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2001
The Status and Distribution of the Topeka Shiner Notropis topeka in Eastern South Dakota
Carmen M. Blausey South Dakota State University
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Recommended Citation Blausey, Carmen M., "The Status and Distribution of the Topeka Shiner Notropis topeka in Eastern South Dakota" (2001). Electronic Theses and Dissertations. 296. https://openprairie.sdstate.edu/etd/296
This Thesis - Open Access is brought to you for free and open access by Open PRAIRIE: Open Public Research Access Institutional Repository and Information Exchange. It has been accepted for inclusion in Electronic Theses and Dissertations by an authorized administrator of Open PRAIRIE: Open Public Research Access Institutional Repository and Information Exchange. For more information, please contact [email protected]. THE STATUS AND DISTRIBUTION OF THE TOPEKA SHINER
Nutropis topeka IN EASTERN SOUTH DAKOTA
By
Carmen M. Blausey
A thesis submitted in partial fulfillment of the requirements for the
l'vlastcr of Science
Major in Wildlire and Fisheries Sciences (Fisheries Specialization)
South Dakota State University
2001 II
The Status and Distribution of the Topeka shiner Notropis topeka in Eastern South
Dakota
This thesis is approved as a creditable and independent investigation by a candidate for the Master of Science degree and is acceptable for meeting the thesis requirements for this degree. Acceptance of this thesis does not imply that the conclusions reached by the candidate are necessarily the conclusions of the major department.
I)r. Charles R. Berry. Y l\lajor Advisor Date
Dr. Charles G. Scalet Head. Wildlife and Fisheries Sciences Date lJl
Acknowledgements
I express my sincere thanks to my advisor Dr. Charles Berry, Jr. for giving me the opportunity to pursue a Master's degree at South Dakota State University. His guidance, support, and incredible amount of patience were very much appreciated to successfully complete this project. Additionally, I'd like to say thanks for helping me to hone my research skills, and increase my awareness and passion for nongame species management.
Thank you to Steve Wall, research associate with this project, for your assistance in the field. I know the days were long and hot, and there were some disagreements, but without your help I would probably still be traversing the South Dakota prairies hunting for Topeka shiners. I also would like to thank Jeff Shearer, Dave Fryda, Craig Milewski,
Jen Powell, Nathan Morey, and Kurt Hodell for your assistance in the field at one time or another. Finally, I would like to thank all of the landowners who gave me permission to work on their property. Without their cooperation, this project truly would not have been a success.
I would like to thank my committee members Dr. W. Carter Johnson, Dr. David
W. Willis, and Dr. Donald Evenson for providing me with their advice and comments to successfully complete this project. Also a big thank you is extended to Dr. Timothy
Wittig for his assistance with statistical analysis. Without his expertise and advice this project would have taken even longer than anticipated to complete. IV
I wish to th ank my parents for their Jove and suppo11, and for always believing in me. Without your guidance and advice I would not be the person I am today.
I want to add and extended thank you to Dave Fryda for editorial comments, advice, and lots of patience and support throughout this project. I will never forget all of the great hunting and fishing outings I had the chance to share with you while in graduate school. Also I would like to take the time to say thanks to all of the other students in the grad office who definitely made my graduate school experience more enjoyable and memorable ... you all know who you are!
Finally, I would like to dedicate this thesis to my Grandpa Custer, who always
had time to take my sister and I fishing on Lake McConaughy for walleyes when we were
kids. If it weren' t for him and all of the memmies of "camping at the Lake", I most
likely would have taken a different path in life.
Funding was provided by the U.S. Fish and Wildlife Service, U.S. Army Corps of
Engineers, Environmental Protection Agency, U.S. Geological Survey- Water Resources
Division, U.S. Geological Survey- Biological Resources Division, and the South Dakota
Cooperative Fish and Wildlife Research Unit, which provided in-kind support. v
Abstract
The Status and Distribution of the Topeka shiner Notropis topeka in Eastern
South Dakota
Carmen M. Blausey
December 2001
The Topeka shiner Notropis topeka is a small (< 75 mm) minnow that inhabits
prairie streams in several north central plains states. Once widespread and abundant
throughout its historic range, the Topeka shiner is now found only in isolated populations. Because of an 80% reduction in occurrence throughout their range, the U.S.
