The Pennsylvania State University

The Graduate School

College of Agricultural Sciences

AQUATIC HABITAT CHARACTERS THAT SUPPORT BOTH THE

BRIDLE SHINER (Notropis bifrenatus) AND THE

IRONCOLOR SHINER (Notropis chalybaeus)

A Dissertation in

Wildlife and Fisheries Science

by

Clare William Hanson, II Captain, United States Navy (retired)

 2013 Clare William Hanson, II

Submitted in Partial Fulfillment of the Requirements for the Degree of

Doctor of Philosophy

December 2013 ii The dissertation of Clare William Hanson, II, was reviewed and approved* by the following:

Jay R. Stauffer Jr. Distinguished Professor of Ichthyology Chair of Committee Dissertation Adviser

Michael C. Saunders Professor of Entomology

Charles A. Cole Associate Professor of Landscape Architecture and Ecology

Jeanette L. Schnars Executive Director, Regional Science Consortium, The Tom Ridge Environmental Center, Erie, PA

Gregory A. Hoover Senior Extension Associate, Department of Entomology Special Signatory

Michael G. Messina Head and Professor, Department of Ecosystem Science and Management

*Signatures are on file in the Graduate School

iii ABSTRACT

The endangered Bridle Shiner, Notropis bifrenatus, and endangered Ironcolor Shiner,

Notropis chalybaeus, co-exist in Marshalls Creek (Delaware River drainage), Monroe County,

Pennsylvania. Although both species were historically widespread, the only known extant populations where these two species occur syntopically is in Marshalls Creek. The primary research goal was to determine the unique aquatic habitat characters of Marshalls Creek that support the syntopic populations of Bridle and Ironcolor shiners. To achieve this goal, research objectives were (1) to examine and discern the aquatic habitat characters (i.e., the combination and interaction of biological, chemical, and physical habitat characters) that are coincident with these two endangered species in Marshalls Creek; (2) to determine if these aquatic habitat characters are commonly found at other historical sites for these two endangered shiners; and (3) to speculate as to why these two endangered shiners currently exist together in Marshalls Creek.

A NetWeaver model was developed to examine aquatic habitat characters of Marshalls Creek research sites and other historical sites on the Atlantic seaboard. NetWeaver model network components were utilized to produce strength of evidence scores (i.e., trueness levels) to compare, contrast, and evaluate aquatic habitat characters to the reference (i.e., benchmark) aquatic habitat characters in Marshalls Creek. This study provided important data and methodology for scientists and resource managers to assess biodiversity and determine favorable habitat for these two endangered shiners, and documented important aquatic habitat character data for fisheries management personnel to manage Bridle and Ironcolor shiner populations.

Key Words: endangered Bridle Shiner, Notropis bifrenatus; endangered Ironcolor Shiner,

Notropis chalybaeus; Marshalls Creek; syntopically; aquatic habitat characters; biological, chemical, and physical habitat characters; biodiversity; fisheries management.

iv TABLE OF CONTENTS

LIST OF FIGURES ...... vii

LIST OF TABLES ...... x

ACKNOWLEDGEMENTS ...... xviii

Chapter 1 Introduction ...... 1

Research Goal and Objectives ...... 1 Research Model ...... 2 Research Hypothesis and Testing ...... 4 Research Approval ...... 5 Research Citations ...... 6 Previous Research ...... 6 Endangered Shiners ...... 6 Bridle Shiner (Notropis bifrenatus) ...... 7 Morphological/Meristic Description ...... 7 Etymology ...... 8 Habitat ...... 9 Feeding ...... 9 Spawning/Development ...... 10 Native Range ...... 11 Ironcolor Shiner (Notropis chalybaeus)...... 13 Morphological/Meristic Description ...... 13 Etymology ...... 14 Habitat ...... 14 Feeding ...... 15 Spawning/Development ...... 15 Native Range ...... 16 Comparisons ...... 18

Chapter 2 Methods and Materials ...... 20

Research Sites ...... 20 Marshalls Creek ...... 23 Other Historical Sites ...... 27 Maryland ...... 27 Delaware ...... 28 Massachusettes ...... 29 Pennsylvania ...... 30 Research Site Collections and Measurements ...... 31 Biological Habitat Characters ...... 32 Fishes ...... 32 Aquatic Macroinvertebrates ...... 33 Aquatic Plants/Algae...... 34

v Chemical Habitat Characters ...... 35 Physical Habitat Characters ...... 36 NetWeaver Model ...... 37 Development and Application ...... 37 Strength of Evidence Scores ...... 41 Biological Habitat Characters Dependency Network ...... 42 Fishes Dependency Network ...... 43 Aquatic Macroinvertebrates Dependency Network ...... 44 Aquatic Plants/Algae Dependency Network ...... 45 Chemical Habitat Characters Dependency Network ...... 46 Physical Habitat Characters Dependency Network ...... 47 Aquatic Habitat Characters Dependency Network ...... 48

Chapter 3 Results ...... 50

Research Site Collections and Measurements ...... 50 Biological Habitat Characters ...... 50 Endangered Shiners...... 50 Fish Associates ...... 52 Aquatic Macroinvertebrates ...... 58 Aquatic Plants/Algae...... 61 Chemical Habitat Characters ...... 63 Physical Habitat Characters ...... 66 NetWeaver Model Strength of Evidence Scores ...... 69 Biological Habitat Characters ...... 70 Fishes ...... 70 Aquatic Macroinvertebrates ...... 73 Aquatic Plants/Algae...... 75 Chemical Habitat Characters ...... 78 Physical Habitat Characters ...... 80 Aquatic Habitat Characters ...... 81 NetWeaver Model Strength of Evidence Score Ratio ...... 83 NetWeaver Model Weighting ...... 84

Chapter 4 Discussion ...... 87

Research Hypothesis and Testing ...... 87 Research Goal and Objectives ...... 88 Determining Favorable Habitat ...... 90 Assessing Biodiversity ...... 92 Fisheries Management Implications ...... 94 Significant Take-aways ...... 95

Appendix A Marshalls Creek Site 0, Pennsylvania ...... 96

Appendix B Marshalls Creek Site 1, Pennsylvania ...... 101

Appendix C Marshalls Creek Site 2, Pennsylvania ...... 108

vi Appendix D Marshalls Creek Site 3, Pennsylvania ...... 115

Appendix E Marshalls Creek Site 4, Pennsylvania ...... 122

Appendix F Marshalls Creek Site 5, Pennsylvania ...... 127

Appendix G Long Marsh Ditch, Maryland ...... 132

Appendix H Zekiah Swamp, Maryland ...... 135

Appendix I Nanticoke River, Delaware ...... 138

Appendix J Gum Branch (mainstream), Delaware ...... 141

Appendix K Gum Branch (headwaters), Delaware ...... 144

Appendix L West Branch, Delaware ...... 147

Appendix M Clifford Road Dam Outlet, Massachusetts ...... 150

Appendix N Eel River, Massachusetts ...... 153

Appendix O Flat Brook, Massachusetts ...... 156

Appendix P Hop Brook, Massachusetts ...... 159

Appendix Q West Branch Farmington River, Massachusetts ...... 162

Appendix R Schenob Brook, Massachusetts ...... 165

Appendix S Dry Brook, Massachusetts ...... 168

Appendix T Sambo Creek, Pennsylvania ...... 171

Appendix U McMichael Creek, Pennsylvania ...... 174

Appendix V Fishes Associations ...... 177

Appendix W Aquatic Macroinvertebrate Associations...... 179

Appendix X Aquatic Plants/Algae Associations ...... 184

Appendix Y NetWeaver Fuzzy Logic Argument Parameters ...... 186

Appendix Z NetWeaver Model Habitat Character Requirements ...... 190

Bibliography ...... 197

vii LIST OF FIGURES

Figure1-1: Bridle Shiner (Notropis bifrenatus)(Kraft et al. 2006) ...... 7

Figure1-2: Native Range of the Bridle Shiner (Notropis bifrenatus)(Page and Burr 1991) .... 12

Figure1-3: Ironcolor Shiner (Notropis chalybaeus)(Kraft et al. 2006) ...... 13

Figure1-4: Native Range of the Ironcolor Shiner (Notropis chalybaeus)(Page and Burr 1991) ...... 17

Figure2-1: Research Sites for the Bridle Shiner in Massachusetts, for the Bridle and Ironcolor Shiner in Pennsylvania, for the Ironcolor Shiner in Maryland, and for the Ironcolor Shiner in Delaware (Delorme 2013) ...... 22

Figure2-2: 3.7 km Reach of Marshalls Creek, Monroe County, Pennsylvania, Where the Bridle and Ironcolor Shiner Co-Exist (Delorme 2013) ...... 23

Figure2-3: Research Sites 0-5 at Marshalls Creek, Monroe County, Pennsylvania (Delorme 2013) ...... 24

Figure2-4: Road Bypass Construction at Marshalls Creek, Monroe County, Pennsylvania (Delorme 2013) ...... 25

Figure2-5: Long Marsh Ditch and Zekiah Swamp; Both are Historical Watersheds in Maryland for the Ironcolor Shiner (Delorme 2013) ...... 27

Figure2-6: Nanticoke River, Gum Branch (mainstream), Gum Branch (headwaters), and West Branch; All are Historical Watersheds for the Ironcolor Shiner in Delaware (Delorme 2013) ...... 28

Figure2-7: Clifford Road Dam Outlet, Eel Creek, Flat Brook, Hop Brook, West Branch Farmington River, Schenob Brook, and Dry Brook; All are Historical Watersheds for the Bridle Shiner in Massachusetts (Delorme 2013) ...... 29

Figure2-8: Sambo Creek, McMichael Creek, and Marshalls Creek Research Sites; Sambo Creek and McMichael Creek are Re-Introduction Watersheds in Pennsylvania for the Bridle and Ironcolor Shiner (Delorme 2013) ...... 30

Figure2-9: NetWeaver Fuzzy Logic Argument for the Simple Data Link Question “Is the American Eel present? 0=No, 1=Yes”. NetWeaver Fuzzy Logic Argument Parameters were based on Collections and Measurements at Marshalls Creek Site 1, PA (the model reference site) (NDE 2013) ...... 38

Figure2-10: NetWeaver Fuzzy Logic Argument for the Simple Data Link Question for “What is the pH?” NetWeaver Fuzzy Logic Argument Parameters were based on Collections and Measurements at Marshalls Creek Site 1, PA (the model reference site) (NDE 2013) ...... 39

viii Figure2-11: Biological Habitat Characters Dependency Network for the NetWeaver Model (NDE 2013) ...... 42

Figure2-12: Fishes Dependency Network for the NetWeaver Model (NDE 2013) ...... 43

Figure2-13: Aquatic Macroinvertebrates Dependency Network for the NetWeaver Model (NDE 2013) ...... 44

Figure2-14: Aquatic Plants/Algae Dependency Network for the NetWeaver Model (NDE 2013) ...... 45

Figure2-15: Chemical Habitat Characters Dependency Network for the NetWeaver Model (NDE 2013)...... 46

Figure2-16: Physical Habitat Characters Dependency Network for the NetWeaver Model (NDE 2013) ...... 47

Figure2-17: Aquatic Habitat Characters Dependency Network for the NetWeaver Model (NDE 2013) ...... 48

Figure3-1: The Number of Aquatic Macroinvertebrate Taxa Collected verses The Number of Collections for Marshalls Creek Site 1, PA ...... 60

FigureA-1: Marshalls Creek Site 0, Pennsylvania ...... 96

FigureB-1: Marshalls Creek Site 1, Pennsylvania (the model reference site) ...... 101

FigureC-1: Marshalls Creek Site 2, Pennsylvania ...... 108

FigureD-1: Marshalls Creek Site 3, Pennsylvania ...... 115

FigureE-1: Marshalls Creek Site 4, Pennsylvania ...... 122

FigureF-1: Marshalls Creek Site 5, Pennsylvania ...... 127

FigureG-1: Long Marsh Ditch, Maryland...... 132

FigureH-1: Zekiah Swamp, Maryland ...... 135

FigureI-1: Nanticoke River, Delaware...... 138

FigureJ-1: Gum Branch (mainstream), Delaware ...... 141

FigureK-1: Gum Branch (headwaters), Delaware ...... 144

FigureL-1: West Branch, Delaware ...... 147

FigureM-1: Clifford Road Dam Outlet, Massachusetts ...... 150

FigureN-1: Eel River, Massachusetts...... 153

ix FigureO-1: Flat Brook, Massachusetts ...... 156

FigureP-1: Hop Brook, Massachusetts ...... 159

FigureQ-1: West Branch Farmington River, Massachusetts ...... 162

FigureR-1: Schenob Brook, Massachusetts ...... 165

FigureS-1: Dry Brook, Massachusetts ...... 168

FigureT-1: Sambo Creek, Pennsylvania ...... 171

FigureU-1: McMichael Creek, Pennsylvania ...... 174

x LIST OF TABLES

Table2-1: Bridle Shiner Endangered Species Status ...... 21

Table2-2: Ironcolor Shiner Endangered Species Status ...... 21

Table2-3: Marshalls Creek Sites 0-5 Remote Chemistry Monitoring Start Dates; and Fishes, Aquatic Macroinvertebrates, and Aquatic Plants/Algae Collection Start Dates ...... 26

Table2-4: NetWeaver Model Logical Node Types and Their Function (NDE 2013) ...... 40

Table3-1: Number of Endangered Shiners Collections and Endangered Shiners Collected and Observed at All Research Sites ...... 51

Table3-2: Number of Fish Associate Collections, Fish Associate Species, Endangered Shiners Predator Species, and Endangered Shiners Non-Predator Species at All Research Sites ...... 53

Table3-3: Exotic Species and Additional (i.e., not found at the model reference site) Exotic Species Collected at All Research Sites ...... 54

Table3-4: Additional (i.e., not found at the model reference site) Endangered Shiners Predator Species Collected at All Research Sites ...... 55

Table3-5: Percentage of Native Species at All Research Sites ...... 58

Table3-6: Number of Aquatic Macroinvertebrate Collections, Aquatic Macroinvertebrate Taxa, Endangered Shiners Edible Aquatic Macroinvertebrate Taxa, and Endangered Shiners Non-Edible Aquatic Macroinvertebrate Taxa at All Research Sites ...... 59

Table3-7: Number of Aquatic Plant/Algae Collections, Aquatic Plant/Algae Species, Endangered Shiners Spawning Plant Species, and Endangered Shiners Non- Spawning Plant/Algae Species at All Research Sites ...... 62

Table3-8: Chemical Habitat Characters (pH, Dissolved Oxygen, and Conductivity) at All Research Sites ...... 63

Table3-9: Chemical Habitat Characters (Alkalinity and Hardness) at All Research Sites ...... 65

Table3-10: Physical Habitat Characters (Water Temperature, Depth, Velocity, Substrate Composition, and Riparian Protection) at All Research Sites...... 66

Table3-11: Physical Habitat Characters (Flow Status, Bank Stability, and Channel Alteration) at All Research Sites ...... 68

Table3-12: Strength of Evidence Scores for Endangered Shiners Predator Species, Endangered Shiners Non-Predator Species, and Native Species at All Research Sites ... 71

xi Table3-13: Strength of Evidence Scores for Additional (i.e., not found at the model reference site) Exotic Species, Additional (i.e., not found at the model reference site) Endangered Shiners Predator Species, and Fishes at All Research Sites ...... 72

Table3-14: Strength of Evidence Scores for Endangered Shiners Edible Aquatic Macroinvertebrate Taxa, Endangered Shiners Non-Edible Aquatic Macroinvertebrate Taxa, and Aquatic Macroinvertebrates at All Research Sites...... 74

Table3-15: Strength of Evidence Scores for Endangered Shiners Spawning Plant Species, Endangered Shiners Non-Spawning Plant/Algae Species, and Aquatic Plants/Algae at All Research Sites ...... 76

Table3-16: Strength of Evidence Scores for Fishes, Aquatic Macroinvertebrates, Aquatic Plants/Algae, and Biological Habitat Characters at All Research Sites ...... 78

Table3-17: Strength of Evidence Scores for Chemical Habitat Characters at All Research Sites ...... 79

Table3-18: Strength of Evidence Scores for Physical Habitat Characters at All Research Sites ...... 80

Table3-19: Strength of Evidence Scores for Biological Habitat Characters, Chemical Habitat Characters, Physical Habitat Characters, and Aquatic Habitat Characters at All Research Sites ...... 82

Table3-20: Strength of Evidence Score Ratio at All Research Sites ...... 83

Table3-21: Strength of Evidence Scores for Aquatic Habitat Characters with (x3) Weighting and (x1) Weighting, and the Corresponding Score Change at All Research Sites ...... 85

Table4-1: NetWeaver Model Sets of Parameters that Determine Favorable Habitat for the Presence of Both Bridle and Ironcolor Shiners, Only Bridle Shiners, and Only Ironcolor Shiners (NDE 2013) ...... 91

TableA-1: Endangered Shiners at Marshalls Creek Site 0, Pennsylvania ...... 97

TableA-2: Fish Associates at Marshalls Creek Site 0, Pennsylvania (in phylogenetic order) ...... 97

TableA-3: Aquatic Macroinvertebrates at Marshalls Creek Site 0, Pennsylvania (in phylogenetic order followed by crustaceans, mollusks, oligochaetes, and leeches) ...... 98

TableA-4: Aquatic Plants/Algae at Marshalls Creek Site 0, Pennsylvania...... 99

TableA-5: Chemical Habitat Characters at Marshalls Creek Site 0, Pennsylvania ...... 100

TableA-6: Physical Habitat Characters at Marshalls Creek Site 0, Pennsylvania ...... 100

TableB-1: Endangered Shiners at Marshalls Creek Site 1, Pennsylvania ...... 102

xii TableB-2: Fish Associates at Marshalls Creek Site 1, Pennsylvania (in phylogenetic order) ...... 102

TableB-3: Aquatic Macroinvertebrates at Marshalls Creek Site 1, Pennsylvania (in phylogenetic order followed by crustaceans, mollusks, oligochaetes, and leeches) ...... 103

TableB-4: Aquatic Plants/Algae at Marshalls Creek Site 1, Pennsylvania ...... 106

TableB-5: Chemical Habitat Characters at Marshalls Creek Site 1, Pennsylvania ...... 106

TableB-6: Physical Habitat Characters at Marshalls Creek Site 1, Pennsylvania ...... 107

TableC-1: Endangered Shiners at Marshalls Creek Site 2, Pennsylvania ...... 109

TableC-2: Fish Associates at Marshalls Creek Site 2, Pennsylvania (in phylogenetic order) ...... 109

TableC-3: Aquatic Macroinvertebrates at Marshalls Creek Site 2, Pennsylvania (in phylogenetic order followed by crustaceans, mollusks, oligochaetes, and leeches) ...... 110

TableC-4: Aquatic Plants/Algae at Marshalls Creek Site 2, Pennsylvania...... 113

TableC-5: Chemical Habitat Characters at Marshalls Creek Site 2, Pennsylvania ...... 114

TableC-6: Physical Habitat Characters at Marshalls Creek Site 2, Pennsylvania ...... 114

TableD-1: Endangered Shiners at Marshalls Creek Site 3, Pennsylvania ...... 116

TableD-2: Fish Associates at Marshalls Creek Site 3, Pennsylvania (in phylogenetic order) ...... 116

TableD-3: Aquatic Macroinvertebrates at Marshalls Creek Site 3, Pennsylvania (in phylogenetic order followed by crustaceans, mollusks, oligochaetes, and leeches) ...... 117

TableD-4: Aquatic Plants/Algae at Marshalls Creek Site 3, Pennsylvania...... 120

TableD-5: Chemical Habitat Characters at Marshalls Creek Site 3, Pennsylvania ...... 121

TableD-6: Physical Habitat Characters at Marshalls Creek Site 3, Pennsylvania ...... 121

TableE-1: Endangered Shiners at Marshalls Creek Site 4, Pennsylvania ...... 123

TableE-2: Fish Associates at Marshalls Creek Site 4, Pennsylvania (in phylogenetic order) ...... 123

TableE-3: Aquatic Macroinvertebrates at Marshalls Creek Site 4, Pennsylvania (in phylogenetic order followed by crustaceans, mollusks, oligochaetes, and leeches) ...... 124

TableE-4: Aquatic Plants/Algae at Marshalls Creek Site 4, Pennsylvania ...... 126

xiii TableE-5: Chemical Habitat Characters at Marshalls Creek Site 4, Pennsylvania ...... 126

TableE-6: Physical Habitat Characters at Marshalls Creek Site 4, Pennsylvania ...... 126

TableF-1: Endangered Shiners at Marshalls Creek Site 5, Pennsylvania ...... 128

TableF-2: Fish Associates at Marshalls Creek Site 5, Pennsylvania (in phylogenetic order) ...... 128

TableF-3: Aquatic Macroinvertebrates at Marshalls Creek Site 5, Pennsylvania (in phylogenetic order followed by crustaceans, mollusks, oligochaetes, and leeches) ...... 129

TableF-4: Aquatic Plants/Algae at Marshalls Creek Site 5, Pennsylvania ...... 130

TableF-5: Chemical Habitat Characters at Marshalls Creek Site 5, Pennsylvania ...... 130

TableF-6: Physical Habitat Characters at Marshalls Creek Site 5, Pennsylvania ...... 131

TableG-1: Endangered Shiners at Long Marsh Ditch, Maryland ...... 133

TableG-2: Fish Associates at Long Marsh Ditch, Maryland (in phylogenetic order) ...... 133

TableG-3: Aquatic Macroinvertebrates at Long Marsh Ditch, Maryland (in phylogenetic order followed by crustaceans, mollusks, oligochaetes, and leeches)...... 133

TableG-4: Aquatic Plants at Long Marsh Ditch, Maryland ...... 134

TableG-5: Chemical Habitat Characters at Long Marsh Ditch, Maryland ...... 134

TableG-6: Physical Habitat Characters at Long Marsh Ditch, Maryland ...... 134

TableH-1: Endangered Shiners at Zekiah Swamp, Maryland ...... 136

TableH-2: Fish Associates at Zekiah Swamp, Maryland (in phylogenetic order) ...... 136

TableH-3: Aquatic Macroinvertebrates at Zekiah, Maryland (in phylogenetic order followed by crustaceans, mollusks, oligochaetes, and leeches) ...... 136

TableH-4: Aquatic Plants at Zekiah Swamp, Maryland ...... 137

TableH-5: Chemical Habitat Characters at Zekiah Swamp, Maryland ...... 137

TableH-6: Physical Habitat Characters at Zekiah Swamp, Maryland ...... 137

TableI-1: Endangered Shiners at Nanticoke River, Delaware ...... 139

TableI-2: Fish Associates at Nanticoke River, Delaware (in phylogenetic order) ...... 139

TableI-3: Aquatic Macroinvertebrates at Nanticoke River, Delaware (in phylogenetic order followed by crustaceans, mollusks, oligochaetes, and leeches)...... 139

xiv TableI-4: Aquatic Plants at Nanticoke River, Delaware ...... 140

TableI-5: Chemical Habitat Characters at Nanticoke River, Delaware...... 140

TableI-6: Physical Habitat Characters at Nanticoke River, Delaware ...... 140

TableJ-1: Endangered Shiners at Gum Branch (mainstream), Delaware ...... 142

TableJ-2: Fish Associates at Gum Branch (mainstream), Delaware (in phylogenetic order) ...... 142

TableJ-3: Aquatic Macroinvertebrates at Gum Branch (mainstream), Delaware (in phylogenetic order followed by crustaceans, mollusks, oligochaetes, and leeches) ...... 142

TableJ-4: Aquatic Plants at Gum Branch (mainstream), Delaware ...... 143

TableJ-5: Chemical Habitat Characters at Gum Branch (mainstream), Delaware ...... 143

TableJ-6: Physical Habitat Characters at Gum Branch (mainstream), Delaware ...... 143

TableK-1: Endangered Shiners at Gum Branch (headwaters), Delaware ...... 145

TableK-2: Fish Associates at Gum Branch (headwaters), Delaware (in phylogenetic order) ...... 145

TableK-3: Aquatic Macroinvertebrates at Gum Branch (headwaters), Delaware (in phylogenetic order followed by crustaceans, mollusks, oligochaetes, and leeches) ...... 145

TableK-4: Aquatic Plants at Gum Branch (headwaters), Delaware ...... 146

TableK-5: Chemical Habitat Characters at Gum Branch (headwaters), Delaware ...... 146

TableK-6: Physical Habitat Characters at Gum Branch (headwaters), Delaware ...... 146

TableL-1: Endangered Shiners at West Branch, Delaware ...... 148

TableL-2: Fish Associates at West Branch, Delaware (in phylogenetic order) ...... 148

TableL-3: Aquatic Macroinvertebrates at West Branch, Delaware (in phylogenetic order followed by crustaceans, mollusks, oligochaetes, and leeches) ...... 148

TableL-4: Aquatic Plants/Algae at West Branch, Delaware ...... 149

TableL-5: Chemical Habitat Characters at West Branch, Delaware ...... 149

TableL-6: Physical Habitat Characters at West Branch, Delaware ...... 149

TableM-1: Endangered Shiners at Clifford Road Dam Outlet, Massachusetts ...... 151

xv TableM-2: Fish Associates at Clifford Road Dam Outlet, Massachusetts (in phylogenetic order) ...... 151

TableM-3: Aquatic Macroinvertebrates at Clifford Road Dam Outlet, Massachusetts (in phylogenetic order followed by crustaceans, mollusks, oligochaetes, and leeches) ...... 151

TableM-4: Aquatic Plants at Clifford Road Dam Outlet, Massachusetts ...... 152

TableM-5: Chemical Habitat Characters at Clifford Road Dam Outlet, Massachusetts ...... 152

TableM-6: Physical Habitat Characters at Clifford Road Dam Outlet, Massachusetts ...... 152

TableN-1: Endangered Shiners at Eel River, Massachusetts ...... 154

TableN-2: Fish Associates at Eel River, Massachusetts (in phylogenetic order) ...... 154

TableN-3: Aquatic Macroinvertebrates at Eel River, Massachusetts (in phylogenetic order followed by crustaceans, mollusks, oligochaetes, and leeches) ...... 154

TableN-4: Aquatic Plants at Eel River, Massachusetts ...... 155

TableN-5: Chemical Habitat Characters at Eel River, Massachusetts ...... 155

TableN-6: Physical Habitat Characters at Eel River, Massachusetts ...... 155

TableO-1: Endangered Shiners at Flat Brook, Massachusetts ...... 157

TableO-2: Fish Associates at Flat Brook, Massachusetts (in phylogenetic order) ...... 157

TableO-3: Aquatic Macroinvertebrates at Flat Brook, Massachusetts (in phylogenetic order followed by crustaceans, mollusks, oligochaetes, and leeches)...... 157

TableO-4: Aquatic Plants at Flat Brook, Massachusetts ...... 158

TableO-5: Chemical Habitat Characters at Flat Brook, Massachusetts ...... 158

TableO-6: Physical Habitat Characters at Flat Brook, Massachusetts ...... 158

TableP-1: Endangered Shiners at Hop Brook, Massachusetts ...... 160

TableP-2: Fish Associates at Hop Brook, Massachusetts (in phylogenetic order) ...... 160

TableP-3: Aquatic Macroinvertebrates at Hop Brook, Massachusetts (in phylogenetic order followed by crustaceans, mollusks, oligochaetes, and leeches)...... 160

TableP-4: Aquatic Plants at Hop Brook, Massachusetts ...... 161

TableP-5: Chemical Habitat Characters at Hop Brook, Massachusetts ...... 161

TableP-6: Physical Habitat Characters at Hop Brook, Massachusetts ...... 161

xvi TableQ-1: Endangered Shiners at West Branch Farmington River, Massachusetts ...... 163

TableQ-2: Fish Associates at West Branch Farmington River, Massachusetts (in phylogenetic order) ...... 163

TableQ-3: Aquatic Macroinvertebrates at West Branch Farmington River, Massachusetts (in phylogenetic order followed by crustaceans, mollusks, oligochaetes, and leeches)... 163

TableQ-4: Aquatic Plants at West Branch Farmington River, Massachusetts ...... 164

TableQ-5: Chemical Habitat Characters at West Branch Farmington River, Massachusetts...... 164

TableQ-6: Physical Habitat Characters at West Branch Farmington River, Massachusetts ... 164

TableR-1: Endangered Shiners at Schenob Brook, Massachusetts ...... 166

TableR-2: Fish Associates at Schenob Brook, Massachusetts (in phylogenetic order) ...... 166

TableR-3: Aquatic Macroinvertebrates at Schenob Brook, Massachusetts (in phylogenetic order followed by crustaceans, mollusks, oligochaetes, and leeches) ...... 166

TableR-4: Aquatic Plants at Schenob Brook, Massachusetts ...... 167

TableR-5: Chemical Habitat Characters at Schenob Brook, Massachusetts ...... 167

TableR-6: Physical Habitat Characters at Schenob Brook, Massachusetts ...... 167

TableS-1: Endangered Shiners at Dry Brook, Massachusetts ...... 169

TableS-2: Fish Associates at Dry Brook, Massachusetts (in phylogenetic order) ...... 169

TableS-3: Aquatic Macroinvertebrates at Dry Brook, Massachusetts (in phylogenetic order followed by crustaceans, mollusks, oligochaetes, and leeches)...... 169

TableS-4: Aquatic Plants at Dry Brook, Massachusetts ...... 170

TableS-5: Chemical Habitat Characters at Dry Brook, Massachusetts ...... 170

TableS-6: Physical Habitat Characters at Dry Brook, Massachusetts ...... 170

TableT-1: Endangered Shiners at Sambo Creek, Pennsylvania ...... 172

TableT-2: Fish Associates at Sambo Creek, Pennsylvania (in phylogenetic order) ...... 172

TableT-3: Aquatic Macroinvertebrates at Sambo Creek, Pennsylvania (in phylogenetic order followed by crustaceans, mollusks, oligochaetes, and leeches)...... 172

TableT-4: Aquatic Plants/Algae at Sambo Creek, Pennsylvania...... 173

xvii TableT-5: Chemical Habitat Characters at Sambo Creek, Pennsylvania ...... 173

TableT-6: Physical Habitat Characters at Sambo Creek, Pennsylvania ...... 173

TableU-1: Endangered Shiners at McMichael Creek, Pennsylvania ...... 175

TableU-2: Fish Associates at McMichael Creek, Pennsylvania (in phylogenetic order) ...... 175

TableU-3: Aquatic Macroinvertebrates at McMichael Creek, Pennsylvania (in phylogenetic order followed by crustaceans, mollusks, oligochaetes, and leeches) ...... 175

TableU-4: Aquatic Plants/Algae at McMichael Creek, Pennsylvania ...... 176

TableU-5: Chemical Habitat Characters at McMichael Creek, Pennsylvania ...... 176

TableU-6: Physical Habitat Characters at McMichael Creek, Pennsylvania ...... 176

TableV-1: Endangered Shiners Predator Species and Endangered Shiners Non-Predator Species (in phylogenetic order) ...... 177

TableV-2: Native Species and Exotic Species (in phylogenetic order) ...... 178

TableW-1: Endangered Shiners Edible Aquatic Macroinvertebrate Taxa and Endangered Shiners Non-Edible Aquatic Macroinvertebrate Taxa (in phylogenetic order followed by crustaceans, mollusks, oligochaetes, and leeches) ...... 179

TableX-1: Endangered Shiners Spawning Plant Species and Endangered Shiners Non- Spawning Plants/Algae Species ...... 184

TableY-1: NetWeaver Fuzzy Logic Argument Parameters. NetWeaver Fuzzy Logic Argument Parameters were Based on Collections and Measurements at Marshalls Creek Site 1, PA (the model reference site) (NDE 2013) ...... 186

TableZ-1: Biological Habitat Character Requirements for All Research Sites (NDE 2013) .. 190

TableZ-2: Chemical Habitat Character Requirements for All Research Sites (NDE 2013) .... 194

TableZ-3: Physical Habitat Character Requirements for All Research Sites (NDE 2013) ..... 195

xviii ACKNOWLEDGEMENTS

I would like to recognize Dr. Jay R. Stauffer, Jr. for his personal mentorship, continued encouragement, fieldwork resources, and vast knowledge of aquatic ecology, systematics, limnology, and ichthyology; Dr. Michael C. Saunders for providing excellent instruction and guidance on the NetWeaver model; Dr. Charles A. Cole for providing excellent insight and instruction on aquatic plant/algae habitat, preservation, and identification; Dr. Jeanette L. Schnars for her excellent discussions and guidance on my research and analysis procedures; and Mr.

Gregory A. Hoover for his superb guidance and outstanding instruction of freshwater entomology.

I would like to recognize Dr. Rich Raisly, Professor at Frostburg State University,

Maryland, for his insight on Bridle and Ironcolor shiner historical locations in Maryland and

Delaware.

I would like to recognize Dr. Kristin Black, Ms. Sarah Maier, and Ms. Sarah Haggerty, staff at the Natural Heritage and Endangered Species Program, Massachusetts Division of

Fisheries and Wildlife, for their help with Bridle Shiner historical locations in Massachusetts.

I would like to recognize Mr. Bruce Miller, President and CEO at Rules of Thumb, Inc., for his exceptional assistance with NetWeaver modeling techniques.

I would like to recognize Emily Hill, BJ Scovern, Jeff Grimm, Carol Leitzell, and Barb

Irwin at the Department of Ecosystem Science and Management, College of Agricultural Science, for their outstanding administrative and technical support.

I would like to recognize the United States Department of Veterans Affairs for providing

Post 9/11 GI Bill Educational Assistance Benefits.

xix My research would not have been possible without the outstanding fieldwork and laboratory assistance from many graduate and undergraduate colleagues including Casey

Weathers, Casey Bradshaw-Wilson, Rich Taylor, Shan Li (Lisa), Shelly Pickett, Brent Smith,

Dave Ryan, Jim Grazio, Sara Mueller, Josh Lynn, Jackie Matzke, Brian Matje, Cindy Nau,

Lingyan Dong (Irene), Brendon Reed, Ben Amos, and Evan Martin.

My entire family provided understanding, patience, and full support. This dissertation is dedicated to my wife, Susan; and my three children, Adam, Sally, and George.

1 Chapter 1

Introduction

Research Goal and Objectives

The endangered Bridle Shiner, Notropis bifrenatus, and endangered Ironcolor Shiner,

Notropis chalybaeus, co-exist in Marshalls Creek (Delaware River drainage), Monroe County,

Pennsylvania. The Bridle Shiner occurred historically in the Susquehanna River and is extant sporadically north of Marshalls Creek and the Ironcolor Shiner south of Marshalls Creek.

Historically, the Bridle and Ironcolor shiner were found throughout the Delaware River drainage in Pennsylvania; however, the only known extant populations where these two endangered species occur syntopically is in Marshalls Creek. Thus, the primary research goal was to determine the unique aquatic habitat characters of Marshalls Creek that support the syntopic populations of Bridle and Ironcolor shiners.

To achieve this goal, specific research objectives of this study were (1) to examine and discern the aquatic habitat characters (i.e., the combination and interaction of biological, chemical, and physical habitat characters) that are coincident with these two endangered species in Marshalls Creek; (2) to determine if these aquatic habitat characters are commonly found at other historical sites for these two endangered shiners; and (3) to speculate as to why these two endangered shiners currently exist together in Marshalls Creek. To address the above, my research documented biological habitat characters (e.g., the presence of fish associates and their trophic relationships to these two endangered shiners), chemical habitat characters (e.g., the preference of pH and dissolved oxygen); and physical habitat characters (e.g., the preference of

2 depth and substrate composition) to determine aquatic habitat characters associated with the presence of both these endangered shiners.

Five primary research focus areas were (1) morphological/meristic description, etymology, habitat, feeding, spawning/development, and native range of these two endangered fishes; (2) biological habitat characters including fish associate, aquatic macroinvertebrate, and aquatic plant/algae community taxa presence, and their trophic and spawning relationship to these two endangered shiners; (3) chemical habitat characters (pH, dissolved oxygen, conductivity, alkalinity, and hardness) and their association with these two endangered shiners; (4) physical habitat characters (water temperature, depth, velocity, substrate composition, riparian protection, flow status, bank stability, and channel alteration) and their association to these two endangered shiners, and (5) NetWeaver2 Knowledge-Base Model development and utilization to examine strength of evidence (i.e., trueness levels) scores of aquatic habitat characters when comparing, contrasting, and evaluating 20 research sites to the Marshalls Creek reference (i.e., benchmark) site. In summary, these research objectives and focus areas provided better documentation of the aquatic habitat characters present in the only syntopic occurrence of the endangered Bridle

Shiner, Notropis bifrenatus, and endangered Ironcolor Shiner, Notropis chalybaeus.

Research Model

NetWeaverTM is a knowledge-base development system used to interpret and evaluate data. NetWeaver is a graphical tool used by engineers that design knowledge-base natural resource management software. Because of NetWeaver’s graphical interface, overall ease of operation, and real-time interface, it was chosen as a fundamental technology and component of the Ecosystem Management Decision Support (EMDS) system (Saunders and Miller 1997;

Boone et al. 2005; NDE 2013). The EMDS system is a Decision Support System (DSS) that is

3 able to integrate multi-taxa inventory data sets for analysis to help researchers and resource managers make sound management decisions more efficiently (Boone et al. 2005).

The EMDS system with its NetWeaver modeling tool component has also been successfully used in a variety of applications including wildlife habitat management, wetlands management, forest ecosystem sustainability, and natural resource condition assessment

(Reynolds et al. 2003; RIDST 2004; Janssen et al. 2005; Annis et al. 2011). NetWeaver modeling has also been used to study and classify lake water chemistry (Saunders et al. 2005), to assess natural resources and watershed conditions at the Delaware Water Gap National Recreation Area and Upper Delaware Scenic and Recreational River (Mahan et al. 2011), and to analyze U.S.

Forest Service projects in various locations (Boone et al. 2005).

Over the years, NetWeaver has evolved and its versatility has increased. The

NetWeaver2 Knowledge-Base Model is the most recent version of NetWeaver. This modeling tool can be used to compare, contrast, and evaluate any ecosystem and produce scores by altering habitat character information. NetWeaver is a characterization mechanism; it compares the inventory of characters of a reference site to the inventory of characters from other research sites.

Concurrently, NetWeaver can be used to study and document ecosystem integrity (NDE 2013).

NetWeaver is used for building and evaluating knowledge networks (Boone et al. 2005).

The modularity of NetWeaver allows the evolution of complex knowledge bases from small, incremental steps (NDE 2013). Key features of NetWeaver include object-based networks of logical propositions and fuzzy logic that provides a complete calculus for knowledge representation and can easily be used by resource managers (Boone et al. 2005; NDE 2013).

I selected NetWeaver as the modeling tool for my research hypothesis because

NetWeaver has been recommended as a DSS for the National Park Service and successfully utilized to examine and discern various characters of a variety of ecosystems (Boone et al. 2005;

4 NDE 2013). For my research, the NetWeaver modeling tool focuses on the endangered Bridle

Shiner and endangered Ironcolor Shiner in various habitats on the Atlantic seaboard.

NetWeaver models can incorporate a wide variety of data sets. In the NetWeaver model,

I developed the wide variety of parameters of the aquatic (i.e., the combination and interaction of biological, chemical, and physical) habitat characters that are coincident with both the Bridle and

Ironcolor shiner.

When comparing five Marshalls Creek research sites and 15 other historical research sites, the aquatic habitat characters of Marshalls Creek Site 1, PA, were used as the domain source and reference (i.e., benchmark) ecosystem for the NetWeaver model that I developed

(other NetWeaver models might use expert opinions as a domain source). The methods for the

NetWeaver model are reported in detail in Chapter 2 (Methods and Materials). NetWeaver model strength of evidence scores (i.e., trueness levels) were produced when comparing a total of 20 research sites to the Marshalls Creek Site 1, PA, reference site. Strength of evidence scores are reported in detail in Chapter 3 (Results).

Research Hypothesis and Testing

To achieve the research goal and research objectives of this study, I developed a

NetWeaver modeling tool to replicate the Marshalls Creek Site 1, PA, research site. This

NetWeaver modeling tool was populated with 21 research sites to determine differences in aquatic habitat characters. Specifically, I used the NetWeaver modeling tool to (1) examine and discern the aquatic habitat characters for the endangered Bridle Shiner and endangered Ironcolor

Shiner in Marshalls Creek, (2) determine if these aquatic habitat characters are commonly found

5 at other historical sites for these two endangered shiners, and (3) give evidence in speculating why these two endangered shiners currently exist together in Marshalls Creek.

Research Hypothesis: A NetWeaver modeling tool can be developed as a research tool to assess the aquatic environment biodiversity and the habitat variability/characters for two endangered shiners (i.e., Notropis bifrenatus and Notropis chalybaeus).

Research Hypothesis Testing: I collected aquatic (biological, chemical, and physical) habitat characters in six Marshalls Creek research sites and 15 other historical research sites along the Atlantic seaboard to populate the NetWeaver model and compare scores with reference system scores.

Research Approval

The Institutional Animal Care and Use Committee (IACUC) of the Office of Research

Protection at The Pennsylvania State University approved this research. IACUC Protocol Review

#34193 approved this research on an annual basis for the last several years (IACUC 2012).

A Scientific Collector Permit and a Special Permit for Collection of Threatened and

Endangered Species were obtained from The Commonwealth of Pennsylvania (PAFRC 2012a,

2012b). A Scientific Collection Permit and Data Release Agreements were obtained from The

Commonwealth of Massachusetts (MADFW 2012a, 2012b, 2012c). A Scientific Collection

Permit and an Endangered Species Permit were obtained from The State of Maryland (MDDNR

2012a, 2012b). A Scientific Collecting Permit was obtained from The State of Delaware

(DEDFW 2012a).

6 Research Citations

Dissertation citations are in accordance with the American Fisheries Society Guide for

Authors and the American Society of Ichthyologists and Herpetologists (AFS 2011; ASIH 2011).

Previous Research

Dr. Jay R. Stauffer, Jr., Distinguished Professor of Ichthyology at The Pennsylvania State

University, and two of his previous graduate students conducted three major research projects concerning the Bridle and Ironcolor shiner in Pennsylvania.

Bethany Finger completed a MSc thesis on the life history and range of Pennsylvania’s endangered Bridle Shiner (Finger 2001). Leslie Leckvarcik completed a MSc thesis on the life history of the Pennsylvania’s Ironcolor Shiner in Marshalls Creek, Monroe County (Leckvarcik

2001). Additionally, Leslie Leckvarcik completed a Ph.D. dissertation on the restoration of the

Pennsylvania’s Bridle and Ironcolor shiner in the Brodhead Creek Watershed, Monroe County

(Leckvarcik 2005). All three of these major research projects provided an in-depth insight and a key foundation to start my research.

Endangered Shiners

These two cyprinids historically were widespread throughout the Atlantic seaboard. Now both species exist in isolated pockets along the Atlantic seaboard with very limited, if any, gene flow. For Pennsylvania, both the Bridle and Ironcolor shiner historically were widespread throughout the Delaware River drainage. The Bridle Shiner historically was also located in the

7 Susquehanna River drainage. Marshalls Creek may be the only isolated pocket on the Atlantic seaboard where both shiner species currently occur sympatrically and syntopically (Page and Burr

1991; Leckvarcik 2001).

Because of the current construction of U.S. Highway 209 at several Marshalls Creek crossings, Dr. Jay R. Stauffer, Jr. is maintaining diverse genetic stocks of both of these two endangered species should re-introduction be required. These fishes are held and bred in aquaria at the University Park Fish Laboratory at The Pennsylvania State University, and the Rock

Springs Fish Laboratory at The Pennsylvania State University (Leckvarcik 2005). Twenty-five adults of both species have been collected every year since 1999 and added to the brood stock.

Endangered, threatened, and candidate (ETC species) collectively account for about thirty percent of Pennsylvania’s native fish diversity. All ETC species are an important component of

Pennsylvania’s fish diversity, and each of these species deserves protection under Pennsylvania

Fish and Boat Commission Code (BWA 2010).

Bridle Shiner (Notropis bifrenatus)

Morphological/Meristic Description

Figure1-1: Bridle Shiner (Notropis bifrenatus)(Kraft et al. 2006).

8 The Bridle Shiner (Fig. 1-1) with brown-black black stripe laterally from spot on caudal fin around snout. Stripe narrower at snout and over only upper lip; light stripe above dark stripe

(Page and Burr 1991). Body form slightly compressed and moderate; deepest and arched below dorsal fin origin. Gravid females often deep bodied (Jenkins and Burkhead 1993). Dorsal fin origin slightly behind pelvic fin origin (Page and Burr 1991). Snout moderately blunt, the slightly subterminal mouth small and oblique (Page and Burr 1991; Jenkins and Burkhead 1993).

Dorsally Bridle Shiner straw yellow with dusty stripe along midline of back. Scales on back with dark outline. Ventrally, Bridle Shiner silver. Lateral line with 33--36 pored scales, often incomplete except for large adults (Page and Burr 1991). The anal fin with 7 rays, dorsal fin with 8 rays, and caudal fin with 19 principal rays (Jenkins and Burkhead 1993). Pharyngeal teeth arrangement 0, 4-4, 0. Maximum adult length 6.5 cm (Page and Burr 1991).

Nuptial males with minute tubercles on nape, head, and pectoral fins. Females nontuberculate. Nuptial males light yellow to bright yellow-gold on the lower side of body.

Nuptial males and females faint yellow on dorsal, caudal, and anal fins (Jenkins and Burkhead

1993). Nuptial females with extended abdomens (Finger 2001).

Etymology

The Bridle Shiner is named for the fish’s “mustached” or “bridled” muzzle. Notropis translates to “back keel” and was probably based on a specimen whose back was ridged owing to shrinkage. The specific epithet bifrenatus means “two bridled” referring to the black preocular bar that crosses the snout (Jenkins and Burkhead 1993).

9 Habitat

The Bridle Shiner’s habitat includes lakes, ponds, sluggish mud-bottomed pools of creeks and small rivers, beaver ponds, marshes, and impoundments (Page and Burr 1991; Jenkins and

Burkhead 1993). They can be found over mud, silt, sand, or detritus in slack-water areas (Lee et al. 1981; Jenkins and Burkhead 1993). The Bridle Shiner inhabits still or slow moving, clear water about 60 cm deep, and inhabits areas of moderate to abundant amounts of vegetation (Lee et al. 1981; Smith 1985; Jenkins and Burkhead 1993; Finger 2001).

The Bridle Shiner usually stays near or on bottom areas (Leckvarcik 2001). Bridle

Shiners use emergent and submerged aquatic vegetation for spawning, foraging, and cover

(Leckvarcik 2005).

In Massachusetts Bridle Shiners tend to occur in habitats with moderate nutrient levels.

They inhabit significant amounts of low submerged aquatic plants such as feather-leaved submerged aquatic plants (e.g., Coontail, Ceratophyllum spp.) and broad-leaved submerged aquatic plants (e.g., Pondweed, Potamogeton spp.) (Chandler 1999). There is a significant negative association between the abundance of Bridle Shiners and the abundance of Largemouth

Bass, Micropterus salmoides. Additionally, in Massachusetts Bridle Shiners are associated with a wide abundance of native fishes and aquatic macroinvertebrates, and are indicators of high water quality conditions (Chandler 1999).

Feeding

The Bridle Shiner feeds by sight during daylight hours (Smith 1985). They feed where there is little current. Food is taken near vegetation and the bottom. Their diet includes plankton; living plant material; algae; small microcrustaceans including copepods (minute planktonic or

10 parasitic crustaceans) and cladocerans (waterfleas); and small aquatic macroinvertebrates including small aquatic insects, amphipods (scuds), water mites, and small mollusks (Lee et al.

1981; Smith 1985; Jenkins and Burkhead 1993; Finger 2001). Small aquatic insects are the most important food items followed by amphipods, copepods, and cladocerans (Lee et al. 1981; Smith

1985; Finger 2001).

In Massachusetts the locations with Bridle Shiners had significantly greater aquatic macroinvertebrate taxa richness. Several aquatic macroinvertebrate taxa were found in greater abundance in the presence of Bridle Shiners including scuds (Gammarus spp.) and small squaregilled mayflies (Caenis spp.) (Chandler 1999).

Spawning/Development

The Bridle Shiner is a broadcast spawner, indiscriminately dispersing eggs over aquatic vegetation with no nest preparation (Finger 2001; Leckvarcik 2001). Spawning occurs between mid-May and mid-July where there are calm pools with minimal current, the water temperature increases to above 17 oC, and the photoperiod is relatively long (Finger 2001; Helfman et al.

2009). Spawning sites are usually about 60 cm deep in openings surrounded by areas of heavy emergent or submerged vegetation (Lee et al. 1981; Smith 1985).

Spawning activity usually occurs in the morning hours with males pursuing females.

Before spawning, the female hovers nearly motionless close to the surface (Lee et al. 1981; Smith

1985; Finger 2001). The male “noses” (bumps) his snout along the female’s lower side and snout

(Jenkins and Burkhead 1993). If the female is not ready to spawn, she moves away to feed.

Chases occur during the spawning act where males may pursue other males or females (Lee et al.

1981; Smith 1985; Finger 2001). During the chase, the male continues to “nose” the female with

11 his snout (Jenkins and Burkhead 1993). These chases can last up to a minute and cover a distance of several meters (Lee et al. 1981; Smith 1985; Finger 2001).

Spawning occurs many times a day (Lee et al. 1981; Smith 1985; Finger 2001). Only a few (6-15) eggs are released each time (Jenkins and Burkhead 1993). The fertilized eggs sink to the bottom, adhere to vegetation and bottom particles, and hatch in about 55 hours depending upon water temperature (Lee et al. 1981; Smith 1985; Jenkins and Burkhead 1993; Finger 2001).

The newly hatched young remain in vegetation at first, and then begin to swim in small groups. By late July, the young are in schools of over 100 or more, and by August they are joining the adult schools (Lee et al. 1981; Smith 1985; Finger 2001). The Bridle Shiner matures in one year with males maturing slightly faster than females. Maximum longevity for both males and females is a little over two years (Jenkins and Burkhead 1993).

Native Range

The Bridle Shiner’s native range (Fig. 1-2) includes the Atlantic Coast drainages from

Maine to the border of North Carolina, mostly north of Pennsylvania (Page and Burr 1991). It is also found in the Lake Ontario/St. Lawrence River basin (Lee et al. 1981; Jenkins and Burkhead

1993).

12

Figure1-2: Native Range of the Bridle Shiner (Notropis bifrenatus)(Page and Burr 1991).

For Pennsylvania, the Bridle Shiner historically inhabited the Susquehanna River drainage and the Delaware River drainage. Populations have significantly decreased and are recently found in one (i.e., Marshalls Creek) of thirty-one other historical locations in

Pennsylvania (Criswell 1998a, 1998b, 1998c; Finger 2001). Several factors including habitat alteration, losses of stream vegetation, urbanization, industrialization, water diversion, industrial and sewage plant discharges, and increased turbidity and sedimentation have all been implicated for this population decline (Finger 2001; Leckvarcik 2001).

The Bridle Shiner was once widespread in Maryland. After extensive collection efforts in areas of historical occurrence since 1984 that resulted in no Bridle Shiners, the extirpation of the Bridle Shiner in Maryland has now been reported. The exact cause of the extirpation is unknown, but declines in other regions have been attributed to increased sedimentation and turbidity, the constant loss of native aquatic vegetation, the increase in non-native plants including Hydrilla, Hydrilla verticillata, and Eurasian Watermilfoil, Myriophyllum spicatum, and

13 the increase of non-native predators including the Largemouth Bass, Micropterus salmoides, and the Channel Catfish, Ictalurus punctatus (Kilian et al. 2010).

Populations of Bridle Shiners in Virginia have been localized and some populations have been extirpated or nearly so (e.g., the Potomac drainage and the Rappahannock drainage).

Habitat alteration (i.e., increased water turbidity and consequent light reduction that impairs growth of submerged aquatic plants and food-sighting ability of the fish) seems to be the general cause of the localization and population decline (Jenkins and Burkhead 1993).

Ironcolor Shiner (Notropis chalybaeus)

Morphological/Meristic Description

Figure1-3: Ironcolor Shiner (Notropis chalybaeus)(Kraft et al. 2006).

Ironcolor Shiner (Fig. 1-3) with black stripe from spot on caudal fin along side around snout. Stripe over both lips and chin. Inside of mouth black (Page and Burr 1991). Body form moderately to well compressed, with some adults quite deep (Jenkins and Burkhead 1993).

Dorsal fin origin above pelvic fin origin. Pointed snout and terminal mouth small and oblique

(Page and Burr 1991; Jenkins and Burkhead 1993).

14 Dorsally, Ironcolor Shiner straw yellow with dusty stripe along back. Scales darkly outlined except above black stripe, with occasional orange-gold streak. Ventrally Ironcolor

Shiner silver-white. Lateral line usually incomplete with 31--37 scales (Page and Burr 1991).

Anal fin with 8 rays, dorsal fin with 8 rays, and caudal fin with 19 principal rays (Jenkins and

Burkhead 1993). Pharyngeal teeth arrangement 2, 4-4, 2. Maximum adult length 6.5 cm (Page and Burr 1991).

Nuptial males with medium-large tubercles on chin, snout, cheek, and pectoral fins.

Females occasionally with tubercles on lower jaw. Nuptial males bright yellow-olive with reddish brown along the side. Nuptial males orange and rosy on all fins. Nuptial females similar color on side and fins, but paler (Jenkins and Burkhead 1993). Nuptial females with extended stomachs (Leckvarcik 2001).

Etymology

The Ironcolor Shiner is named for the fish’s shining dark lateral stripe. Notropis translates to “back keel” and was probably based on a specimen whose back was ridged owing to shrinkage. The specific epithet chalybaeus means steel or iron (Jenkins and Burkhead 1993).

Habitat

The Ironcolor Shiner’s habitat includes well-vegetated, clear, sand-bottomed pools; and very slow runs of swamps, creeks, streams, and small rivers (Page and Burr 1991; Jenkins and

Burkhead 1993). Non-tidal Coastal Plain lakes and ponds with sandy substrates also provide good habitat (Leckvarcik 2001).

15 The Ironcolor Shiner usually stays in the mid-water or near surface areas (Lee et al.

1981). Ironcolor Shiners use emergent and submerged aquatic vegetation for spawning, foraging, and cover (Leckvarcik 2005).

Feeding

The Ironcolor Shiner feeds by sight during daylight hours (Leckvarcik 2001). The

Ironcolor Shiner’s diet mostly includes small aquatic insects, some terrestrial insects, and plant material (Lee et al. 1981; Jenkins and Burkhead 1993; Leckvarcik 2001). They also fed on a variety of small crustaceans and mollusks, which they shred with their pharyngeal teeth

(Leckvarcik 2001).

In Pennsylvania their small aquatic insect diet mostly includes Ephemeroptera (mayflies), certain Trichoptera (caddisflies) and certain Diptera (true flies). Their crustacean diet includes cladocerans (waterfleas) and copepods (minute planktonic or parasitic crustaceans) (Leckvarcik

2001).

Spawning/Development

The Ironcolor Shiner is a broadcast spawner, indiscriminately dispersing these eggs over aquatic vegetation with no nest preparation. Spawning occurs between May and August depending on region, and is controlled by temperature and photoperiod. Spawning locations include areas of relatively low flow with heavy submerged and emergent vegetation and sandy bottoms (Jenkins and Burkhead 1993; Leckvarcik 2001; Helfman et al. 2009).

Females are fractional spawners and produce multiple clutches of mature eggs throughout the spawning season (Leckvarcik 2001). Gravid females can hold over 200 eggs (Jenkins and

16 Burkhead 1993). During spawning, males swim alongside a female and often dash across pools to separate females. Males also chase and nip other males. The fertilized eggs sink and stick to aquatic vegetation and particles on the stream bottom (Leckvarcik 2001).

Newly hatched young remain in thick vegetation for about 60 days. At this time they leave the protection of vegetation and join adult schools (Leckvarcik 2001). The Ironcolor Shiner matures in one year with males and females maturing simultaneously. Longevity for both males and females is over two years (Jenkins and Burkhead 1993).

Native Range

The Ironcolor Shiner’s native range (Fig. 1-4) is highly fragmented and includes the lowlands of the Atlantic Coast, Gulf Coast, and Mississippi River drainages from New York to

Florida to Texas mostly south of Pennsylvania (Page and Burr 1991). The Ironcolor Shiner’s native range also includes sporadic areas of the southern Great Lakes region in Wisconsin,

Illinois, and Indiana (Lee et al. 1981). Except in the Southeast, most populations are disjointed

(Jenkins and Burkhead 1993).

17

Figure1-4: Native Range of the Ironcolor Shiner (Notropis chalybaeus)(Page and Burr 1991).

The Ironcolor Shiner has disappeared from some areas of New Jersey. Populations in

Iowa have been reported as extirpated. Populations in Delaware and Virginia are uncommon

(Leckvarcik 2001).

The Ironcolor Shiner populations in Pennsylvania have significantly decreased. The only known population in Pennsylvania is in Marshalls Creek, a part of the Delaware River drainage.

Several factors including habitat alteration, losses of stream vegetation, water diversion, industrial and sewage plant discharges, and increased turbidity also have all been implicated for this population decline (Leckvarcik 2001).

Populations of the Ironcolor Shiner in Virginia have peculiarities. They are absent from most of the Chesapeake basin. They are found, however, in the relatively small Piankatank River drainage that is isolated between the Rappahannock and York River drainages. They are well distributed in southeast corner of Virginia along the North Carolina border. The Bridle and

Ironcolor shiner are the most diminutive of shiners in Virginia. The poor success of the Ironcolor

18 Shiner populations in Virginia parallels that of the Bridle Shiner populations in Virginia (Jenkins and Burkhead 1993).

Comparisons

Morphologically, the Bridle and Ironcolor shiners are very similar in appearance, shape, and size. Both species have similar scale, snout, and fin structure; have similar color from above, laterally, and from below; and grow to a maximum length of about 6.5 cm. A key to separating these two species is to look directly at their mouth from a frontal view. The Bridle Shiner will only have a darkened upper lip (looks like a moustache), while the Ironcolor Shiner has both a darkened upper and lower lip (Page and Burr 1991).

Habitat preference is very similar. Both species prefer to live in clear, relatively deep, very slow moving water in streams, creeks, small rivers, ponds, and lakes. Both species prefer a mud and sand mixture for substrate habitat, and use emergent and submerged aquatic vegetation for spawning, foraging, and cover (Jenkins and Burkhead 1993; Finger 2001; Leckvarcik 2001).

While living in the same water column, Bridle Shiners generally stay near the bottom and

Ironcolor Shiners generally stay near mid-depth to near the surface (Finger 2001).

Feeding preferences are very similar. The macroinvertebrate diet of both species includes Ephemeroptera (mayflies) taxa, Trichoptera (caddisflies) taxa, Diptera (true flies) taxa,

Amphipoda (scuds) taxa, Gastropoda (snails) taxa and Bivalvia (clams) taxa (Lee et al. 1981;

Smith 1985; Jenkins and Burkhead 1993; Finger 2001; Leckvarcik 2001).

Both species are broadcast spawners, indiscriminately dispersing their eggs over aquatic vegetation with no nest preparation. Both species spawn from late May to mid-August when water temperatures are higher and photoperiods are longer. Both species deposit eggs on emergent and submerged plants. Spawning plants for both species include Ceratophyllum (i.e.,

19 coontail species, feather-leaved submerged aquatic plants) and Potamogeton (i.e., pondweed species, broad-leaved submerged aquatic plants) (Lee et al. 1981; Jenkins and Burkhead 1993;

Finger 2001; Leckvarcik 2001; Helfman et al. 2009).

Native ranges for the Bridle and Ironcolor shiner are different. Both native ranges, however historically overlap in New York, New Jersey, Pennsylvania, Delaware, Maryland and

Virginia. Marshalls Creek, Pennsylvania, is in the region where both native ranges currently overlap (Page and Burr 1991).

20 Chapter 2

Methods and Materials

Research Sites

In 2010 I initiated collection of aquatic habitat character data in Marshalls Creek, where five research sites were already established. In 2011 a sixth site was established in Marshalls

Creek. In 2012 I expanded my aquatic habitat character research data by visiting other rivers, streams, creeks, and brooks that historically yielded endangered shiners. To the northeast of

Pennsylvania, I visited seven Massachusetts watersheds that historically yielded the Bridle

Shiner. To the south of Pennsylvania, I visited two Maryland and four Delaware watersheds that historically yielded the Ironcolor Shiner. Additionally, I visited two sites in eastern Pennsylvania near Marshalls Creek where Bridle and Ironcolor shiners were re-introduced in 2004 and 2005.

Bridle and Ironcolor shiner endangered species status for these states are listed in Table2-

1 and Table2-2. New York and New Jersey species status are added as interesting information from Pennsylvania bordering states. Massachusetts is not mentioned in the Table2-2 because it is beyond the native range for the Ironcolor Shiner.

21 Table2-1: Bridle Shiner Endangered Species Status.

State Endangered Special Concern Not listed Massachusetts x New York x New Jersey x Pennsylvania x Delaware x Maryland x*

* Endangered/extirpated for Maryland in 2010 (Kilian et al. 2011)

(DEDFW 2012b; MADFW 2012d; MDDNR 2012c; NJDEP 2012; NYDEC 2013; PAC 2013)

Table2-2: Ironcolor Shiner Endangered Species Status.

State Endangered Special Concern Not Listed New York x New Jersey x Pennsylvania x Delaware x Maryland x

(DEDFW 2012b; MADFW 2012d; MDDNR 2012c; NJDEP 2012; NYDEC 2013; PAC 2013)

22 All research sites historically yielded Bridle and/or Ironcolor shiners. I collected aquatic habitat character data at 21 of these historical sites in Pennsylvania, Maryland, Delaware, and

Massachusetts (Fig. 2-1).

Seven Bridle Shiner Research Sites in MA

Eight Bridle Shiner and Ironcolor Shiner Research Sites in PA (including the six research sites in Marshalls Creek)

Two Ironcolor Shiner Research Sites in MD

Four Ironcolor Shiner Research Sites In DE

Figure2-1: Research Sites for the Bridle Shiner in Massachusetts, for the Bridle and Ironcolor Shiner in Pennsylvania, for the Ironcolor Shiner in Maryland, and for the Ironcolor Shiner in Delaware (Delorme 2013).

23 Marshalls Creek

Marshalls Creek (Delaware River drainage, Monroe County, Pennsylvania) is approximately 42 km long. Marshalls Creek headwaters flow from the Pocono escarpment, and the entire drainage area is 69.4 square kilometers (BWA 2010). Marshalls Creek water quality is designated as a high quality cold-water fishery by the Pennsylvania Code water quality standards

(Leckvarcik 2005). The Bridle and Ironcolor shiner inhabit a 3.7 km reach of Marshalls Creek

(Fig. 2-2).

3.7 km

Figure2-2: 3.7 km Reach of Marshalls Creek, Monroe County, Pennsylvania, Where the Bridle and Ironcolor Shiner Co-Exist (Delorme 2013).

24 I sampled six Marshalls Creek sites (Sites 0-5). Site 0 is the farthest downstream. Site 5 is the farthest upstream (Fig. 2-3).

Site 5

Site 4

Site 3

Site 2

Site 1

Site 0

Figure2-3: Research Sites 0-5 at Marshalls Creek, Monroe County, Pennsylvania (Delorme 2013).

25 Because of the presence of endangered shiners and the related Environmental Impact

Statements, Dr. Jay R. Stauffer, Jr. and his Penn State graduate students have been working with the Pennsylvania Department of Transportation to monitor Marshalls Creek since 2001 (PDT

1999a, 1999b). Road bypass construction around the town of Marshalls Creek began in

September 2010 and was completed in August 2013 (Fig. 2-4).

Site 5

Road bypass

Site 0

Figure2-4: Road Bypass Construction at Marshalls Creek, Monroe County, Pennsylvania (Delorme 2013).

26 For the last three years, Dr. Jay R. Stauffer, Jr. and his Penn State graduate students have been remotely monitoring Marshalls Creek water chemistry (PDT 2012). For many years fish species and aquatic macroinvertebrate taxa have also been collected to monitor stream health.

I have collected fishes and benthic macroinvertebrates and recorded remote monitoring data since March 2010; moreover since January 2011, I have been collecting aquatic plant/algae species (Table 2-3).

Table2-3: Marshalls Creek Sites 0-5 Remote Chemistry Monitoring Start Dates; and Fishes, Aquatic Macroinvertebrates, and Aquatic Plants/Algae Collection Start Dates.

Remote Aquatic Aquatic Location Chemistry Fishes Macroinvertebrates Plants/Algae Site 0 1 August 2010 11 October 2006 17 December 2010 17 January 2011 Site 1 1 August 2010 11 October 2006 3 August 2001 17 January 2011 Site 2 1 August 2010 11 October 2006 3 August 2001 17 January 2011 Site 3 1 August 2010 11 October 2006 3 August 2001 17 January 2011 Site 4 1 August 2010 8 June 2011 5 March 2011 17 January 2011 Site 5 8 June 2011 8 June 2011 3 August 2011 28 October 2011

27 Other Historical Sites

Maryland

The two historical sites for the Ironcolor Shiner that I sampled in Maryland were Long

Marsh Ditch and Zekiah Swamp (Fig. 2-5).

Long Marsh Ditch

Zekiah Swamp

Figure2-5: Long Marsh Ditch and Zekiah Swamp; Both are Historical Watersheds in Maryland for the Ironcolor Shiner (Delorme 2013).

28 Delaware

The four historical sites for the Ironcolor Shiner that I sampled in Delaware were

Nanticoke River, Gum Branch (mainstream), Gum Branch (headwaters), and West Branch (Fig.

2-6).

West Branch

Gum Branch (headwaters)

Nanticoke River

Gum Branch (mainstream)

Figure2-6: Nanticoke River, Gum Branch (mainstream), Gum Branch (headwaters), and West Branch; All are Historical Watersheds for the Ironcolor Shiner in Delaware (Delorme 2013).

29 Massachusetts

The seven historical sites that I sampled in Massachusetts for the Bridle Shiner were

Clifford Road Dam Outlet, Eel Creek, Flat Brook, Hop Brook, West Branch Farmington River,

Schenob Brook, and Dry Brook (Fig. 2-7).

Flat Brook

W. Branch Farmington River

Hop Brook

Eel Creek/ Clifford Rd Dam Outlet

Schenob Brook

Dry Brook

Figure2-7: Clifford Road Dam Outlet, Eel Creek, Flat Brook, Hop Brook, West Branch Farmington River, Schenob Brook, and Dry Brook; All are Historical Watersheds Sambofor the Bridle Shiner in Massachusetts (Delorme 2013). Creek

McMichael s Creek

30 Pennsylvania

The two additional historical sites that I sampled in Pennsylvania for both species of endangered shiners were Sambo Creek and McMichael Creek (Fig. 2-8). Thousands of Bridle and Ironcolor shiners were propagated and released into these two Pennsylvania watersheds in the

Delaware River drainage as part of a restoration project in 2003 and 2004 (Leckvarcik 2005).

Marshalls Creek Research Sites

Sambo Creek

McMichael Creek

Figure2-8: Sambo Creek, McMichael Creek, and Marshalls Creek Research Sites; Sambo Creek and McMichael Creek are Re-Introduction Watersheds in Pennsylvania for the Bridle and Ironcolor Shiner (Delorme 2013).

31 Research Site Collections and Measurements

I electrofished for fishes, used D-frame kick nets for aquatic macroinvertebrates, hand collected aquatic plants/algae, used various water chemistry analyses for chemical habitat characters, and used Rapid Bioassessment Protocols (RBPs) for physical habitat characters

(Barbour et al. 1999).

In order to create NetWeaver model dependency networks (discussed later in this chapter), I associated biological habitat character taxa (i.e., fish associates, aquatic macronvertebrates, and aquatic plants/algae) based on their relationship to these two endangered shiners. Existing literature and website data were utilized to associate taxa data. Based on morphological, meristic, and/or phylogenetic characteristics, all biological habitat character taxa were associated into the following groups:

a. Fish associates groups - (1) endangered shiner predator species and (2) endangered

shiners non-predator species,

b. Aquatic macroinvertebrates groups - (1) edible aquatic macroinvertebrate

taxa consumed by endangered shiners and (2) non-edible aquatic

macroinverebrate taxa associated with endangered shiners, and

c. Aquatic plants/algae groups - (1) spawning plant species used by endangered

shiners and (2) non-spawning plant/algae species associated with endangered

shiners.

32 Biological Habitat Characters

Fishes

For all research sites, fishes were collected using standard electrofishing procedures and guidance (Reynolds 1996). Fishes were collected with battery powered backpack electrofishing gear (i.e., Smith-Root, LR-24, set at pulsed 300 volts direct current) using one pass completion in

100 m reaches. Due to private property restrictions, one pass completion in 50 m reaches were used in five of the other historical research sites (i.e., Eel River, MA; Flat Brook, MA; Schenob

Brook, MA; Sambo Creek, PA; and McMichael Creek, PA).

Fishes were sorted, counted, and identified using a field guide (Page and Burr 1991).

For Marshalls Creek research sites, all sport fishes and endangered species were immediately released, and some fishes were labeled with stream location information and placed in permanent storage in The Pennsylvania State University Fish Museum. For all the other historical research sites, pictures were taken of all fishes to document the species collected and all fishes were then released.

For Marshall Creek research sites, annual collections have occurred every summer for several years. For all the other historical research sites, collections occurred only once in the summer of 2012.

In order to create NetWeaver model dependency networks (discussed later in this chapter), I associated trophic relationships of these two endangered shiners with fish associates and correlated the native/exotic status of fishes. Based on morphological, meristic, and/or phylogenetic characteristics, fish associates were associated into the following groups: (1) endangered shiner predator species and (2) endangered shiners non-predator species. For the purposes of this study endangered shiners predator species were piscivores, and endangered

33 shiners predator species were those that I determined preyed on endangered shiners.

Additionally, all fishes were correlated into native fish species or exotic fish species. Existing literature data (i.e., Lee et al. 1981, Page and Burr 1991, Jenkins and Burkhead 1993) were used for these relationships.

Aquatic Macroinvertebrates

Aquatic macroinvertebrates were collected using a standard D-frame kick net with a

1,200-micrometer mesh (Mackey et al. 1984). The net was placed facing upstream. The substrate directly upstream of the net was kicked and agitated for 20 seconds by the operator so that dislodged aquatic macroinvertebrates were swept into the net by the current. Ten of these kick samples (20 seconds duration for each) were taken across the width of stream. Each aquatic macroinvertebrate sample was labeled with stream location information and stored in a 2-liter plastic container with 70% ethanol.

In the laboratory aquatic macroinvertebrates were identified to order, family, or genus depending on specimen type (Peckarsky et al. 1990; Merritt et al. 2008). Common names for orders, families, and genera were found in several references (McCafferty 1998; Voshell 2002;

ADW 2013; EOL 2013; VanDyk 2013). All specimens were stored in the laboratory of Dr. Jay

R. Stauffer, Jr. at The Pennsylvania State University.

For Marshalls Creek research sites, collections have occurred for several years every

March, August, and December; and the same location was always used for each research site collection. For all the other historical research sites, collections occurred only once in the summer of 2012.

In order to create NetWeaver model dependency networks (discussed later in this chapter), I associated trophic relationships of these two endangered shiners with aquatic

34 macroinvertebrates. Based on morphological, meristic, and/or phylogenetic characteristics, aquatic macroinvertebrate taxa were associated into the following groups: (1) edible aquatic macroinvertebrate taxa consumed by endangered shiners and (2) non-edible aquatic macroinverebrate taxa associated with endangered shiners. Edible aquatic macroinvertebrate taxa were those that I determined were consumed by these two endangered shiners. Existing literature data (i.e., Peckarsky et al. 1990; McCafferty 1998; Voshell 2002; Merritt et al. 2008) and feeding preference data of these two endangered shiners (See Chapter 1) were used for these relationships.

Aquatic Plants/Algae

Aquatic plants/algae were collected by hand in 100 m reaches. Due to private property restrictions, 50 m reaches were used for hand collections in five of the other historical research sites (i.e., Eel River, MA; Flat Brook, MA; Schenob Brook, MA; Sambo Creek, PA; and

McMichael Creek, PA). Each aquatic plant/algae sample was labeled with stream location information and stored in a 2-liter plastic container with freshwater.

In the laboratory aquatic plants/algae were rinsed and drip-dried. Aquatic plant/algae specimens were then laid as flat as possible between sheets of newspaper. A cardboard drier then separated each specimen. A plant press was used to stack and hold specimens for one month to dry. Each specimen was identified to the genus/species level using two references (Fassett 1957;

USDA 2012). Common names were found in two references (Fassett 1957; USDA 2012). All specimens were stored in the laboratory of Dr. Jay R. Stauffer, Jr. at The Pennsylvania State

University.

For Marshalls Creek Sites 0-4, PA, aquatic plants/algae were collected in January, March,

April, June, August, and October over a two-year period. For Marshalls Creek Site 5, PA, aquatic

35 plants/algae were collected in June, August, and October over a one-year period. For all the other historical research sites, collections occurred only once in the summer of 2012.

In order to create NetWeaver model dependency networks (discussed later in this chapter), I associated spawning relationships of these two endangered shiners with aquatic plants/algae. Based on morphological, meristic, and/or phylogenetic characteristics, aquatic plants/algae species were associated into the following groups: (1) spawning plant species used by endangered shiners and (2) non-spawning plant/algae species associated with endangered shiners. Spawning plant species were those that I determined were used by these two endangered shiners during spawning. Existing literature (i.e., Fassett 1957), website data (i.e., USDA 2012), and habitat and spawning preference data of these two endangered shiners (see Chapter 1) were used for these relationships.

Chemical Habitat Characters

For all Marshalls Creek sites, water chemistry was remotely monitored at the Marshalls

Creek Site 4, PA, (located upstream of the all road construction) and Marshalls Creek Site 0, PA,

(located downstream of all road construction) in order to determine if road construction was altering the chemical composition of Marshalls Creek. This remote monitoring system (i.e., Hach

Company sondes (calibrated monthly), Stevens Company transmission equipment) monitors pH, conductivity (microsiemens/cm), and dissolved oxygen (mg/liter) reporting results for the two sites every 30 minutes on a website (PDT 2012). I used water chemistry data from January 2011 to December 2012 to calculate ranges for pH, conductivity, and dissolved oxygen.

For all the other historical sites, water chemistry was measured using a portable chemistry monitoring kit (i.e., YSI Professional Plus (calibrated monthly)). This kit monitors pH, conductivity (microsiemens/cm), and dissolved oxygen (mg/liter). For all sites, alkalinity and

36 hardness were analyzed at each research site using commercial aquaria test strips. Test strips were held in the water for two seconds, dried for one minute, and then compared to a color chart to determine alkalinity (ppm) and hardness (ppm) levels.

Physical Habitat Characters

For all Marshalls Creek sites, water temperature (oC) was remotely monitored (i.e., Hach

Company sondes (calibrated monthly), Stevens Company transmission equipment) at the

Marshalls Creek Site 4, PA, (located upstream of all road construction) and Marshalls Creek Site

0, PA, (located downstream of all road construction) in order to determine if road construction is affecting stream health. This remote monitoring system monitors water temperature and reports results for the two sites every 30 minutes on a website (PDT 2012). I used water temperatures from January 2011 to December 2012 to calculate a range for water temperature for all research sites. For all the other historical research sites, water temperature (oC) was measured using a portable temperature monitoring kit (i.e., YSI Professional Plus (calibrated monthly)).

For all sites, water velocity (cm/sec) and depth (cm) measurements were obtained using a portable flow meter (i.e., Flo-Mate, Model 2000, Portable Flow Meter (calibrated monthly)) and associated sliding rod. For streams < 0.75 m, water velocity measurements were taken at 60% of total depth (this approximates mean column velocity). For streams 0.75 m, water velocity measurements were taken at 20% and 80% of total depth (from the top) and the average of these two velocities was calculated to get the mean column velocity.

For all sites, Rapid Bioassessment Protocols from the United States Environmental

Protection Agency were used to evaluate physical habitat characters including substrate composition (% mud/sand), riparian protection (% erosion), flow status (% flow to both banks), bank stability (% bank erosion), and channel alteration (% altered) (Barbour et al. 1999).

37

NetWeaver Model

Development and Application

I used NetWeaver software as a tool to construct various dependency networks for a reference ecosystem. The NetWeaver model I developed was a collection of simple data link questions, fuzzy logic arguments, dependency network (i.e., goal) groups, and dependency networks (i.e., goals) with their associated logic nodes. For a completed knowledge base, each dependency chain ended with a simple data link question. I developed 116 simple data link questions in the NetWeaver model (NDE 2013).

Fuzzy logic deals with reasoning that is approximate rather than exact or fixed, and it involves the concept of partial truth, where the truth value may range from completely false to completely true (NDE 2013). NetWeaver fuzzy logic is less arbitrary than the confidence factor approach used in rule-based systems (Negoita 1985, NDE 2013). NetWeaver fuzzy logic is concerned with “aboutness” and provides a metric for expressing a degree to which an observation on some variable belongs to a set that represents a concept (NDE 2013).

NetWeaver fuzzy logic arguments were created for all 116 simple data link questions in the NetWeaver model (Appendix Y). NetWeaver fuzzy logic argument parameters were based on collections and measurements at Marshalls Creek Site 1, PA (the model reference site). As indicated earlier in this chapter, biological habitat character taxa (i.e., fish associates, aquatic macronvertebrates, and aquatic plants/algae) were associated into groups (e.g., endangered shiner predator species) based on their relationship to endangered shiners. To make the NetWeaver fuzzy logic concept clear, two examples of NetWeaver fuzzy logic arguments are illustrated.

The first illustration of a NetWeaver fuzzy logic argument involves presence (true) or absence (false) of the American Eel, Anguilla rostrata, which was collected in Marshalls Creek

38 Site 1, PA (the model reference site). A simple data link question would be “Is the American Eel

present? 0=No, 1=Yes”. A NetWeaver fuzzy logic argument for this simple data link question

was created (Fig 2-9). The fuzzy set membership is shown on the Y-axis with -1.0 indicating no

fuzzy membership (i.e., false) and +1.0 indicating complete membership (i.e., true). The value

for the number entered (0 = No, 1 = Yes) is shown on the X-axis with “1 = Yes” fully satisfying

the argument (i.e, +1.0, true) and “0 = No” being an unacceptable number value (i.e., -1.0, false)

(NDE 2013).

2

(1.0,1.0) 1

0 -1 0 1 2

-1

Fuzzy Set Membership Set Fuzzy (0.0,-1.0)

-2

Is the American Eel present? 0=No, 1=Yes

Number entered: 0 = No, 1 = Yes

Figure2-9: NetWeaver Fuzzy Logic Argument for the Simple Data Link Question “Is the American Eel present? 0=No, 1=Yes”. NetWeaver Fuzzy Logic Argument Parameters were based on Collections and Measurements at Marshalls Creek Site 1, PA (the model reference site) (NDE 2013).

The second illustration of a NetWeaver fuzzy logic argument involves the range for the

value for pH that was measured in Marshalls Creek Site 1, PA (the model reference site). A

simple data link question would be “What is the pH?” A NetWeaver fuzzy logic argument for

this simple data link question was created (Fig 2-10). The fuzzy set membership is shown on the

39 Y-axis with -1.0 indicating no fuzzy membership (i.e., false) and +1.0 indicating complete

membership (i.e., true). The value for pH is shown on the X-axis with pH values between 5.8 and

8.5 (the range of pH measured at Marshalls Creek Site 1, PA) fully satisfying the argument (i.e,

+1.0, true). Values of pH between 5.6 and 5.8 and between 8.5 and 8.7 represent a certain

percentage of fuzzy membership. Values of pH < 5.6 and values of pH > 8.7 are unacceptable pH

values (i.e., -1.0, false) (NDE 2013).