Fish and Wildlife Service listed the Topeka shiner as endangered in January 1999. At the time, limited information on habitat preferences and dist1ibution existed for this species
in South Dakota. The objectives of this study were to measure local habitat features and
water quality conditions at the reach scale at Topeka shiner study sites, create a model
using these data to determine favorable habitat conditions. and identify fish species
commonly associated with Topeka shiners. Fish and habitat data were collected at 61
tributary sites of the James, Vermillion, and Big Sioux rivers from June through
September in 1999 and 2000. Sample sites in 1999 were based on historic Topeka shiner
records in the South Dakota Natural Heritage Database. Sample sites in 2000 were based
on a draft GIS model identifying potential Topeka shiner streams. Fish were collected
with seines between block nets. and standard procedures were used to measure physical
and hydrological features of stream reaches. Cyprinids dominated the fish community
for each river basin during both sample years. Insectivores and omnivores were the VI dominant trophic classes for each river basin for both sample years. Fish community associations for Topeka shiners were based on two stepwise logistic regression models: abundance of individual species at each site. and presence or absence of individual species at each site. The abundance model indicated that Topeka shiners were most commonly associated with orangespotted sunfish Lepomis Izumi/is and tadpole madtoms
Noturns gyrinus. The presence/absence model showed that Topeka shiners were typically associated with red shiners Notropis lutre11sis, tadpole madtoms Noturns gyrinus, black bullheads Ameiurus melas, and bigmouth shiners Notropis dorsalis.
Habitat preferences were based on three stepwise logistic regression models: physical habitat water quality, and substrate composition at the reach scale. The physical habitat
model indicated that Topeka shiners are associated with stream reaches that had low
animal use, overhanging vegetation, stream bank vegetation comprised of sedges/rushes,
low depositional zones, and run macrohabitat. The water quality model did not indicate
any favorable or preferred conditions. The substrate model indicated that Topeka shiners
are associated with stream reaches that had fine gravel or cobble substrates. The results
of my study will lead to a better understanding of Topeka shiner distribution and habitat,
and aid federal and state agencies in making management decisions that provide for
protection and preservation of this species. vii
Table of Contents
Page
Abstract ...... vi
List of Symbols and Abbreviations ...... ix
List of Fish Species ...... x
List of Tables ...... xii
List of Figures ...... xiv
List of Appendices ...... xv
Chapter I. Introduction and Study Arca
Introduction ...... I
Study Arca ...... 6
James River Basin ...... 6
Vermillion River Basin ...... I 0
Big Sioux River Basin ...... l l
Chapter 2. Fish Communities of Tributaries to the James. Vermillion, and Big Sioux Rivers
lntrodlll:tion ...... 15
ivlethods ...... 17
Results ...... 22
James River Basin Tributaries ...... 22
Vermillion Ri1·er Basin Tributaries ...... 23
Big Sioux River Basin Tributaries ...... 24
Trophic Classes ...... 24 VIII
Community Aleasures ...... 26
Topeka shiner Abundance ...... 32
J.enr;th and Condition <~/Topeka shiners ...... 37
S/Jecies Associated with Topeka shiners ...... 37
Discussion ...... 39
Conclusion ...... 45
Chapter 3. Habitat Preferences and Distribution of the Topeka shiner
Introduction ...... 46
Methods ...... 47
Results ...... 59
Physical Hahitat Model...... 60
S'11bstrate Compos ii ion Model ...... 63
/Voter Quality ,\!ode/ ...... 68
Discussion ...... 72
Cone! us ion ...... 85
Literature cited ...... 87
Appendices ...... 96 IX
LIST OF SYMBOLS AND ABBREVIATIONS
ANOV A- analysis of variance m- meter
BSR- Big Sioux River basin mg- milligram cm- centimeter mm- millimeter
CPUA- catch per unit area µS- m1cros1emens o C- degrees Celcius m/s- meters per second df- degrees of freedom m3/s- cubic meters per second e.g.- for example NTU- nepholimeter unit
ESA- endangered species act RBF- right bankfull g- gram REW - right edge water
GIS- geographic information system RTB- right-top-of-bank
GPS- global positioning system SE- standard error
JMR- James River basin STR 1- 1A stream width
K- Fulton-type index of well being STR2- 1/2 stream width
km- kilometer STR3- % stream width
L- liter TL- total length
LBF- left bankfull UTM- universal transverse mercator