1.5

(5.8,1.0) (8.5,1.0) 1

0.5

0 5 5.5 6 6.5 7 7.5 8 8.5 9 9.5 -0.5

Fuzzy Set Membership Set Fuzzy -1 (5.6,-1.0) (8.7,-1.0) -1.5

What is the pH?

pH

Figure2-10: NetWeaver Fuzzy Logic Argument for the Simple Data Link Question for “What is the pH?” NetWeaver Fuzzy Logic Argument Parameters were based on Collections and Measurements at Marshalls Creek Site 1, PA (the model reference site) (NDE 2013).

An example of a dependency network group for the NetWeaver model was titled “Fish”.

The dependency network group “Fish” contained all the simple data link questions (e.g., the

American Eel simple data link question above) for Marshalls Creek Site 1, PA (the model

reference site) (NDE 2013). There were seven dependency network groups (i.e., Fish, Macros,

40 Plants, Biological Habitat, Chemical Habitat, Physical Habitat, and Aquatic Habitat) in the

NetWeaver model that I developed.

NetWeaver software uses several logic nodes to define the logical dependency of a network on antecedent networks and simple data links (Table 2-4) (NDE 2013). I used a UNION node in most NetWeaver dependency networks because that was best suited for my analysis of comparing aquatic habitat characters for each research site. Because of certain simple data link questions, I used a NOT node in two applications within the fishes dependency network in order to give Marshalls Creek Site 1, PA (the model reference site) the highest strength of evidence score (discussed later in this chapter) of 200.

Table2-4: NetWeaver Model Logical Node Types and Their Function (NDE 2013).

Node Function

UNION A UNION node is the weighted average. Functionally, a UNION node performs a weighted average of all antecedents.

OR An OR node is true when any one of its antecedents is true. An OR node is false when all of its antecedents are false. Functionally, an OR node passes the value of its most true antecedent.

AND An AND node is true when all of its antecedents are true. An AND node is false when any one of its antecedents is false. Functionally, an AND node performs a weighted average of the values of its antecedents unless one of the antecedents is fully false.

NOT A NOT node inverts the value of its antecedent.

SOR A SOR node (sequential OR) is a special class of node designed to select between alternative decision scenarios where there is a definite hierarchy of quality level associated with each possible data gathering method.

XOR A XOR node (exclusive OR) is true when one and only one of its antecedents is true.

41 Dependency networks for biological habitat characters, chemical habitat characters, physical habitat characters, and aquatic habitat characters were created. A detailed description of dependency network approaches/assumptions and strength of evidence scores for the NetWeaver model that I developed is reported below.

Strength of Evidence Scores

This NetWeaver model was constructed in three steps. First, the model was built on an empirical reference data set. Second, an empirical input data set was entered into the model.

Third, strength of evidence scores (i.e., trueness levels) were produced from the model that compares the empirical input data set to the empirical reference data set (NDE 2013).

As indicated earlier (Chapter 1) Marshalls Creek Site 1, PA, aquatic (i.e., biological, chemical, and physical) habitat characters were used as the empirical reference data set. Each of the aquatic habitat characters at my other 20 research sites were then entered separately into the model as an empirical input data set. Strength of evidence scores were then produced from the model that compare the aquatic habitat characters at my other 20 research sites to the Marshalls

Creek Site 1, PA, reference aquatic habitat characters (NDE 2013).

For any given empirical input data set, a NetWeaver model produces strength of evidence scores with a range from -1.0 to +1.0. All strength of evidence scores between -1.0 and +1.0 indicate a trueness level. A score of -1.0 (100% false) is the lowest strength of evidence score possible and a score of +1.0 (100% true) is the highest strength of evidence score possible. When the empirical reference site data (i.e., the Marshalls Creek Site 1, PA, reference aquatic habitat characters) are entered into a NetWeaver model, the highest strength of evidence score of +1.0

(100% true) is always achieved because a NetWeaver model is built with the empirical reference data set (NDE 2013).

42 To simplify the strength of evidence score, I converted the -1.0 to +1.0 strength of evidence score range (a 2.0 difference) to a 0.0 to 200.0 strength of evidence score range, where

0.0 (a -1.0 NetWeaver model strength of evidence score, 100% false) is the lowest converted strength of evidence score possible and 200.0 (a +1.0 NetWeaver model strength of evidence score, 100% true) was the highest converted strength of evidence score possible. A converted strength of evidence score of 200.0 was always achieved for the Marshalls Creek Site 1, PA, reference aquatic habitat characters because it was the empirical reference data set (NDE 2013).

Biological Habitat Characters Dependency Network

The biological habitat characters dependency network (Fig. 2-11) was the weighted average (i.e., UNION node) strength of evidence score (i.e., trueness level) for fishes, aquatic macroinvertebrates, and aquatic plants/algae (NDE 2013).

Biological Habitat Characters

UNION node

Aquatic Aquatic Fishes Macroinvertebrates Plants/Algae

Figure2-11: Biological Habitat Characters Dependency Network for the NetWeaver Model (NDE 2013).

43 Fishes Dependency Network

The fishes dependency network (Fig. 2-12) was the weighted average (i.e., UNION node) strength of evidence score (i.e., trueness level) for endangered shiners predator species, additional

(i.e., not found at the model reference site) endangered shiners predator species, endangered shiners non-predator species, native species, and additional (i.e., not found at the model reference site) exotic species (NDE 2013). As indicated earlier, a NOT node was used in two applications within this dependency network. The only time the presence of Bridle and/or Ironcolor shiners was used in any of the NetWeaver model dependency networks was in the percentage of native species calculation (Chapter 3).

Fishes

UNION node

Endangered Native Additional Exotic Additional Endangered Shiners Species Species Endangered Shiners Predator (NOT node used) Shiners Non-Predator Species Predator Species Species (NOT node used)

Figure2-12: Fishes Dependency Network for the NetWeaver Model (NDE 2013).

44 Aquatic Macroinvertebrates Dependency Network

The aquatic macroinvertebrate dependency network (Fig. 2-13) was the weighted average

(i.e., UNION node) strength of evidence score (i.e., trueness level) for edible aquatic macroinvertebrate taxa consumed by endangered shiners and non-edible aquatic macroinvertebrate taxa associated with endangered shiners. Because of the importance of edible aquatic macroinvertebrate taxa consumed by these two endangered shiners to the feeding preference data reported in Chapter 1, edible aquatic macroinvertebrate taxa consumed by endangered shiners were weighted by a factor of three (I chose a factor of three, others may decide to use a different factor.)(NDE 2013).

Aquatic Macroinveretebrates

UNION node

Endangered Shiners Endangered Shiners Edible Non-Edible Aq. Macroinvertebrate Aq. Macroinvertebrate Taxa Taxa (x 3)

Figure2-13: Aquatic Macroinvertebrates Dependency Network for the NetWeaver Model (NDE 2013).

45 Aquatic Plants/Algae Dependency Network

The aquatic plant/algae dependency network (Fig. 2-14) was the weighted average (i.e.,

UNION node) strength of evidence score (i.e., trueness level) for spawning plant species used by endangered shiners and non-spawning plant/algae species associated with endangered shiners.

Because of the importance of spawning plant species used by these two endangered shiners to the spawning preference data reported in Chapter 1, spawning plant species used by endangered shiners were weighted by a factor of three (I chose a factor of three, others may decide to use a different factor.) (NDE 2013).

Aquatic Plants/Algae

UNION node

Endangered Shiners Endangered Shiners Spawning Non-Spawning Plant Plant/Algae Species Species (x 3)

Figure2-14: Aquatic Plants/Algae Dependency Network for the NetWeaver Model (NDE 2013).

46 Chemical Habitat Characters Dependency Network

The chemical habitat characters dependency network (Fig. 2-15) was the weighted average (i.e., UNION node) strength of evidence score (i.e., trueness level) for pH, dissolved oxygen (mg/liter), conductivity (microsiemens/cm), alkalinity (ppm), and hardness (ppm) (NDE

2013).

Chemical Habitat Characters

UNION node

Dissolved pH Conductivity Alkalinity Hardness Oxygen

Figure2-15: Chemical Habitat Characters Dependency Network for the NetWeaver Model (NDE 2013).

47 Physical Habitat Characters Dependency Network

The physical habitat characters dependency network (Fig. 2-16) was the weighted average (i.e., UNION node) strength of evidence score (i.e., trueness level) for water temperature

(oC), depth (cm), velocity (cm/sec), substrate composition (% mud/sand), riparian protection (% erosion), flow status (% flow to both banks), bank stability (% bank erosion), and channel alteration (% altered). Because of the importance of depth, velocity, and substrate composition to the habitat preference data of these two endangered shiners reported in Chapter 1, each was weighted by a factor of three (I chose a factor of three, others may decide to use a different factor.) (NDE 2013).

Physical Habitat Characters

UNION node

Water Depth Velocity Substrate Composition Riparian Flow Bank Channel Temperature (x 3) (x 3) Protection Status Stability Alteration (x 3)

Figure2-16: Physical Habitat Characters Dependency Network for the NetWeaver Model (NDE 2013).

48 Aquatic Habitat Characters Dependency Network

The aquatic habitat characters dependency network (Fig. 2-17) was the weighted average

(i.e., UNION node) strength of evidence score (i.e., trueness level) for biological habitat characters, chemical habitat characters, and physical habitat characters (NDE 2013).

Aquatic Habitat Characters

UNION node

Biological Habitat Chemical Habitat Physical Habitat Characters Characters Characters

Figure2-17: Aquatic Habitat Characters Dependency Network for the NetWeaver Model (NDE 2013).

With all the above NetWeaver simple data links, dependency network groups, fuzzy logic arguments, and dependency networks, I developed a NetWeaver model that represented the complex aquatic (i.e., biological, chemical, and physical) habitat characters for Marshalls Creek

Site 1, PA, reference site. Over 150 biological, chemical, and physical habitat characters were

49 part of this NetWeaver modeling tool. Other historical sites from Maryland, Delaware,

Massachusetts, and Pennsylvania, including other Marshalls Creek sites were compared, contrasted, and evaluated by the NetWeaver model using the Marshalls Creek Site 1, PA, reference ecosystem. All of these NetWeaver model network components were utilized to produce strength of evidence scores (i.e., trueness levels) to compare the input aquatic habitat characters of 20 research sites to the reference aquatic habitat characters of Marshalls Creek Site

1, PA (NDE 2013).

50 Chapter 3

Results

Research Site Collections and Measurements

The number of collections for fishes, aquatic macroinvertebrates, aquatic plants/algae, and certain chemical/physical habitat characters varied for research sites. Raw data collection was utilized, and the data results from research site collections and measurements were not standardized.

Biological Habitat Characters

Endangered Shiners

Throughout the study 21 research sites were sampled (Appendixes A-U), and the endangered shiners were collected and observed, including a total of 389 Bridle and 433

Ironcolor shiners (Table 3-1). Bridle and Ironcolor shiners were listed as native species

(Appendix V). As indicated earlier (Chapter 2) the only time the presence of Bridle and/or

Ironcolor shiners was used in any of the NetWeaver model dependency networks was in the percentage of native species calculation (discussed later in this chapter). These data were used in the NetWeaver model dependency networks to produce strength of evidence scores (Chapters 1 and 2).

51 Table3-1: Number of Endangered Shiners Collections and Endangered Shiners Collected and Observed at All Research Sites.

Endangered Shiner Bridle Shiners Ironcolor Shiners Location Collections Collected/Observed Collected/Observed Marshalls Creek Site 1, PA 7 261/1000+ 307/1000+ (model reference site)

Marshalls Creek Site 0, PA 7 8/0 4/0 Marshalls Creek Site 2, PA 7 44/0 35/0 Marshalls Creek Site 3, PA 7 50/0 71/0 Marshalls Creek Site 4, PA 2 0/0 0/0 Marshalls Creek Site 5, PA 2 0/0 0/0 Long Marsh Ditch, MD 1 0/0 0/0 Zekiah Swamp, MD 1 0/0 0/0 Nanticoke River, DE 1 0/0 7/100+ Gum Branch (main.), DE 1 0/0 4/50+ Gum Branch (head.), DE 1 0/0 5/200+ West Branch, DE 1 0/0 0/0 Clifford Rd Dam Outlet, MA 1 2/10+ 0/0 Eel Creek, MA 1 0/0 0/0 Flat Brook, MA 1 6/35+ 0/0 Hop Brook, MA 1 9/200+ 0/0 W. Branch Farm. River, MA 1 0/0 0/0 Schenob Brook, MA 1 0/0 0/0 Dry Brook, MA 1 9/20+ 0/0 Sambo Creek, PA 1 0/0 0/0 McMichael Creek, PA 1 0/0 0/0

Marshalls Creek Site 1, PA, clearly (by two orders of magnitude) contained the largest populations of Bridle and Ironcolor shiners (Table 3-1). Therefore, all aquatic (i.e., biological, chemical, and physical) habitat characters from Marshalls Creek Site 1, PA, were used as a model reference (i.e., benchmark) data set for the NetWeaver model (Chapters 1 and 2).

52 Fish Associates

Throughout the study 21 research sites were sampled (Appendixes A-U), and 31 species of fish associates were collected (Table 3-2), including 16 endangered shiners predator species and 15 endangered shiners non-predator species (Appendix V). As indicated earlier (Chapter 2) for the purposes of this study endangered shiners predator species were piscivores, and endangered shiners predator species were those that I determined preyed on these two endangered shiners. These data were used in the NetWeaver model dependency networks to produce strength of evidence scores (Chapters 1 and 2).

53 Table3-2: Number of Fish Associate Collections, Fish Associate Species, Endangered Shiners Predator Species, and Endangered Shiners Non-Predator Species at All Research Sites.

Endangered Endangered Fish Fish Shiners Shiners Associate Associate Predator Non-Predator Location Collections Species Species Species Marshalls Creek Site 1, PA 7 16 9 7 (model reference site)

Marshalls Creek Site 0, PA 7 13 8 5 Marshalls Creek Site 2, PA 7 20 10 10 Marshalls Creek Site 3, PA 7 20 9 11 Marshalls Creek Site 4, PA 2 18 8 10 Marshalls Creek Site 5, PA 2 12 6 6 Long Marsh Ditch, MD 1 10 4 6 Zekiah Swamp, MD 1 5 3 2 Nanticoke River, DE 1 2 2 0 Gum Branch (main.), DE 1 9 4 5 Gum Branch (head.), DE 1 7 3 4 West Branch, DE 1 7 3 4 Clifford Rd Dam Outlet, MA 1 4 4 0 Eel Creek, MA 1 5 4 1 Flat Brook, MA 1 1 1 0 Hop Brook, MA 1 6 3 3 W. Branch Farm. River, MA 1 5 4 1 Schenob Brook, MA 1 1 1 0 Dry Brook, MA 1 3 2 1 Sambo Creek, PA 1 7 3 4 McMichael Creek, PA 1 5 2 3

For Marshalls Creek research sites, the number of fish associate species collected when sampling seven times at a research site was relatively the same as the number of fish associate species collected when sampling two times at a research site (Table 3-2). Marshalls Creek Site 1,

PA, (the model reference site) was ranked second with the maximum number of endangered shiners predator species (Table 3-2), and both Bridle and Ironcolor shiners were collected in this research site (Table 3-1). Additionally, Marshalls Creek Site 5, PA, had the least amount of

54 endangered shiners predator species (Table 3-2), yet no endangered shiners were collected at this research site (Table 3-1).

Throughout the study, five exotic species and three additional (i.e., not found at the model reference site) exotic species were collected (Table 3-3). Many of these exotic species had been residents in the ecosystem for many years, however I grouped them all together for my analysis. Concurrently, seven additional (i.e., not found at the model reference site) endangered shiners predator species were collected (Table 3-4). These data were used in the NetWeaver model dependency networks to produce strength of evidence scores (Chapters 1 and 2).

Table3-3: Exotic Species and Additional (i.e., not found at the model reference site) Exotic Species Collected at All Research Sites.

Additional Location Exotic Species Exotic Species Marshalls Creek Site 1, PA Brown Trout N/A (model reference site) (Salmo trutta) Bluegill (Lepomis macrochirus)

Marshalls Creek Site 0, PA Smallmouth Bass Smallmouth Bass (Micropterus dolomieu) (Micropterus dolomieu) Marshalls Creek Site 2, PA Brown Trout Largemouth Bass (Salmo trutta) (Micropterus salmoides) Bluegill (Lepomis macrochirus) Largemouth Bass (Micropterus salmoides) Marshalls Creek Site 3, PA Brown Trout Largemouth Bass (Salmo trutta) (Micropterus salmoides) Bluegill (Lepomis macrochirus) Largemouth Bass (Micropterus salmoides) Marshalls Creek Site 4, PA Brown Trout None (Salmo trutta) Bluegill (Lepomis macrochirus)

55

Marshalls Creek Site 5, PA Brown Trout None (Salmo trutta) Bluegill (Lepomis macrochirus) Long Marsh Ditch, MD Bluegill None (Lepomis macrochirus) Zekiah Swamp, MD None None Nanticoke River, DE None None Gum Branch (main.), DE None None Gum Branch (head.), DE None None West Branch, DE None None Clifford Rd Dam Outlet, MA Bluegill None (Lepomis macrochirus) Eel Creek, MA Largemouth Bass Largemouth Bass (Micropterus salmoides) (Micropterus salmoides) Flat Brook, MA None None Hop Brook, MA Bluegill None (Lepomis macrochirus) W. Branch Farm. River, MA Bluegill None (Lepomis macrochirus) Schenob Brook, MA Bluegill None (Lepomis macrochirus) Dry Brook, MA Bluegill None (Lepomis macrochirus) Sambo Creek, PA Grass Carp Grass Carp (Ctenopharyngodon idella) (Ctenopharyngodon idella) McMichael Creek, PA Brown Trout None (Salmo trutta)

Table3-4: Additional (i.e., not found at the model reference site) Endangered Shiners Predator Species Collected at All Research Sites.

Additional Endangered Shiners Location Predator Species Marshalls Creek Site 1, PA N/A (model reference site)

Marshalls Creek Site 0, PA Brook Trout (Salvelinus fontinalus) Smallmouth Bass (Micropterus dolomieu)

56 Marshalls Creek Site 2, PA Brook Trout (Salvelinus fontinalus) Largemouth Bass (Micropterus salmoides) Marshalls Creek Site 3, PA Margined Madtom (Notorus insignis) Largemouth Bass (Micropterus salmoides) Marshalls Creek Site 4, PA Brook Trout (Salvelinus fontinalus) Marshalls Creek Site 5, PA Brook Trout (Salvelinus fontinalus) Long Marsh Ditch, MD Tadpole Madtom (Notorus gyninus) Pirate Perch (Aphredoderus sayanus) Zekiah Swamp, MD None Nanticoke River, DE None Gum Branch (main.), DE Tadpole Madtom (Notorus gyninus) Pirate Perch (Aphredoderus sayanus) Gum Branch (head.), DE Tadpole Madtom (Notorus gyninus) Pirate Perch (Aphredoderus sayanus) West Branch, DE Tadpole Madtom (Notorus gyninus) Clifford Rd Dam Outlet, MA None Eel Creek, MA Largemouth Bass (Micropterus salmoides) Margined Madtom (Notorus insignis) Flat Brook, MA None Hop Brook, MA None W. Branch Farm. River, MA None Schenob Brook, MA None Dry Brook, MA None Sambo Creek, PA Grass Pickerel (Esox americanus) McMichael Creek, PA None

57 Marshalls Creek Site 1, PA, (the model reference site) yielded none of the following exotic species: Smallmouth Bass, Micropterus dolomieu; Largemouth Bass, Micropterus salmoides; or Grass Carp, Ctenopharyngodon idella (Table 3-3). Marshalls Creek Site 1, PA,

(the model reference site) yielded none of the following endangered shiners predator species:

Smallmouth Bass, Micropterus dolomieu; Largemouth Bass, Micropterus salmoides; Brook

Trout, Salvelinus fontinalus; Margined Madtom, Notorus insignis; Tadpole Madtom, Notorus gyninus; Pirate Perch, Aphredoderus sayanus; or Grass Pickerel, Esox americanus (Table 3-4).

Throughout the study, 31 species of fish associates were collected, including 26 native species and five exotic species (Appendix V). The percentage of native species at all research sites was calculated (Table 3-5), and as indicated earlier (Chapter 2) this was the only time the presence of Bridle and/or Ironcolor shiners was used in any of the NetWeaver model dependency networks. These data were used in the NetWeaver model dependency networks to produce strength of evidence scores (Chapters 1 and 2).

58 Table3-5: Percentage of Native Species at All Research Sites.

Location Native Species (%) Marshalls Creek Site 1, PA 88.8 (model reference site)

Marshalls Creek Site 0, PA 93.3 Marshalls Creek Site 2, PA 86.4 Marshalls Creek Site 3, PA 86.4 Marshalls Creek Site 4, PA 88.8 Marshalls Creek Site 5, PA 83.3 Long Marsh Ditch, MD 90.0 Zekiah Swamp, MD 100.0 Nanticoke River, DE 100.0 Gum Branch (main.), DE 100.0 Gum Branch (head.), DE 100.0 West Branch, DE 100.0 Clifford Rd Dam Outlet, MA 80.0 Eel River, MA 80.0 Flat Brook, MA 100.0 Hop Brook, MA 85.7 W. Branch Farm. River, MA 80.0 Schenob Brook, MA 0.0 Dry Brook, MA 75.0 Sambo Creek, PA 85.7 McMichael Creek, PA 80.0

Excluding Marshalls Creek research sites, six other historical research sites had 100% native species (Table 3-5). Of these six other historical research sites, Bridle Shiners were collected in one of these six research sites, and Ironcolor Shiners were collected in three sites

(Table 3-1).

Aquatic Macroinvertebrates

Throughout the study, 21 research sites were sampled (Appendixes A-U), and 207 aquatic macroinvertebrate taxa were collected (Table 3-6), including 76 edible aquatic

59 macroinvertebrate taxa consumed by endangered shiners and 131 non-edible aquatic macroinvertebrate taxa associated with endangered shiners (Appendix W). As indicated earlier

(Chapter 2) edible aquatic macroinvertebrate taxa were those that I determined were consumed by these two endangered shiners. These data were used in the NetWeaver model dependency networks to produce strength of evidence scores (Chapters 1 and 2).

Table3-6: Number of Aquatic Macroinvertebrate Collections, Aquatic Macroinvertebrate Taxa, Endangered Shiners Edible Aquatic Macroinvertebrate Taxa, and Endangered Shiners Non- Edible Aquatic Macroinvertebrate Taxa at All Research Sites.

Endangered Endangered Shiners Shiners Aquatic Aquatic Edible Non-Edible Macro. Macro. Aquatic Aquatic Location Collections Taxa Macro. Taxa Macro. Taxa Marshalls Creek Site 1, PA 33 127 60 67 (model reference site)

Marshalls Creek Site 0, PA 5 65 24 41 Marshalls Creek Site 2, PA 33 153 65 88 Marshalls Creek Site 3, PA 33 152 57 95 Marshalls Creek Site 4, PA 4 81 32 49 Marshalls Creek Site 5, PA 3 49 27 22 Long Marsh Ditch, MD 1 12 6 6 Zekiah Swamp, MD 1 12 8 4 Nanticoke River, DE 1 11 8 3 Gum Branch (main.), DE 1 16 9 7 Gum Branch (head.), DE 1 18 7 11 West Branch, DE 1 13 7 6 Clifford Rd Dam Outlet, MA 1 20 14 6 Eel Creek, MA 1 14 11 3 Flat Brook, MA 1 11 4 7 Hop Brook, MA 1 16 5 11 W. Branch Farm. River, MA 1 12 7 5 Schenob Brook, MA 1 22 8 14 Dry Brook, MA 1 11 7 4 Sambo Creek, PA 1 13 8 5 McMichael Creek, PA 1 13 9 4

60 The highest amount of edible aquatic macroinvertebrate taxa consumed by endangered shiners collected for all research sites was 65 (Table 3-6). Both Bridle and Ironcolor shiners were collected in this research site (Table 3-1). The lowest amount of edible aquatic macroinvertebrate taxa consumed by endangered shiners collected for all research sites was four (Table 3-6). Bridle

Shiners were collected in this research site (Table 3-1).

The number of aquatic macroinvertebrate taxa increased when collecting 33 times at

Marshalls Creek Sites 1, 2, and 3, PA, when compared to collecting a few times at Marshalls

Creek Site 0, 4, and 5, PA (Table 3-6). Overall as the number of collections increased to 33 for a research site, fewer aquatic macroinvertebrate taxa were added to the total aquatic macroinvertebrate taxa list for that research site. To illustrate, the number of aquatic macroinvertebrate taxa collected verses the number of collections for Marshalls Creek Site 1, PA, was plotted (Fig. 3-1). This was a practical laboratory example of rarefaction and the law of diminishing returns.

The Number of Aquatic Macroinvertebrate Taxa Collected verses The Number of Collections # of Taxa 140 120 100 80 60 Marshalls Creek Site 1, PA 40 20 0 0 5 10 15 20 25 30 # of Collections

Figure3-1: Number of Aquatic Macroinvertebrate Taxa Collected verses The Number of Collections for Marshalls Creek Site 1, PA.

61 Aquatic Plants/Algae

Throughout the study 21 research sites were sampled (Appendixes A-U), and 33 aquatic plant/algae species were collected (Table 3-7), including 17 spawning plant species used by endangered shiners and 16 non-spawning plant/algae species associated with endangered shiners

(Appendix X). As indicated earlier (Chapter 2) spawning plant species were those that I determined were used by these two endangered shiners during spawning. These data were used in the NetWeaver model dependency networks to produce strength of evidence scores (Chapters 1 and 2).

62 Table3-7: Number of Aquatic Plant/Algae Collections, Aquatic Plant/Algae Species, Endangered Shiners Spawning Plant Species, and Endangered Shiners Non-Spawning Plant/Algae Species at All Research Sites.

Endangered Endangered Shiners Shiners Aquatic Aquatic Spawning Non-Spawning Plant/Algae Plant/Algae Plant Plant/Algae Location Collections Species Species Species Marshalls Creek Site 1, PA 7 16 8 8 (model reference site)

Marshalls Creek Site 0, PA 7 10 3 7 Marshalls Creek Site 2, PA 7 13 8 5 Marshalls Creek Site 3, PA 7 11 7 4 Marshalls Creek Site 4, PA 7 10 3 7 Marshalls Creek Site 5, PA 4 8 4 4 Long Marsh Ditch, MD 1 5 3 2 Zekiah Swamp, MD 1 4 3 1 Nanticoke River, DE 1 5 4 1 Gum Branch (main.), DE 1 4 4 0 Gum Branch (head.), DE 1 4 4 0 West Branch, DE 1 4 1 3 Clifford Rd Dam Outlet, MA 1 3 2 1 Eel Creek, MA 1 3 2 1 Flat Brook, MA 1 2 2 0 Hop Brook, MA 1 6 3 3 W. Branch Farm. River, MA 1 2 0 2 Schenob Brook, MA 1 5 5 0 Dry Brook, MA 1 1 1 0 Sambo Creek, PA 1 4 3 1 McMichael Creek, PA 1 2 1 1

The highest amount of spawning plant species used by endangered shiners was eight in two research sites (Table 3-7). Both Bridle and Ironcolor shiners were collected in these two research sites (Table 3-1).

63 Chemical Habitat Characters

Throughout the study, 21 research sites were sampled (Appendixes A-U), and five chemical habitat characters (pH, dissolved oxygen, conductivity, alkalinity, and hardness) were measured (Tables 3-8 and 3-9). These data were used in the NetWeaver model dependency networks to produce strength of evidence scores (Chapters 1 and 2).

Table3-8: Chemical Habitat Characters (pH, Dissolved Oxygen, and Conductivity) at All Research Sites.

Dissolved Oxygen Conductivity Location pH (mg/liter) (microsiemens/cm) Marshalls Creek Site 1, PA 5.8-8.5 7.5-15.0 80-290 (model reference site)

Marshalls Creek Site 0, PA 5.8- 8.5 7.5-15.0 80-290 Marshalls Creek Site 2, PA 5.8-8.5 7.5-15.0 80-290 Marshalls Creek Site 3, PA 5.8-8.5 7.5-15.0 80-290 Marshalls Creek Site 4, PA 5.8-8.5 7.5-15.0 80-290 Marshalls Creek Site 5, PA 5.8-8.5 7.5-15.0 80-290 Long Marsh Ditch, MD 6.28 10.87 495 Zekiah Swamp, MD 7.45 4.36 111 Nanticoke River, DE 6.57 7.66 290 Gum Branch (main.), DE 7.50 7.77 106 Gum Branch (head.), DE 7.06 7.65 82 West Branch, DE 6.83 9.41 164 Clifford Rd Dam Outlet, MA 7.25 8.74 122 Eel Creek, MA 7.68 7.26 123 Flat Brook, MA 7.67 0.93 439 Hop Brook, MA 7.17 2.50 143 W. Branch Farm. River, MA 7.90 6.53 205 Schenob Brook, MA 8.06 4.12 256 Dry Brook, MA 7.82 4.09 208 Sambo Creek, PA 7.39 6.24 290 McMichael Creek, PA 7.77 12.8 311

64 For Marshalls Creek research sites, a wide range for dissolved oxygen (i.e., 7.5 mg/liter to 15.0 mg/liter) and conductivity (i.e., 80 microsiemens/cm to 290 microsiemens/cm) was measured (Table 3-8). Both Bridle and Ironcolor shiners where collected in four of these six research sites (Table 3-1).

For the other historical research sites, the highest measurement for dissolved oxygen where endangered shiners were collected was 8.74 mg/liter (Table 3-8). Bridle Shiners were collected in this research site (Table 3-1). The lowest measurement for dissolved oxygen where endangered shiners were collected was 0.93 mg/liter (Table 3-8). Bridle Shiners were collected in this research site (Table 3-1).

For the other historical research sites, the highest measurement for conductivity where endangered shiners were collected was 439 microsiemens/cm (Table 3-8). Bridle Shiners were collected in this research site (Table 3-1). The lowest measurement for conductivity where endangered shiners were collected was 82 microsiemens/cm (Table 3-8). Ironcolor Shiners were collected in this research site (Table 3-1).

65 Table3-9: Chemical Habitat Characters (Alkalinity and Hardness) at All Research Sites.

Alkalinity Hardness Location (ppm) (ppm) Marshalls Creek Site 1, PA 20-50 50-75 (model reference site)

Marshalls Creek Site 0, PA 20- 50 50- 75 Marshalls Creek Site 2, PA 20-50 50-75 Marshalls Creek Site 3, PA 20-50 50-75 Marshalls Creek Site 4, PA 20-50 50-75 Marshalls Creek Site 5, PA 20-50 50-75 Long Marsh Ditch, MD 40 75 Zekiah Swamp, MD 40 120 Nanticoke River, DE 50 75 Gum Branch (main.), DE 40 70 Gum Branch (head.), DE 30 75 West Branch, DE 40 75 Clifford Rd Dam Outlet, MA 40 25 Eel Creek, MA 20 25 Flat Brook, MA 180 150 Hop Brook, MA 120 75 W. Branch Farm. River, MA 40 75 Schenob Brook, MA 120 150 Dry Brook, MA 120 150 Sambo Creek, PA 70 150 McMichael Creek, PA 40 75

The highest alkalinity measurement was 180 ppm (Table 3-9). Bridle Shiners were collected in this research site (Table 3-1). The highest hardness measurements were 150 ppm at four research sites (Table 3-9). Bridle Shiners were collected in two of these four research sites

(Table 3-1). The lowest hardness measurements were 25 ppm at two research sites (Table 3-9).

Bridle Shiners were collected in one of these two research sites (Table 3-1).

66 Physical Habitat Characters

Throughout the study, 21 research sites were sampled (Appendixes A-U), and eight physical habitat characters (water temperature, depth, velocity, substrate composition, riparian protection, flow status, bank stability, and channel alteration) were measured (Tables 3-10 and 3-

11). These data were used in the NetWeaver model dependency networks to produce strength of evidence scores (Chapters 1 and 2).

Table3-10: Physical Habitat Characters (Water Temperature, Depth, Velocity, Substrate Composition, and Riparian Protection) at All Research Sites.

Water Substrate Riparian Temp. Depth Vel. Composition Protection Location (deg. C) (cm) (cm/sec) (% mud/sand) (% erosion) Marshalls Creek Site 1, PA 0.5-26.0 100 17.6 80 5 (model reference site)

Marshalls Creek Site 0, PA 0.5-26.0 54 36.6 50 5 Marshalls Creek Site 2, PA 0.5-26.0 69 38.0 60 5 Marshalls Creek Site 3, PA 0.5-26.0 68 25.0 60 10 Marshalls Creek Site 4, PA 0.5-26.0 44 50.0 20 10 Marshalls Creek Site 5, PA 0.5-26.0 89 61.0 20 10 Long Marsh Ditch, MD 21.6 44 2.0 90 5 Zekiah Swamp, MD 23.7 8 14.0 80 20 Nanticoke River, DE 19.6 65 11.2 90 20 Gum Branch (main.), DE 20.7 44 30.0 90 5 Gum Branch (head.), DE 24.0 22 10.0 90 60 West Branch, DE 24.5 10 12.0 80 5 Clifford Rd Dam Outlet, MA 25.7 48 3.0 70 5 Eel Creek, MA 24.4 28 7.0 70 10 Flat Brook, MA 21.3 80 6.0 80 10 Hop Brook, MA 24.7 28 2.0 80 10 W. Branch Farm. River, MA 26.2 24 5.0 40 10 Schenob Brook, MA 22.6 60 1.0 90 30 Dry Brook, MA 21.6 20 2.0 80 5 Sambo Creek, PA 21.4 30 2.0 50 5 McMichael Creek, PA 21.3 21 17.0 30 15

67 For Marshalls Creek research sites, a wide range for water temperature (i.e., 0.5 oC to

26.0 oC) was measured (Table 3-10). Both Bridle and Ironcolor shiners were collected in four of these six research sites (Table 3-1). Additionally, the depth, velocity, and substrate composition of mud/sand for Marshalls Creek Site 1, PA, (the model reference site) was measured (Table 3-

10), and these set of measurements were ideal for both the Bridle and Ironcolor shiner’s spawning and habitat preferences (Chapter 1). Both Bridle and Ironcolor shiners were collected in

Marshalls Creek Site 1, PA (Table 3-1).

At other historical research sites, the depth, velocity, and substrate composition of mud/sand in two research sites (i.e., Nanticoke River, DE, and Flat Brook, MA) were measured

(Table 3-10), and these set of measurements were relatively close to both the Bridle and Ironcolor shiner’s spawning and habitat preferences (Chapter 1). Bridle Shiners were collected in one (i.e.,

Flat Book, MA) of these two research sites and Ironcolor Shiners were collected in one (i.e.,

Nanticoke River, DE) of these two research sites (Table 3-1).

For depth, the lowest measurements were 8 cm and 10 cm (Table 3-10). No endangered shiners were collected in these research sites (Table 3-1). For velocity, the highest measurements were 61 cm/sec and 50 cm/sec (Table 3-10). No endangered shiners were collected in these research sites (Table 3-1).

For substrate composition, the lowest measurements were of 20% mud/sand at two research sites and 30% mud/sand at one research site (Table 3-10). No endangered shiners were collected in these research sites (Table 3-1). For riparian protection, the highest measurement was 60% erosion (Table 3-10). Bridle Shiners were collected in the 60% erosion research site

(Table 3-1).

68

Table3-11: Physical Habitat Characters (Flow Status, Bank Stability, and Channel Alteration) at All Research Sites.

Bank Channel Flow Status Stability Alteration Location (% flow to both banks) (% bank erosion) (% altered) Marshalls Creek Site 1, PA 95 10 5 (model reference site)

Marshalls Creek Site 0, PA 95 5 20 Marshalls Creek Site 2, PA 95 5 10 Marshalls Creek Site 3, PA 95 10 5 Marshalls Creek Site 4, PA 95 10 20 Marshalls Creek Site 5, PA 90 10 20 Long Marsh Ditch, MD 90 10 10 Zekiah Swamp, MD 25 10 5 Nanticoke River, DE 95 5 5 Gum Branch (main.), DE 95 5 10 Gum Branch (head.), DE 95 50 30 West Branch, DE 95 5 10 Clifford Rd Dam Outlet, MA 95 5 5 Eel Creek, MA 90 10 15 Flat Brook, MA 90 10 10 Hop Brook, MA 95 10 20 W. Branch Farm. River, MA 95 10 5 Schenob Brook, MA 90 30 20 Dry Brook, MA 95 5 5 Sambo Creek, PA 95 10 5 McMichael Creek, PA 95 10 5

For flow status, the lowest measurement was 25% flow to both banks (Table 3-11). No endangered shiners were collected in this research site (Table 3-1).

For bank stability, the highest measurements were 50% bank erosion and 30% bank erosion (Table 3-11). Ironcolor Shiners were collected in the 50% bank erosion research site

(Table 3-1). No endangered shiners were collected in the 30% bank erosion research site (Table

3-1).

69 For channel alteration, the highest measurement was 30% altered (Table 3-11). Ironcolor

Shiners were collected in this research site (Table 3-1).

I only had one opportunity to visit and collect aquatic habitat character data at each of the other historical research sites. If resources and time had permitted, it would have been advantageous to visit and collect additional data again at all the other historical research sites.

Repeated visits would have allowed for an increased database, and possibly more insight on the aquatic habitat characters required for both the Bridle and Ironcolor shiner.

All the data from Marshalls Creek research sites provided insight on the aquatic habitat characters within a small section of one aquatic ecosystem. When considering the seven years of collecting fishes, the eleven years of collecting aquatic macroinvertebrates, the two years of collecting aquatic plants/algae, and the over two years of remote water chemistry and water temperature monitoring, I believe the 3.7 km reach of Marshalls Creek that harbors both Bridle and Ironcolor shiners was on a very short list of the most studied aquatic habitat characters of a

Pennsylvania watershed.

NetWeaver Model Strength of Evidence Scores

Using the NetWeaver model dependency networks (Chapter 2) and the research site collections and measurements data reported above, the NetWeaver model produced a wide range of strength of evidence scores at all research sites. As indicated earlier (Chapter 2) the only time the presence of Bridle and/or Ironcolor shiners was used in any of the NetWeaver model dependency networks was in the native species strength of evidence score.

70 Biological Habitat Characters

Fishes

The NetWeaver model produced strength of evidence scores for endangered shiners predator species, endangered shiners non-predator species, native species, additional (i.e., not found at the model reference site) exotic species, additional (i.e., not found at the model reference site) endangered shiners predator species, and fishes at all research sites (Tables 3-12 and 3-13).

As indicated earlier (Chapter 2) the fishes strength of evidence score was the weighted average of the strength of evidence scores for endangered shiners predator species, endangered shiners non- predator species, native species, additional (i.e., not found at the model reference site) exotic species, and additional (i.e., not found at the model reference site) endangered shiners predator species.

71 Table3-12: Strength of Evidence Scores for Endangered Shiners Predator Species, Endangered Shiners Non-Predator Species, and Native Species at All Research Sites.

Endangered Endangered Shiners Predator Shiners Non-Predator Native Location Species Species Species Marshalls Creek Site 1, PA 200.0 200.0 200.0 (model reference site)

Marshalls Creek Site 0, PA 142.9 114.3 200.0 Marshalls Creek Site 2, PA 171.4 200.0 187.6 Marshalls Creek Site 3, PA 171.4 200.0 187.6 Marshalls Creek Site 4, PA 142.9 200.0 200.0 Marshalls Creek Site 5, PA 142.9 114.3 171.6 Long Marsh Ditch, MD 85.7 85.7 200.0 Zekiah Swamp, MD 85.7 57.1 200.0 Nanticoke River, DE 57.1 0.0 200.0 Gum Branch (main.), DE 114.3 85.7 200.0 Gum Branch (head.), DE 85.7 57.1 200.0 West Branch, DE 85.7 85.7 200.0 Clifford Rd Dam Outlet, MA 85.7 0.0 154.6 Eel River, MA 85.7 0.0 154.6 Flat Brook, MA 28.6 0.0 200.0 Hop Brook, MA 85.7 0.0 184.0 W. Branch Farm. River, MA 57.1 28.6 154.6 Schenob Brook, MA 28.6 0.0 0.0 Dry Brook, MA 28.6 0.0 128.9 Sambo Creek, PA 85.7 57.1 184.0 McMichael Creek, PA 57.1 57.1 154.6

The highest strength of evidence score (besides the model reference site) for endangered shiners predator species for all research sites was 171.4 for two research sites (Table 3-12). Both

Bridle and Ironcolor shiners were collected in these two research sites (Table 3-1).

The highest strength of evidence score (besides the model reference site) for endangered shiners non-predator species was 200.0 for three research sites (Table 3-12). Both Bridle and

Ironcolor shiners were collected in two of these three research sites (Table 3-1).

72 The highest strength of evidence score (besides the model reference site) for native species was 200.0 for nine research sites (Table 3-12). Both Bridle and Ironcolor shiners were collected in one of these nine research sites, Bridle Shiners were collected in one of these nine research sites, and Ironcolor Shiners were collected in three of these nine research sites (Table 3-

1).

Table3-13: Strength of Evidence Scores for Additional (i.e., not found at the model reference site) Exotic Species, Additional (i.e., not found at the model reference site) Endangered Shiners Predator Species, and Fishes at All Research Sites.

Additional Additional Exotic Endangered Shiners Location Species Predator Species Fishes Marshalls Creek Site 1, PA 200.0 200.0 200.0 (model reference site)

Marshalls Creek Site 0, PA 66.7 0.0 104.8 Marshalls Creek Site 2, PA 66.7 0.0 125.1 Marshalls Creek Site 3, PA 66.7 0.0 125.1 Marshalls Creek Site 4, PA 200.0 0.0 148.6 Marshalls Creek Site 5, PA 200.0 0.0 125.8 Long Marsh Ditch, MD 200.0 0.0 114.3 Zekiah Swamp, MD 200.0 200.0 148.6 Nanticoke River, DE 200.0 200.0 131.4 Gum Branch (main.), DE 200.0 0.0 120.0 Gum Branch (head.), DE 200.0 0.0 108.6 West Branch, DE 200.0 100.0 134.3 Clifford Rd Dam Outlet, MA 200.0 200.0 128.1 Eel River, MA 66.7 0.0 61.4 Flat Brook, MA 200.0 200.0 125.7 Hop Brook, MA 200.0 200.0 133.9 W. Branch Farm. River, MA 200.0 200.0 128.1 Schenob Brook, MA 200.0 200.0 85.7 Dry Brook, MA 200.0 200.0 111.5 Sambo Creek, PA 66.7 0.0 78.7 McMichael Creek, PA 200.0 200.0 133.8

73 The highest strength of evidence score (besides the model reference site) for additional exotic species was 200.0 for 15 research sites (Table 3-13). Bridle Shiners were collected in four of these 15 research sites and Ironcolor Shiners were collected in three of these 15 research sites

(Table 3-1).

The highest strength of evidence score (besides the model reference site) for additional endangered shiners predator species was 200.0 for nine research sites (Table 3-13). Bridle

Shiners were collected in four of these nine research sites and Ironcolor Shiners were collected in one of these nine research sites (Table 3-1).

The highest strength of evidence score (besides the model reference site) for fishes was

148.6 for two research sites (Table 3-13). No endangered shiners were collected in these two research sites (Table 3-1).

Aquatic Macroinvertebrates

The NetWeaver model produced strength of evidence scores for edible aquatic macroinvertebrate taxa consumed by endangered shiners, non-edible aquatic macroinvertebrate taxa associated with endangered shiners, and aquatic macroinvertebrates at all research sites

(Table 3-14). As indicated earlier (Chapter 2) the aquatic macroinvertebrates strength of evidence score was the weighted average of the strength of evidence scores for edible aquatic macroinvertebrate taxa consumed by endangered shiners (x3 weighting) and non-edible aquatic macroinvertebrate taxa associated with endangered shiners.

74 Table3-14: Strength of Evidence Scores for Endangered Shiners Edible Aquatic Macroinvertebrate Taxa, Endangered Shiners Non-Edible Aquatic Macroinvertebrate Taxa, and Aquatic Macroinvertebrates at All Research Sites.

Endangered Shiners Endangered Shiners Edible Aquatic Non-Edible Aquatic Aquatic Location Macro. Taxa Macro. Taxa Macros. Marshalls Creek Site 1, PA 200.0 200.0 200.0 (model reference site)

Marshalls Creek Site 0, PA 146.7 127.8 141.9 Marshalls Creek Site 2, PA 193.3 177.8 189.4 Marshalls Creek Site 3, PA 193.3 172.2 188.1 Marshalls Creek Site 4, PA 160.0 122.2 150.6 Marshalls Creek Site 5, PA 120.0 77.8 109.4 Long Marsh Ditch, MD 46.7 27.8 41.9 Zekiah Swamp, MD 60.0 22.2 50.6 Nanticoke River, DE 53.3 22.2 45.6 Gum Branch (main.), DE 66.7 44.4 61.1 Gum Branch (head.), DE 53.3 50.0 52.5 West Branch, DE 46.7 27.8 41.9 Clifford Rd Dam Outlet, MA 86.7 33.3 73.3 Eel River, MA 73.3 22.2 60.6 Flat Brook, MA 33.3 33.3 33.3 Hop Brook, MA 40.0 50.0 42.5 W. Branch Farm. River, MA 46.7 33.3 43.3 Schenob Brook, MA 60.0 50.0 57.5 Dry Brook, MA 53.3 27.8 46.9 Sambo Creek, PA 53.3 27.8 46.9 McMichael Creek, PA 53.3 27.8 46.9

The highest strength of evidence score (besides the model reference site) for edible aquatic macroinvertebrate taxa consumed by endangered shiners was 193.3 for two research sites

(Table 3-14). Both Bridle and Ironcolor shiners were collected in these two research sites (Table

3-1).

75 The highest strength of evidence score (besides the model reference site) for non-edible aquatic macroinvertebrate taxa associated with endangered shiners was 177.8 (Table 3-14). Both

Bridle and Ironcolor shiners were collected in this research site (Table 3-1).

The highest strength of evidence score (besides the model reference site) for aquatic macroinvertebrates was 189.4 (Table 3-14). Both Bridle and Ironcolor shiners were collected in this research site (Table 3-1).

Aquatic Plants/Algae

The NetWeaver model produced strength of evidence scores for spawning plant species used by endangered shiners, non-spawning plant/algae species associated with endangered shiners, and aquatic plants/algae at all research sites (Table 3-15). As indicated earlier (Chapter

2) the aquatic plants/algae strength of evidence score was the weighted average of the strength of evidence scores for spawning plant species used by endangered shiners (x3 weighting) and non- spawning plant/algae species associated with endangered shiners.

76 Table3-15: Strength of Evidence Scores for Endangered Shiners Spawning Plant Species, Endangered Shiners Non-Spawning Plant/Algae Species, and Aquatic Plants/Algae at All Research Sites.

Endangered Endangered Shiners Shiners Spawning Non-Spawning Aquatic Location Plant Species Plant/Algae Species Plants/Algae Marshalls Creek Site 1, PA 200.0 200.0 200.0 (model reference site)

Marshalls Creek Site 0, PA 100.0 88.9 97.2 Marshalls Creek Site 2, PA 175.0 88.9 153.5 Marshalls Creek Site 3, PA 150.0 111.1 140.3 Marshalls Creek Site 4, PA 100.0 111.1 102.8 Marshalls Creek Site 5, PA 100.0 66.7 91.7 Long Marsh Ditch, MD 75.0 44.4 67.4 Zekiah Swamp, MD 50.0 22.2 43.1 Nanticoke River, DE 75.0 44.4 67.4 Gum Branch (main.), DE 50.0 22.2 43.1 Gum Branch (head.), DE 75.0 22.2 61.8 West Branch, DE 25.0 66.7 35.4 Clifford Rd Dam Outlet, MA 50.0 22.2 43.1 Eel River, MA 75.0 22.2 61.8 Flat Brook, MA 50.0 0.0 37.5 Hop Brook, MA 25.0 66.7 35.4 W. Branch Farm. River, MA 0.0 22.2 5.6 Schenob Brook, MA 75.0 0.0 56.2 Dry Brook, MA 25.0 0.0 18.7 Sambo Creek, PA 75.0 44.4 67.4 McMichael Creek, PA 50.0 44.4 48.6

The highest strength of evidence score (besides the model reference site) for spawning plant species used by endangered shiners was 175.0 (Table 3-15). Both Bridle and Ironcolor shiners were collected in this research site (Table 3-1).

The highest strength of evidence score (besides the model reference site) for non- spawning plant/algae species associated with endangered shiners was 111.1 for two research sites

77 (Table 3-15). Both Bridle and Ironcolor shiners were collected in one of these two research sites

(Table 3-1).

The highest strength of evidence score (besides the model reference site) for aquatic plants/algae was 153.5 (Table 3-15). Both Bridle and Ironcolor shiners were collected in this research site (Table 3-1).

The NetWeaver model produced strength of evidence scores for fishes, aquatic macroinvertebrates, aquatic plants/algae, and biological habitat characters at all research sites

(Table 3-16). As indicated earlier (Chapter 2) the biological habitat characters strength of evidence score was the weighted average of the strength of evidence scores for fishes, aquatic macroinvertebrates, and aquatic plants/algae.

78 Table3-16: Strength of Evidence Scores for Fishes, Aquatic Macroinvertebrates, Aquatic Plants/Algae, and Biological Habitat Characters at All Research Sites.

Biological Aquatic Aquatic Habitat Location Fishes Macros. Plants/Algae Characters Marshalls Creek Site 1, PA 200.0 200.0 200.0 200.0 (model reference site)

Marshalls Creek Site 0, PA 104.8 141.9 97.2 114.6 Marshalls Creek Site 2, PA 125.1 189.4 153.5 156.0 Marshalls Creek Site 3, PA 125.1 188.1 140.3 151.2 Marshalls Creek Site 4, PA 148.6 150.6 102.8 134.0 Marshalls Creek Site 5, PA 125.8 109.4 91.7 109.0 Long Marsh Ditch, MD 114.3 41.9 67.4 74.5 Zekiah Swamp, MD 148.6 50.6 43.1 80.7 Nanticoke River, DE 131.4 45.6 67.4 81.4 Gum Branch (main.), DE 120.0 61.1 43.1 74.7 Gum Branch (head.), DE 108.6 52.5 61.8 74.3 West Branch, DE 134.3 41.9 35.4 70.5 Clifford Rd Dam Outlet, MA 128.1 73.3 43.1 81.5 Eel River, MA 61.4 60.6 61.8 61.3 Flat Brook, MA 125.7 33.3 37.5 65.5 Hop Brook, MA 133.9 42.5 35.4 70.6 W. Branch Farm. River, MA 128.1 43.3 5.6 59.0 Schenob Brook, MA 85.7 57.5 56.2 66.5 Dry Brook, MA 111.5 46.9 18.7 59.1 Sambo Creek, PA 78.7 46.9 67.4 64.3 McMichael Creek, PA 133.8 46.9 48.6 76.4

The highest strength of evidence score (besides the model reference site) for biological habitat characters was 156.0 (Table 3-16). Both Bridle and Ironcolor shiners were collected in this research site (Table 3-1).

Chemical Habitat Characters

The NetWeaver model produced strength of evidence scores for chemical habitat characters at all research sites (Table 3-17). As indicated earlier (Chapter 2) the chemical habitat

79 characters strength of evidence score was the weighted average of the strength of evidence scores for pH, dissolved oxygen (mg/liter), conductivity (microsiemens/cm), alkalinity (ppm), and hardness (ppm).

Table3-17: Strength of Evidence Scores for Chemical Habitat Characters at All Research Sites.

Location Chemical Habitat Characters Marshalls Creek Site 1, PA 200.0 (model reference site)

Marshalls Creek Site 0, PA 200.0 Marshalls Creek Site 2, PA 200.0 Marshalls Creek Site 3, PA 200.0 Marshalls Creek Site 4, PA 200.0 Marshalls Creek Site 5, PA 200.0 Long Marsh Ditch, MD 160.0 Zekiah Swamp, MD 120.0 Nanticoke River, DE 200.0 Gum Branch (main.), DE 200.0 Gum Branch (head.), DE 200.0 West Branch, DE 200.0 Clifford Rd Dam Outlet, MA 160.0 Eel River, MA 140.8 Flat Brook, MA 40.0 Hop Brook, MA 120.0 W. Branch Farm. River, MA 160.0 Schenob Brook, MA 80.0 Dry Brook, MA 80.0 Sambo Creek, PA 80.0 McMichael Creek, PA 160.0

The highest strength of evidence score (besides the model reference site) for chemical habitat characters was 200.0 for nine research sites (Table 3-17). Both Bridle and Ironcolor shiners were collected in three of these nine research sites and Ironcolor Shiners were collected in three of these nine research sites (Table 3-1).

80 Physical Habitat Characters

The NetWeaver model produced strength of evidence scores for physical habitat characters at all research sites (Table 3-18). As indicated earlier (Chapter 2) the physical habitat characters strength of evidence score was the weighted average of the strength of evidence scores for water temperature (oC), depth (cm)(x3 weighting), velocity (cm/sec)(x3 weighting), substrate composition (% mud/sand)(x3 weighting), riparian protection (% erosion), flow status (% flow to both banks), bank stability (% bank erosion), and channel alteration (% altered).

Table3-18: Strength of Evidence Scores for Physical Habitat Characters at All Research Sites.

Location Physical Habitat Characters Marshalls Creek Site 1, PA 200.0 (model reference site)

Marshalls Creek Site 0, PA 60.6 Marshalls Creek Site 2, PA 83.0 Marshalls Creek Site 3, PA 93.2 Marshalls Creek Site 4, PA 52.4 Marshalls Creek Site 5, PA 82.2 Long Marsh Ditch, MD 148.8 Zekiah Swamp, MD 128.6 Nanticoke River, DE 155.7 Gum Branch (main.), DE 109.5 Gum Branch (head.), DE 114.3 West Branch, DE 152.4 Clifford Rd Dam Outlet, MA 135.7 Eel River, MA 117.9 Flat Brook, MA 169.8 Hop Brook, MA 138.1 W. Branch Farm. River, MA 103.8 Schenob Brook, MA 119.3 Dry Brook, MA 157.1 Sambo Creek, PA 114.3 McMichael Creek, PA 104.8

81 The highest strength of evidence score (besides the model reference site) for physical habitat characters was 169.8 (Table 3-18). Bridle Shiners were collected in this research site

(Table 3-1).

Aquatic Habitat Characters

The NetWeaver model produced strength of evidence scores for biological habitat characters (discussed above), chemical habitat characters (discussed above), physical habitat characters (discussed above), and aquatic habitat characters at all research sites (Table 3-19).

As indicated earlier (Chapter 2) the aquatic habitat characters strength of evidence score was the weighted average of the strength of evidence scores for biological habitat characters, chemical habitat characters, and physical habitat characters.

82 Table3-19: Strength of Evidence Scores for Biological Habitat Characters, Chemical Habitat Characters, Physical Habitat Characters, and Aquatic Habitat Characters at All Research Sites.

Biological Chemical Physical Aquatic Habitat Habitat Habitat Habitat Location Characters Characters Characters Characters Marshalls Creek Site 1, PA 200.0 200.0 200.0 200.0 (model reference site)

Marshalls Creek Site 0, PA 114.6 200.0 60.6 125.1 Marshalls Creek Site 2, PA 156.0 200.0 83.0 146.3 Marshalls Creek Site 3, PA 151.2 200.0 93.2 148.1 Marshalls Creek Site 4, PA 134.0 200.0 52.4 128.8 Marshalls Creek Site 5, PA 109.0 200.0 82.2 130.4 Long Marsh Ditch, MD 74.5 160.0 148.8 127.8 Zekiah Swamp, MD 80.7 120.0 128.6 109.8 Nanticoke River, DE 81.4 200.0 155.7 145.7 Gum Branch (main.), DE 74.7 200.0 109.5 128.1 Gum Branch (head.), DE 74.3 200.0 114.3 129.5 West Branch, DE 70.5 200.0 152.4 141.0 Clifford Rd Dam Outlet, MA 81.5 160.0 135.7 125.7 Eel River, MA 61.3 140.8 117.9 106.6 Flat Brook, MA 65.5 40.0 169.8 91.8 Hop Brook, MA 70.6 120.0 138.1 109.6 W. Branch Farm. River, MA 59.0 160.0 103.8 107.6 Schenob Brook, MA 66.5 80.0 119.3 88.6 Dry Brook, MA 59.1 80.0 157.1 98.7 Sambo Creek, PA 64.3 80.0 114.3 86.2 McMichael Creek, PA 76.4 160.0 104.8 113.7

The highest strength of evidence score (besides the model reference site) for aquatic habitat characters was 148.1 (Table 3-19). Both Bridle and Ironcolor shiners were collected in this research site (Table 3-1).

83 NetWeaver Model Strength of Evidence Score Ratio

A strength of evidence score ratio (%) (i.e., [the strength of evidence score for the aquatic habitat characters at a research site / the strength of evidence score for the aquatic habitat characters at the model reference site] x 100) was calculated to help determine how the aquatic habitat characters at a research site compared to the aquatic habitat characters at the model research site. As the strength of evidence score ratio (Table 3-20) increases for a research site, there was an increasing similarity to the aquatic habitat characters at the model reference site.

Table3-20: Strength of Evidence Score Ratio at All Research Sites.

Strength of Evidence Score Ratio Location (%) Marshalls Creek Site 1, PA 100.0 (model reference site)

Marshalls Creek Site 0, PA 62.6 Marshalls Creek Site 2, PA 73.2 Marshalls Creek Site 3, PA 74.1 Marshalls Creek Site 4, PA 64.4 Marshalls Creek Site 5, PA 65.2 Long Marsh Ditch, MD 63.9 Zekiah Swamp, MD 54.9 Nanticoke River, DE 72.8 Gum Branch (main.), DE 64.1 Gum Branch (head.), DE 64.8 West Branch, DE 70.5 Clifford Rd Dam Outlet, MA 62.9 Eel River, MA 53.3 Flat Brook, MA 45.9 Hop Brook, MA 55.0 W. Branch Farm. River, MA 53.8 Schenob Brook, MA 44.3 Dry Brook, MA 49.4 Sambo Creek, PA 43.1 McMichael Creek, PA 56.9

84 The highest strength of evidence score ratio (besides the model reference site) was 74.1%

(Table 3-20). Both Bridle and Ironcolor shiners were collected in this research site (Table 3-1).

NetWeaver Model Weighting

Because of the importance of various aquatic habitat characters, various NetWeaver model dependency network aquatic habitat characters were weighted by a factor of three (i.e.,

(x3) weighting)(Chapter 2). These various aquatic habitat characters were edible aquatic macroinvertebrates taxa consumed by endangered shiners, spawning plants species used by endangered shiners, depth (cm), velocity (cm/sec), and substrate composition (% mud/sand).

For comparison purposes and to examine the impact of weighting, a second NetWeaver model was created where all NetWeaver model dependency network aquatic habitat characters were weighted by a factor of one (i.e., no weighting, (x1) weighting) (NDE 2013). NetWeaver models produced strength of evidence scores for aquatic habitat characters with (x3) weighting and (x1) weighting (Table 3-21).

As indicated earlier (Chapter 2) the percentage of native species at all research sites was calculated (Table 3-5), and this was the only time the presence of Bridle and/or Ironcolor shiners was used in NetWeaver model dependency networks. Only (x1) weighting was used for the percentage of native species calculation (Table 3-5).

85 Table3-21: Strength of Evidence Scores for Aquatic Habitat Characters with (x3) Weighting and (x1) Weighting, and the Corresponding Score Change at All Research Sites.

Aquatic Aquatic Habitat Characters Habitat Characters Corresponding Location with (x3) Weighting with (x1) Weighting Score Change Marshalls Creek Site 1, PA 200.0 200.0 0.0 (model reference site)

Marshalls Creek Site 0, PA 125.1 138.0 (+) 12.9 Marshalls Creek Site 2, PA 146.3 157.9 (+) 11.6 Marshalls Creek Site 3, PA 148.1 159.4 (+) 11.3 Marshalls Creek Site 4, PA 128.8 141.1 (+) 12.3 Marshalls Creek Site 5, PA 130.4 135.9 (+) 5.5 Long Marsh Ditch, MD 127.8 130.3 (+) 2.5 Zekiah Swamp, MD 109.8 106.8 (-) 3.0 Nanticoke River, DE 145.7 144.6 (-) 1.1 Gum Branch (main.), DE 128.1 137.4 (+) 9.3 Gum Branch (head.), DE 129.5 123.2 (-) 6.3 West Branch, DE 141.0 146.4 (+) 5.4 Clifford Rd Dam Outlet, MA 125.7 132.4 (+) 6.7 Eel River, MA 106.6 108.3 (+) 1.7 Flat Brook, MA 91.8 89.5 (-) 2.3 Hop Brook, MA 109.6 112.2 (+) 2.6 W. Branch Farm. River, MA 107.6 117.1 (+) 9.5 Schenob Brook, MA 88.6 79.4 (-) 9.2 Dry Brook, MA 98.7 103.4 (+) 4.7 Sambo Creek, PA 86.2 96.6 (+) 10.4 McMichael Creek, PA 113.7 122.4 (+) 8.7

The NetWeaver model with (x1) weighting resulted in 15 research sites increasing their aquatic habitat characters strength of evidence score, and five research sites decreasing their aquatic habitat characters strength of evidence score (Table 3-21). The maximum difference for increasing aquatic habitat characters strength of evidence scores was 12.9 and the maximum difference for decreasing aquatic habitat characters strength of evidence scores was 9.2 (Table 3-

21).

86 As indicated earlier, the highest strength of evidence score (besides the model reference site) for aquatic habitat characters with (x3) weighting was 148.1 (Tables 3-19 and 3-21); and the highest strength of evidence score ratio for this research site (i.e., Marshalls Creek Site 3, PA) was 74.1% (Table 3-20). The highest strength of evidence score (besides the model reference site) for aquatic habitat characters with (x1) weighting was 159.4 (Table 3-21), and the highest strength of evidence score ratio for this research site (i.e., Marshalls Creek Site 3, PA, the same research site as above) was 79.7% (Table 3-20). The (x1) weighting strength of evidence score ratio for this research site increased by 5.6% when compared to the (x3) weighting strength of evidence score ratio for this research site. Both Bridle and Ironcolor shiners were collected in this research site (Table 3-1).

87 Chapter 4

Discussion

Research Hypothesis and Testing

Research Hypothesis (Chapter 1): A NetWeaver modeling tool can be developed as a research tool to assess the aquatic environment biodiversity and the habitat variability/characters for two endangered shiners (i.e., Notropis bifrenatus and Notropis chalybaeus).

Research Hypothesis Testing (Chapter 1): I collected aquatic (biological, chemical, and physical) habitat characters in six Marshalls Creek research sites and 15 other historical research sites along the Atlantic seaboard to populate the NetWeaver model and compare scores with reference system scores.

In all cases research sites with the highest NetWeaver strength of evidence scores for various aquatic habitat characters resulted in a closer similarity to the model reference site

(Chapter 3). In 15 of 16 cases (the strength of evidence score for “Fishes” was the exception), research sites with the highest NetWeaver strength of evidence scores for various aquatic habitat characters resulted in finding a population of endangered shiners (Chapter 3). Therefore, a

NetWeaver modeling tool was successfully developed as a research tool to assess the aquatic environment biodiversity and the habitat variability/characters for two endangered shiners (i.e.,

Notropis bifrenatus and Notropis chalybaeus). More importantly, various interacting and discerned aquatic habitat characters data from NetWeaver model dependency networks (Chapter

2) and their associated stength of evidence scores (Chapter 3) produced insight that was not

88 evident by univariate examination of the collection and measurement data at research sites

(Chapter 3 and Appendixes A-U).

Research Goal and Objectives

As indicated earlier (Chapter 1) the primary research goal of this study was to determine the unique aquatic habitat characters of Marshalls Creek that support the syntopic populations of

Bridle and Ironcolor Shiners. To achieve this goal, the specific research objectives of this study were (1) to examine and discern the aquatic habitat characters (i.e., the combination and interaction of biological, chemical, and physical habitat characters) that are coincident with these two endangered species in Marshalls Creek; (2) to determine if these aquatic habitat characters are commonly found at other historical sites for these two endangered shiners; and (3) to speculate as to why these two endangered shiners currently exist together in Marshalls Creek

(Chapter 1). Each of these research objectives is discussed below.

This study examined and discerned the aquatic habitat characters that supported these two endangered shiners by collecting and measuring aquatic habitat characters at 21 research sites

(Chapters 2 and 3) and using a NetWeaver modeling tool and its associated dependency networks

(Chapters 1 and 2). NetWeaver strength of evidence scores for biological, chemical, and physical habitat characters produced a strength of evidence score for aquatic habitat characters for each research site, and these aquatic habitat character scores were then compared to the aquatic habitat character score of Marshalls Creeks Site 1, PA (the model reference site) (Chapter 3). Both

Bridle and Ironcolor shiners were present at this model reference site (Chapter 3).

This study determined that the aquatic habitat characters found at Marshalls Creek Site 1,

PA, are not commonly found at other historical sites for these two endangered shiners. My criteria for commonly found aquatic habitat characters was to have over half of the other

89 historical sites produce a strength of evidence score ratio 90% . No strength of evidence score ratios were 90.0% (Chapter 3). The highest strength of evidence score ratio for Marshalls

Creek sites (besides the model reference site) was 74.1%, and the highest strength of evidence score ratio for other historical sites (besides the model reference site) was 72.8% (Chapter 3).

I postulated that Marshalls Creek (i.e., the Marshalls Creek Site 1, PA) harbored both

Bridle and Ironcolor shiners in relatively large numbers because of a unique combination and complex interaction of aquatic habitat characters; thus, I needed to document habitat, feeding, and spawning preferences of these two endangered shiners (Chapter 1); native range overlap for these two endangered species (Chapter 1); NetWeaver model attributes and dependency networks

(Chapters 1 and 2); collection and measurement data for all research sites (Chapter 3); and

NetWeaver model strength of evidence scores for various aquatic habitat characters at all research sites (Chapter 3). The unique combination and complex interaction of aquatic habitat characters at Marshalls Creek Site 1, PA, included: (1) an absence of fish associates especially the two exotic/endangered shiners predator species of Smallmouth Bass, Micropterus dolomieu, and

Largemouth Bass, Micropterus salmoides (Chapter 3); (2) a presence of aquatic macroinvertebrate taxa, especially the 60 edible aquatic macroinvertebrate taxa consumed by endangered shiners including Ephemeroptera (mayflies) taxa, Trichoptera (caddisflies) taxa,

Diptera (true flies) taxa, Amphipoda (scuds) taxa, Gastropoda (snails) taxa and Bivalvia (clams) taxa (Chapters 1, 2, and 3); (3) a presence of aquatic plant/algae species, especially the eight spawning plant species used by endangered shiners including Ceratophyllum (i.e., coontail species, feather-leaved submerged aquatic plants) and Potamogeton (i.e., pondweed species, broad-leaved submerged aquatic plants)(Chapters 1, 2, and 3); (4) satisfactory measurements for chemical habitat characters for endangered shiners (Chapter 3); and (5) satisfactory measurements for physical habitat characters especially depth (>100 cm), velocity (17.6 cm/sec),

90 and substrate composition (80% mud/sand) that are ideal for both the Bridle and Ironcolor shiner’s spawning and habitat preferences (Chapters 1 and 3).

In summary, this study included adequate background information for these two endangered shiners (Chapter 1), sufficient aquatic habitat characters collections and measurements at 21 research sites (Chapters 2 and 3), and a successsfully developed NetWeaver modeling tool with its strength of evidence scores (Chapters 1, 2, and 3). This study compared the aquatic habitat characters found in the Marshalls Creek reference site to the other Marshalls

Creek sites and other historical sites along the Atlantic seaboard where there were two endangered shiner species, one endangered shiner species, or neither (Chapters 1, 2, and 3). This study documented what was unique about Marshalls Creek that support the syntopic population of Bridle and Ironcolor shiners (Chapters 1, 2, and 3).

Determining Favorable Habitat

Examining differences between and among research sites is a logical step in order to speculate as to which habitat characters (i.e, biological, chemical, and/or physical) determine favorable habitat for the presence of these two endangered shiners. Using the Marshalls Creek

Site 1, PA (the model reference site) as the standard for comparison, biological, chemical, and physical habitat character requirements were documented for all research sites (Appendix Z) by reviewing all populated NetWeaver model dependency networks, simple data links, and their respective strength of evidence scores (Chapters 2 and 3). These NetWeaver model habitat character requirements were examined, compared, and correlated to a general set of parameters

(i.e., minimum requirements) to determine favorable habitat for the presence of both Bridle and

Ironcolor shiners, only Bridle Shiners, and only Ironcolor Shiners (Table 4-1).

91 Table4-1: NetWeaver Model Sets of Parameters that Determine Favorable Habitat for the Presence of Both Bridle and Ironcolor Shiners, Only Bridle Shiners, and Only Ironcolor Shiners (NDE 2013).

Presence of Both Presence of Presence of NetWeaver Model Bridle and Only Only Sets of Parameters Ironcolor Shiners Bridle Shiners Ironcolor Shiners Biological Habitat Characters Fishes* En. Sh. Predators (genera) > 5 of 7 > 1 of 7 > 2 of 7 En. Sh. Non-Predators (genera) > 4 of 7 > 0 of 7 > 0 of 7 Native Fishes (%) > 86.4 > 75.0 100 Aquatic Macroinvertebrates En. Sh. Edible (families) > 22 of 30 > 5 of 30 > 8 of 30 En. Sh. Non-Edible (families) > 23 of 36 > 6 of 36 > 4 of 36 Aquatic Plants/Algae En. Sh. Spawning (genera) > 4 of 8 > 1 of 8 > 2 of 8 En. Sh. Non-Spawning (genera) > 4 of 9 > 0 of 9 > 2 of 9 Chemical Habitat Characters pH 5.80 - 8.50 7.17 - 7.82 6.57 - 7.50 Dissolved Oxygen (mg/liter) 7.5 - 15.0 0.93 - 8.74 7.65 - 7.77 Conductivity (microsiemens/cm) 80 - 290 122 - 439 82 - 290 Alkalinity (ppm) 20 - 50 40 - 180 30 - 50 Hardness (ppm) 50 - 75 25 - 150 70 - 75 Physical Habitat Characters Water Temperature (deg. C) 0.5 - 26.0 21.3 - 25.7 19.6 - 24.0 Depth (cm) > 54 > 20 > 22 Velocity (cm/sec) < 38.0 < 6.0 < 30.0 Substrate Composition (% mud/sand) > 50 > 70 > 90 Riparian Protection (% erosion) < 10 < 10 < 60 Flow Status (% flow to both banks) > 95 > 90 > 95 Bank Stability (% bank erosion) < 10 < 10 < 50 Channel Alteration (% altered) < 20 < 20 < 30

*The presence of exotic and/or additional endangered shiner predator fishes (including Smallmouth Bass, Micropterus dolomieu; Largemouth Bass, Micropterus salmoides; Brook Trout, Salvelinus fontinalus; Margined Madtom, Notorus insignis; Tadpole Madtom, Notorus gyninus; Pirate Perch, Aphredoderus sayanus; Grass Pickerel, Esox americanus; and/or Grass Carp, Ctenopharyngodon idella) to determine the presence of both Bridle and Ironcolor shiners, only Bridle Shiners, and only Ironcolor Shiners is unresolved and requires further research and study.

92 With data indicated earlier (Appendixes V, W, Y, and Z; Chapters 2 and 3) and

NetWeaver model sets of parameters (Table 4-1), scientists and resource managers can assess certain biological, chemical, and physical ecosystem elements needed to predict the presence of these endangered shiners. For example, column 1 of Table 4-1 lists the minimum requirements for the sets of parameters necessary to support the presence of both shiner species, and could be used to assess sites for re-introduction of both shiner species.

Accessing Biodiversity

The loss of biodiversity of natural systems (i.e., the loss of the variety of life forms and processes of natural systems) is directly related to the over-consumptive and overgrown human population (Barlow 2000; Helfman et al. 2009). Habitat alteration, overharvesting, pollution, and introduced species are all primary agents for the loss of biodiversity (Helfman et al. 2009). The loss of species due to introductions has had detrimental impacts on native aquatic faunas throughout the world (Courtenay and Stauffer 1984; Stauffer et al. 1988). Understanding the complex effects of human activities on aquatic ecosystems presents a challenge to ecologists, biologists, and resource managers.

Historically, the assessment of ecosystems has centered on the biodiversity of the flora and fauna. The biodiversity of any system is anchored on the number of species in that system, the functional aspects of each species, and the genetic and phenotypic diversity and uniqueness of the system. Biotic assessment methods and tools for lotic systems using fish and macroinvertebrate assemblages have been studied and used by ecologists, biologists, and fisheries managers for many years (Ney 1999). The equitability of the distribution of individual species in a sample, community, or habitat (i.e., evenness) and the number of these species in a sample, community, or habitat (i.e., richness) commonly function together to define biodiversity (Cole

93 1994). Biodiversity indices consider both evenness and richness in mathematical (e.g., Shannon-

Weaver diversity index, Brillouin diversity index) formulas. Biodiversity indices have the potential for comparing and contrasting sites, where high values of diversity indices generally mean relatively unspoiled systems and low values of diversity indices generally mean some degree of degradation (Ney 1999). It should be noted, however that zoogeographic constraints result in some pristine environs that do not support high biodiversity (e.g., headwater streams isolated by waterfalls).

Similar to the concepts in biodiversity indices, the NetWeaver model developed for this study may also be a relevant and useful biotic assessment method and tool. Several attributes of this NetWeaver model were to utilize (1) the presence and absence data for fish associate species, aquatic macroinvertebrate taxa, and aquatic plant/algae species (Chapters 2 and 3); (2) endangered shiners predator fish species, endangered shiners non-predator fish species, native fish species, and exotic fish species data (Chapters 2 and 3); (3) edible and non-edible aquatic macroinvertebrate taxa data consumed by or associated with endangered shiners (Chapters 2 and

3), (4) spawning plant and non-spawning plant/algae species data used by or associated with endangered shiners (Chapters 2 and 3), (5) the combination of fishes, aquatic macroinvertebrates, and aquatic plants/algae habitat character data to produce biological habitat character data relative to endangered shiners (Chapters 2 and 3), (6) chemical and physical habitat character data relative to endangered shiners (Chapters 2 and 3), (7) the combination of biological, chemical, and physical habitat character data to produce aquatic habitat character data relative to endangered shiners (Chapters 2 and 3), and (8) reference (i.e., benchmark) research site data for comparisons with other research site data (Chapters 2 and 3).

With these attributions, the NetWeaver model developed for this study produced strength of evidence scores to compare, contrast, and evaluate aquatic habitat character data relative to these two endangered shiners (Chapter 3). This NetWeaver model can assist aquatic ecologists,

94 biologists, and resource managers to assess certain biological, chemical, and physical ecosystem elements; the relationships of fishes, aquatic macroinvertebrates, and aquatic plants/algae to endangered and threatened fish species; and the potential uniqueness of aquatic ecosystem biodiversity. Further, this NetWeaver model may provide a method to predict the effect of biodiversity component changes; and present ecologists, biologists, and resource managers much needed data to make decisions that will both protect the biodiversity of a system and increase the potential of that biodiversity to recover should it be impacted.

Fisheries Management Implications

Many state and federal resource agencies have legal mandates to prevent the loss of native fishes. Recovery of endangered and threatened fishes has become an important activity of fisheries biologists and managers. Fisheries management personnel use various approaches in the management of endangered and threatened fishes including maintaining and enhancing historic populations; protecting, expanding, or restoring habitat; moving specimens to refuges; rearing and stocking in new or formerly occupied areas; minimizing introductions and undesirable effects of nonnative organisms; and controlling exploitation (Rahel et al. 1999). Biological, chemical, and physical descriptions of fisheries resources are essential to effective fisheries management

(Ney 1999).

Persons that want to evaluate any species of concern may learn all NetWeaver model techniques (Chapters 1 and 2), code NetWeaver model dependency networks and logic that provides a complete calculus for knowledge representation (Chapters 1 and 2), and most importantly, may get real-time verification from a NetWeaver model (NDA 2013). Additionally, fisheries management personnel can revisit resource assessments and management approaches as new data are received, generate new reports, ground proof the predictions, and identify any

95 significant trends (NDE 2013). This study with its NetWeaver modeling tool provides important aquatic habitat character data for fisheries management personnel to manage the Bridle and

Ironcolor shiners, maintain and enhance historic populations; protect, expand, or restore habitat; and predict where re-introductions of these endangered species are plausible.

Significant Take-aways

This study (1) focused on the combination and interaction of biological, chemical, and physical habitat that were present when both the endangered Bridle Shiner and endangered

Ironcolor Shiner occurred (Chapters 2 and 3); (2) developed a NetWeaver model to examine and discern the aquatic habitat character data of Marshalls Creek research sites and other historical sites along the Atlantic seaboard (Chapters 1, 2, and 3); (3) developed a NetWeaver model structure that pertains to any targeted species (e.g., eliminate exotic species, propagate sport species, and manage endangered and threatened species)(Chapters 1, 2, and 3); (4) utilized

NetWeaver model strength of evidence scores produced from dependency network components to compare, contrast, and evaluate aquatic habitat characters to the Marshalls Creek reference site

(Chapter 3); (5) created important data for scientists and resource managers to assess certain biological, chemical, and physical ecosystem elements needed to determine the presence of these two endangered shiners (Chapter 4); (6) provided important data and methodology for scientists and resource managers to assess biodiversity (Chapter 4); and (7) documented important aquatic habitat character data for fisheries management personnel to manage Bridle and Ironcolor shiner populations (Chapter 4). Overall, this study provided a documentation of the unique aquatic habitat characters that support the syntopic populations of the endangered Bridle Shiner, Notropis bifrenatus, and endangered Ironcolor Shiner, Notropis chalybaeus (Chapters 1, 2, 3, and 4).

96 Appendix A

Marshalls Creek Site 0, Pennsylvania

Description

FigureA-1: Marshalls Creek Site 0, Pennsylvania.

Historical Site: Bridle and Ironcolor shiner

Collection Dates: Fishes - 11 October 2006*, 8 May 2007*, 10 June 2008*, 7 May 2009*, 24 May 2010*, 8 June 2011*, and 4 June 2012 (*I did not collect, but I am using collection data)

Aquatic Macroinvertebrates - 17 December 2010, 5 March 2011, 3 August 2011, 14 December 2011, and 8 March 2012

Aquatic Plants - 17 January 2011, 5 March 2011, 7 April 2011, 28 October 2011, 5 June 2012, 1 August 2012, and 5 October 2012

Type: High Gradient Current: Pool (40%), Run (50%), and Riffle (10%) Reach: 100 meters Drainage: Delaware County: Monroe

97 Latitude: N41.01422 Longitude: W075.12988 Collection Number: CWH-12-69

Biological Habitat Characters

Endangered Shiners

TableA-1: Endangered Shiners at Marshalls Creek Site 0, Pennsylvania. Individuals Scientific Name Common Name Collected/Released Individuals Observed Notropis bifrenatus Bridle Shiner 8 0 Notropis chalybaeus Ironcolor Shiner 4 0

Fish Associates

TableA-2: Fish Associates at Marshalls Creek Site 0, Pennsylvania (in phylogenetic order).

Scientific Name Common Name Anguilla rostrata American Eel Salvelinus fontinalus Brook Trout Esox niger Chain Pickerel Exoglossum maxillingua Cutlips Minnow Luxilus cornutus Common Shiner Catostomus commersoni White Sucker Erimyzon oblongus Creek Chubsucker Ameiurus nebulosus Brown Bullhead Enneacanthus gloriosus Bluespotted Sunfish Lepomis auritus Redbreast Sunfish Lepomis gibbosus Pumpinseed Micropterus dolomieu Smallmouth Bass Etheostoma olmstedi Tessellated Darter

98 Aquatic Macroinvertebrates

TableA-3: Aquatic Macroinvertebrates at Marshalls Creek Site 0, Pennsylvania (in phylogenetic order followed by crustaceans, mollusks, oligochaetes, and leeches).