LEW- left edge water VMR- Vermillion River basin
LTB- left top-of-bank x
LIST OF FISI I SPECIES
Catostomidae Centrarchidae
River carpsucker Carpiodes carpio Black crappie Pomoxis a111111laris
Shorthead redhorse Moxostoma macrolepidotum White crappie P. 11igro111aculatus
White sucker Catostomus commersoni Bluegill Lepomis macrochirus
Green sunfish L. cyanellus
Clupeidae Orangespotted sunfish L. humilis
Gizzard shad Dorsoma cepedianum Largemouth bass Micropterus sa/moides
Cyprinidae Esocidae
Central stoneroller Campostoma anoma/11111 Northern pike Esox /11cius
Emerald shiner Notropis atherinoides
Bigmouth shiner N. dorsalis Fundulidae
Red shiner N. lutrensis Plains topminnow F1111dul11s sciadicus
Sand shiner N. stramineus
Topeka shiner N. topeka Hiodontidae
Common carp Cyprinus carpio Goldeye lliodon alosoides
Brassy minnow Hybognathus hanki11soni
Plains minnow H. placitus Ictaluridae
Bluntnose minnow Pimephales notatus Black bullhead Ameiurus me/as
Fathead minnow P. promelas Channel catfish /cta/urus p1111ctat11s
Common shiner Luxilus cornutus Stonecat Not11111s flavus
Black.nose dace Rhinicltthys atrat11l11s Tadpole madtom N. gyri1111s xi
Longnose dace R. cataracrae
Creek chub Semotilus atromaculatus
Percidac
Iowa darter Etheostoma exile
Johnny darter E. nigrum
Yellow perch Perea flavescens
Blackside darter Percina maculata
Walleye Stizostedion vitreum xii
List of Tables Table Page
Table 2-1. List of fish species sampled in tributaries of the James, Vermillion, and Big Sioux River basins. including historical and present study records ...... 18
Table 2-2. Total numbers fish captured for tributaries of the James. Vermillion. and Big Sioux Rivers. and percentage of Topeka shiners captured 1999-2000 ...... 22
Table 2-3. Species richness and species diversity for James River tributaries during 1999 and 2000 sampling seasons ...... 29
Table 2-4. Species richness and species diversity for Vermillion River tributaries during 1999 and 2000 sampling seasons ...... 30
Table 2-5. Species richness and species diversity for Big Sioux River tributaries during 1999 and 2000 sampling seasons ...... 31
Table 2-6. Total number of and catch per unit area for Topeka shiners captured in Vcnnillion River tributaries during 1999 ...... 33
Table 2-7. Total number of and catch per unit area for Topeka shiners captured in .Tames River tributaries during 1999 ...... 34
Table 2-8. Total number of and catch per unit area for Topeka shiners captured in Big Sioux River tributaries during 1999 ...... 35
Table 2-9. Total number of and catch per unit area for Topeka shiners captured in tributaries to the James. Vermillion. and Big Sioux Rivers during 2000 ...... 36
Table 2-10. Fish associated with the Topeka shiner in eastern South Dakota ...... 43
Table 3-1. Legal description of South Dakota streams sampled during June through September 1999. numbt:r of Topeka shiners sampled in each stream. and UTM coordinates for each sample site ...... 48
Table 3-2. L1:gal description of South Dakota streams sampled during .June through August 2000. number of Topeka shiners sampled in each stream. and UTM coordinates for each sample site ...... 50
Table 3-3. ~ labitat variables measured at tributary sample sites throughout the James. V1:rmillion, and Big Sioux River basins in 1999 and 2000 ...... 53
Table 3-4. Bed substrate size classification ...... 56 xiii
Table 3-5. Water characteristics measured at transects along sites sampled throughout the James, Vermillion. and Big Sioux River basins in 1999 and 2000 ...... 57
Table 3-6. Substrate composition at Topeka shiner presence sites for .lames. Vermillion. and Big Sioux River tributaries. J 999 ...... 64
Table 3-7. Substrate composition at Topeka shiner pn:sencc sites for .lames. Vermillion. and Big Sioux River tributaries. 2000 ...... 66
Table 3-8. Substrate composition at Topeka shiner absence sites for James. Vermillion, and Big Sioux River tributaries. 1999 ...... 67
Table 3-9. Substrate composition at Topeka shiner absence sites for James. Vermillion. and Big Sioux River tributaries. 2000 ...... 69
Table 3-10. Average velocity and discharge for each site sampled during June through September 1999 in eastern South Dakota ...... 73
Table 3-11. Average velocity and discharge for each site sampled during June through August 2000 in eastern South Dakota ...... 75 xiv
List of Figures
Figure Page
Figure 1-1. Photograph of breeding male Topeka shiner sampled from Six Mile Creek. 13rookings County. South Dakota. 2000 ...... 2
Figure 1-2. Photograph of breeding male Topeka shiner sampled from Pipestone Creek. Moody County, South Dakota. 1999 ...... 2
Figure 1-3. Map illustrating the historical distribution of the Topeka shiner throughout six no1th central plains states ...... 4
Figure 1-4. Map illustrating the James, Vermillion. and Big Sioux River tributary study sites ...... 7
Figure 1-5. Mean monthly discharge (cubic feet per second) of the James River; water years 1929-1999 ...... 9
Figure 1-6. Mean monthly discharge (cubic feet per second) of the Vermillion River: \Vater years 1984-1999 ...... I 2
Figure 1-7. rvkan monthly discharg1: (cubic feet per second) of the Big Sioux River: water years 1929-1999 ...... 14
Figure 2-1. Relative abundance of six trophic dasses sampled from Big Sioux River tributaries during 1999 and 2000 ...... 25
Figure 2-2. Relative abundance of six trophic classes sampled from Vermillion River tributaries during 1999 and 2000 ...... 27
Figure 2-3. Relative abundance of six trophic classes sampled from James River tributaries during 1999 and 2000 ...... 28
Figure 3-1. Illustration of horizontal measurements taken at transects in streams of the James. Vermillion. and Big Sioux Rivers ...... 54
Figure 3-2. Illustration of vertical measurements taken at transects in streams of the James. Vermillion. and Big Sioux Rivers ...... 58 xv
List of Appendices Appendix Pugc
Appendix 1. Total number of individuals sampled by species for sites located within the James River basin sampled from June through September 1999 in eastern South Dakota ...... 96
Appendix 2. Total number of individuals sampled by species for sites located within the James River basin sampled from June through August 2000 in eastern South Dakota ...... 98
Appendix 3. Total number of individuals sampled by species for sites located within the Vermillion River basin sampkd from June through September 1999 in eastern South Dakota ...... 100
Appendix 4. Total number of individuals sampled by species for sites located within the Vermillion River basin sampled from .lune through August 2000 in eastern South Dakota ...... I 02
Appendix 5. Total number of individuals sampled by species for sites located within the Big Sioux River watershed during June through September 1999 in eastern South Dakota ...... I 04
Appendix 6. Total number of individuals sampled by species for sites located within the Big Sioux River basin sampled .lune through August 2000 in eastern South Dakota ...... 106
Appendix 7. Photographs taken at various sites \Vhere Topeka shiners \Vere captured throughout eastern South Dakota from I 999-2000 ...... I 08
Appendix 8. \:\'atcr temperature. turbidity. secchi depth. dissolved oxygen. and conductivity for 31 streams sampled from .lune through September 1999 in eastern South Dakota ...... 110
Appendix 9. Water temperature. turbidity. secchi depth. dissolved oxygen. and conductivity for 28 streams sampled from June through August 2000 in eastern South Dakota ...... 112 Chapter 1. Introduction and Study Area
Introduction
The Topeka shiner Notropis topeka is a small minnow belonging to the family
Cyprinidae. It was first identified in 1884 by C.H. Gilbert in Shunganunga Creek, a tributary to the Kansas River, Shawnee County, Kansas (Minckley and Cross 1959).
Mature adults average 40 to 50 millimeters (mm) in total length, and attain maximum lengths up to 75 mm. Distinctive characteristics include a discrete chevron-like black spot located at the base of the caudal fin, a dusky stripe running the entire length of the lateral line, a body that is a dark olivaceous color, and a distinct dark stripe preceding the dorsal fin. Breeding males exhibit orange-red fins, and the head also has an orange tint
(Figure 1-1, Figure l-2)(Cross 1967; Pflieger 1997; Harlan and Speaker 1987; Tabor
1993; Cross and Collins 1995; Tabor 1998).
In January 1999, the Topeka shiner was listed as federally endangered by the U.S.
Fish and Wildlife Service (USFWS), under Section 4 of the Endangered Species Act
(ESA). Section 4 of the ESA uses several criteria to determine whether a species should be listed as endangered or threatened including a) present or threatened destruction, modification, or curtailment of its habitat or range, b) overutilization for commercial, recreational. scientific, or educational purposes, c) disease or predation, d) inadequacy of existing regulatory mechanisms, and e) other natural or human-induced factors affecting its continued existence (ESA 1983; Tabor 1998). 2
Figure 1-1. Breeding male Topeka shiner sampled from Six Mile Creek, Brookings County, South Dakota, 2000.