Class/Order Family Genus Common Name Ephemeroptera Ameletidae Ameletus combmouthed minnow mayflies Ephemeroptera Baetidae Baetis small minnow mayflies Ephemeroptera Ephemerellidae Ephemerella spiny crawler mayflies Ephemeroptera Heptageniidae Maccaffertium flatheaded mayflies Ephemeroptera Heptageniidae Stenacron flatheaded mayflies Ephemeroptera Isonychiidae Isonychia brushlegged mayflies Ephemeroptera Leptohyphidae Tricorythodes little stout crawler mayflies Ephemeroptera Leptophlebiidae Leptophlebia pronggilled mayflies Odonata Aeshnidae Boyeria darners Odonata Coenagrionidae Argia narrowwinged damselflies Odonata Coenagrionidae Nehalennia narrowwinged damselflies Odonata Gomphidae Gomphus clubtails Odonata Gomphidae Hagenius clubtails Odonata Gomphidae Lanthus clubtails Odonata Gomphidae Progomphus clubtails Odonata Libellulidae Erythemis skimmers Plecoptera Nemouridae Paranemoura spring stoneflies Plecoptera Peltoperlidae Peltoperla roachlike stoneflies Plecoptera Perlidae Acroneuria common stoneflies Plecoptera Perlidae Paragnetina common stoneflies Plecoptera Perlidae Perlesta common stoneflies Plecoptera Perlodidae Isoperla perlodid stoneflies Plecoptera Taeniopterygidae Taeniopteryx winter stoneflies Coleoptera Elmidae Ancyronyx riffle beetles Coleoptera Elmidae Dubiraphia riffle beetles Coleoptera Elmidae Optioservus riffle beetles Coleoptera Elmidae Promoresia riffle beetles Coleoptera Elmidae Stenelmis riffle beetles Coleoptera Psephenidae Ectopria water pennies Coleoptera Psephenidae Psephenus water pennies Megaloptera Corydalidae Corydalus dobsonflies Megaloptera Corydalidae Neohermes fishflies Megaloptera Corydalidae Nigronia fishflies Megaloptera Sialiidae Sialis alderflies Trichoptera Beraeidae Beraea small eastern caddisflies Trichoptera Brachycentridae Micrasema humpless casemaker caddisflies Trichoptera Helicopsychidae Helicopsyche snailcase caddisflies Trichoptera Hydropsychidae Cheumatopsyche netspinning caddisflies Trichoptera Hydropsychidae Hydropsyche netspinning caddisflies Trichoptera Lepidostomatidae Lepidostoma bizarre caddisflies Trichoptera Leptoceridae Leptocerus longhorned caddisflies Trichoptera Leptoceridae Mystacides longhorned caddisflies

99 Trichoptera Limnephilidae Pseudostenophylax northern caddisflies Trichoptera Molannidae Molanna hood casemaker caddisflies Trichoptera Philopotamidae Chimarra fingernet caddisflies Trichoptera Phryganeidae Phryganea giant casemaker caddisflies Trichoptera Polycentropodidae Polycentropus tubemaker caddisflies Trichoptera Rhyacophilidae Rhyacophila freeliving caddisflies Trichoptera Uenoidae Neophylax stonecase caddisflies Lepidoptera Crambidae Petrophila crambid snout moths Diptera Athericidae Atherix watersnipe flies Diptera Chironomidae * midges Diptera Simuliidae Simulium black flies Diptera Tipulidae Antocha crane flies Diptera Tipulidae Tipula crane flies Amphipoda Gammaridae Gammarus scuds Amphipoda Hyalellidae Hyalella scuds Isopoda Asellidae Caecidotea sowbugs Bivalvia Sphaeriidae * fingernail clams Gastropoda Physidae * bladder snails Gastropoda Planorbidae * ram's horn snails Gastropoda Valvatidae * valve snails Gastropoda Viviparidae * river snails Hirudinea * * leeches Oligochaeta * * aquatic worms

Aquatic Plants/Algae

TableA-4: Aquatic Plants/Algae at Marshalls Creek Site 0, Pennsylvania. Scientific Name Common Name Brassica Mustard Caltha palustris Marsh Marigold Cladophora Nuisance Algae Drepanocladus Moss Elodea canadensis Canadian Waterweed Leersia oryzoides Rice Cut-grass Najas flexilis Bushy Pondweed Potamogeton crispus Curly Pondweed Sagittaria Arrowhead Viola lanceolata Big White Violet

100 Chemical Habitat Characters

TableA-5: Chemical Habitat Characters at Marshalls Creek Site 0, Pennsylvania. pH 5.8 - 8.5 Dissolved Oxygen (mg/liter) 7.5 - 15.0 Conductivity (microsiemens/cm) 80 – 290 Alkalinity (ppm) 20 – 50 Hardness (ppm) 50 – 75

Physical Habitat Characters

TableA-6: Physical Habitat Characters at Marshalls Creek Site 0, Pennsylvania. Water Temperature (degrees C) 0.5 - 26.0 Depth (cm) 54 Velocity (cm/sec) 36.6 Substrate (% mud/sand) 50 Riparian Protection (% erosion) 5 Flow Status (% flow to both banks) 95 Bank Stability (% bank erosion) 5 Channel Alteration (% altered) 20

Other Marshalls Creek Site 0, Pennsylvania, 2011-2012 data including numbers of fish specimens and macroinvertebrate specimens are available from Dr. Jay R. Stauffer, Jr.

101 Appendix B

Marshalls Creek Site 1, Pennsylvania

Description

FigureB-1: Marshalls Creek Site 1, Pennsylvania (the model reference site).

Historical Site: Bridle and Ironcolor shiner

Collection Dates: Fishes - 11 October 2006*, 8 May 2007*, 10 June 2008*, 7 May 2009*, 24 May 2010*, 8 June 2011*, and 4 June 2012 (*I did not collect, but I am using collection data)

Aquatic Macroinvertebrates - 3 August 2001*, 5 December 2001*, 21 March 2002*, 23 August 2002*, 15 December 2002*, 28 March 2003*, 1 September 2003*, 28 December 2003*, 1 April 2004*, 7 September 2004*, 3 December 2004*, 31 March 2005*, 2 August 2005*, 3 December 2005*, 25 March 2006*, 31 August 2006*, 22 December 2006*, 23 March 2007*, 22 August 2007*, 9 December 2007*, 13 March 2008*, 10 September 2008*, 17 December 2008*, 20 March 2009*, 2 September 2009*, 5 January 2010*, 27 March 2010, 4 August 2010, 17 December 2010, 5 March 2011, 3 August 2011, 14 December 2011, and 8 March 2012 (*I did not collect, but I am using collection data)

Aquatic Plants - 17 January 2011, 5 March 2011, 7 April 2011, 28 October 2011, 5 June 2012, 1 August 2012, and 5 October 2012

102 Type: High Gradient Current: Pool (100%) Reach: 100 meters Drainage: Delaware County: Monroe Latitude: N41.03138 Longitude: W075.12639 Collection Number: CWH-12-69

Biological Habitat Characters

Endangered Shiners

TableB-1: Endangered Shiners at Marshalls Creek Site 1, Pennsylvania. Individuals Scientific Name Common Name Collected/Released Individuals Observed Notropis bifrenatus Bridle Shiner 261 1000+ Notropis chalybaeus Ironcolor Shiner 307 1000+

Fish Associates

TableB-2: Fish Associates at Marshalls Creek Site 1, Pennsylvania (in phylogenetic order). Anguilla rostrata American Eel Salmo trutta Brown Trout Umbra pygmaea Eastern Mudminnow Esox niger Chain Pickerel Exoglossum maxillingua Cutlips Minnow Semotilus corporalis Fall Fish Catostomus commersoni White Sucker Erimyzon oblongus Creek Chubsucker Ameiurus nebulosus Brown Bullhead Enneacanthus gloriosus Bluespotted Sunfish Lepomis auritus Redbreast Sunfish Lepomis gibbosus Pumpinseed Lepomis macrochirus Bluegill Etheostoma olmstedi Tessellated Darter Perca flavescens Yellow Perch Percina peltata Shield Darter

103 Aquatic Macroinvertebrates

TableB-3: Aquatic Macroinvertebrates at Marshalls Creek Site 1, Pennsylvania (in phylogenetic order followed by crustaceans, mollusks, oligochaetes, and leeches).

Class/Order Family Genus Common Name Ephemeroptera Ameletidae Ameletus combmouthed minnow mayflies Ephemeroptera Baetidae Baetis small minnow mayflies Ephemeroptera Baetidae Callibaetis small minnow mayflies Ephemeroptera Baetidae Centroptilum small minnow mayflies Ephemeroptera Caenidae Caenis small squaregilled mayflies Ephemeroptera Ephemerellidae Attenella spiny crawler mayflies Ephemeroptera Ephemerellidae Drunella spiny crawler mayflies Ephemeroptera Ephemerellidae Ephemerella spiny crawler mayflies Ephemeroptera Ephemerellidae Eurylophella spiny crawler mayflies Ephemeroptera Ephemerellidae Serratella spiny crawler mayflies Ephemeroptera Ephemeridae Hexagenia common burrower mayflies Ephemeroptera Ephemeridae Litobrancha common burrower mayflies Ephemeroptera Heptageniidae Epeorus flatheaded mayflies Ephemeroptera Heptageniidae Heptagenia flatheaded mayflies Ephemeroptera Heptageniidae Maccaffertium flatheaded mayflies Ephemeroptera Heptageniidae Nixe flatheaded mayflies Ephemeroptera Heptageniidae Stenacron flatheaded mayflies Ephemeroptera Isonychiidae Isonychia brushlegged mayflies Ephemeroptera Leptohyphidae Tricorythodes little stout crawler mayflies Ephemeroptera Leptophlebiidae Leptophlebia pronggilled mayflies Ephemeroptera Leptophlebiidae Paraleptophlebia pronggilled mayflies Ephemeroptera Siphlonuridae Siphlonurus primitive minnow mayflies Odonata Aeshnidae Aeshna darners Odonata Aeshnidae Basiaeschna darners Odonata Aeshnidae Boyeria darners Odonata Calopterygidae Calopteryx broadwinged damselflies Odonata Coenagrionidae Amphiagrion narrowwinged damselflies Odonata Coenagrionidae Argia narrowwinged damselflies Odonata Coenagrionidae Chromagrion narrowwinged damselflies Odonata Coenagrionidae Enallagma narrowwinged damselflies Odonata Coenagrionidae Ischnura narrowwinged damselflies Odonata Coenagrionidae Nehalennia narrowwinged damselflies Odonata Corduliidae Epitheca emeralds Odonata Corduliidae Helocordulia emeralds Odonata Corduliidae Neurocordulia emeralds Odonata Corduliidae Somatochlora emeralds Odonata Gomphidae Arigomphus clubtails Odonata Gomphidae Dromogomphus clubtails Odonata Gomphidae Gomphus clubtails Odonata Gomphidae Lanthus clubtails Odonata Gomphidae Ophiogomphus clubtails Odonata Gomphidae Stylogomphus clubtails

104 Odonata Lestidae Lestes spreadwings Odonata Libellulidae Erythemis skimmers Odonata Macromiidae Macromia cruisers Plecoptera Nemouridae Paranemoura spring stoneflies Plecoptera Nemouridae Shipsa spring stonefies Plecoptera Perlidae Acroneuria common stoneflies Plecoptera Perlidae Perlesta common stoneflies Plecoptera Taeniopterygidae Taeniopteryx winter stoneflies Hemiptera Corixidae Palmacorixa water boatmans Hemiptera Veliidae Microvelia broadshouldered water striders Coleoptera Elmidae Ancronyx riffle beetles Coleoptera Elmidae Dubiraphia riffle beetles Coleoptera Elmidae Optioservus riffle beetles Coleoptera Elmidae Promoresia riffle beetles Coleoptera Elmidae Stenelmis riffle beetles Coleoptera Haliplidae Haliplus crawling water beetles Coleoptera Psephenidae Dicranopselaphus water pennies Coleoptera Psephenidae Ectopria water pennies Coleoptera Psephenidae Psephenus water pennies Neuroptera Sisyridae Climacia spongillaflies Megaloptera Corydalidae Corydalus dobsonflies Megaloptera Corydalidae Nigronia fishflies Megaloptera Sialiidae Sialis alderflies Trichoptera Apataniidae Apatania early smoky wing sedges Trichoptera Brachycentridae Brachycentrus humpless casemaker caddisflies Trichoptera Brachycentridae Micrasema humpless casemaker caddisflies Trichoptera Goeridae Goera weighted casemaker caddisflies Trichoptera Helicopsychidae Helicopsyche snailcase caddisflies Trichoptera Hydropsychidae Cheumatopsyche netspinning caddisflies Trichoptera Hydropsychidae Hydropsyche netspinning caddisflies Trichoptera Hydropsychidae Parapsyche netspinning caddisflies Trichoptera Hydropsychidae Potamyia netspinning caddisflies Trichoptera Hydroptilidae Agraylea micro caddisflies Trichoptera Hydroptilidae Hydroptila micro caddisflies Trichoptera Hydroptilidae Leucotrichia micro caddisflies Trichoptera Hydroptilidae Stactobiella micro caddisflies Trichoptera Lepidostomatidae Lepidostoma bizarre caddisflies Trichoptera Leptoceridae Ceraclea longhorned caddisflies Trichoptera Leptoceridae Leptocerus longhorned caddisflies Trichoptera Leptoceridae Mystacides longhorned caddisflies Trichoptera Leptoceridae Oecetis longhorned caddisflies Trichoptera Leptoceridae Setodes longhorned caddisflies Trichoptera Leptoceridae Triaenodes longhorned caddisflies Trichoptera Limnephilidae Chyranda northern caddisflies Trichoptera Limnephilidae Onocosmoecus northern caddisflies Trichoptera Limnephilidae Platycentropus northern caddisflies Trichoptera Limnephilidae Pseudostenophylax northern caddisflies Trichoptera Limnephilidae Psychoglypha northern caddisflies Trichoptera Molannidae Molanna hood casemaker caddisflies

105

Trichoptera Odontoceridae Psilotreta mortarjoint casemaker caddisflies Trichoptera Philopotamidae Chimarra fingernet caddisflies Trichoptera Philopotamidae Dolophilodes fingernet caddisflies Trichoptera Phryganeidae Agrypnia giant casemaker caddisflies Trichoptera Polycentropodidae Cernotina tubemaker caddisflies Trichoptera Polycentropodidae Cyrnellus tubemaker caddisflies Trichoptera Polycentropodidae Neureclipsis tubemaker caddisflies Trichoptera Polycentropodidae Phylocentropus tubemaker caddisflies Trichoptera Polycentropodidae Polycentropus tubemaker caddisflies Trichoptera Psychomyiidae Lype nettube caddisflies Trichoptera Psychomyiidae Psychomyia nettube caddisflies Trichoptera Rhyacophilidae Rhyacophila freeliving caddisflies Trichoptera Sericostomatidae Agarodes bushtailed caddisflies Trichoptera Uenoidae Neophylax stonecase caddisflies Diptera Ceratopogonidae Bezzia biting midges Diptera Ceratopogonidae Dasyhelea biting midges Diptera Chironomidae * midges Diptera Empididae Clinocera dance flies Diptera Empididae Dolichocephala dance flies Diptera Simuliidae Prosimulium black flies Diptera Simuliidae Simulium black flies Diptera Tabanidae Chrysops deer flies Diptera Tabanidae Tabanus horse flies Diptera Tipulidae Antocha crane flies Diptera Tipulidae Tipula crane flies Amphipoda Gammaridae Gammarus scuds Amphipoda Hyalellidae Hyalella scuds Decapoda Cambaridae * crayfish Isopoda Asellidae Caecidotea sowbugs Bivalvia Sphaeriidae * fingernail clams Gastropoda Physidae * bladder snails Gastropoda Planorbidae * ram's horn snails Gastropoda Valvatidae * valve snails Gastropoda Viviparidae * river snails Hirudinea * * leeches Oligochaeta * * aquatic worms

106 Aquatic Plants/Algae

TableB-4: Aquatic Plants/Algae at Marshalls Creek Site 1, Pennsylvania. Scientific Name Common Name Brassica Mustard Ceratophyllum demersum Coontail Cladophora Nuisance Algae Cyperaceae Sedge Elodea canadensis Canadian Waterweed Hippuris vulgaris Mare's-tail Hydrocotyle americana Water Pennywort Iridaceae Iris Juncus effuses Soft Rush Leersia oryzoides Rice Cut-grass Lythrum salicaria Purple Loosestrife Najas flexilis Bushy Pondweed Podostemum ceratophyllum River Weed Potamogeton americanus American Pondweed Potamogeton crispus Curly Pondweed Symplocarpus foetidus Skunk Cabbage

Chemical Habitat Characters

TableB-5: Chemical Habitat Characters at Marshalls Creek Site 1, Pennsylvania. pH 5.8 - 8.5 Dissolved Oxygen (mg/liter) 7.5 - 15.0 Conductivity (microsiemens/cm) 80 – 290 Alkalinity (ppm) 20 – 50 Hardness (ppm) 50 – 75

107 Physical Habitat Characters

TableB-6: Physical Habitat Characters at Marshalls Creek Site 1, Pennsylvania. Water Temperature (degrees C) 0.5 - 26.0 Depth (cm) 100 Velocity (cm/sec) 17.6 Substrate (% mud/sand) 80 Riparian Protection (% erosion) 5 Flow Status (% flow to both banks) 95 Bank Stability (% bank erosion) 10 Channel Alteration (% altered) 5

Other Marshalls Creek Site 1, Pennsylvania, 2001-2012 data including numbers of fish specimens and macroinvertebrate specimens are available from Dr. Jay R. Stauffer, Jr.

108 Appendix C

Marshalls Creek Site 2, Pennsylvania

Description

FigureC-1: Marshalls Creek Site 2, Pennsylvania.

Historical Site: Bridle and Ironcolor shiner

Collection Dates: Fishes - 11 October 2006*, 8 May 2007*, 10 June 2008*, 7 May 2009*, 24 May 2010*, 8 June 2011*, and 4 June 2012 (*I did not collect, but I am using collection data)

Aquatic Macroinvertebrates - 3 August 2001*, 5 December 2001*, 21 March 2002*, 23 August 2002*, 15 December 2002*, 28 March 2003*, 1 September 2003*, 28 December 2003*, 1 April 2004*, 7 September 2004*, 3 December 2004*, 31 March 2005*, 2 August 2005*, 3 December 2005*, 25 March 2006*, 31 August 2006*, 22 December 2006*, 23 March 2007*, 22 August 2007*, 9 December 2007*, 13 March 2008*, 10 September 2008*, 17 December 2008*, 20 March 2009*, 2 September 2009*, 5 January 2010*, 27 March 2010, 4 August 2010, 17 December 2010, 5 March 2011, 3 August 2011, 14 December 2011, and 8 March 2012 (*I did not collect, but I am using collection data)

Aquatic Plants - 17 January 2011, 5 March 2011, 7 April 2011, 28 October 2011, 5 June 2012, 1 August 2012, and 5 October 2012

109 Type: High Gradient Current: Pool (50%), Run (40%) and Riffle (10%) Reach: 100 meters Drainage: Delaware County: Monroe Latitude: N41.03476 Longitude: W075.12407 Collection Number: CWH-12-69

Biological Habitat Characters

Endangered Shiners

TableC-1: Endangered Shiners at Marshalls Creek Site 2, Pennsylvania. Individuals Scientific Name Common Name Collected/Released Individuals Observed Notropis bifrenatus Bridle Shiner 44 0 Notropis chalybaeus Ironcolor Shiner 35 0

Fish Associates

TableC-2: Fish Associates at Marshalls Creek Site 2, Pennsylvania (in phylogenetic order). Scientific Name Common Name Anguilla rostrata American Eel Salmo trutta Brown Trout Salvelinus fontinalus Brook Trout Umbra pygmaea Eastern Mudminnow Esox niger Chain Pickerel Exoglossum maxillingua Cutlips Minnow Luxilus cornutus Common Shiner Rhinichthys atratulus Blacknose Dace Rhinichthys cataractae Longnose Dace Semotilus corporalis Fall Fish Catostomus commersoni White Sucker Erimyzon oblongus Creek Chubsucker Ameiurus nebulosus Brown Bullhead Enneacanthus gloriosus Bluespotted Sunfish Lepomis auritus Redbreast Sunfish Lepomis gibbosus Pumpinseed Lepomis macrochirus Bluegill Micropterus salmoides Largemouth Bass

110

Etheostoma olmstedi Tessellated Darter Percina peltata Shield Darter

Aquatic Macroinvertebrates

TableC-3: Aquatic Macroinvertebrates at Marshalls Creek Site 2, Pennsylvania (in phylogenetic order followed by crustaceans, mollusks, oligochaetes, and leeches).

Class/Order Family Genus Common Name Ephemeroptera Ameletidae Ameletus combmouthed minnow mayflies Ephemeroptera Baetidae Acentrella small minnow mayflies Ephemeroptera Baetidae Baetis small minnow mayflies Ephemeroptera Baetidae Callibaetis small minnow mayflies Ephemeroptera Baetidae Centroptilum small minnow mayflies Ephemeroptera Caenidae Caenis small squaregilled mayflies Ephemeroptera Ephemerellidae Attenella spiny crawler mayflies Ephemeroptera Ephemerellidae Drunella spiny crawler mayflies Ephemeroptera Ephemerellidae Ephemerella spiny crawler mayflies Ephemeroptera Ephemerellidae Eurylophella spiny crawler mayflies Ephemeroptera Ephemerellidae Serratella spiny crawler mayflies Ephemeroptera Heptageniidae Epeorus flatheaded mayflies Ephemeroptera Heptageniidae Heptagenia flatheaded mayflies Ephemeroptera Heptageniidae Leucrocuta flatheaded mayflies Ephemeroptera Heptageniidae Maccaffertium flatheaded mayflies Ephemeroptera Heptageniidae Nixe flatheaded mayflies Ephemeroptera Heptageniidae Stenacron flatheaded mayflies Ephemeroptera Isonychiidae Isonychia brushlegged mayflies Ephemeroptera Leptohyphidae Tricorythodes little stout crawler mayflies Ephemeroptera Leptophlebiidae Leptophlebia pronggilled mayflies Ephemeroptera Leptophlebiidae Paraleptophlebia pronggilled mayflies Ephemeroptera Potamanthidae Anthopotamus hacklegilled burrower mayflies Ephemeroptera Siphlonuridae Siphlonurus primitive minnow mayflies Odonata Aeshnidae Aeshna darners Odonata Aeshnidae Boyeria darners Odonata Calopterygidae Calopteryx broadwinged damselflies Odonata Coenagrionidae Argia narrowwinged damselflies Odonata Coenagrionidae Chromagrion narrowwinged damselflies Odonata Coenagrionidae Enallagma narrowwinged damselflies Odonata Coenagrionidae Ischnura narrowwinged damselflies Odonata Coenagrionidae Nehalennia narrowwinged damselflies Odonata Corduliidae Neurocordulia emeralds Odonata Gomphidae Arigomphus clubtails Odonata Gomphidae Gomphus clubtails Odonata Gomphidae Hagenius clubtails Odonata Gomphidae Lanthus clubtails Odonata Gomphidae Ophiogomphus clubtails

111 Odonata Gomphidae Progomphus clubtails Odonata Gomphidae Stylogomphus clubtails Odonata Lestidae Lestes spreadwings Odonata Libellulidae Erythemis skimmers Odonata Macromiidae Macromia cruisers Plecoptera Capniidae Allocapnia small winter stoneflies Plecoptera Chloroperlidae Alloperla green stoneflies Plecoptera Chloroperlidae Sweltsa green stoneflies Plecoptera Chloroperlidae Utaperla green stoneflies Plecoptera Leuctridae Leuctra rolledwinged stoneflies Plecoptera Leuctridae Paraleuctra rolledwinged stoneflies Plecoptera Nemouridae Amphinemura spring stoneflies Plecoptera Nemouridae Nemoura spring stoneflies Plecoptera Nemouridae Ostrocerca spring stoneflies Plecoptera Nemouridae Paraneumora spring stoneflies Plecoptera Nemouridae Prostoia spring stoneflies Plecoptera Nemouridae Shipsa spring stoneflies Plecoptera Peltoperlidae Peltoperla roachlike stoneflies Plecoptera Perlidae Acroneuria common stoneflies Plecoptera Perlidae Agnetina common stoneflies Plecoptera Perlidae Attaneuria common stoneflies Plecoptera Perlidae Neoperla common stoneflies Plecoptera Perlidae Paragnetina common stoneflies Plecoptera Perlidae Perlinella common stoneflies Plecoptera Pteronarcyidae Pteronarcys giant stoneflies Plecoptera Taeniopterygidae Strophopteryx winter stoneflies Plecoptera Taeniopterygidae Taeniopteryx winter stoneflies Hemiptera Belostomatidae Belostoma giant water bugs Hemiptera Corixidae Palmacorixa water boatmans Hemiptera Notonectidae Buenoa back swimmers Hemiptera Pleidae Neoplea pygmy back swimmers Coleoptera Elmidae Ancyronyx riffle beetles Coleoptera Elmidae Dubiraphia riffle beetles Coleoptera Elmidae Macronychus riffle beetles Coleoptera Elmidae Microcylloepus riffle beetles Coleoptera Elmidae Optioservus riffle beetles Coleoptera Elmidae Oulimnius riffle beetles Coleoptera Elmidae Promoresia riffle beetles Coleoptera Elmidae Stenelmis riffle beetles Coleoptera Gyrinidae Gyrinus whirligig beetles Coleoptera Haliplidae Haliplus crawling water beetles Coleoptera Hydrophilidae Berosus water scavenger beetles Coleoptera Hydrophilidae Hydrophilus water scavenger beetles Coleoptera Psephenidae Ectopria water pennies Coleoptera Psephenidae Psephenus water pennies Megaloptera Corydalidae Corydalus dobsonflies Megaloptera Corydalidae Neohermes fishflies Megaloptera Corydalidae Nigronia fishflies Megaloptera Sialiidae Sialis alderflies

112 Trichoptera Apataniidae Apatania early smoky wing sedges Trichoptera Beraeidae Beraea small eastern caddisflies Trichoptera Brachycentridae Brachycentrus humpless casemaker caddisflies Trichoptera Brachycentridae Micrasema humpless casemaker caddisflies Trichoptera Glossosomatidae Glossosoma little black caddisflies Trichoptera Goeridae Goera weighted casemaker caddisflies Trichoptera Helicopsychidae Helicopsyche snailcase caddisflies Trichoptera Hydropsychidae Arctopsyche netspinning caddisflies Trichoptera Hydropsychidae Cheumatopsyche netspinning caddisflies Trichoptera Hydropsychidae Hydropsyche netspinning caddisflies Trichoptera Hydropsychidae Macrostemum netspinning caddisflies Trichoptera Hydropsychidae Parapsyche netspinning caddisflies Trichoptera Hydroptilidae Agraylea micro caddisflies Trichoptera Hydroptilidae Leucotrichia micro caddisflies Trichoptera Hydroptilidae Stactobiella micro caddisflies Trichoptera Lepidostomatidae Lepidostoma bizarre caddisflies Trichoptera Leptoceridae Ceraclea longhorned caddisflies Trichoptera Leptoceridae Mystacides longhorned caddisflies Trichoptera Leptoceridae Oecetis longhorned caddisflies Trichoptera Leptoceridae Setodes longhorned caddisflies Trichoptera Limnephilidae Anabolia northern caddisflies Trichoptera Limnephilidae Hesperophylax northern caddisflies Trichoptera Limnephilidae Lernachus northern caddisflies Trichoptera Limnephilidae Platycentropus northern caddisflies Trichoptera Limnephilidae Pseudostenophylax northern caddisflies Trichoptera Limnephilidae Psychoglypha northern caddisflies Trichoptera Limnephilidae Pycnopsyche northern caddisflies Trichoptera Molannidae Molanna hood casemaker caddisflies Trichoptera Odontoceridae Psilotreta mortarjoint casemaker caddisflies Trichoptera Philopotamidae Chimarra fingernet caddisflies Trichoptera Philopotamidae Dolophilodes fingernet caddisflies Trichoptera Philopotamidae Wormaldia fingernet caddisflies Trichoptera Polycentropodidae Cernotina tubemaker caddisflies Trichoptera Polycentropodidae Cyrnellus tubemaker caddisflies Trichoptera Polycentropodidae Neureclipsis tubemaker caddisflies Trichoptera Polycentropodidae Nyctiophlyax tubemaker caddisflies Trichoptera Polycentropodidae Phylocentropus tubemaker caddisflies Trichoptera Polycentropodidae Polycentropus tubemaker caddisflies Trichoptera Psychomyiidae Lype nettube caddisflies Trichoptera Psychomyiidae Psychomyia nettube caddisflies Trichoptera Rhyacophilidae Rhyacophila freeliving caddisflies Trichoptera Uenoidae Neophylax stonecase caddisflies Lepidoptera Crambidae Petrophila crambid snout moths Diptera Athericidae Atherix watersnipe flies Diptera Ceratopogonidae Dasyhelea biting midges Diptera Chironomidae * midges Diptera Empididae Hemerodromia dance flies Diptera Simuliidae Cnephia black flies Diptera Simuliidae Prosimulium black flies

113 Diptera Simuliidae Simulium black flies Diptera Simuliidae Twinia black flies Diptera Tabanidae Chrysops deer flies Diptera Tabanidae Merycomyia horse flies Diptera Tabanidae Tabanus horse flies Diptera Tipulidae Antocha crane flies Diptera Tipulidae Tipula crane flies Amphipoda Gammaridae Gammarus scuds Amphipoda Hyalellidae Hyalella scuds Decapoda Cambaridae * crayfish Isopoda Asellidae Caecidotea sowbugs Bivalvia Sphaeriidae * fingernail clams Gastropoda Physidae * bladder snails Gastropoda Planorbidae * ram's horn snails Gastropoda Valvatidae * valve snails Gastropoda Viviparidae * river snails Hirudinea * * leeches Oligochaeta * * aquatic worms

Aquatic Plants/Algae

TableC-4: Aquatic Plants/Algae at Marshalls Creek Site 2, Pennsylvania. Scientific Name Common Name Brassica Mustard Caltha palustris Marsh Marigold Ceratophyllum demersum Coontail Cladophora Nuisance Algae Cyperaceae Sedge Elodea canadensis Canadian Waterweed Hippuris vulgaris Mare's-tail Najas flexilis Bushy Pondweed Podostemum ceratophyllum River Weed Potamogeton americanus American Pondweed Potamogeton crispus Curly Pondweed Stuckenia pectinata Sago Pondweed Viola lanceolata Big White Violet

114 Chemical Habitat Characters

TableC-5: Chemical Habitat Characters at Marshalls Creek Site 2, Pennsylvania. pH 5.8 - 8.5 Dissolved Oxygen (mg/liter) 7.5 - 15.0 Conductivity (microsiemens/cm) 80 - 290 Alkalinity (ppm) 20 - 50 Hardness (ppm) 50 - 75

Physical Habitat Characters

TableC-6: Physical Habitat Characters at Marshalls Creek Site 2, Pennsylvania. Water Temperature (degrees C) 0.5 - 26.0 Depth (cm) 69 Velocity (cm/sec) 38.0 Substrate (% mud/sand) 60 Riparian Protection (% erosion) 5 Flow Status (% flow to both banks) 95 Bank Stability (% bank erosion) 5 Channel Alteration (% altered) 10

Other Marshalls Creek Site 2, Pennsylvania, 2001-2012 data including numbers of fish specimens and macroinvertebrate specimens are available from Dr. Jay R. Stauffer, Jr.

115 Appendix D

Marshalls Creek Site 3, Pennsylvania

Description

FigureD-1: Marshalls Creek Site 3, Pennsylvania.

Historical Site: Bridle and Ironcolor shiner

Collection Dates: Fishes - 11 October 2006*, 8 May 2007*, 10 June 2008*, 7 May 2009*, 24 May 2010*, 8 June 2011*, and 4 June 2012 (*I did not collect, but I am using collection data)

Aquatic Macroinvertebrates - 3 August 2001*, 5 December 2001*, 21 March 2002*, 23 August 2002*, 15 December 2002*, 28 March 2003*, 1 September 2003*, 28 December 2003*, 1 April 2004*, 7 September 2004*, 3 December 2004*, 31 March 2005*, 2 August 2005*, 3 December 2005*, 25 March 2006*, 31 August 2006*, 22 December 2006*, 23 March 2007*, 22 August 2007*, 9 December 2007*, 13 March 2008*, 10 September 2008*, 17 December 2008*, 20 March 2009*, 2 September 2009*, 5 January 2010*, 27 March 2010, 4 August 2010, 17 December 2010, 5 March 2011, 3 August 2011, 14 December 2011, and 8 March 2012 (*I did not collect, but I am using collection data)

Aquatic Plants - 17 January 2011, 5 March 2011, 7 April 2011, 28 October 2011, 5 June 2012, 1 August 2012, and 5 October 2012

116 Type: High Gradient Current: Pool (75%) and Run (25%) Reach: 100 meters Drainage: Delaware County: Monroe Latitude: N41.03997 Longitude: W075.12270 Collection Number: CWH-12-69

Biological Habitat Characters

Endangered Shiners

TableD-1: Endangered Shiners at Marshalls Creek Site 3, Pennsylvania. Individuals Scientific Name Common Name Collected/Released Individuals Observed Notropis bifrenatus Bridle Shiner 50 0 Notropis chalybaeus Ironcolor Shiner 71 0

Fish Associates

TableD-2: Fish Associates at Marshalls Creek Site 3, Pennsylvania (in phylogenetic order).

Scientific Name Common Name Anguilla rostrata American Eel Salmo trutta Brown Trout Umbra pygmaea Eastern Mudminnow Esox niger Chain Pickerel Exoglossum maxillingua Cutlips Minnow Luxilus cornutus Common Shiner Rhinichthys atratulus Blacknose Dace Rhinichthys cataractae Longnose Dace Semotilus corporalis Fall Fish Catostomus commersoni White Sucker Erimyzon oblongus Creek Chubsucker Ameiurus nebulosus Brown Bullhead Noturus insignis Margined Madtom Enneacanthus gloriosus Bluespotted Sunfish Lepomis auritus Redbreast Sunfish Lepomis gibbosus Pumpinseed Lepomis macrochirus Bluegill Micropterus salmoides Largemouth Bass

117

Etheostoma olmstedi Tessellated Darter Percina peltata Shield Darter

Aquatic Macroinvertebrates

TableD-3: Aquatic Macroinvertebrates at Marshalls Creek Site 3, Pennsylvania (in phylogenetic order followed by crustaceans, mollusks, oligochaetes, and leeches).

Class/Order Family Genus Common Name Ephemeroptera Ameletidae Ameletus combmouthed minnow mayflies Ephemeroptera Baetidae Baetis small minnow mayflies Ephemeroptera Baetidae Callibaetis small minnow mayflies Ephemeroptera Baetidae Centroptilum small minnow mayflies Ephemeroptera Caenidae Caenis small squaregilled mayflies Ephemeroptera Ephemerellidae Drunella spiny crawler mayflies Ephemeroptera Ephemerellidae Ephemerella spiny crawler mayflies Ephemeroptera Ephemerellidae Eurylophella spiny crawler mayflies Ephemeroptera Ephemerellidae Serratella spiny crawler mayflies Ephemeroptera Heptageniidae Epeorus flatheaded mayflies Ephemeroptera Heptageniidae Heptagenia flatheaded mayflies Ephemeroptera Heptageniidae Maccaffertium flatheaded mayflies Ephemeroptera Heptageniidae Stenacron flatheaded mayflies Ephemeroptera Isonychiidae Isonychia brushlegged mayflies Ephemeroptera Leptohyphidae Tricorythodes little stout crawler mayflies Ephemeroptera Leptophlebiidae Leptophlebia pronggilled mayflies Ephemeroptera Leptophlebiidae Paraleptophlebia pronggilled mayflies Ephemeroptera Siphlonuridae Siphlonurus primitive minnow mayflies Odonata Aeshnidae Aeshna darners Odonata Aeshnidae Boyeria darners Odonata Aeshnidae Gomphaeshna darners Odonata Calopterygidae Calopteryx broadwinged damselflies Odonata Calopterygidae Hetaerina broadwinged damselflies Odonata Coenagrionidae Amphiagrion narrowwinged damselflies Odonata Coenagrionidae Argia narrowwinged damselflies Odonata Coenagrionidae Chromagrion narrowwinged damselflies Odonata Coenagrionidae Enallagma narrowwinged damselflies Odonata Coenagrionidae Ischnura narrowwinged damselflies Odonata Coenagrionidae Nehalennia narrowwinged damselflies Odonata Cordulegastridae Cordulegaster flying adders Odonata Corduliidae Helocordulia emeralds Odonata Corduliidae Neurocordulia emeralds Odonata Gomphidae Arigomphus clubtails Odonata Gomphidae Gomphus clubtails Odonata Gomphidae Hagenius clubtails Odonata Gomphidae Lanthus clubtails

118

Odonata Gomphidae Ophiogomphus clubtails Odonata Gomphidae Progomphus clubtails Odonata Gomphidae Stylogomphus clubtails Odonata Libellulidae Erythemis skimmers Odonata Macromiidae Macromia cruisers Odonata Petaluridae Tachopteryx petaltails Plecoptera Chloroperlidae Alloperla green stoneflies Plecoptera Chloroperlidae Sweltsa green stoneflies Plecoptera Leuctridae Leuctra rolledwinged stoneflies Plecoptera Leuctridae Paraleuctra rolledwinged stoneflies Plecoptera Nemouridae Nemoura spring stoneflies Plecoptera Nemouridae Ostrocerca spring stoneflies Plecoptera Nemouridae Paranemoura spring stoneflies Plecoptera Nemouridae Prostoia spring stoneflies Plecoptera Nemouridae Zapada spring stoneflies Plecoptera Peltoperlidae Peltoperla roachlike stoneflies Plecoptera Perlidae Acroneuria common stoneflies Plecoptera Perlidae Agnetina common stoneflies Plecoptera Perlidae Neoperla common stoneflies Plecoptera Perlidae Paragnetina common stoneflies Plecoptera Perlodidae Clioperla perlodid stoneflies Plecoptera Perlodidae Hydroperla perlodid stoneflies Plecoptera Perlodidae Isogenoides perlodid stoneflies Plecoptera Perlodidae Isoperla perlodid stoneflies Plecoptera Pteronarcyidae Pteronarcys giant stoneflies Plecoptera Taeniopterygidae Strophopteryx winter stoneflies Plecoptera Taeniopterygidae Taeniopteryx winter stoneflies Hemiptera Belostomatidae Belostoma giant water bugs Hemiptera Corixidae Palmacorixa water boatmans Hemiptera Naucoridae Pelocoris creeping water bugs Hemiptera Notonectidae Notonecta back swimmers Coleoptera Elmidae Ancyronyx riffle beetles Coleoptera Elmidae Dubiraphia riffle beetles Coleoptera Elmidae Macronychus riffle beetles Coleoptera Elmidae Microcylloepus riffle beetles Coleoptera Elmidae Optioservus riffle beetles Coleoptera Elmidae Promoresia riffle beetles Coleoptera Elmidae Stenelmis riffle beetles Coleoptera Gyrinidae Gyrinus whirligig beetles Coleoptera Haliplidae Haliplus crawling water beetles Coleoptera Hydrophilidae Berosus water scavenger beetles Coleoptera Psephenidae Ectopria water pennies Coleoptera Psephenidae Psephenus water pennies Megaloptera Corydalidae Corydalus dobsonflies Megaloptera Corydalidae Neohermes fishflies Megaloptera Corydalidae Nigronia fishflies Megaloptera Sialiidae Sialis alderflies

119

Trichoptera Apataniidae Apatania early smoky wing sedges Trichoptera Beraeidae Beraea small eastern caddisflies Trichoptera Brachycentridae Adicrophleps humpless casemaker caddisflies Trichoptera Brachycentridae Brachycentrus humpless casemaker caddisflies Trichoptera Brachycentridae Micrasema humpless casemaker caddisflies Trichoptera Glossosomatidae Glossosoma little black caddisflies Trichoptera Helicopsychidae Helicopsyche snailcase caddisflies Trichoptera Hydropsychidae Arctopsyche netspinning caddisflies Trichoptera Hydropsychidae Cheumatopsyche netspinning caddisflies Trichoptera Hydropsychidae Homoplectra netspinning caddisflies Trichoptera Hydropsychidae Hydropsyche netspinning caddisflies Trichoptera Hydropsychidae Macrostemum netspinning caddisflies Trichoptera Hydropsychidae Parapsyche netspinning caddisflies Trichoptera Hydroptilidae Hydroptila micro caddisflies Trichoptera Hydroptilidae Leucotrichia micro caddisflies Trichoptera Lepidostomatidae Lepidostoma bizarre caddisflies Trichoptera Lepidostomatidae Theliopsyche bizarre caddisflies Trichoptera Leptoceridae Ceraclea longhorned caddisflies Trichoptera Leptoceridae Leptocerus longhorned caddisflies Trichoptera Leptoceridae Mystacides longhorned caddisflies Trichoptera Leptoceridae Nectopsyche longhorned caddisflies Trichoptera Leptoceridae Oecetis longhorned caddisflies Trichoptera Leptoceridae Setodes longhorned caddisflies Trichoptera Leptoceridae Triaenodes longhorned caddisflies Trichoptera Limnephilidae Hesperophylax northern caddisflies Trichoptera Limnephilidae Nemotaulis northern caddisflies Trichoptera Limnephilidae Onocosmoecus northern caddisflies Trichoptera Limnephilidae Platycentropus northern caddisflies Trichoptera Limnephilidae Pseudostenophylax northern caddisflies Trichoptera Limnephilidae Psychoglypha northern caddisflies Trichoptera Limnephilidae Pycnopsyche northern caddisflies Trichoptera Molannidae Molanna hood casemaker caddisflies Trichoptera Odontoceridae Psilotreta mortarjoint casemaker caddisflies Trichoptera Philopotamidae Chimarra fingernet caddisflies Trichoptera Polycentropodidae Cernotina tubemaker caddisflies Trichoptera Polycentropodidae Cyrnellus tubemaker caddisflies Trichoptera Polycentropodidae Neureclipsis tubemaker caddisflies Trichoptera Polycentropodidae Nyctiophlyax tubemaker caddisflies Trichoptera Polycentropodidae Phylocentropus tubemaker caddisflies Trichoptera Polycentropodidae Polycentropus tubemaker caddisflies Trichoptera Psychomyiidae Lype nettube caddisflies Trichoptera Psychomyiidae Psychomyia nettube caddisflies Trichoptera Rhyacophilidae Rhyacophila freeliving caddisflies Trichoptera Sericostomatidae Agarodes bushtailed caddisflies Trichoptera Uenoidae Neophylax stonecase caddisflies Lepidoptera Crambidae Petrophila crambid snout moths Diptera Athericidae Atherix watersnipe flies

120

Diptera Ceratopogonidae Dasyhelea biting midges Diptera Chironomidae * midges Diptera Empididae Clinocera dance flies Diptera Empididae Hemerodromia dance flies Diptera Simuliidae Prosimulium black flies Diptera Simuliidae Simulium black flies Diptera Tabanidae Chrysops deer flies Diptera Tipulidae Antocha crane flies Diptera Tipulidae Tipula crane flies Amphipoda Gammaridae Gammarus scuds Amphipoda Hyalellidae Hyalella scuds Decapoda Cambaridae * crayfish Isopoda Asellidae Caecidotea sowbugs Bivalvia Sphaeriidae * fingernail clams Gastropoda Lymnaeidae * pond snails Gastropoda Physidae * bladder snails Gastropoda Planorbidae * ram's horn snails Gastropoda Valvatidae * valve snails Gastropoda Viviparidae * river snails Hirudinea * * leeches Oligochaeta * * aquatic worms

Aquatic Plants/Algae

TableD-4: Aquatic Plants/Algae at Marshalls Creek Site 3, Pennsylvania. Scientific Name Common Name Brassica Mustard Ceratophyllum demersum Coontail Cladophora Nuisance Algae Cyperaceae Sedge Elodea canadensis Canadian Waterweed Hippuris vulgaris Mare's-tail Leersia oryzoides Rice Cut-grass Najas flexilis Bushy Pondweed Potamogeton americanus American Pondweed Potamogeton crispus Curly Pondweed Stuckenia pectinata Sago Pondweed

121 Chemical Habitat Characters

TableD-5: Chemical Habitat Characters at Marshalls Creek Site 3, Pennsylvania. pH 5.8 - 8.5 Dissolved Oxygen (mg/liter) 7.5 - 15.0 Conductivity (microsiemens/cm) 80 - 290 Alkalinity (ppm) 20 - 50 Hardness (ppm) 50 - 75

Physical Habitat Characters

TableD-6: Physical Habitat Characters at Marshalls Creek Site 3, Pennsylvania. Water Temperature (degrees C) 0.5 - 26.0 Depth (cm) 68 Velocity (cm/sec) 25.0 Substrate (% mud/sand) 60 Riparian Protection (% erosion) 10 Flow Status (% flow to both banks) 95 Bank Stability (% bank erosion) 10 Channel Alteration (% altered) 5

Other Marshalls Creek Site 3, Pennsylvania, 2001-2012 data including numbers of fish specimens and macroinvertebrate specimens are available from Dr. Jay R. Stauffer, Jr.