Figure 1-2. Breeding male Topeka shiner sampled from Pipestone Creek, Moody County, South Dakota, 1999. 3
Topeka shiners typically are found in small, low order. prairie streams with high water quality and cool temperatures. These streams generally now throughout the year, but some become intermittent during the summer months. When surface flow ceases. pool levels and cool temperatures in these streams are maintained by percolation through the streambed, spring flow, or groundwater seepage (Cross 1967: Pnieger 1997: Tabor
1993). Topeka shiners are usually found over gravel, cobble, or sand substrates, although clay hardpan and bedrock covered by a layer of silt are also utilized (Minckley and Cross
1959). Topeka shiners are limnetic and found primarily in pools and runs. and rarely in riffles.
The Topeka shiner was once widespread and abundant in low order tributary streams throughout the central prairie region of the United States. Historically, they were found in portions of South Dakota, Minnesota, Nebraska. Iowa, Missouri, and Kansas
(Figure l-3) (Bailey and Allum 1962: Tabor 1993, 1998). South Dakota is located on the northern edge of the species range. Currently the Topeka shiner is found in highly fragmented populations throughout its range. Potential causes for decline include increased sedimentation from agricultural practices (e.g., feedlots, conversion of prairie grasses to row crops, and overgrazing). construction of watershed impoundments for flood control. and predation by non-native stocked species (Minckley and Cross 1959;
Pflieger 1997: Tabor 1993; Layher 1993; Mammoliti 1995; Tabor 1998). Within South
Dakota. distribution of Topeka shiners includes the James. Vermillion, and Big Sioux
River drainages (Bailey and Allum 1962: Braaten 1993: Tabor 1993, 1998). One report I 1 r I 4
Figure 1-3. Historical distribution of the Topeka shiner throughout six north central plains states (i.e., Minnesota, South Dakota, Nebraska, Iowa, Kansas, and Missouri). 5 documents Topeka shiner presence in the Grand, Moreau, and Cheyenne river embayments to Lake Oahe (Beckman and Elrod 1971). However, since that study
Topeka shiners have not been documented in western rivers in South Dakota.
Several studies have recently investigated habitat requirements of the Topeka shiner in Kansas and Minnesota (Schrank et al. 2001: Hatch 2001, Professor, University of Minnesota, St. Paul, personal communication), but little infmmation on habitat preferences exists for the South Dakota portion of the range. This study was the first comprehensive assessment of Topeka shiner habitat and distribution in South Dakota.
The goal of this study was to assess habitat conditions at historic and recent presence/absence sites of Topeka shiners in South Dakota, and use the data to 1) identify
favorable habitat conditions needed at the stream reach scale, and 2) recommend critical
habitat associated with this species. Specific objectives were to:
a) measure local habitat features and water quality conditions at the reach scale
at presence and absence sites of Topeka shiners;
b) create a statistical model using habitat features and water quality conditions to
determine favorable habitat associations for Topeka shiner presence, and
c) identify fish community structure at presence and absence sites to determine
fish species commonly associated with Topeka shiners. 6
Study Area
This study was conducted on mainstem portions and tribucaries of the James.
Vermillion, and Big Sioux rivers in eastern South Dakota (Figure 1-4). These three river basins drain the Central Lowlands physiographic region in eastern South Dakota. before reaching their confluence with the Missouri River.
James River Basin
The James River originates near Fessenden, North Dakota. It flows approximately 1,200 km before emptying into the Missouri River near Yankton, South
Dakota. The James River basin encompasses approximately 57 ,000 krn2 of land area with about 21.000 km2 located in southeastern North Dakota and 36,000 km2 in eastern
South Dakota (Walsh 1992; Berry el al. 1993: Schumacher 1995). Primary land use within the James River basin is intensive row crop agriculture (com and wheat) and pasture used for livestock grazing. Decreased riparian zones caused by agricultural activities have resulted in overland runoff and erosion, leading to increased sedimentation rates within the basin.
The basin lies within the James River Lowland and James River Highlands physiographic regions (Johnson et al. 1995). The James River Lowland is situated between the Missouri and Prairie Coteaus. Topography in this region is dominated by gently undulating ground moraine with drift interspersed throughout. The James River 7
MCPHERSON MARSHALL I - "- ._I EDMU:i DAY I \.,. , ? POTTER FAULK
Figure 1-4. James, Ve1million, and Big Sioux River tributary study sites. Light colored circles indicate Topeka shiner presence at study sites; dark colored circles indicate Topeka shiner absence at study sites. 8
Highlands is located near the southern end of the James River Lowland. Topography for this area consists of till underlying bedrock plateaus.