122 Appendix E

Marshalls Creek Site 4, Pennsylvania

Description

FigureE-1: Marshalls Creek Site 4, Pennsylvania.

Historical Site: No

Collection Dates: Fishes - 8 June 2011* and 4 June 2012 (*I did not collect, but I am using collection data)

Aquatic Macroinvertebrates - 5 March 2011, 3 August 2011, 14 December 2011, and 8 March 2012

Aquatic Plants - 17 January 2011, 5 March 2011, 7 April 2011, 28 October 2011, 5 June 2012, 1 August 2012, and 5 October 2012

Type: High Gradient Current: Pool (30%), Run (60%), and Riffle (10%) Reach: 100 meters Drainage: Delaware County: Monroe Latitude: N41.04240 Longitude: W075.12840 Collection Number: CWH-12-69

123 Biological Habitat Characters

Endangered Shiners

TableE-1: Endangered Shiners at Marshalls Creek Site 4, Pennsylvania. Individuals Scientific Name Common Name Collected/Released Individuals Observed Notropis bifrenatus Bridle Shiner 0 0 Notropis chalybaeus Ironcolor Shiner 0 0

Fish Associates

TableE-2: Fish Associates at Marshalls Creek Site 4, Pennsylvania (in phylogenetic order). Scientific Name Common Name Anguilla rostrata American Eel Salmo trutta Brown Trout Salvelinus fontinalus Brook Trout Umbra pygmaea Eastern Mudminnow Exoglossum maxillingua Cutlips Minnow Luxilus cornutus Common Shiner Rhinichthys atratulus Blacknose Dace Rhinichthys cataractae Longnose Dace Semotilus corporalis Fall Fish Catostomus commersoni White Sucker Erimyzon oblongus Creek Chubsucker Ameiurus nebulosus Brown Bullhead Enneacanthus gloriosus Bluespotted Sunfish Lepomis auritus Redbreast Sunfish Lepomis gibbosus Pumpinseed Lepomis macrochirus Bluegill Etheostoma olmstedi Tessellated Darter Percina peltata Shield Darter

124 Aquatic Macroinvertebrates

TableE-3: Aquatic Macroinvertebrates at Marshalls Creek Site 4, Pennsylvania (in phylogenetic order followed by crustaceans, mollusks, oligochaetes, and leeches).

Class/Order Family Genus Common Name Ephemeroptera Ameletidae Ameletus combmouthed minnow mayflies Ephemeroptera Baetidae Baetis small minnow mayflies Ephemeroptera Ephemerellidae Ephemerella spiny crawler mayflies Ephemeroptera Ephemerellidae Eurylophella spiny crawler mayflies Ephemeroptera Ephemerellidae Serratella spiny crawler mayflies Ephemeroptera Heptageniidae Maccaffertium flatheaded mayflies Ephemeroptera Isonychiidae Isonychia brushlegged mayflies Ephemeroptera Leptohyphidae Tricorythodes little stout crawler mayflies Ephemeroptera Leptophlebiidae Leptophlebia pronggilled mayflies Ephemeroptera Leptophlebiidae Paraleptophlebia pronggilled mayflies Odonata Aeshnidae Boyeria darners Odonata Coenagrionidae Argia narrowwinged damselflies Odonata Coenagrionidae Nehalennia narrowwinged damselflies Odonata Gomphidae Gomphus clubtails Odonata Gomphidae Stylogomphus clubtails Plecoptera Chloroperlidae Utaperla green stoneflies Plecoptera Leuctridae Paraleuctra rolledwinged stoneflies Plecoptera Nemouridae Nemoura spring stoneflies Plecoptera Nemouridae Paranemoura spring stoneflies Plecoptera Peltoperlidae Peltoperla roachlike stoneflies Plecoptera Perlidae Acroneuria common stoneflies Plecoptera Perlidae Agnetina common stoneflies Plecoptera Perlodidae Isoperla perlodid stoneflies Plecoptera Pteronarcyidae Pteronarcys giant stoneflies Plecoptera Taeniopterygidae Taeniopteryx winter stoneflies Hemiptera Veliidae Rhagovelia broadshouldered water striders Coleoptera Elmidae Dubiraphia riffle beetles Coleoptera Elmidae Microcylloepus riffle beetles Coleoptera Elmidae Optioservus riffle beetles Coleoptera Elmidae Promoresia riffle beetles Coleoptera Elmidae Stenelmis riffle beetles Coleoptera Psephenidae Ectopria water pennies Coleoptera Psephenidae Psephenus water pennyies Megaloptera Corydalidae Nigronia dobsonflies Megaloptera Sialiidae Sialis alderflies Trichoptera Beraeidae Beraea small eastern caddisflies Trichoptera Brachycentridae Micrasema humpless casemaker caddisflies Trichoptera Helicopsychidae Helicopsyche snailcase caddisflies

125

Trichoptera Hydropsychidae Cheumatopsyche netspinning caddisflies Trichoptera Hydropsychidae Hydropsyche netspinning caddisflies Trichoptera Lepidostomatidae Lepidostoma bizarre caddisflies Trichoptera Leptoceridae Ceraclea longhorned caddisflies Trichoptera Leptoceridae Mystacides longhorned caddisflies Trichoptera Leptoceridae Nectopsyche longhorned caddisflies Trichoptera Limnephilidae Hesperophylax northern caddisflies Trichoptera Limnephilidae Pseudostenophylax northern caddisflies Trichoptera Limnephilidae Pycnopsyche northern caddisflies Trichoptera Molannidae Molanna hood casemaker caddisflies Trichoptera Philopotamidae Chimarra fingernet caddisflies Trichoptera Polycentropodidae Cyrnellus tubemaker caddisflies Trichoptera Polycentropodidae Nyctiophylax tubemaker caddisflies Trichoptera Polycentropodidae Polycentropus tubemaker caddisflies Trichoptera Rhyacophilidae Rhyacophila freeliving caddisflies Trichoptera Uenoidae Neophylax stonecase caddisflies Diptera Athericidae Atherix watersnipe flies Diptera Ceratopogonidae Bezzia biting midges Diptera Chironomidae * midges Diptera Empididae Hemerodromia dance flies Diptera Simuliidae Simulium black flies Diptera Tipulidae Antocha crane flies Diptera Tipulidae Pedicia crane flies Diptera Tipulidae Tipula crane flies Amphipoda Gammaridae Gammarus scuds Amphipoda Hyalellidae Hyalella scuds Isopoda Asellidae Caecidotea sowbugs Bivalvia Sphaeriidae * fingernail clams Gastropoda Physidae * bladder snails Gastropoda Planorbidae * ram's horn snails Gastropoda Valvatidae * valve snails Gastropoda Viviparidae * river snails Hirudinea * * leeches Oligochaeta * * aquatic worms

126 Aquatic Plants/Algae

TableE-4: Aquatic Plants/Algae at Marshalls Creek Site 4, Pennsylvania. Scientific Name Common Name Brassica Mustard Caltha palustris Marsh Marigold Ceratophyllum demersum Coontail Cladophora Nuisance Algae Elodea canadensis Canadian Waterweed Hippuris vulgaris Mare's-tail Iridaceae Iris Leersia oryzoides Rice Cut-grass Rumex Dock Viola lanceolata Big White Violet

Chemical Habitat Characters

TableE-5: Chemical Habitat Characters at Marshalls Creek Site 4, Pennsylvania. pH 5.8 - 8.5 Dissolved Oxygen (mg/liter) 7.5 - 15.0 Conductivity (microsiemens/cm) 80 - 290 Alkalinity (ppm) 20 - 50 Hardness (ppm) 50 - 75

Physical Habitat Characters

TableE-6: Physical Habitat Characters at Marshalls Creek Site 4, Pennsylvania. Water Temperature (degrees C) 0.5 - 26.0 Depth (cm) 44 Velocity (cm/sec) 50.0 Substrate (% mud/sand) 20 Riparian Protection (% erosion) 10 Flow Status (% flow to both banks) 95 Bank Stability (% bank erosion) 10 Channel Alteration (% altered) 20

Other Marshalls Creek Site 4, Pennsylvania, 2011-2012 data including numbers of fish specimens and macroinvertebrate specimens are available from Dr. Jay R. Stauffer, Jr.

127 Appendix F

Marshalls Creek Site 5, Pennsylvania

Description

FigureF-1: Marshalls Creek Site 5, Pennsylvania.

Historical Site: No

Collection Dates: Fishes - 8 June 2011* and 4 June 2012 (*I did not collect, but I am using collection data)

Aquatic Macroinvertebrates - 3 August 2011, 14 December 2011, and 8 March 2012

Aquatic Plants - 28 October 2011, 5 June 2012, 1 August 2012, and 5 October 2012

Type: High Gradient Current: Run (80%) and Riffle (20%) Reach: 100 meters Drainage: Delaware County: Monroe Latitude: N41.05170 Longitude: W075.13660 Collection Number: CWH-12-69

128 Biological Habitat Characters

Endangered Shiners

TableF-1: Endangered Shiners at Marshalls Creek Site 5, Pennsylvania. Individuals Scientific Name Common Name Collected/Released Individuals Observed Notropis bifrenatus Bridle Shiner 0 0 Notropis chalybaeus Ironcolor Shiner 0 0

Fish Associates

TableF-2: Fish Associates at Marshalls Creek Site 5, Pennsylvania (in phylogenetic order). Scientific Name Common Name Anguilla rostrata American Eel Salmo trutta Brown Trout Salvelinus fontinalus Brook Trout Exoglossum maxillingua Cutlips Minnow Rhinichthys atratulus Blacknose Dace Catostomus commersoni White Sucker Hypentelium nigricans Northern Hog Sucker Enneacanthus gloriosus Bluespotted Sunfish Lepomis macrochirus Bluegill Etheostoma olmstedi Tessellated Darter Perca flavescens Yellow Perch Percina peltata Shield Darter

129 Aquatic Macroinvertebrates

TableF-3: Aquatic Macroinvertebrates at Marshalls Creek Site 5, Pennsylvania (in phylogenetic order followed by crustaceans, mollusks, oligochaetes, and leeches).

Class/Order Family Genus Common Name Ephemeroptera Ameletidae Ameletus combmouthed minnow mayflies Ephemeroptera Baetidae Baetis small minnow mayflies Ephemeroptera Ephemerellidae Ephemerella spiny crawler mayflies Ephemeroptera Ephemerellidae Serratella spiny crawler mayflies Ephemeroptera Heptageniidae Epeorus flatheaded mayflies Ephemeroptera Heptageniidae Maccaffertium flatheaded mayflies Ephemeroptera Isonychiidae Isonychia brushlegged mayflies Ephemeroptera Leptohyphidae Tricorythodes little stout crawler mayflies Ephemeroptera Leptophlebiidae Leptophlebia pronggilled mayflies Ephemeroptera Leptophlebiidae Paraleptophlebia pronggilled mayflies Odonata Gomphidae Stylogomphus clubtails Plecoptera Leuctridae Leuctra rolledwinged stoneflies Plecoptera Peltoperlidae Peltoperla roachlike stoneflies Plecoptera Perlidae Acroneuria common stoneflies Plecoptera Perlidae Agnetina common stoneflies Plecoptera Pteronarcyidae Pteronarcys giant stoneflies Plecoptera Taeniopterygidae Taeniopteryx winter stoneflies Coleoptera Elmidae Promoresia riffle beetles Coleoptera Elmidae Stenelmis riffle beetles Coleoptera Psephenidae Ectopria water pennies Coleoptera Psephenidae Psephenus water pennies Megaloptera Corydalidae Nigronia dobsonflies Megaloptera Sialiidae Sialis alderflies Trichoptera Beraeidae Beraea small eastern caddisflies Trichoptera Glossosomatidae Glossosoma little black caddisflies Trichoptera Helicopsychidae Helicopsyche snailcase caddisflies Trichoptera Hydropsychidae Cheumatopsyche netspinning caddisflies Trichoptera Hydropsychidae Hydropsyche netspinning caddisflies Trichoptera Lepidostomatidae Lepidostoma bizarre caddisflies Trichoptera Lepidostomatidae Theliopsyche bizarre caddisflies Trichoptera Limnephilidae Pseudostenophylax northern caddisflies Trichoptera Molannidae Molanna hood casemaker caddisflies Trichoptera Philopotamidae Chimarra fingernet caddisflies Trichoptera Polycentropodidae Neureclipsis tubemaker caddisflies Trichoptera Polycentropodidae Polycentropus tubemaker caddisflies Trichoptera Rhyacophilidae Rhyacophila freeliving caddisflies Trichoptera Uenoidae Neophylax stonecase caddisflies

130

Lepidoptera Crambidae Petrophila crambid snout moths Diptera Athericidae Atherix watersnipe flies Diptera Chironomidae * midges Diptera Empididae Hemerodromia dance flies Diptera Simuliidae Simulium black flies Diptera Tipulidae Antocha crane flies Diptera Tipulidae Hexatoma crane flies Diptera Tipulidae Pedicia crane flies Diptera Tipulidae Tipula crane flies Amphipoda Gammaridae Gammarus scuds Bivalvia Sphaeriidae * fingernail clams Oligochaeta * * aquatic worms

Aquatic Plants/Algae

TableF-4: Aquatic Plants/Algae at Marshalls Creek Site 5, Pennsylvania. Scientific Name Common Name Caltha palustris Marsh Marigold Cladophora Nuisance Algae Drepanocladus Moss Elodea canadensis Canadian Waterweed Hippuris vulgaris Mare's-tail Leersia oryzoides Rice Cut-grass Podostemum ceratophyllum River Weed Stuckenia pectinata Sago Pondweed

Chemical Habitat Characters

TableF-5: Chemical Habitat Characters at Marshalls Creek Site 5, Pennsylvania. pH 5.8 - 8.5 Dissolved Oxygen (mg/liter) 7.5 - 15.0 Conductivity (microsiemens/cm) 80 - 290 Alkalinity (ppm) 20 - 50 Hardness (ppm) 50 - 75

131 Physical Habitat Characters

TableF-6: Physical Habitat Characters at Marshalls Creek Site 5, Pennsylvania. Water Temperature (degrees C) 0.5 - 26.0 Depth (cm) 89 Velocity (cm/sec) 61.0 Substrate (% mud/sand) 20 Riparian Protection (% erosion) 10 Flow Status (% flow to both banks) 90 Bank Stability (% bank erosion) 10 Channel Alteration (% altered) 20

Other Marshalls Creek Site 5, Pennsylvania, 2011-2012 data including numbers of fish specimens and macroinvertebrate specimens are available from Dr. Jay R. Stauffer, Jr.

132 Appendix G

Long Marsh Ditch, Maryland

Description

FigureG-1: Long Marsh Ditch, Maryland.

Historical Site: Ironcolor Shiner

Collection Date: 19 June 2012

Type: Low Gradient Current: Pool (100%) Reach: 100 meters Drainage: Chesapeake County: Caroline Latitude: N39.09972 Longitude: W075.83985 Nearest Road Crossing: Taylor Road Collection Number: CWH-12-22

133 Biological Habitat Characters

Endangered Shiners

TableG-1: Endangered Shiners at Long Marsh Ditch, Maryland. Individuals Scientific Name Common Name Collected/Released Individuals Observed Notropis bifrenatus Bridle Shiner 0 0 Notropis chalybaeus Ironcolor Shiner 0 0

Fish Associates

TableG-2: Fish Associates at Long Marsh Ditch, Maryland (in phylogenetic order). Anguilla rostrata American Eel Umbra pygmaea Eastern Mudminnow Luxilus cornutus Common Shiner Semotilus corporalis Fall Fish Noturus gyninus Tadpole Madtom Aphredoderus sayanus Pirate Perch Enneacanthus gloriosus Bluespotted Sunfish Lepomis gibbosus Pumpinseed Lepomis macrochirus Bluegill Etheostoma olmstedi Tessellated Darter

Aquatic Macroinvertebrates

TableG-3: Aquatic Macroinvertebrates at Long Marsh Ditch, Maryland (in phylogenetic order followed by crustaceans, mollusks, oligochaetes, and leeches).

Class/Order Family Genus Common Name Ephemeroptera Baetidae Baetis small minnow mayflies Odonata Gomphidae Gomphus clubtails Hemiptera Corixidae Palmacorixa water boatmans Coleoptera Elmidae Dubiraphia riffle beetles Coleoptera Elmidae Stenelmis riffle beetles Coleoptera Haliplidae Haliplus crawling water beetles Coleoptera Haliplidae Peltodytes crawling water beetles Trichoptera Polycentropodidae Phylocentropus tubemaker caddisflies Diptera Chironomidae * midges

134

Diptera Empididae Hemerodromia dance flies Amphipoda Gammaridae Gammarus scuds Bivalvia Sphaeriidae * fingernail clams

Aquatic Plants

TableG-4: Aquatic Plants at Long Marsh Ditch, Maryland. Scientific Name Common Name Cyperaceae Sedge Elatine Waterwort Hydrocotyle americana Water Pennywort Najas flexilis Bushy Pondweed Rumex Dock

Chemical Habitat Characters

TableG-5: Chemical Habitat Characters at Long Marsh Ditch, Maryland. pH 6.28 Dissolved Oxygen (mg/liter) 10.87 Conductivity (microsiemens/cm) 495 Alkalinity (ppm) 40 Hardness (ppm) 75

Physical Habitat Characters

TableG-6: Physical Habitat Characters at Long Marsh Ditch, Maryland. Water Temperature (degrees C) 21.6 Depth (cm) 44 Velocity (cm/sec) 2.0 Substrate (% mud/sand) 90 Riparian Protection (% erosion) 5 Flow Status (% flow to both banks) 90 Bank Stability (% bank erosion) 10 Channel Alteration (% altered) 10

135 Appendix H

Zekiah Swamp, Maryland

Description

FigureH-1: Zekiah Swamp, Maryland.

Historical Site: Ironcolor Shiner

Collection Date: 21 June 2012

Type: Low Gradient Current: Run (50%) and Riffle (50%) Reach: 100 meters Drainage: Chesapeake County: Charles Latitude: N38.55915 Longitude: W075.85517 Nearest Road Crossing: Route 5 Collection Number: CWH-12-28

136 Biological Habitat Characters

Endangered Shiners

TableH-1: Endangered Shiners at Zekiah Swamp, Maryland. Individuals Scientific Name Common Name Collected/Released Individuals Observed Notropis bifrenatus Bridle Shiner 0 0 Notropis chalybaeus Ironcolor Shiner 0 0

Fish Associates

TableH-2: Fish Associates at Zekiah Swamp, Maryland (in phylogenetic order). Scientific Name Common Name Anguilla rostrata American Eel Umbra pygmaea Eastern Mudminnow Esox niger Chain Pickerel Lepomis gibbosus Pumpinseed Etheostoma olmstedi Tessellated Darter

Aquatic Macroinvertebrates

TableH-3: Aquatic Macroinvertebrates at Zekiah, Maryland (in phylogenetic order followed by crustaceans, mollusks, oligochaetes, and leeches).

Class/Order Family Genus Common Name Ephemeroptera Baetidae Baetis small minnow mayflies Ephemeroptera Heptageniidae Maccaffertium flatheaded mayflies Coleoptera Elmidae Dubiraphia riffle beetles Coleoptera Elmidae Stenelmis riffle beetles Trichoptera Hydropsychidae Hydropsyche netspinning caddisflies Diptera Chironomidae * midges Diptera Simuliidae Simulium black flies Amphipoda Gammaridae Gammarus scuds Amphipoda Hyalellidae Hyalella scuds Isopoda Asellidae Caecidotea sowbugs Gastropoda Viviparidae * river snails Oligochaeta * * aquatic worms

137 Aquatic Plants

TableH-4: Aquatic Plants at Zekiah Swamp, Maryland. Scientific Name Common Name Alisma Water Plantain Elatine Waterwort Najas flexilis Bushy Pondweed Sparganium Bur Reed

Chemical Habitat Characters

TableH-5: Chemical Habitat Characters at Zekiah Swamp, Maryland. pH 7.45 Dissolved Oxygen (mg/liter) 4.36 Conductivity (microsiemens/cm) 111 Alkalinity (ppm) 40 Hardness (ppm) 120

Physical Habitat Characters

TableH-6: Physical Habitat Characters at Zekiah Swamp, Maryland. Water Temperature (degrees C) 23.7 Depth (cm) 8 Velocity (cm/sec) 14.0 Substrate (% mud/sand) 80 Riparian Protection (% erosion) 20 Flow Status (% flow to both banks) 25 Bank Stability (% bank erosion) 10 Channel Alteration (% altered) 5

138 Appendix I

Nanticoke River, Delaware

Description

FigureI-1: Nanticoke River, Delaware.

Historical Site: Ironcolor Shiner

Collection Date: 20 June 2012

Type: Low Gradient Current: Pool (50%) and Run (50%) Reach: 100 meters Drainage: Chesapeake County: Sussex Latitude: N38.75795 Longitude: W075.58757 Nearest Road Crossing: Fawn Road Collection Number: CWH-12-23

139 Biological Habitat Characters

Endangered Shiners

TableI-1: Endangered Shiners at Nanticoke River, Delaware. Individuals Scientific Name Common Name Collected/Released Individuals Observed Notropis bifrenatus Bridle Shiner 0 0 Notropis chalybaeus Ironcolor Shiner 7 100+

Fish Associates

TableI-2: Fish Associates at Nanticoke River, Delaware (in phylogenetic order). Scientific Name Common Name Anguilla rostrata American Eel Enneacanthus gloriosus Bluespotted Sunfish

Aquatic Macroinvertebrates

TableI-3: Aquatic Macroinvertebrates at Nanticoke River, Delaware (in phylogenetic order followed by crustaceans, mollusks, oligochaetes, and leeches).

Ephemeroptera Baetidae Baetis small minnow mayflies Ephemeroptera Leptohyphidae Tricorythodes little stout crawler mayflies Odonata Coenagrionidae Argia narrowwinged damselflies Coleoptera Haliplidae Peltodytes crawling water beetles Trichoptera Leptoceridae Triaenodes longhorned caddisflies Diptera Ceratopogonidae Serromyia biting midges Diptera Chironomidae * midges Amphipoda Hyalellidae Hyalella scuds Bivalvia Sphaeriidae * fingernail clams Gastropoda Lymnaeidae * pond snails Gastropoda Physidae * bladder snails

140 Aquatic Plants

TableI-4: Aquatic Plants at Nanticoke River, Delaware. Scientific Name Common Name Cyperaceae Sedge Elatine Waterwort Hippuris vulgaris Mare's-tail Myriophyllum Water Milfoil Najas flexilis Bushy Pondweed

Chemical Habitat Characters

TableI-5: Chemical Habitat Characters at Nanticoke River, Delaware. pH 6.57 Dissolved Oxygen (mg/liter) 7.66 Conductivity (microsiemens/cm) 290 Alkalinity (ppm) 50 Hardness (ppm) 75

Physical Habitat Characters

TableI-6: Physical Habitat Characters at Nanticoke River, Delaware. Water Temperature (degrees C) 19.6 Depth (cm) 65 Velocity (cm/sec) 11.2 Substrate (% mud/sand) 90 Riparian Protection (% erosion) 20 Flow Status (% flow to both banks) 95 Bank Stability (% bank erosion) 5 Channel Alteration (% altered) 5

141 Appendix J

Gum Branch (mainstream), Delaware

Description

FigureJ-1: Gum Branch (mainstream), Delaware.

Historical Site: Ironcolor Shiner

Collection Date: 20 June 2012

Type: Low Gradient Current: Pool (50%) and Run (50%) Reach: 100 meters Drainage: Chesapeake County: Sussex Latitude: N38.74778 Longitude: W075.55366 Nearest Road Crossing: Redder Road Collection Number: CWH-12-24

142 Biological Habitat Characters

Endangered Shiners

TableJ-1: Endangered Shiners at Gum Branch (mainstream), Delaware. Individuals Scientific Name Common Name Collected/Released Individuals Observed Notropis bifrenatus Bridle Shiner 0 0 Notropis chalybaeus Ironcolor Shiner 4 50+

Fish Associates

TableJ-2: Fish Associates at Gum Branch (mainstream), Delaware (in phylogenetic order). Anguilla rostrata American Eel Umbra pygmaea Eastern Mudminnow Esox niger Chain Pickerel Semotilus corporalis Fall Fish Noturus gyninus Tadpole Madtom Aphredoderus sayanus Pirate Perch Enneacanthus gloriosus Bluespotted Sunfish Lepomis gibbosus Pumpinseed Etheostoma olmstedi Tessellated Darter

Aquatic Macroinvertebrates

TableJ-3: Aquatic Macroinvertebrates at Gum Branch (mainstream), Delaware (in phylogenetic order followed by crustaceans, mollusks, oligochaetes, and leeches).

Class/Order Family Genus Common Name Ephemeroptera Baetidae Baetis small minnow mayflies Ephemeroptera Heptageniidae Maccaffertium flatheaded mayflies Odonata Aeshnidae Boyeria darners Odonata Gomphidae Gomphus clubtails Hemiptera Corixidae Palmacorixa water boatmans Coleoptera Elmidae Stenelmis riffle beetles Coleoptera Haliplidae Peltodytes crawling water beetles Megaloptera Sialiidae Sialis alderfly Trichoptera Limnephilidae Pseudostenophylax northern caddisflies

143

Diptera Chironomidae * midges Diptera Simuliidae Simulium black flies Diptera Tipulidae Tipula crane flies Amphipoda Gammaridae Gammarus scuds Amphipoda Hyalellidae Hyalella scuds Bivalvia Sphaeriidae * fingernail clams Gastropoda Physidae * bladder snails

Aquatic Plants

TableJ-4: Aquatic Plants at Gum Branch (mainstream), Delaware. Scientific Name Common Name Polygonum Smartweed Potamogeton crispus Curly Pondweed Sparganium Bur Reed Utricularia Bladderwort

Chemical Habitat Characters

TableJ-5: Chemical Habitat Characters at Gum Branch (mainstream), Delaware. pH 7.50 Dissolved Oxygen (mg/liter) 7.77 Conductivity (microsiemens/cm) 106 Alkalinity (ppm) 40 Hardness (ppm) 70

Physical Habitat Characters

TableJ-6: Physical Habitat Characters at Gum Branch (mainstream), Delaware. Water Temperature (degrees C) 20.7 Depth (cm) 44 Velocity (cm/sec) 30.0 Substrate (% mud/sand) 90 Riparian Protection (% erosion) 5 Flow Status (% flow to both banks) 95 Bank Stability (% bank erosion) 5 Channel Alteration (% altered) 10

144 Appendix K

Gum Branch (headwaters), Delaware

Description

FigureK-1: Gum Branch (headwaters), Delaware.

Historical Site: Ironcolor Shiner

Collection Date: 20 June 2012

Type: Low Gradient Current: Pool (100%) Reach: 100 meters Drainage: Chesapeake County: Sussex Latitude: N38.76818 Longitude: W075.51612 Nearest Road Crossing: Oak Road Collection Number: CWH-12-25

145 Biological Habitat Characters

Endangered Shiners

TableK-1: Endangered Shiners at Gum Branch (headwaters), Delaware. Individuals Scientific Name Common Name Collected/Released Individuals Observed Notropis bifrenatus Bridle Shiner 0 0 Notropis chalybaeus Ironcolor Shiner 15 200+

Fish Associates

TableK-2: Fish Associates at Gum Branch (headwaters), Delaware (in phylogenetic order). Scientific Name Common Name Esox niger Chain Pickerel Semotilus corporalis Fall Fish Noturus gyninus Tadpole Madtom Aphredoderus sayanus Pirate Perch Enneacanthus gloriosus Bluespotted Sunfish Lepomis gibbosus Pumpinseed Etheostoma olmstedi Tessellated Darter

Aquatic Macroinvertebrates

TableK-3: Aquatic Macroinvertebrates at Gum Branch (headwaters), Delaware (in phylogenetic order followed by crustaceans, mollusks, oligochaetes, and leeches).

Class/Order Family Genus Common Name Ephemeroptera Ameletidae Ameletus combmouthed minnow mayflies Ephemeroptera Leptohyphidae Tricorythodes little stout crawler mayflies Odonata Aeshnidae Boyeria darners Odonata Coenagrionidae Enallagma narrowwinged damselflies Hemiptera Corixidae Palmacorixa water boatmans Coleoptera Elmidae Stenelmis riffle beetles Coleoptera Haliplidae Haliplus crawling water beetles Coleoptera Hydrophilidae Berosus water scavenger beetles Coleoptera Noteridae Hydrocanthus burrowing water beetles Megaloptera Sialiidae Sialis alderflies Trichoptera Limnephilidae Pseudostenophylax northern caddisflies

146

Lepidoptera Crambidae Petrophila crambid snout moths Diptera Chironomidae * midges Diptera Tabanidae Chrysops deer flies Amphipoda Gammaridae Gammarus scuds Amphipoda Hyalellidae Hyalella scuds Decapoda Cambaridae * crayfish Gastropoda Physidae * bladder snails

Aquatic Plants

TableK-4: Aquatic Plants at Gum Branch (headwaters), Delaware. Scientific Name Common Name Callitriche Water Starwort Najas flexilis Bushy Pondweed Potamogeton crispus Curly Pondweed Sparganium Bur Reed

Chemical Habitat Characters

TableK-5: Chemical Habitat Characters at Gum Branch (headwaters), Delaware. pH 7.06 Dissolved Oxygen (mg/liter) 7.65 Conductivity (microsiemens/cm) 82 Alkalinity (ppm) 30 Hardness (ppm) 75

Physical Habitat Characters

TableK-6: Physical Habitat Characters at Gum Branch (headwaters), Delaware. Water Temperature (degrees C) 24.0 Depth (cm) 22 Velocity (cm/sec) 10.0 Substrate (% mud/sand) 90 Riparian Protection (% erosion) 60 Flow Status (% flow to both banks) 95 Bank Stability (% bank erosion) 50 Channel Alteration (% altered) 30

147 Appendix L

West Branch, Delaware

Description

FigureL-1: West Branch, Delaware.

Historical Site: Ironcolor Shiner

Collection Date: 20 June 2012

Type: Low Gradient Current: Run (100%) Reach: 100 meters Drainage: Chesapeake County: Sussex Latitude: N38.77395 Longitude: W075.52642 Nearest Road Crossing: Tucker Road Collection Number: CWH-12-26

148 Biological Habitat Characters

Endangered Shiners

TableL-1: Endangered Shiners at West Branch, Delaware. Individuals Scientific Name Common Name Collected/Released Individuals Observed Notropis bifrenatus Bridle Shiner 0 0 Notropis chalybaeus Ironcolor Shiner 0 0

Fish Associates

TableL-2: Fish Associates at West Branch, Delaware (in phylogenetic order). Anguilla rostrata American Eel Umbra pygmaea Eastern Mudminnow Semotilus corporalis Fall Fish Noturus gyninus Tadpole Madtom Enneacanthus gloriosus Bluespotted Sunfish Lepomis gibbosus Pumpinseed Etheostoma olmstedi Tessellated Darter

Aquatic Macroinvertebrates

TableL-3: Aquatic Macroinvertebrates at West Branch, Delaware (in phylogenetic order followed by crustaceans, mollusks, oligochaetes, and leeches).

Class/Order Family Genus Common Name Ephemeroptera Baetidae Baetis small minnow mayflies Odonata Aeshnidae Boyeria darners Coleoptera Elmidae Stenelmis riffle beetles Coleoptera Gyrinidae Gyrinus whirligig beetles Megaloptera Sialiidae Sialis alderflies Trichoptera Hydropsychidae Cheumatopsyche netspinning caddisflies Trichoptera Hydropsychidae Hydropsyche netspinning caddisflies Lepidoptera Crambidae Petrophila crambid snout moths Diptera Chironomidae * midges Amphipoda Gammaridae Gammarus scuds Amphipoda Hyalellidae Hyalella scuds

149

Gastropoda Physidae * bladder snails Hirudinea * * leeches

Aquatic Plants/Algae

TableL-4: Aquatic Plants/Algae at West Branch, Delaware. Scientific Name Common Name Cladophora Nuisance Algae Elatine Waterwort Leersia oryzoides Rice Cut-grass Rumex Dock

Chemical Habitat Characters

TableL-5: Chemical Habitat Characters at West Branch, Delaware. pH 6.83 Dissolved Oxygen (mg/liter) 9.41 Conductivity (microsiemens/cm) 164 Alkalinity (ppm) 40 Hardness (ppm) 75

Physical Habitat Characters

TableL-6: Physical Habitat Characters at West Branch, Delaware. Water Temperature (degrees C) 24.5 Depth (cm) 10 Velocity (cm/sec) 12.0 Substrate (% mud/sand) 80 Riparian Protection (% erosion) 5 Flow Status (% flow to both banks) 95 Bank Stability (% bank erosion) 5 Channel Alteration (% altered) 10

150 Appendix M

Clifford Road Dam Outlet, Massachusetts

Description

FigureM-1: Clifford Road Dam Outlet, Massachusetts.

Historical Site: Bridle Shiner

Collection Date: 23 July 2012

Type: Low Gradient Current: Pool (100%) Reach: 100 meters Drainage: Atlantic County: Sussex Latitude/Longitude: not released on request of the Natural Heritage & Endangered Species Program, Massachusetts Division of Fisheries & Wildlife Nearest Road Crossing: not released on request of the Natural Heritage & Endangered Species Program, Massachusetts Division of Fisheries & Wildlife Collection Number: CWH-12-59

151 Biological Habitat Characters

Endangered Shiners

TableM-1: Endangered Shiners at Clifford Road Dam Outlet, Massachusetts. Individuals Scientific Name Common Name Collected/Released Individuals Observed Notropis bifrenatus Bridle Shiner 2 10+ Notropis chalybaeus Ironcolor Shiner 0 0

Fish Associates

TableM-2: Fish Associates at Clifford Road Dam Outlet, Massachusetts (in phylogenetic order). Scientific Name Common Name Anguilla rostrata American Eel Lepomis gibbosus Pumpinseed Lepomis macrochirus Bluegill Perca flavescens Yellow Perch

Aquatic Macroinvertebrates

TableM-3: Aquatic Macroinvertebrates at Clifford Road Dam Outlet, Massachusetts (in phylogenetic order followed by crustaceans, mollusks, oligochaetes, and leeches).