Climate within the basin is classified as sub-humid continental. Seasonal
temperatures range from -10.0 ° C to 32.0 ° C, with an average of 13.2 ° C in 1999
(USGS 2000). Annual precipitation for the basin averages 46 cm in North Dakota and 56 cm in South Dakota (Berry et al. 1993). Seasonal flow patterns are somewhat
predictable, indicated by the hydrograph based on mean monthly discharge for water
years 1929-1999 (Figure 1-5). Generally. discharge peaks in April, and returns to base flows October through February. During the summer months when extended periods of dry weather are common, many tributaries to the James River become intermittent.
During 1999 tributary sample sites were perennial; however, several tributaries in 2000 experienced intermittency (personal observation). Principal recreational and beneficial
uses of the tributaiies include boating, fishing, and domestic water supply (SD DENR
1994). Assigned water quality conditions include warmwater permanent fish life
propagation (water quality conditions are acceptable for long-term sustainability of
aquatic organisms). warmwater semipermanent fish life propagation (water quality
conditions are acceptable to suppot1 aquatic organisms, but natural conditions will cause
occasional fish kills), and warmwater marginal fish life propagation (water quality
conditions are acceptable to support aquatic organisms, but natural conditions will cause
frequent fish kills) (SD DENR 1994). 9
2000
1800
1600
1400 Ul u - 1200 -Q) Cl.....
200
0
Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec Month
Figure l-5. Mean monthly discharge (cfs) of the James River near Scotland, South Dakota: water years 1929-1999 (USGS 2000). 10
Venni/lion River Basin
The Vermillion River basin encompasses approximately 6.700 km2 and flows entirely within eastern South Dakota before reaching its confluence with the Missouri
River near Vermillion, South Dakota (Braaten 1993). Headwaters begin as two forks, the
East and West, originating in Kingsbury County and McCook County respectively, before merging to fo1m the mainstem of the Vermillion River near Parker. South Dakota.
Both headwater regions of the East and West forks often become intermittent. especially during droughts. Predominant land use within the watershed is row crop agriculture and pasture used for livestock grazing. Consequently, channelization and sedimentation from agricultural practices has caused degradation of water quality in this basin (Underhill
1959).
The Vermillion River basin lies within two physiographic regions, the Prairie
Coteau and Missouri River Valley Floodplain (Johnson et al. 1995). Turkey Ridge, located in the southern portion of the Prairie Coteau, best characterizes most of the
Vermillion River basin. and was included in the Prairie Coteau region based on its similar glacial history and soil series. The Missouri River Floodplain is located in the southernmost portion of the Vermillion River basin, and is comprised mainly of floodplain deposits.
Climate is classified as sub-humid continental and temperatures ranged from
-4.0 ° C to 28.0 ° C in 1999 (USGS 2000). Average annual precipitation is approximately 6lcm. 75 % of which falls during the growing season (Schmulbach and
Braaten 1993). Mean annual discharge was 14.21 m3/s with 1.0 m3/s being the lowest II daily mean, and 77.0 m3/s being the highest daily mean in l999 (USGS 2000). The hydrograph depicts seasonal fluctuations in flow, and discharge usually peaks first in
April, followed by a second peak in June (Figure 1-6). In years of drought, only the lower 29 km of the basin contained flowing water, indicating that several tributaries in the upper reaches of the basin may have become intermittent (Schmulbach and Braaten
1993). Portions of the mainstem Vermillion River were intermittent in 1951, 1955, and
1958 with water flowing only in the lower 29 kilometers (Underhill 1959), and several tributaries were intermittent in 2000 (personal observation). Principal recreational uses of the tributaries designated by the SD DENR ( 1994) include boating and fishing.
Assigned water quality condition is warm water marginal fish life propagation.
Big Sioux River Basin
The Big Sioux River basin encompasses 23,325 km2 of land area in portions of eastern South Dakota, southwestern Minnesota, and northwestern Iowa. The headwaters originate in north-central Grant County, South Dakota, and flow southeast through South
Dakota, before reaching its confluence with the Missouri River near Sioux City, Iowa
(Dieterman and Berry 1995). Com, wheat. and soybeans are the main crops cultivated within this agriculturally dominated watershed, while pasture for livestock grazing is also common. In addition to these land use practices. this watershed also supports the largest human population in South Dakota, with Sioux Falls contributing a considerable amount 12
1400
1200
1000 Ul -0 800 -Q) C>.... ca ..r:: 0 600 en 'C c: ca 400 Q) ~ 200
0
Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec Month
Figure 1-6. Mean monthly discharge (cfs} of the Vermillion River near Vermillion, South Dakota; water years 1984-1999 (USGS 2000). 13 to the overall population (Dietennan and BeITy 1995). The Big Sioux River basin lies
within two physiographic regions. the Prairie Coteau and Southeastern Loess Hills
(Johnson et al. 1995). The Prairie Coteau region has a highly variable landscape formed
by a series of glacial advances, most of which is comprised of Carey substage-age till.
Seasonal temperatures range from -3.0 °C to 35.0 °C, and averaged 13.9 °C in
1999. Annual discharge ranged from 12. l m3/s (lowest daily mean) to 292 m3/s (highest
daily mean), with an overall mean of 66 m3/s for 1999 (USGS 2000). Seasonal fluctuations in discharge are apparent from the hydrograph for water years 1929-1999
(Figure 1-7), with two peaks usually occurring in April and June. The hydrograph reflects the high precipitation that the area receives during the spring and early summer
months. Principal recreational uses of tributaiies includes swimming, wading, boating. and fishing (SD DENR 1994). Assigned water quality conditions include wannwater semipermanent fish life propagation and warrnwater marginal fish life propagation (SD
DENR 1994). Several streams (e.g., Split Rock Creek, Pipestone Creek, Flandreau
Creek, Beaver Creek, and Medary Creek) may have alternate water quality guidelines
because these streams originate in Minnesota. 14
3500
3000
(j) 2500 -~ Q) ....O> 2000 ('() .r:. (.) II) :0 1500 c ('() Q) ~ 1000
500
0 Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec Month
Figure 1-7. Mean monthly discharge (cfs) of the Big Sioux River near Akron, Iowa; water years 1929-1999 (USGS 2000). 15
Chapter 2
Fish communities of tributaries to the James, Vermillion, and Big Sioux rivers
Introduction
Several studies of fish communities have been conducted on main stem portions of the James (Schumacher 1995; Walsh 1992), Vermillion (Underhill 1959; Braaten
1993), and Big Sioux rivers (Nickum and Sinning 1971; Dieterman and Be1ry 1995), but less work has been done on the tributaries. Bailey and Allum ( 1962) and Churchill and
Over ( 1933) collected fish species from several tributary and main stem sites of the
James, Vermillion, and Big Sioux rivers in eastern South Dakota, but few sites contained
Topeka shiners. Churchill and Over (1933) published a comprehensive list of South
Dakota fishes (81 species), but did not provide quantitative data on distribution and abundance of various species, including Topeka shiners.
Previous investigations have provided insight into the fish communities of these t1ibutaries. Several studies conducted on the James River and its tributaries from 1975 to
1992 reported a total of 57 species present in the basin (Berry et al. 1993); 31 species were found exclusively in tributaries (Shearer 2001). Topeka shiners were found al nine of 16 sites; species that dominated the tributary fish communities were red shiners
Notropis lutrensis. bigmouth shiners Notropis dorsalis. sand shiners Notropis stramineus, black bullheads Ameiurus me/as, and green sunfish Lepomis cyanellus.
Dieterman and Be1Ty (1995) sampled 20 tributaries to the Big Sioux River and collected 34 species. but did not find Topeka shiners. However in 1997, students from
South Dakota State University collected Topeka shiners from Medary Creek. a stream 16 previously sampled by Dietemrnn (Berry 1997, Professor, South Dakota State University,
Brookings, unpublished data; Tabor 1998). Investigators may have misidentified the rare
Topeka shiner as the more common sand shiner. The two species are very similar in size and appearance, distinguished by orange-red fins in males during the breeding season. and a distinct chevron spot at the base of the caudal fin of Topeka shiners. The fish community in tributaries sampled by Dieterman and Berry ( 1995) was dominated by
black bullhead, white sucker Catostomus commersoni, creek chub Semotilus atromaculatus, emerald shiner Notropis atheri11oides. common shiner Lzu:ilus conwtus,
bigmouth shiner, sand shiner, and johnny darter Etheostoma 11igrum.
Braaten ( 1993) sampled several sites on the main stem of the Vermillion River
and its t1ibutaries, and collected 38 species. Topeka shiners were found at five sites, and
the fish community was dominated mainly by fathead minnows Pimephales promelas,
brassy minnows Hybog11athus hankinsoni, orangespotted sunfish Lepomis Izumi/is, and
black bullheads.