Class/Order Family Genus Common Name Ephemeroptera Heptageniidae Maccaffertium flatheaded mayflies Ephemeroptera Leptohyphidae Tricorythodes little stout crawler mayflies Odonata Coenagrionidae Enallagma narrowwinged damselflies Coleoptera Elmidae Microcylloepus riffle beetles Coleoptera Elmidae Stenelmis riffle beetles Megaloptera Sialiidae Sialis alderflies Trichoptera Hydropsychidae Cheumatopsyche netspinning caddisflies Trichoptera Hydropsychidae Hydropsyche netspinning caddisflies Trichoptera Philopotamidae Chimarra fingernet caddisflies Diptera Athericidae Atherix watersnipe flies Diptera Chironomidae * midges Diptera Simuliidae Simulium black flies Diptera Tabanidae Chrysops deer flies

152

Diptera Tipulidae Tipula crane flies Amphipoda Gammaridae Gammarus scuds Isopoda Asellidae Caecidotea sowbugs Bivalvia Sphaeriidae * fingernail clams Gastropoda Physidae * bladder snails Gastropoda Planorbidae * ram's horn snails Hirudinea * * leeches

Aquatic Plants

TableM-4: Aquatic Plants at Clifford Road Dam Outlet, Massachusetts. Scientific Name Common Name Hippuris vulgaris Mare's-tail Rumex Dock Sparganium americanum American Bur Reed

Chemical Habitat Characters

TableM-5: Chemical Habitat Characters at Clifford Road Dam Outlet, Massachusetts. pH 7.25 Dissolved Oxygen (mg/liter) 8.74 Conductivity (microsiemens/cm) 122 Alkalinity (ppm) 40 Hardness (ppm) 25

Physical Habitat Characters

TableM-6: Physical Habitat Characters at Clifford Road Dam Outlet, Massachusetts. Water Temperature (degrees C) 25.7 Depth (cm) 48 Velocity (cm/sec) 3.0 Substrate (% mud/sand) 70 Riparian Protection (% erosion) 5 Flow Status (% flow to both banks) 95 Bank Stability (% bank erosion) 5 Channel Alteration (% altered) 5

153 Appendix N

Eel River, Massachusetts

Description

FigureN-1: Eel River, Massachusetts.

Historical Site: Bridle Shiner

Collection Date: 23 July 2012

Type: Low Gradient Current: Pool (75%) and Run (25%) Reach: 50 meters Drainage: Atlantic County: Sussex Latitude/Longitude: not released on request of the Natural Heritage & Endangered Species Program, Massachusetts Division of Fisheries & Wildlife Nearest Road Crossing: not released on request of the Natural Heritage & Endangered Species Program, Massachusetts Division of Fisheries & Wildlife Collection Number: CWH-12-60

154 Biological Habitat Characters

Endangered Shiners

TableN-1: Endangered Shiners at Eel River, Massachusetts. Individuals Scientific Name Common Name Collected/Released Individuals Observed Notropis bifrenatus Bridle Shiner 0 0 Notropis chalybaeus Ironcolor Shiner 0 0

Fish Associates

TableN-2: Fish Associates at Eel River, Massachusetts (in phylogenetic order). Scientific Name Common Name Anguilla rostrata American Eel Noturus insignis Margined Madtom Lepomis gibbosus Pumpinseed Micropterus salmoides Largemouth Bass Perca flavescens Yellow Perch

Aquatic Macroinvertebrates

TableN-3: Aquatic Macroinvertebrates at Eel River, Massachusetts (in phylogenetic order followed by crustaceans, mollusks, oligochaetes, and leeches).

Class/Order Family Genus Common Name Ephemeroptera Ameletidae Ameletus combmouthed minnow mayflies Ephemeroptera Baetidae Baetis small minnow mayflies Ephemeroptera Heptageniidae Maccaffertium flatheaded mayflies Coleoptera Elmidae Stenelmis riffle beetles Trichoptera Hydropsychidae Cheumatopsyche netspinning caddisflies Trichoptera Hydropsychidae Hydropsyche netspinning caddisflies Trichoptera Philopotamidae Chimarra fingernet caddisflies Diptera Chironomidae * midges Diptera Simuliidae Simulium black flies Amphipoda Gammaridae Gammarus scuds Amphipoda Hyalellidae Hyalella scuds Bivalvia Sphaeriidae * fingernail clams

155

Hirudinea * * leeches Oligochaeta * * aquatic worms

Aquatic Plants

TableN-4: Aquatic Plants at Eel River, Massachusetts. Scientific Name Common Name Hippuris vulgaris Mare's-tail Potamogeton gramineus Pondweed Vallisneria americana American Tape Grass

Chemical Habitat Characters

TableN-5: Chemical Habitat Characters at Eel River, Massachusetts. pH 7.68 Dissolved Oxygen (mg/liter) 7.26 Conductivity (microsiemens/cm) 123 Alkalinity (ppm) 20 Hardness (ppm) 25

Physical Habitat Characters

TableN-6: Physical Habitat Characters at Eel River, Massachusetts. Water Temperature (degrees C) 24.4 Depth (cm) 28 Velocity (cm/sec) 7.0 Substrate (% mud/sand) 70 Riparian Protection (% erosion) 10 Flow Status (% flow to both banks) 90 Bank Stability (% bank erosion) 10 Channel Alteration (% altered) 15

156 Appendix O

Flat Brook, Massachusetts

Description

FigureO-1: Flat Brook, Massachusetts.

Historical Site: Bridle Shiner

Collection Date: 25 July 2012

Type: Low Gradient Current: Pool (100%) Reach: 50 meters Drainage: Housatonic County: Berkshire Latitude/Longitude: not released on request of the Natural Heritage & Endangered Species Program, Massachusetts Division of Fisheries & Wildlife Nearest Road Crossing: not released on request of the Natural Heritage & Endangered Species Program, Massachusetts Division of Fisheries & Wildlife Collection Number: CWH-12-61

157 Biological Habitat Characters

Endangered Shiners

TableO-1: Endangered Shiners at Flat Brook, Massachusetts. Individuals Scientific Name Common Name Collected/Released Individuals Observed Notropis bifrenatus Bridle Shiner 6 35+ Notropis chalybaeus Ironcolor Shiner 0 0

Fish Associates

TableO-2: Fish Associates at Flat Brook, Massachusetts (in phylogenetic order). Scientific Name Common Name Lepomis gibbosus Pumpinseed

Aquatic Macroinvertebrates

TableO-3: Aquatic Macroinvertebrates at Flat Brook, Massachusetts (in phylogenetic order followed by crustaceans, mollusks, oligochaetes, and leeches).

Class/Order Family Genus Common Name Ephemeroptera Heptageniidae Stenacron flatheaded mayflies Ephemeroptera Siphlonuridae Siphlonurus primitive minnow mayflies Odonata Coenagrionidae Ischnura narrowwinged damselflies Odonata Lestidae Lestes spreadwings Hemiptera Corixidae Palmacorixa water boatmans Hemiptera Notonectidae Buenoa back swimmers Coleoptera Gyrinidae Gyrinus whirligig beetles Diptera Chironomidae * midges Amphipoda Hyalellidae Hyalella scuds Decapoda Cambaridae * crayfish Isopoda Asellidae Caecidotea sowbugs

158 Aquatic Plants

TableO-4: Aquatic Plants at Flat Brook, Massachusetts. Scientific Name Common Name Potamogeton crispus Curly Pondweed Potamogeton gramineus Pondweed

Chemical Habitat Characters

TableO-5: Chemical Habitat Characters at Flat Brook, Massachusetts. pH 7.67 Dissolved Oxygen (mg/liter) 0.93 Conductivity (microsiemens/cm) 439 Alkalinity (ppm) 180 Hardness (ppm) 150

Physical Habitat Characters

TableO-6: Physical Habitat Characters at Flat Brook, Massachusetts. Water Temperature (degrees C) 21.3 Depth (cm) 80 Velocity (cm/sec) 6.0 Substrate (% mud/sand) 80 Riparian Protection (% erosion) 10 Flow Status (% flow to both banks) 90 Bank Stability (% bank erosion) 10 Channel Alteration (% altered) 10

159 Appendix P

Hop Brook, Massachusetts

Description

FigureP-1: Hop Brook, Massachusetts.

Historical Site: Bridle Shiner

Collection Date: 25 July 2012

Type: Low Gradient Current: Pool (75%) and Run (25%) Reach: 100 meters Drainage: Housatonic County: Berkshire Latitude/Longitude: not released on request of the Natural Heritage & Endangered Species Program, Massachusetts Division of Fisheries & Wildlife Nearest Road Crossing: not released on request of the Natural Heritage & Endangered Species Program, Massachusetts Division of Fisheries & Wildlife Collection Number: CWH-12-62

160 Biological Habitat Characters

Endangered Shiners

TableP-1: Endangered Shiners at Hop Brook, Massachusetts. Individuals Collected Scientific Name Common Name Released Individuals Observed Notropis bifrenatus Bridle Shiner 9 200+ Notropis chalybaeus Ironcolor Shiner 0 0

Fish Associates

TableP-2: Fish Associates at Hop Brook, Massachusetts (in phylogenetic order). Scientific Name Common Name Esox niger Chain Pickerel Luxilus cornutus Common Shiner Notemigonus crysoleucas Golden Shiner Notropis atherinoides Emerald Shiner Ameiurus nebulosus Brown Bullhead Lepomis macrochirus Bluegill

Aquatic Macroinvertebrates

TableP-3: Aquatic Macroinvertebrates at Hop Brook, Massachusetts (in phylogenetic order followed by crustaceans, mollusks, oligochaetes, and leeches).

Class/Order Family Genus Common Name Ephemeroptera Heptageniidae Maccaffertium flatheaded mayflies Ephemeroptera Leptohyphidae Tricorythodes little stout crawler mayflies Ephemeroptera Siphlonuridae Siphlonurus primitive minnow mayflies Odonata Gomphidae Gomphus clubtails Odonata Libellulidae Tramea skimmers Hemiptera Corixidae Palmacorixa water boatmans Coleoptera Dytiscidae Rhantus predaceous diving beetles Coleoptera Elmidae Stenelmis riffle beetles Coleoptera Hydrophilidae Hydrophilus water scavenger beetles Coleoptera Psephenidae Psephenus water pennies Coleoptera Scirtidae Scirtes marsh beetles Trichoptera Limnephilidae Pseudostenophylax northern caddisflies

161

Diptera Chironomidae * midges Amphipoda Hyalellidae Hyalella scuds Decapoda Cambaridae * crayfish Hirudinea * * leeches

Aquatic Plants

TableP-4: Aquatic Plants at Hop Brook, Massachusetts. Scientific Name Common Name Cyperaceae Sedge Elatine Waterwort Juncus effusus Soft Rush Polygonum Smartweed Sparganium Bur Reed Viola lanceolata Big White Violet

Chemical Habitat Characters

TableP-5: Chemical Habitat Characters at Hop Brook, Massachusetts. pH 7.17 Dissolved Oxygen (mg/liter) 2.50 Conductivity (microsiemens/cm) 143 Alkalinity (ppm) 120 Hardness (ppm) 75

Physical Habitat Characters

TableP-6: Physical Habitat Characters at Hop Brook, Massachusetts. Water Temperature (degrees C) 24.7 Depth (cm) 28 Velocity (cm/sec) 2.0 Substrate (% mud/sand) 80 Riparian Protection (% erosion) 10 Flow Status (% flow to both banks) 95 Bank Stability (% bank erosion) 10 Channel Alteration (% altered) 20

162 Appendix Q

West Branch Farmington River, Massachusetts

Description

FigureQ-1: West Branch Farmington River, Massachusetts.

Historical Site: Bridle Shiner

Collection Date: 25 July 2012

Type: Low Gradient Current: Run (100%) Reach: 100 meters Drainage: Housatonic County: Berkshire Latitude/Longitude: not released on request of the Natural Heritage & Endangered Species Program, Massachusetts Division of Fisheries & Wildlife Nearest Road Crossing: not released on request of the Natural Heritage & Endangered Species Program, Massachusetts Division of Fisheries & Wildlife Collection Number: CWH-12-63

163 Biological Habitat Characters

Endangered Shiners

TableQ-1: Endangered Shiners at West Branch Farmington River, Massachusetts. Individuals Scientific Name Common Name Collected/Released Individuals Observed Notropis bifrenatus Bridle Shiner 0 0 Notropis chalybaeus Ironcolor Shiner 0 0

Fish Associates

TableQ-2: Fish Associates at West Branch Farmington River, Massachusetts (in phylogenetic order). Scientific Name Common Name Esox niger Chain Pickerel Exoglossum maxillingua Cutlips Minnow Lepomis autritus Redbreast Sunfish Lepomis gibbosus Pumpinseed Lepomis macrochirus Bluegill

Aquatic Macroinvertebrates

TableQ-3: Aquatic Macroinvertebrates at West Branch Farmington River, Massachusetts (in phylogenetic order followed by crustaceans, mollusks, oligochaetes, and leeches).

Class/Order Family Genus Common Name Ephemeroptera Ameletidae Ameletus combmouthed minnow mayflies Ephemeroptera Caenidae Caenis small squaregilled mayflies Ephemeroptera Heptageniidae Maccaffertium flatheaded mayflies Ephemeroptera Heptageniidae Stenacron flatheaded mayflies Coleoptera Elmidae Stenelmis riffle beetles Coleoptera Psephenidae Psephenus water pennies Megaloptera Sialiidae Sialis alderflies Diptera Chironomidae * midges Diptera Tabanidae Chrysops deer flies Amphipoda Hyalellidae Hyalella scuds Decapoda Cambaridae * crayfish Isopoda Asellidae Caecidotea sowbugs

164 Aquatic Plants

TableQ-4: Aquatic Plants at West Branch Farmington River, Massachusetts.

Scientific Name Common Name Nupar Yellow Water Lily Sagittaria Arrowhead

Chemical Habitat Characters

TableQ-5: Chemical Habitat Characters at West Branch Farmington River, Massachusetts. pH 7.90 Dissolved Oxygen (mg/liter) 6.53 Conductivity (microsiemens/cm) 205 Alkalinity (ppm) 40 Hardness (ppm) 75

Physical Habitat Characters

TableQ-6: Physical Habitat Characters at West Branch Farmington River, Massachusetts. Water Temperature (degrees C) 26.2 Depth (cm) 24 Velocity (cm/sec) 5.0 Substrate (% mud/sand) 40 Riparian Protection (% erosion) 10 Flow Status (% flow to both banks) 95 Bank Stability (% bank erosion) 10 Channel Alteration (% altered) 5

165 Appendix R

Schenob Brook, Massachusetts

Description

FigureR-1: Schenob Brook, Massachusetts.

Historical Site: Bridle Shiner

Collection Date: 26 July 2012

Type: Low Gradient Current: Pool (100%) Reach: 50 meters Drainage: Housatonic County: Berkshire Latitude/Longitude: not released on request of the Natural Heritage & Endangered Species Program, Massachusetts Division of Fisheries & Wildlife Nearest Road Crossing: not released on request of the Natural Heritage & Endangered Species Program, Massachusetts Division of Fisheries & Wildlife Collection Number: CWH-12-65

166 Biological Habitat Characters

Endangered Shiners

TableR-1: Endangered Shiners at Schenob Brook, Massachusetts. Individuals Scientific Name Common Name Collected/Released Individuals Observed Notropis bifrenatus Bridle Shiner 0 0 Notropis chalybaeus Ironcolor Shiner 0 0

Fish Associates

TableR-2: Fish Associates at Schenob Brook, Massachusetts (in phylogenetic order). Scientific Name Common Name Lepomis macrochirus Bluegill

Aquatic Macroinvertebrates

TableR-3: Aquatic Macroinvertebrates at Schenob Brook, Massachusetts (in phylogenetic order followed by crustaceans, mollusks, oligochaetes, and leeches).

Class/Order Family Genus Common Name Ephemeroptera Leptohyphidae Tricorythodes little stout crawler mayflies Ephemeroptera Siphlonuridae Siphlonurus primitive minnow mayflies Odonata Aeshnidae Basiaeschna darners Odonata Coenagrionidae Enallagma narrowwinged damselflies Hemiptera Corixidae Trichocorixa water boatmans Hemiptera Notonectidae Buenoa back swimmers Hemiptera Veliidae Microvelia broadshouldered water striders Coleoptera Dytiscidae Coptotomus predaceous diving beetles Coleoptera Elmidae Dubiraphia riffle beetles Coleoptera Elmidae Optioservus riffle beetles Coleoptera Haliplidae Haliplus crawling water beetles Coleoptera Haliplidae Peltodytes crawling water beetles Coleoptera Hydrophilidae Hydrochus water scavenger beetles Megaloptera Sialiidae Sialis alderflies Diptera Chironomidae * midges Diptera Tabanidae Tabanus horse flies

167

Amphipoda Gammaridae Gammarus scuds Decapoda Cambaridae * crayfish Bivalvia Sphaeriidae * fingernail clams Gastropoda Physidae * bladder snails Gastropoda Planorbidae * ram's horn snails

Aquatic Plants

TableR-4: Aquatic Plants at Schenob Brook, Massachusetts. Scientific Name Common Name Ceratophyllum demersum Coontail Elatine Waterwort Potamogeton crispus Curly Pondweed Potamogeton gramineus Pondweed Sparganium Bur Reed

Chemical Habitat Characters

TableR-5: Chemical Habitat Characters at Schenob Brook, Massachusetts. pH 8.06 Dissolved Oxygen (mg/liter) 4.12 Conductivity (microsiemens/cm) 256 Alkalinity (ppm) 120 Hardness (ppm) 150

Physical Habitat Characters

TableR-6: Physical Habitat Characters at Schenob Brook, Massachusetts. Water Temperature (degrees C) 22.6 Depth (cm) 60 Velocity (cm/sec) 1.0 Substrate (% mud/sand) 90 Riparian Protection (% erosion) 30 Flow Status (% flow to both banks) 90 Bank Stability (% bank erosion) 30 Channel Alteration (% altered) 20

168 Appendix S

Dry Brook, Massachusetts

Description

FigureS-1: Dry Brook, Massachusetts.

Historical Site: Bridle Shiner

Collection Date: 26 July 2012

Type: Low Gradient Current: Pool (100%) Reach: 100 meters Drainage: Housatonic County: Berkshire Latitude/Longitude: not released on request of the Natural Heritage & Endangered Species Program, Massachusetts Division of Fisheries & Wildlife Nearest Road Crossing: not released on request of the Natural Heritage & Endangered Species Program, Massachusetts Division of Fisheries & Wildlife Collection Number: CWH-12-64

169 Biological Habitat Characters

Endangered Shiners

TableS-1: Endangered Shiners at Dry Brook, Massachusetts. Individuals Scientific Name Common Name Collected/Released Individuals Observed Notropis bifrenatus Bridle Shiner 9 20+ Notropis chalybaeus Ironcolor Shiner 0 0

Fish Associates

TableS-2: Fish Associates at Dry Brook, Massachusetts (in phylogenetic order). Scientific Name Common Name Notropis hudsonius Spottail Shiner Lepomis gibbosus Pumpinseed Lepomis macrochirus Bluegill

Aquatic Macroinvertebrates

TableS-3: Aquatic Macroinvertebrates at Dry Brook, Massachusetts (in phylogenetic order followed by crustaceans, mollusks, oligochaetes, and leeches).

Class/Order Family Genus Common Name Ephemeroptera Caenidae Caenis small squaregilled mayflies Ephemeroptera Ephemeridae Litobrancha common burrower mayflies Odonata Gomphidae Gomphus clubtails Hemiptera Corixidae Palmacorixa water boatmans Coleoptera Elmidae Stenelmis riffle beetles Megaloptera Sialiidae Sialis alderflies Trichoptera Hydropsychidae Cheumatopsyche netspinning caddisflies Trichoptera Philopotamidae Chimarra fingernet caddisflies Diptera Chironomidae * midges Amphipoda Gammaridae Gammarus scuds Amphipoda Hyalellidae Hyalella scuds

170 Aquatic Plants

TableS-4: Aquatic Plants at Dry Brook, Massachusetts.

Scientific Name Common Name Sparganium americanum American Bur Reed

Chemical Habitat Characters

TableS-5: Chemical Habitat Characters at Dry Brook, Massachusetts. pH 7.82 Dissolved Oxygen (mg/liter) 4.09 Conductivity (microsiemens/cm) 208 Alkalinity (ppm) 120 Hardness (ppm) 150

Physical Habitat Characters

TableS-6: Physical Habitat Characters at Dry Brook, Massachusetts. Water Temperature (degrees C) 21.6 Depth (cm) 20 Velocity (cm/sec) 2.0 Substrate (% mud/sand) 80 Riparian Protection (% erosion) 5 Flow Status (% flow to both banks) 95 Bank Stability (% bank erosion) 5 Channel Alteration (% altered) 5

171 Appendix T

Sambo Creek, Pennsylvania

Description

FigureT-1: Sambo Creek, Pennsylvania.

Historical Site: Bridle and Ironcolor shiner (re-introduced in 2003/2004)

Collection Date: 7 Aug 2012

Type: High Gradient Current: Pool (75%) and Run (25%) Reach: 50 meters Drainage: Delaware County: Monroe Latitude: N41.02320 Longitude: W075.18182 Nearest Road Crossing: Fawn Road Collection Number: CWH-12-67

172 Biological Habitat Characters

Endangered Shiners

TableT-1: Endangered Shiners at Sambo Creek, Pennsylvania. Individuals Scientific Name Common Name Collected/Released Individuals Observed Notropis bifrenatus Bridle Shiner 0 0 Notropis chalybaeus Ironcolor Shiner 0 0

Fish Associates

TableT-2: Fish Associates at Sambo Creek, Pennsylvania (in phylogenetic order). Scientific Name Common Name Anguilla rostrata American Eel Esox americanus Grass Pickerel Ctenopharyngodon idella Grass Carp Rhinichthys atratulus Blacknose Dace Catostomus commersoni White Sucker Lepomis gibbosus Pumpinseed Etheostoma olmstedi Tessellated Darter

Aquatic Macroinvertebrates

TableT-3: Aquatic Macroinvertebrates at Sambo Creek, Pennsylvania (in phylogenetic order followed by crustaceans, mollusks, oligochaetes, and leeches).

Class/Order Family Genus Common Name Odonata Coenagrionidae Amphiagrion narrowwinged damselflies Odonata Gomphidae Stylogomphus clubtails Hemiptera Mesoveliidae Mesovelia water treaders Coleoptera Elmidae Stenelmis riffle beetles Coleoptera Psephenidae Psephenus water pennies Trichoptera Hydropsychidae Hydropsyche netspinning caddisflies Trichoptera Philopotamidae Chimarra fingernet caddisflies Trichoptera Polycentropodidae Neureclipsis tubemaker caddisflies Trichoptera Polycentropodidae Polycentropus tubemaker caddisflies Trichoptera Rhyacophilidae Rhyacophila freeliving caddisflies Diptera Chironomidae * midges

173

Amphipoda Gammaridae Gammarus scuds Gastropoda Viviparidae * river snails

Aquatic Plants/Algae

TableT-4: Aquatic Plants/Algae at Sambo Creek, Pennsylvania. Scientific Name Common Name Ceratophyllum demersum Coontail Cladophora Nuisance Algae Najas flexilis Bushy Pondweed Sparganium Bur Reed

Chemical Habitat Characters

TableT-5: Chemical Habitat Characters at Sambo Creek, Pennsylvania. pH 7.39 Dissolved Oxygen (mg/liter) 6.24 Conductivity (microsiemens/cm) 290 Alkalinity (ppm) 70 Hardness (ppm) 150

Physical Habitat Characters

TablT-6: Physical Habitat Characters at Sambo Creek, Pennsylvania. Water Temperature (degrees C) 21.4 Depth (cm) 30 Velocity (cm/sec) 2.0 Substrate (% mud/sand) 50 Riparian Protection (% erosion) 5 Flow Status (% flow to both banks) 95 Bank Stability (% bank erosion) 10 Channel Alteration (% altered) 5

174 Appendix U

McMichael Creek, Pennsylvania

Description

FigureU-1: McMichael Creek, Pennsylvania.

Historical Site: Bridle and Ironcolor shiner (re-introduced in 2003/2004)

Collection Date: 7 Aug 2012

Type: High Gradient Current: Pool (75%) and Run (25%) Reach: 50 meters Drainage: Delaware County: Monroe Latitude: N40.93480 Longitude: W075.31352 Nearest Road Crossing: Old Mill Road Collection Number: CWH-12-68

175 Biological Habitat Characters

Endangered Shiners

TableU-1: Endangered Shiners at McMichael Creek, Pennsylvania. Individuals Scientific Name Common Name Collected/Released Individuals Observed Notropis bifrenatus Bridle Shiner 0 0 Notropis chalybaeus Ironcolor Shiner 0 0

Fish Associates

TableU-2: Fish Associates at McMichael Creek, Pennsylvania (in phylogenetic order). Scientific Name Common Name Anguilla rostrata American Eel Salmo trutta Brown Trout Rhinichthys atratulus Blacknose Dace Catostomus commersoni White Sucker Etheostoma olmstedi Tessellated Darter

Aquatic Macroinvertebrates

TableU-3: Aquatic Macroinvertebrates at McMichael Creek, Pennsylvania (in phylogenetic order followed by crustaceans, mollusks, oligochaetes, and leeches).

Class/Order Family Genus Common Name Ephemeroptera Heptageniidae Maccaffertium flatheaded mayflies Ephemeroptera Heptageniidae Stenacron flatheaded mayflies Ephemeroptera Isonychiidae Isonychia brushlegged mayflies Ephemeroptera Siphlonuridae Siphlonurus primitive minnow mayflies Plecoptera Perlidae Acroneuria common stoneflies Coleoptera Psephenidae Psephenus water pennies Megaloptera Corydalidae Nigronia dobsonflies Trichoptera Hydropsychidae Cheumatopsyche netspinning caddisflies Trichoptera Hydropsychidae Hydropsyche netspinning caddisflies Trichoptera Polycentropodidae Polycentropus tubemaker caddisflies Diptera Chironomidae * midges

176

Amphipoda Gammaridae Gammarus scuds Oligochaeta * * aquatic worms

Aquatic Plants/Algae

TableU-4: Aquatic Plants/Algae at McMichael Creek, Pennsylvania. Scientific Name Common Name Cladophora Nuisance Algae Najas flexilis Bushy Pondweed

Chemical Habitat Characters

TableU-5: Chemical Habitat Characters at McMichael Creek, Pennsylvania. pH 7.77 Dissolved Oxygen (mg/liter) 12.8 Conductivity (microsiemens/cm) 311 Alkalinity (ppm) 40 Hardness (ppm) 75

Physical Habitat Characters

TableU-6: Physical Habitat Characters at McMichael Creek, Pennsylvania. Water Temperature (degrees C) 21.3 Depth (cm) 21 Velocity (cm/sec) 17.0 Substrate (% mud/sand) 30 Riparian Protection (% erosion) 15 Flow Status (% flow to both banks) 95 Bank Stability (% bank erosion) 10 Channel Alteration (% altered) 5

177 Appendix V

Fishes Associations

TableV-1: Endangered Shiners Predator Species and Endangered Shiners Non-Predator Species (in phylogenetic order).

Endangered Endangered Shiners Shiners Predator Non-Predator Scientific Name Common Name Species Species Anguilla rostrata American Eel x Salmo trutta Brown Trout x Salvelinus fontinalus Brook Trout x Umbra pygmaea Eastern Mudminnow x Esox americanus Grass Pickerel x Esox niger Chain Pickerel x Ctenopharyngodon idella Grass Carp x Exoglossum maxillingua Cutlips Minnow x Luxilus cornutus Common Shiner x Notemigonus crysoleucas Golden Shiner x Notropis atherinoides Emerald Shiner x Notropis hudsonius Spottail Shiner x Rhinichthys atratulus Blacknose Dace x Rhinichthys cataractae Longnose Dace x Semotilus corporalis Fall Fish x Catostomus commersoni White Sucker x Erimyzon oblongus Creek Chubsucker x Hypentelium nigricans Northern Hog Sucker x Ameiurus nebulosus Brown Bullhead x Noturus gyninus Tadpole Madtom x Noturus insignis Margined Madtom x Aphredoderus sayanus Pirate Perch x Enneacanthus gloriosus Bluespotted Sunfish x Lepomis auritus Redbreast Sunfish x Lepomis gibbosus Pumpinseed x Lepomis macrochirus Bluegill x Micropterus dolomieu Smallmouth Bass x Micropterus salmoides Largemouth Bass x Etheostoma olmstedi Tessellated Darter x Perca flavescens Yellow Perch x Percina peltata Shield Darter x

178 TableV-2: Native Species and Exotic Species (in phylogenetic order).

Scientific Name Common Name Native Fish Exotic Fish Anguilla rostrata American Eel x Salmo trutta Brown Trout x Salvelinus fontinalus Brook Trout x Umbra pygmaea Eastern Mudminnow x Esox americanus Grass Pickerel x Esox niger Chain Pickerel x Ctenopharyngodon idella Grass Carp x Exoglossum maxillingua Cutlips Minnow x Luxilus cornutus Common Shiner x Notemigonus crysoleucas Golden Shiner x Notropis atherinoides Emerald Shiner x Notropis bifrenatus Bridle Shiner x Notropis chalybaeus Ironcolor Shiner x Notropis hudsonius Spottail Shiner x Rhinichthys atratulus Blacknose Dace x Rhinichthys cataractae Longnose Dace x Semotilus corporalis Fall Fish x Catostomus commersoni White Sucker x Erimyzon oblongus Creek Chubsucker x Hypentelium nigricans Northern Hog Sucker x Ameiurus nebulosus Brown Bullhead x Noturus gyninus Tadpole Madtom x Noturus insignis Margined Madtom x Aphredoderus sayanus Pirate Perch x Enneacanthus gloriosus Bluespotted Sunfish x Lepomis auritus Redbreast Sunfish x Lepomis gibbosus Pumpinseed x Lepomis macrochirus Bluegill x Micropterus dolomieu Smallmouth Bass x Micropterus salmoides Largemouth Bass x Etheostoma olmstedi Tessellated Darter x Perca flavescens Yellow Perch x Percina peltata Shield Darter x

179 Appendix W

Aquatic Macroinvertebrate Associations

TableW-1: Endangered Shiners Edible Aquatic Macroinvertebrate Taxa and Endangered Shiners Non-Edible Aquatic Macroinvertebrate Taxa (in phylogenetic order followed by crustaceans, mollusks, oligochaetes, and leeches).

En. Sh. En. Sh. Non- Edible Edible Aq. Aq. Macro. Macro.

Taxa Taxa

Order/Family Genus Common Name x Ameletidae Ameletus combmouthed minnow mayflies x Baetidae Acentrella small minnow mayflies x Baetidae Baetis small minnow mayflies x Baetidae Callibaetis small minnow mayflies x Baetidae Centroptilum small minnow mayflies x Caenidae Caenis small squaregilled mayflies x Ephemerellidae Attenella spiny crawler mayflies x Ephemerellidae Drunella spiny crawler mayflies x Ephemerellidae Ephemerella spiny crawler mayflies x Ephemerellidae Eurylophella spiny crawler mayflies x Ephemerellidae Serratella spiny crawler mayflies x Ephemeridae Hexagenia common burrow mayflies x1 Ephemeridae Litobrancha common burrow mayflies x1 Heptageniidae Epeorus flatheaded mayflies x Heptageniidae Heptagenia flatheaded mayflies x Heptageniidae Leucrocuta flatheaded mayflies x Heptageniidae Maccaffertium flatheaded mayflies x Heptageniidae Nixe flatheaded mayflies x Heptageniidae Stenacron flatheaded mayflies x Isonychiidae Isonychia brushlegged mayflies x Leptohyphidae Tricorythodes little stout crawler mayflies x Leptophlebiidae Leptophlebia pronggilled mayflies x Leptophlebiidae Paraleptophlebia pronggilled mayflies x Potamanthidae Anthopotamus hacklegilled burrower mayflies x Siphlonuridae Siphlonurus primitive minnow mayflies x Aeshnidae Aeshna darners x Aeshnidae Basiaeschna darners x Aeshnidae Boyeria darners x Aeshnidae Gomphaeshna darners x Calopterygidae Calopteryx broadwinged damselflies x Calopterygidae Hetaerina broadwinged damselflies x

180 Coenagrionidae Amphiagrion narrowwinged damselflies x Coenagrionidae Argia narrowwinged damselflies x Coenagrionidae Chromagrion narrowwinged damselflies x Coenagrionidae Enallagma narrowwinged damselflies x Coenagrionidae Ischnura narrowwinged damselflies x Coenagrionidae Nehalennia narrowwinged damselflies x Cordulegastridae Cordulegaster flying adders x Corduliidae Epitheca emeralds x Corduliidae Helocordulia emeralds x Corduliidae Neurocordulia emeralds x Corduliidae Somatochlora emeralds x Gomphidae Arigomphus clubtails x Gomphidae Dromogomphus clubtails x Gomphidae Gomphus clubtails x Gomphidae Hagenius clubtails x Gomphidae Lanthus clubtails x Gomphidae Ophiogomphus clubtails x Gomphidae Progomphus clubtails x Gomphidae Stylogomphus clubtails x Lestidae Lestes spreadwings x Libellulidae Erythemis skimmers x Libellulidae Tramea skimmers x Macromiidae Macromia cruisers x Petaluridae Tachopteryx petaltails x Capniidae Allocapnia small winter stoneflies x Chloroperlidae Alloperla green stoneflies x Chloroperlidae Sweltsa green stoneflies x Chloroperlidae Utaperla green stoneflies x Leuctridae Leuctra rolledwinged stoneflies x Leuctridae Paraleuctra rolledwinged stoneflies x Nemouridae Amphinemura spring stoneflies x Nemouridae Nemoura spring stoneflies x Nemouridae Ostrocerca spring stoneflies x Nemouridae Paraneumora spring stoneflies x Nemouridae Prostoia spring stoneflies x Nemouridae Shipsa spring stoneflies x Nemouridae Zapada spring stoneflies x Peltoperlidae Peltoperla roachlike stoneflies x Perlidae Acroneuria common stoneflies x Perlidae Agnetina common stoneflies x Perlidae Attaneuria common stoneflies x Perlidae Neoperla common stoneflies x Perlidae Paragnetina common stoneflies x Perlidae Perlesta common stoneflies x Perlidae Perlinella common stoneflies x Perlodidiae Clioperla perlodid stoneflies x Perlodidiae Hydroperla perlodid stoneflies x Perlodidiae Isogenoides perlodid stoneflies x Perlodidiae Isoperla perlodid stoneflies x

181 Pteronarcyidae Pteronarcys giant stoneflies x Taeniopterygidae Strophopteryx winter stoneflies x Taeniopterygidae Taeniopteryx winter stoneflies x Belostomatidae Belostoma giant water bugs x Corixidae Palmacorixa water boatmans x Corixidae Trichocorixa water boatmans x Mesoveliidae Mesovelia water treaders x Naucoridae Pelocoris creeping water bugs x Notonectidae Buenoa back swimmers x Notonectidae Notonecta back swimmers x Pleidae Neoplea pygmy back swimmers x Veliidae Microvelia broadshouldered water striders x Veliidae Rhagovelia broadshouldered water striders x Dytiscidae Coptotomus predaceous diving beetle x Dytiscidae Rhantus predaceous diving beetle x Elmidae Ancyronyx riffle beetles x Elmidae Dubiraphia riffle beetles x Elmidae Macronychus riffle beetles x Elmidae Microcylloepus riffle beetles x Elmidae Optioservus riffle beetles x Elmidae Oulimnius riffle beetles x Elmidae Promoresia riffle beetles x Elmidae Stenelmis riffle beetles x Gyrinidae Gyrinus whirligig beetles x Haliplidae Haliplus crawling water beetles x Haliplidae Peltodytes crawling water beetles x Hydrophilidae Berosus water scavenger beetles x Hydrophilidae Hydrohus water scavenger beetles x Hydrophilidae Hydrophilus water scavenger beetles x Noteridae Hydrocanthus burrowing water beetles x Psephenidae Dicranopselaphus water pennies x Psephenidae Ectopria water pennies x Psephenidae Psephenus water pennies x Scirtidae Scirtes marsh beetles x Sisyridae Climacia spongillaflies x Corydalidae Corydalus dobsonflies x Corydalidae Neohermes fishflies x Corydalidae Nigronia fishflies x Sialiidae Sialis alderflies x Apataniidae Apatania early smoky wing sedges x Beraeidae Beraea small eastern caddisflies x Brachycentridae Adicrophleps humpless casemaker caddisflies x Brachycentridae Brachycentrus humpless casemaker caddisflies x Brachycentridae Micrasema humpless casemaker caddisflies x Glossosomatidae Glossosoma little black caddisflies x Goeridae Goera weighted casemaker caddisflies x Helicopsychidae Helicopsyche snailcase caddisflies x Hydropsychidae Arctopsyche netspinning caddisflies x Hydropsychidae Cheumatopsyche netspinning caddisflies x

182 Hydropsychidae Homoplectra netspinning caddisflies x Hydropsychidae Hydropsyche netspinning caddisflies x Hydropsychidae Macrostemum netspinning caddisflies x Hydropsychidae Parapsyche netspinning caddisflies x Hydropsychidae Potamyia netspinning caddisflies x Hydroptilidae Agraylea micro caddisflies x Hydroptilidae Hydroptila micro caddisflies x Hydroptilidae Leucotrichia micro caddisflies x Hydroptilidae Stactobiella micro caddisflies x Lepidostomatidae Lepidostoma bizarre caddisflies x Lepidostomatidae Theliopsyche bizarre caddisflies x Leptoceridae Ceraclea longhorned caddisflies x Leptoceridae Leptocerus longhorned caddisflies x Leptoceridae Mystacides longhorned caddisflies x Leptoceridae Nectopsyche longhorned caddisflies x Leptoceridae Oecetis longhorned caddisflies x Leptoceridae Setodes longhorned caddisflies x Leptoceridae Triaenodes longhorned caddisflies x Limnephilidae Anabolia northern caddisflies x Limnephilidae Chyranda northern caddisflies x Limnephilidae Hesperophylax northern caddisflies x Limnephilidae Lernachus northern caddisflies x Limnephilidae Nemotaulis northern caddisflies x Limnephilidae Onocosmoecus northern caddisflies x Limnephilidae Platycentropus northern caddisflies x Limnephilidae Pseudostenophylax northern caddisflies x Limnephilidae Psychoglypha northern caddisflies x Limnephilidae Pycnopsyche northern caddisflies x Molannidae Molanna hood casemaker caddisflies x Odontoceridae Psilotreta mortarjoint casemaker caddisflies x Philopotamidae Chimarra fingernet caddisflies x Philopotamidae Dolophilodes fingernet caddisflies x Philopotamidae Wormaldia fingernet caddisflies x Philopotamidae Agrypnia giant casemaker caddisflies x Phryganeidae Phryganea giant casemaker caddisflies x Polycentropodidae Cernotina tubemaker caddisflies x Polycentropodidae Cyrnellus tubemaker caddisflies x Polycentropodidae Neureclipsis tubemaker caddisflies x Polycentropodidae Nyctiophlyax tubemaker caddisflies x Polycentropodidae Phylocentropus tubemaker caddisflies x Polycentropodidae Polycentropus tubemaker caddisflies x Psychomyiidae Lype nettube caddisflies x Psychomyiidae Psychomyia nettube caddisflies x Rhyacophilidae Rhyacophila freeliving caddisflies x Sericostomatidae Agarodes bushtailed caddisflies Uenoidae Neophylax stonecase caddisflies x Crambidae Petrophila crambid snout moths x Athericidae Atherix watersnipe flies x Ceratopogonidae Bezzia biting midges x

183 Ceratopogonidae Dasyhelea biting midges x Ceratopogonidae Serromyia biting midges x Chironomidae * midges x Empididae Clinocera dance flies x Empididae Dolichocephala dance flies x Empididae Hemerodromia dance flies x Simuliidae Cnephia black flies x Simuliidae Prosimulium black flies x Simuliidae Simulium black flies x Simuliidae Twinia black flies x Tabanidae Chrysops deer flies x Tabanidae Merycomyia horse flies x Tabanidae Tabanus horse flies x Tipulidae Antocha crane flies x Tipulidae Hexatoma crane flies x Tipulidae Pedicia crane flies x Tipulidae Tipula crane flies x Gammaridae Gammarus scuds x Hyalellidae Hyalella scuds x Cambaridae * crayfish x Asellidae Caecidotea sowbugs x Sphaeriidae * fingernail clams x Lymnaeidae * pond snails x Physidae * bladder snails x Planorbidae * ram's horn snails x Valvatidae * valve snails x Viviparidae * river snails x Hirudinea * leeches x Oligachaeta * aquatic worms x

x1 edible if exposed on the substrate

184 Appendix X

Aquatic Plant/Algae Associations

TableX-1: Endangered Shiners Spawning Plant Species and Endangered Shiners Non-Spawning Plants/Algae Species.

Endangered Endangered Shiners Shiners Spawning Non-Spawning Plant Plant/Algae Scientific Name Common Name Species Species Alisma Water Plantain x Brassica Mustard x Callitriche Water Starwort x Catha palustris Marsh Marigold x Ceratophyllum demersum Coontail x Cladophora Nuisance Algae x Cyperaceae Sedge x Drepanocladus Moss x Elatine Waterwort x Elodea canadensis Canadian Waterweed x Hippuris vulgaris Mare's-tail x Hydrocotyle americana Water Pennywort x Iridaceae Iris x Juncus effuses Soft Rush x Leersia oryzoides Rice Cut-grass x Lythrum salicaria Purple Loosestrife x Myriophyllum Water Milfoil x Najas flexilis Bushy Pondweed x Nupar Yellow Water Lily x Podostemum ceratophyllum River Weed x Polygonum Smartweed x Potamogeton americanus American Pondweed x Potamogeton crispus Curly Pondweed x Potamogeton gramineus Pondweed x Rumex Dock x Sagittaria Arrowhead x Sparganium Bur Reed x Sparganium americanum American Bur Reed x Stuckenia pectinata Sago Pondweed x Symplocarpus foetidus Skunk Cabbage x

185

Utricularia Bladderwort x Vallisneria americana American Tape Grass x Viola lanceolata Big White Violet x

186 Appendix Y

NetWeaver Fuzzy Logic Agrument Parameters

TableY-1: NetWeaver Fuzzy Logic Argument Parameters. NetWeaver Fuzzy Logic Argument Parameters were Based on Collections and Measurements at Marshalls Creek Site 1, PA (the model reference site) (NDE 2013).

Fuzzy Fuzzy Fuzzy Fuzzy Membership Membership Membership Membership Y = -1.0 Y = +1.0 Y = +1.0 Y = -1.0 Simple Data Link False True True False Chemical Habitat Characters pH? X = 5.6 X = 5.8 X = 8.5 X = 8.7 Dissolved Oxygen (mg/liter)? X = 7.0 X = 7.5 X = 15 X = 15.5 Conductivity (microsiemens/cm)? X = 60.0 X = 80.0 X = 290.0 X = 310.0 Alkalinity (ppm)? X = 10.0 X = 20.0 X = 50.0 X = 60.0 Hardness (ppm)? X = 40.0 X = 50.0 X = 75.0 X = 85.0 Physical Habitat Characters Temperature (deg C)? X = 0.0 X = 0.5 X = 26.0 X = 26.5 Depth (cm)? X = 50.0 X = 100.0 n/a n/a Velocity (cm/sec)? n/a n/a X = 17.6 X = 27.6 Substrate (% mud/sand)? X = 60.0 X = 80.0 n/a n/a Riparian Protection (% erosion)? n/a n/a X = 5.0 X = 20.0 Flow Status (% flow to both banks)? X = 75.0 X = 95.0 n/a n/a Bank Stability (% bank erosion)? n/a n/a X = 10.0 X = 25.0 Channel Alteration (% altered)? n/a n/a X = 5.0 X = 20.0 Biological Habitat Characters Fishes Endangered Shiners Predators Anquilla? 0=No, 1=Yes X = 0 X =1 n/a n/a Salmo? 0=No, 1=Yes X = 0 X =1 n/a n/a Esox? 0=No, 1=Yes X = 0 X =1 n/a n/a Ameiurus? 0=No, 1=Yes X = 0 X =1 n/a n/a Enneacanthus? 0=No, 1=Yes X = 0 X =1 n/a n/a Lepomis? 0=No, 1=Yes X = 0 X =1 n/a n/a Perca? 0=No, 1=Yes X = 0 X =1 n/a n/a Endangered Shiners Non-Predators Umbra? 0=No, 1=Yes X = 0 X =1 n/a n/a Catostomus? 0=No, 1=Yes X = 0 X =1 n/a n/a Exoglossum? 0=No, 1=Yes X = 0 X =1 n/a n/a Semotilus? 0=No, 1=Yes X = 0 X =1 n/a n/a

187

Erimyron? 0=No, 1=Yes X = 0 X =1 n/a n/a Etheostoma? 0=No, 1=Yes X = 0 X =1 n/a n/a Percina? 0=No, 1=Yes X = 0 X =1 n/a n/a Additional Exotic Food Competition? 0=No, 1=Yes X = 0 X =1 n/a n/a Habitat Competition? 0=No, 1=Yes X = 0 X =1 n/a n/a Habitat Degradation? 0=No, 1=Yes X = 0 X =1 n/a n/a Additional En. Sh. Predator Adult Predator? 0=No, 1=Yes X = 0 X =1 n/a n/a Fry Predator? 0=No, 1=Yes X = 0 X =1 n/a n/a Native Fishes Species Native Fishes (%)? X = 50.0 X = 88.8 n/a n/a Aquatic Macroinvertebrates Endangered Shiners Edible Ameletidae? 0=No, 1=Yes X = 0 X =1 n/a n/a Baetidae? 0=No, 1=Yes X = 0 X =1 n/a n/a Caenidae? 0=No, 1=Yes X = 0 X =1 n/a n/a Ephemerellidae? 0=No, 1=Yes X = 0 X =1 n/a n/a Ephemeridae? 0=No, 1=Yes X = 0 X =1 n/a n/a Heptageniidae? 0=No, 1=Yes X = 0 X =1 n/a n/a Isonychiidae? 0=No, 1=Yes X = 0 X =1 n/a n/a Leptohyphidae? 0=No, 1=Yes X = 0 X =1 n/a n/a Leptophiebiidae? 0=No, 1=Yes X = 0 X =1 n/a n/a Siphlonuridae? 0=No, 1=Yes X = 0 X =1 n/a n/a Hydropsychidae? 0=No, 1=Yes X = 0 X =1 n/a n/a Hydroptilidae? 0=No, 1=Yes X = 0 X =1 n/a n/a Philopotamidae? 0=No, 1=Yes X = 0 X =1 n/a n/a Polycentropodidae? 0=No, 1=Yes X = 0 X =1 n/a n/a Psychomyiidae? 0=No, 1=Yes X = 0 X =1 n/a n/a Rhyacophilidae? 0=No, 1=Yes X = 0 X =1 n/a n/a Ceratopogonidae? 0=No, 1=Yes X = 0 X =1 n/a n/a Chironomidae? 0=No, 1=Yes X = 0 X =1 n/a n/a Empididae? 0=No, 1=Yes X = 0 X =1 n/a n/a Simuliidae? 0=No, 1=Yes X = 0 X =1 n/a n/a Tabanidae? 0=No, 1=Yes X = 0 X =1 n/a n/a Tipulidae? 0=No, 1=Yes X = 0 X =1 n/a n/a Gammaridae? 0=No, 1=Yes X = 0 X =1 n/a n/a Hyalellidae? 0=No, 1=Yes X = 0 X =1 n/a n/a Sphaeriidae? 0=No, 1=Yes X = 0 X =1 n/a n/a Physidae? 0=No, 1=Yes X = 0 X =1 n/a n/a Planorbidae? 0=No, 1=Yes X = 0 X =1 n/a n/a Valvatidae? 0=No, 1=Yes X = 0 X =1 n/a n/a Viviparidae? 0=No, 1=Yes X = 0 X =1 n/a n/a Edible Taxa? 0=No, 1=Yes X = 0 X =1 n/a n/a

188

Endangered Shiners Non-Edible Aeshnidae? 0=No, 1=Yes X = 0 X =1 n/a n/a Calopterygidae? 0=No, 1=Yes X = 0 X =1 n/a n/a Coenagrionidae? 0=No, 1=Yes X = 0 X =1 n/a n/a Corduliidae? 0=No, 1=Yes X = 0 X =1 n/a n/a Gomphidae? 0=No, 1=Yes X = 0 X =1 n/a n/a Lestidae? 0=No, 1=Yes X = 0 X =1 n/a n/a Libellulidae? 0=No, 1=Yes X = 0 X =1 n/a n/a Macromiidae? 0=No, 1=Yes X = 0 X =1 n/a n/a Nemouridae? 0=No, 1=Yes X = 0 X =1 n/a n/a Perlidae? 0=No, 1=Yes X = 0 X =1 n/a n/a Taeniopterygidae? 0=No, 1=Yes X = 0 X =1 n/a n/a Corixidae? 0=No, 1=Yes X = 0 X =1 n/a n/a Veliidae? 0=No, 1=Yes X = 0 X =1 n/a n/a Elmidae? 0=No, 1=Yes X = 0 X =1 n/a n/a Haliplidae? 0=No, 1=Yes X = 0 X =1 n/a n/a Psephenidae? 0=No, 1=Yes X = 0 X =1 n/a n/a Sisyridae? 0=No, 1=Yes X = 0 X =1 n/a n/a Corydalidae? 0=No, 1=Yes X = 0 X =1 n/a n/a Sialiidae? 0=No, 1=Yes X = 0 X =1 n/a n/a Apataniidae? 0=No, 1=Yes X = 0 X =1 n/a n/a Brachycentridae? 0=No, 1=Yes X = 0 X =1 n/a n/a Goeridae? 0=No, 1=Yes X = 0 X =1 n/a n/a Helicopsychidae? 0=No, 1=Yes X = 0 X =1 n/a n/a Lepidostomatidae? 0=No, 1=Yes X = 0 X =1 n/a n/a Leptoceridae? 0=No, 1=Yes X = 0 X =1 n/a n/a Limnephilidae? 0=No, 1=Yes X = 0 X =1 n/a n/a Molannidae? 0=No, 1=Yes X = 0 X =1 n/a n/a Odontoceridae? 0=No, 1=Yes X = 0 X =1 n/a n/a Phryganeidae? 0=No, 1=Yes X = 0 X =1 n/a n/a Sericostomatidae? 0=No, 1=Yes X = 0 X =1 n/a n/a Uenoidae? 0=No, 1=Yes X = 0 X =1 n/a n/a Cambaridae? 0=No, 1=Yes X = 0 X =1 n/a n/a Asellidae? 0=No, 1=Yes X = 0 X =1 n/a n/a Hirudinea? 0=No, 1=Yes X = 0 X =1 n/a n/a Oligachaeta? 0=No, 1=Yes X = 0 X =1 n/a n/a Non-Edible Taxa? 0=No, 1=Yes X = 0 X =1 n/a n/a Aquatic Plants/Algae Endangered Shiners Spawning Ceratophyllum? 0=No, 1=Yes X = 0 X =1 n/a n/a Elodea? 0=No, 1=Yes X = 0 X =1 n/a n/a Hippuris? 0=No, 1=Yes X = 0 X =1 n/a n/a Hydrocotyle? 0=No, 1=Yes X = 0 X =1 n/a n/a Najas? 0=No, 1=Yes X = 0 X =1 n/a n/a

189

Podostemum? 0=No, 1=Yes X = 0 X =1 n/a n/a Potamogeton? 0=No, 1=Yes X = 0 X =1 n/a n/a Spawning Taxa? 0=No, 1=Yes X = 0 X =1 n/a n/a Endangered Shiners Non-Spawning Brassica? 0=No, 1=Yes X = 0 X =1 n/a n/a Cladophora? 0=No, 1=Yes X = 0 X =1 n/a n/a Cyperaceae? 0=No, 1=Yes X = 0 X =1 n/a n/a Iridaceae? 0=No, 1=Yes X = 0 X =1 n/a n/a Juncus? 0=No, 1=Yes X = 0 X =1 n/a n/a Leersia? 0=No, 1=Yes X = 0 X =1 n/a n/a Lythrum? 0=No, 1=Yes X = 0 X =1 n/a n/a Symplocarpus? 0=No, 1=Yes X = 0 X =1 n/a n/a Non-Spawning Taxa? 0=No, 1=Yes X = 0 X =1 n/a n/a

190 Appendix Z

NetWeaver Model Habitat Character Requirements

TableZ-1: Biological Habitat Character Requirements for All Research Sites (NDE 2013).

Endangered Shiners Location Collected Biological Habitat Character Requirements Marshalls Creek Site 1, PA Bridle & None (Standard) (model reference site) Ironcolor

Marshalls Creek Site 0, PA Bridle & Brook Trout, Salvelinus fontinalus Ironcolor Smallmouth Bass, Micropterus dolomieu 5 of 7 En. Sh. Predators 4 of 7 En. Sh. Non-Predators 22 of 30 En. Sh. Edible Aq. Macros 23 of 36 En. Sh. Non-Edible Aq. Macros 4 of 8 Spawning Plants 4 of 9 Non-Spawning Plants/Algae Marshalls Creek Site 2, PA Bridle & Brook Trout, Salvelinus fontinalus Ironcolor Largemouth Bass, Micropterus salmoides 6 of 7 En. Sh. Predators Native Fishes 86.4% (88.8% standard) 29 of 30 En. Sh. Edible Aq. Macros 32 of 36 En. Sh. Non-Edible Aq. Macros 7 of 8 Spawning Plants 4 of 9 Non-Spawning Plants/Algae Marshalls Creek Site 3, PA Bridle & Largemouth Bass, Micropterus salmoides Ironcolor Margined Madtom, Notorus insignis 6 of 7 En. Sh. Predators Native Fishes 86.4% (88.8% standard) 29 of 30 En. Sh. Edible Aq. Macros 31 of 36 En. Sh. Non-Edible Aq. Macros 6 of 8 Spawning Plants 5 of 9 Non-Spawning Plants/Algae Marshalls Creek Site 4, PA None Brook Trout, Salvelinus fontinalus 5 of 7 En. Sh. Predators 24 of 30 En. Sh. Edible Aq. Macros 22 of 36 En. Sh. Non-Edible Aq. Macros 4 of 8 Spawning Plants 5 of 9 Non-Spawning Plants/Algae Marshalls Creek Site 5, PA None Brook Trout, Salvelinus fontinalus

191

5 of 7 En. Sh. Predators 4 of 7 En. Sh. Non-Predators Native Fishes 83.3% (88.8% standard) 18 of 30 En. Sh. Edible Aq. Macros 14 of 36 En. Sh. Non-Edible Aq. Macros 4 of 8 Spawning Plants 3 of 9 Non-Spawning Plants/Algae Long Marsh Ditch, MD None Tadpole Madtom, Notorus gyninus Pirate Perch, Aphredoderus sayanus 3 of 7 En. Sh. Predators 3 of 7 En. Sh. Non-Predators 7 of 30 En. Sh. Edible Aq. Macros 5 of 36 En. Sh. Non-Edible Aq. Macros 3 of 8 Spawning Plants 2 of 9 Non-Spawning Plants/Algae Zekiah Swamp, MD None 3 of 7 En. Sh. Predators 2 of 7 En. Sh. Non-Predators 9 of 30 En. Sh. Edible Aq. Macros 4 of 36 En. Sh. Non-Edible Aq. Macros 2 of 8 Spawning Plants 2 of 9 Non-Spawning Plants/Algae Nanticoke River, DE Ironcolor 2 of 7 En. Sh. Predators 0 of 7 En. Sh. Non-Predators 8 of 30 En. Sh. Edible Aq. Macros 4 of 36 En. Sh. Non-Edible Aq. Macros 3 of 8 Spawning Plants 2 of 9 Non-Spawning Plants/Algae Gum Branch (main.), DE Ironcolor Tadpole Madtom, Notorus gyninus Pirate Perch, Aphredoderus sayanus 4 of 7 En. Sh. Predators 3 of 7 En. Sh. Non-Predators 10 of 30 En. Sh. Edible Aq. Macros 8 of 36 En. Sh. Non-Edible Aq. Macros 2 of 8 Spawning Plants 2 of 9 Non-Spawning Plants/Algae Gum Branch (head.), DE Ironcolor Tadpole Madtom, Notorus gyninus Pirate Perch, Aphredoderus sayanus 3 of 7 En. Sh. Predators 2 of 7 En. Sh. Non-Predators 8 of 30 En. Sh. Edible Aq. Macros 8 of 36 En. Sh. Non-Edible Aq. Macros 3 of 8 Spawning Plants 2 of 9 Non-Spawning Plants/Algae West Branch, DE None Tadpole Madtom, Notorus gyninus 3 of 7 En. Sh. Predators

192

3 of 7 En. Sh. Non-Predators 7 of 30 En. Sh. Edible Aq. Macros 5 of 36 En. Sh. Non-Edible Aq. Macros 2 of 8 Spawning Plants 3 of 9 Non-Spawning Plants/Algae Clifford Rd Dam Outlet, MA Bridle 3 of 7 En. Sh. Predators 0 of 7 En. Sh. Non-Predators Native Fishes 80.0% (88.8% standard) 13 of 30 En. Sh. Edible Aq. Macros 6 of 36 En. Sh. Non-Edible Aq. Macros 2 of 8 Spawning Plants 1 of 9 Non-Spawning Plants/Algae Eel River, MA None Largemouth Bass, Micropterus salmoides Margined Madtom, Notorus insignis 3 of 7 En. Sh. Predators 0 of 7 En. Sh. Non-Predators Native Fishes 80.0% (88.8% standard) 11 of 30 En. Sh. Edible Aq. Macros 4 of 36 En. Sh. Non-Edible Aq. Macros 3 of 8 Spawning Plants 1 of 9 Non-Spawning Plants/Algae Flat Brook, MA Bridle 1 of 7 En. Sh. Predators 0 of 7 En. Sh. Non-Predators 5 of 30 En. Sh. Edible Aq. Macros 6 of 36 En. Sh. Non-Edible Aq. Macros 2 of 8 Spawning Plants 0 of 9 Non-Spawning Plants/Algae Hop Brook, MA Bridle 3 of 7 En. Sh. Predators 0 of 7 En. Sh. Non-Predators Native Fishes 87.5% (88.8% standard) 6 of 30 En. Sh. Edible Aq. Macros 9 of 36 En. Sh. Non-Edible Aq. Macros 1 of 8 Spawning Plants 3 of 9 Non-Spawning Plants/Algae W. Branch Farm. River, MA None 2 of 7 En. Sh. Predators 1 of 7 En. Sh. Non-Predators Native Fishes 80.0% (88.8% standard) 7 of 30 En. Sh. Edible Aq. Macros 6 of 36 En. Sh. Non-Edible Aq. Macros 0 of 8 Spawning Plants 0 of 8 Non-Spawning Plants/Algae Schenob Brook, MA None 1 of 7 En. Sh. Predators 0 of 7 En. Sh. Non-Predators Native Fishes 0.0% (88.8% standard) 9 of 30 En. Sh. Edible Aq. Macros

193

9 of 36 En. Sh. Non-Edible Aq. Macros 3 of 8 Spawning Plants 0 of 9 Non-Spawning Plants/Algae Dry Brook, MA Bridle 1 of 7 En. Sh. Predators 0 of 7 En. Sh. Non-Predators Native Fishes 75.0% (88.8% standard) 8 of 30 En. Sh. Edible Aq. Macros 9 of 36 En. Sh. Non-Edible Aq. Macros 1 of 8 Spawning Plants 0 of 9 Non-Spawning Plants/Algae Sambo Creek, PA None Grass Carp, Ctenopharyngodon idella Grass Pickerel, Esox americanus 3 of 7 En. Sh. Predators 2 of 7 En. Sh. Non-Predators Native Fishes 87.5% (88.8% standard) 8 of 30 En. Sh. Edible Aq. Macros 5 of 36 En. Sh. Non-Edible Aq. Macros 3 of 8 Spawning Plants 2 of 9 Non-Spawning Plants/Algae McMichael Creek, PA None 2 of 7 En. Sh. Predators 2 of 7 En. Sh. Non-Predators Native Fishes 87.5% (80.0% standard) 8 of 30 En. Sh. Edible Aq. Macros 5 of 36 En. Sh. Non-Edible Aq. Macros 2 of 8 Spawning Plants 2 of 9 Non-Spawning Plants/Algae

194 TableZ-2: Chemical Habitat Character Requirements for All Research Sites (NDE 2013).

Endangered Shiners Location Collected Chemical Habitat Character Requirements Marshalls Creek Site 1, PA Bridle & None (Standard) (model reference site) Ironcolor

Marshalls Creek Site 0, PA Bridle & None Ironcolor Marshalls Creek Site 2, PA Bridle & None Ironcolor Marshalls Creek Site 3, PA Bridle & None Ironcolor Marshalls Creek Site 4, PA None None Marshalls Creek Site 5, PA None None Long Marsh Ditch, MD None Conductivity high (495 microsiemens/cm) Zekiah Swamp, MD None Dissolved Oxygen low (4.36 mg/liter) Hardness high (120 ppm) Nanticoke River, DE Ironcolor None Gum Branch (main.), DE Ironcolor None Gum Branch (head.), DE Ironcolor None West Branch, DE None None Clifford Rd Dam Outlet, MA Bridle Hardness low (25 ppm) Eel River, MA None Dissolved Oxygen low (7.30 mg/liter) Hardness low (25 ppm) Flat Brook, MA Bridle Dissolved Oxygen low (0.93 mg/liter) Conductivity high (439 microsiemens/cm) Alkalinity high (180 ppm) Hardness high (150 ppm) Hop Brook, MA Bridle Dissolved Oxygen low (2.50 mg/liter) Alkalinity high (120 ppm) W. Branch Farm. River, MA None Dissolved Oxygen low (6.53 mg/liter) Schenob Brook, MA None Dissolved Oxygen low (4.12 mg/liter) Alkalinity high (120 ppm) Hardness high (150 ppm) Dry Brook, MA Bridle Dissolved Oxygen low (4.09 mg/liter) Alkalinity high (120 ppm) Hardness high (150 ppm) Sambo Creek, PA None Dissolved Oxygen low (6.24 mg/liter) Alkalinity high (70 ppm) Hardness high (150 ppm) McMichael Creek, PA None Conductivity high (311 microsiemens/cm)

195 TableZ-3: Physical Habitat Character Requirements for All Research Sites (NDE 2013).

Endangered Shiners Location Collected Physical Habitat Character Requirements Marshalls Creek Site 1, PA Bridle & None (Standard) (model reference site) Ironcolor

Marshalls Creek Site 0, PA Bridle & Depth low (54 cm) Ironcolor Velocity high (36.6 cm/sec) Substrate Composition low (50% mud/sand) Channel Alteration high (20% altered) Marshalls Creek Site 2, PA Bridle & Depth low (69 cm) Ironcolor Velocity high (38.0 cm/sec) Substrate Composition low (60% mud/sand) Channel Alteration high (10% altered) Marshalls Creek Site 3, PA Bridle & Depth low (68 cm) Ironcolor Velocity high (25.0 cm/sec) Substrate Composition low (60% mud/sand) Marshalls Creek Site 4, PA None Depth low (44 cm) Velocity high (50.0 cm/sec) Substrate Composition low (20% mud/sand) Riparian Protection high (60% erosion) Channel Alteration high (20% altered) Marshalls Creek Site 5, PA None Depth low (89 cm) Velocity high (61.0 cm/sec) Substrate Composition low (20% mud/sand) Riparian Protection high (10% erosion) Channel Alteration high (20% altered) Long Marsh Ditch, MD None Depth low (44 cm) Flow Status low (90% flow to both banks) Channel Alteration high (10% altered) Zekiah Swamp, MD None Depth low (8 cm) Riparian Protection high (20% erosion) Flow Status low (25% flow to both banks) Nanticoke River, DE Ironcolor Depth low (65 cm) Riparian Protection high (20% erosion) Gum Branch (main.), DE Ironcolor Depth low (44 cm) Velocity high (30.0 cm/sec) Channel Alteration high (10% altered) Gum Branch (head.), DE Ironcolor Depth low (22 cm) Riparian Protection high (60% erosion) Bank Stability low (50% bank erosion)

196

Channel Alteration high (30% altered) West Branch, DE None Depth low (10 cm) Channel Alteration high (10% altered) Clifford Rd Dam Outlet, MA Bridle Depth low (48 cm) Substrate Composition low (70% mud/sand) Eel River, MA None Depth low (28 cm) Substrate Composition low (70% mud/sand) Riparian Protection high (10% erosion) Flow Status low (90% flow to both banks) Channel Alteration high (15% altered) Flat Brook, MA Bridle Depth low (80 cm) Riparian Protection high (10% erosion) Flow Status low (90% flow to both banks) Channel Alteration high (10% altered) Hop Brook, MA Bridle Depth low (28 cm) Riparian Protection high (10% erosion) Channel Alteration high (20% altered) W. Branch Farm. River, MA None Water Temperature high (26.2 deg C) Depth low (24 cm) Substrate Composition low (40% mud/sand) Riparian Protection high (10% erosion) Schenob Brook, MA None Depth low (60 cm) Riparian Protection high (30% erosion) Flow Status low (90% flow to both banks) Bank Stability low (30% bank erosion) Channel Alteration high (20% altered) Dry Brook, MA Bridle Depth low (20 cm) Sambo Creek, PA None Depth low (30 cm) Substrate Composition low (50% mud/sand) McMichael Creek, PA None Depth low (21 cm) Substrate Composition low (30% mud/sand) Riparian Protection high (15% erosion)

197 Bibliography

ADW (Animal Diversity Web). 2013. University of Michigan Museum of Zoology, Ann Arbor, Michigan. Available: www.animaldiversity.ummz.umich.edu (January 2013).

AFS (American Fisheries Society). 2011. Transactions of the American Fisheries Society, Guide for Authors. Bethesda, Maryland.

Annis G., M. DeBacker, D. Diamond, L. Elliott, A. Garringer, P. Hanberry, K. James, R. Lee, S. Leis, M. Morey, and D. Pursell. 2011. Pea Ridge National Military Park Natural Resource Condition Assessment. Natural Resource Report NPS/HTLN/NRR— 2011/426. National Park Service, Fort Collins, Colorado.

ASIH (American Society of Ichthyologists and Herpetologists). 2011. Copeia. Allen Press, Inc., Lawrence, Kansas.

Barbour, M. T., J. Gerritsen, B. D. Snyder, and J. B. Stribling. 1999. Rapid Bioassessment Protocols for Use in Streams and Wadeable Rivers: Periphyton, Benthic Macroinvertebrates and Fish, Second Edition. EPA841-B-99-002. U. S. Environmental Protection Agency, Office of Water, Washington, D.C.

Barlow, G. W. 2000. The Cichlid Fishes. Nature's Grand Experiment in Evolution. Perseus Publishing, Cambridge, Massachusetts.

Boone, J. H., C. G. Mahan, and K. C. Kim. 2005. Biodiversity Inventory: Approaches, Analysis, and Synthesis. Technical Report NPS/NER/NRTR -- 2005/015. U. S. Department of the Interior, National Park Service, Northeast Region, Philadelphia, Pennsylvania.

BWA (Brodhead Watershed Association). 2010. Brodhead Watershed Association, Henryville, Pennsylvania. Available: www.brodheadwatershed.org (March 2013).

Chandler, M. 1999. Characterizing the abiotic and biotic environment for the Bridle Shiner, Notropis bifrenatus, a state listed species of special concern. New England Aquarium, Boston, Massachusetts.

Cole, G. A. 1994. Textbook of Limnology, Fourth Edition. Waveland Press, Inc., Long Grove, Illinois.

Courtenay, W. R., Jr., and J. R. Stauffer, Jr. 1984. Biology, Distribution and Management of Exotic Fishes. Johns Hopkins University Press, Baltimore, Maryland.

Criswell, R. W. 1998a. Report on Fish Surveys in Lehigh and Northampton Counties, Pennsylvania. Completion Report to PA Fish and Boat Commission, Bellefonte, Pennsylvania.

Criswell, R. W. 1998b. Report on Fish Surveys in Bucks County, Pennsylvania. Completion Report to PA Fish and Boat Commission, Bellefonte, Pennsylvania.

198 Criswell, R. W. 1998c. Status of the Bridle Shiner [Notropis bifrenatus (Cope)] and Ironcolor Shiner [Notropis chalybaeus (Cope)] in Pennsylvania. Completion Report to PA Fish and Boat Commission, Bellefonte, Pennsylvania.

DEDFW (Delaware Division of Fish & Wildlife). 2012a. Scientific Collecting Permit No. 2012- 028F, Effective 5/14/2012. Department of Natural Resources and Environmental Control, Dover, Delaware.

DEDFW (Delaware Division of Fish & Wildlife). 2012b. Delaware's Endangered Species. National Heritage and Endangered Species Program. Department of Natural Resources and Environmental Control, Dover, Delaware. Available: www.dnrec.delaware.gov/fw/NHESP (January 2013).

Delorme. 2013. 2010 Delorme (www.delorme.com) TOPO North AmericaTM. Delorme, Yarmouth, Maine.

EOL (Encyclopedia of Life). 2013. Available: www.eol.org (January 2013).

Fassett, N. C. 1957. A Manual of Aquatic Plants. The University of Wisconsin Press, Madison, Wisconsin.

Finger, B. A. 2001. Life History and Range of Pennsylvania’s Endangered Bridle Shiner, Notropis bifrenatus (Cope). Master of Science thesis. The Pennsylvania State University, University Park, Pennsylvania.

Helfman, G. S., B. B. Collette, D. E. Facey, and B. W. Bowen. 2009. The Diversity of Fishes. Second Edition. Wiley-Blackwell, West Sussex, United Kingdom.

IACUC (Institutional Animal Care and Use Committee). 2012. Restoration of the Pennsylvania Endangered Bridle Shiner and Ironcolor Shiner. Annual Review (IACUC# 34193), Annual Renewal, Effective 2 May 2012. Biosafety and Radiation Programs, Office of Research Protections, The Pennsylvania State University, University Park, Pennsylvania.

Janssen, R., H. Goosena, M. L. Verhoevenb, J. T. A. Verhoevenb, A. Q. A. Omtzigta, and E. Maltby. 2005. Decision Support for Integrated Wetland Management. Environmental Modeling and Software 30: 215-299.

Jenkins, R. E., and N. M. Burkhead. 1993. Freshwater Fishes of Virginia. American Fisheries Society, Bethesda, Maryland.

Kilian, J. V., R. L. Raesly, S. A. Stranko, A. J. Becker, and E. Durell. 2011. Extirpation of the Bridle Shiner (Notropis bifrenatus) from Maryland. Northeastern Naturist, Issue 18/2.

Kraft, C. E., D. M. Carlson, and M. Carlson. 2006. Inland Fishes of New York. Department of Natural Resources, Cornell University, and the New York State Department of Environmental Conservation, Albany, New York.

199 Leckvarcik, L. G. 2001. Life History of the Ironcolor Shiner, Notropis chalybaeus (Cope), in Marshalls Creek, Monroe County, Pennsylvania. Master of Science thesis. The Pennsylvania State University, University Park, Pennsylvania.

Leckvarcik, L. G. 2005. Restoration of the Pennsylvania-Endangered Bridle Shiner, Notropis bifrenatus (Cope), and Ironcolor Shiner, Notropis chalybaeus (Cope), in Brodhead Creek Watershed, Monroe County. Doctoral dissertation. The Pennsylvania State University, University Park, Pennsylvania.

Lee, D. S., C. R. Gilbert, C. H. Hocutt, R. E. Jenkins, D. E. McAllister, and J. R. Stauffer, Jr. 1981. Atlas of North American Freshwater Fishes. North Carolina State Museum of Natural History, Raleigh, North Carolina.

Mackey, A. P., D. A. Cooling, and A. D. Berrie. 1984. An Evaluation of Sampling Strategies for Qualitative Surveys for Marco-Invertebrates in Rivers, Using Pond Nets. Journal of Applied Ecology, Vol. 21, No. 2, pp. 515-534.

MADFW (Massachusetts Division of Fisheries & Wildlife). 2012a. Scientific Collection Permit#:178.12SCF, Effective 6/21/2012. Department of Fish and Game, Boston, Massachusetts.

MADFW (Massachusetts Division of Fisheries & Wildlife). 2012b. Data Release Agreement for the release of a report entitled Characterizing the Abiotic and Biotic Environment for the Bridle Shiner, Notropis bifrenatus, a State Listed Species of Concern. Natural Heritage & Endangered Species Program, Westborough, Massachusetts.

MADFW (Massachusetts Division of Fisheries & Wildlife). 2012c. Data Release Agreement for Element Occurrence Data for Notropis bifrenatus within Massachusetts. Natural Heritage & Endangered Species Program, Westborough, Massachusetts.

MADFW (Massachusetts Division of Fisheries & Wildlife). 2012d. Massachusetts List of Endangered, Threatened and Special Concern Species. Department of Fish and Game, Boston, Massachusetts. Available: www.mass.gov/dfwele/dfw/nhesp/species_info (January 2013).

Mahan, C. G., B. J. Miller, M. C. Saunders, and J. A. Young. 2011. Assessment of Natural Resources and Watershed Conditions for Delaware Water Gap National Recreation Area and Upper Delaware Scenic and Recreational River. U.S.D.I. National Park Service, Natural Resource Report NPS/NER/NRR 2011/429-NPS 620/108557; 647/108557, July 2011, 90pp.

Merritt, R. W., K. W. Cummins, and M. B. Berg. 2008. An Introduction to the Aquatic insects of North America. Kendall Hunt Publishing Company, Dubuque, Iowa.

McCafferty, W. P. 1998. Aquatic Entomology. Jones and Bartlett Publishers, Sudbury, Massachusetts.

200 MDDNR (Maryland Department of Natural Resources). 2012a. Scientific Collection Permit Number SCP201285, Effective 06-11-2012. Fisheries Service, Department of Natural Resources, Annapolis, Maryland.

MDDNR (Maryland Department of Natural Resources). 2012b. Endangered Species Permit Number: 52244, Effective 06-06-12. Wildlife and Heritage Service, Department of Natural Resources, Annapolis, Maryland.

MDDNR (Maryland Department of Natural Resources). 2012c. Threatened and Endangered Fish Species and Fish Species in Need of Conservation in Maryland. Department of Natural Resources, Annapolis, Maryland. Available: www.dnr.state.md.us/fisheries/management/endangered (January 2013).

Negoita, C. V. 1985. Expert Systems and Fuzzy Systems. Benjamin/Cummings Publishing Company. San Francisco, California.

Ney, J. J. 1999. Practical Use of Biological Statistics. Pages 167-191 in C. C. Kohler and W. A. Hubert, editors. Inland Fisheries Management in North America, Second Edition. American Fisheries Society, Bethesda, Maryland.

NDE (NetWeaver2 Developer/Explorer). 2013. Rules of Thumb, Inc. Northeast, Pennsylvania.

NJDEP (New Jersey Department of Environmental Protection). 2012. New Jersey's Endangered and Threatened Wildlife. Division of Fish and Wildlife, Trenton, New Jersey. Available: www.nj.gov/dep (January 2013).

NYDEC (New York Department of Environmental Conservation) 2013. Endangered & Threatened Fishes of New York. Bureau of Fisheries, Albany, New York. Available: www.dec.ny.gov (January 2013).

PAC (Pennsylvania Code). 2013. Chapter 75, Endangered Species. Commonwealth of Pennsylvania, Harrisburg, Pennsylvania. Available: www.pacode.com (January 2013).

PAFBC (Pennsylvania Fish and Boat Commission). 2012a. Chapter 75.4 Special Permit for Collection of Threatened and Endangered Species Scientific Collectors’ Permit No. 590 Type I, Effective February 29, 2012. Natural Diversity Section, Environmental Services Division, Bureau of Fisheries, Bellefonte, Pennsylvania.

PAFBC (Pennsylvania Fish and Boat Commission). 2012b. Scientific Collector Permit No. 590 Type I, Effective March 02, 2012. Natural Diversity Section, Environmental Services Division, Bureau of Fisheries, Bellefonte, Pennsylvania.

Page, L. M. and R. M. Burr. 1991. The Petersen Field Guide Series: A Field Guide to Freshwater Fishes. Houghton Mifflin Company, New York, New York.

201 PDT (Pennsylvania Department of Transportation). 1999a. Marshalls Creek Traffic Survey, Detailed Effects Assessment of Proposed Draft Environmental Impact Statement and Supplemental Environmental Impact Statement Relocation Alternative Modifications Developed to Minimize Effects on Notropis bifrenatus and Notropis chalybaeus (Final). Harrisburg, Pennsylvania.

PDT (Pennsylvania Department of Transportation). 1999b. Final Environmental Impact Statement and Section 404 Permit Application. Harrisburg, Pennsylvania.

PDT (Pennsylvania Department of Transportation). 2011. Logger Data for Marshalls Creek. The Penn State University/Stevens-Connect Services. Available: penndot-stevens.com (January 2011 – December 2012).

Peckarsky, B. L., P. R. Fraissinet, M. A. Penton, and D. J. Conklin. 1990. Freshwater Macroinvertebrates of Northeastern North America. Cornell University Press, Ithaca, New York.

Rahel, F. J., R. T. Muth, and C. A. Carlson. 1999. Endangered Species Management. Pages 431-454 in C. C. Kohler and W. A. Hubert, editors. Inland Fisheries Management in North America, Second Edition. American Fisheries Society, Bethesda, Maryland.

Reynolds, J. B. 1996. Electrofishing. Pages 221-253 in B. R. Murphy and D. W. Willis, editors. Fisheries Techniques, Second Edition. American Fisheries Society, Bethesda, Maryland.

Reynolds, K. M., K. N. Johnson, and S. N. Gordon. 2003. The Science/Policy Interface in Logic-Based Evaluation of Forest Ecosystem Sustainability. Forest Policy and Economics 5:433-446.

RIDST (Redlands Institute Decision Support Team). 2004. Desert Tortoise Habitat Potential Knowledge Base. Redlands Institute, Redlands, California.

Saunders, M. C. and B. J. Miller. 1997. A graphical tool for knowledge engineers designing natural resource management software: NetWeaverTM. ACSM/ASPRS Annual Convention: Resource Technology, Volume 4:380-389.

Saunders, M. C., T. J. Sullivan, B. L. Nash, K. A. Tomnessen, and B. J. Miller. 2005. A Knowledge-Based Approach for Classifying Lake Water Chemistry. Knowledge Based Systems. Volume 18/1:47-54.

Smith, C. L. 1985. The Inland Fishes of New York State. New York State Department of Environmental Conservation, Albany, New York.

Stauffer, J. R., Jr., S. E. Boltz, and J. M. Boltz. 1988. Thermal tolerance of the Blue Tilapia, Oreochromis aureas, in the Susquehanna River. North American Journal of Fisheries Management 8(3):329-332.

USDA (United States Department of Agriculture). 2012. Natural Resources Conservation Service, Washington, D. C. Available: www.plants.usda.gov (January 2011 – November 2012).

202 VanDyk, J. 2013. BugGuide. Iowa State University Entomology Department. Ames, Iowa. Available: www.bugguide.net (January 2013).

Voshell, J. R. 2002. A Guide to Common Freshwater Invertebrates of North America. The McDonald & Woodward Publishing Company, Blacksburg, Virginia.

203 VITA

Clare William Hanson, II Captain, United States Navy (retired)

Education 2013 The Pennsylvania State University, University Park, Pennsylvania Doctor of Philosophy, Wildlife and Fisheries Science 1993 Naval War College, Newport, Rhode Island Master of Arts, National Security and Strategic Studies 1978 The Pennsylvania State University, University Park, Pennsylvania Bachelor of Science, Nuclear Engineering

Teaching Experience at The Pennsylvania State University Fall 2012 Teaching Assistant for Freshwater Entomology (ENT 425) Fall 2012 Teaching Assistant for Scholarship and Research Integrity (SARI) May 2012 Teaching Assistant for Field Ichthyology (WFS 497) Jan 2012 The Pennsylvania State University Graduate School Teaching Certificate Fall 2011 Teaching Assistant for Fisheries Science (WFS 410) Fall 2011 Teaching Assistant for Scholarship and Research Integrity (SARI) 2006-2009 Professor of Naval Science, The Pennsylvania State University, Instructor for Leadership and Ethics (NAV SCI 402)

Leadership/Management Experience in the United States Navy 1978-2009 Commissioned Active Duty Naval Officer with service in the Atlantic and Pacific Submarine Force, the Department of Defense (DoD), the North Atlantic Treaty Organization (NATO), and the Multi-National Security Transition Command-Iraq (MNSTC-I)

Presentation Fall 2011 Regional Science Consortium, The Tom Ridge Environmental Center, Erie, Pennsylvania