Cunningham and Hickey (1997) sampled 36 sites within the Big Sioux and James
river drainage basins. Twenty-eight species were reported for Big Sioux River
tributmies, and 33 species were reported for James River tributmies. Topeka shiners
were found at four sites, all within the James River basin. In 1998, Cunningham and
Hickey (1999) sampled 33 main stem and tributary sites to the James, Vermillion, and
Big Sioux rivers, and found Topeka shiners at four sites in each river basin. Twenty
eight species were recorded from Big Sioux River tributaries. 19 species from Vermillion
River tributaries. and 21 species from James River tributaries in 1998. The fish 17 communities for these two studies were mainly composed of red shiners. sand shiners, bigmouth shiners, and black bullheads.
Results of these studies provided a comprehensive ichthyofaunal list for tributaries in these basins. and indicated that the Topeka shiner was fairly widespread but
uncommon (Table 2-1 ). These studies provided a list of known sites for sampling during
the first year of my study.
Primary objectives of this portion of the study were to document the distribution
and status of Topeka shiner populations and to determine fish species most commonly
associated with Topeka shiners. Additionally. I wanted to document relative abundance.
species richness, and species diversity at each sample site to further assess the fish communities present in eastern South Dakota prairie streams.
Methods
Sample sites in 1999 were selected based on histmical records from the South
Dakota Natural Heritage Database (SDGFP). and studies cited above. Sample sites for
2000 were determined from GIS analysis that matched land use data at known sites to
landuse data for other river reaches (Wall et al. 2001). Sites sampled in 2000 were
classified as high, medium, or low probability of Topeka shiner presence. Fish were
sampled after water quality measurements were made, and prior to physical habitat
measurements. to minimize disturbance within the stream reach. Block nets consisting of
4.7 mm (bar-measure) mesh were placed at the first and thirteenth transect for each reach,
and securely fastened to the substrate with rocks or rebar hooks. A bag seine (4.5 m long 18
Table 2-1. List of fish species sampled in tributaries of the James. Vermillion. and Big Sioux River basins. including historical and present study records (Braaten 1993: Dietennan and Berry 1995; Cunningham and Hickey 1997: Cunningham and Hickey 1998: Shearer 2001). Trophic class and tolerance were modified from Barbour et al. (l 999) and Bazata (1991 ). res~ctivel~ . Present Species Trophic classa. I listorical study Common name toleranceb record (1999- 2000) Catostomidae Carpiodes carpio River carpsucker 0 x· x Moxosto111a 111acrolepidot11111 Shorthead redhorse IN x x Catosto11111s commersoni White sucker O.T x x Cypri1111s cyprinus Quillback 0 x Cyclept11s e/011gatus Blue sucker I.I x /ctiolms cypri11ellus Bigmouth buffalo 0 x Clupeidae Dorsoma cepedia1111111 Gizzard shad FF.T x x Cyprinidae Campostoma a110111a/11111 Central stoneroller 1-1, T x x Notropis atherinoides Emerald shiner IN x x N. dorsalis Bigmouth shiner IN x x N. lutrensis Red shiner O. T x x N. stra111i11e11s ' Sand shiner IN x x N. topeka Topeka shiner IN . I x x Cypri1111s carpio Common carp 0 x x Hybog11at/111s ha11kinso11i Brassy minnow 0 x x H. placit11s Plains minnow H x Pimeplwles 11otat11s Bluntnose minnow O.T x x P. promelas Fathead minnow o:r x x L11xi/11s com11tus Common shiner IN x x Rlriniclrthys atrat11/11s Blacknose dace G.T x x R. cataractae Longnose dace IN. I x x Se111otil11s atromac11lar11s Creek chub G.T x x Notemigo1111s crysole11cas Golden shiner I x Percidae Etlreostoma exile Iowa darter IN x x E. 11ignm1 Johnny darter IN x x Perea flavescens Yell ow perch p x x Percina 111ac11/ata 131ackside darter IN x Stizastedion vitre11111 Walleye p x x Percichthyidae Marone clrrysops White bass p x Centrarchidae Po111oxis aw111laris White crappie p x x P. 11igro111ac11lat11s Black crappie p x x Lepomis macrocl1irus Bluegill IN x x L lr11111ilis Orangespotted sunlish IN x x L cya11el/11s Green sunfish G, T x x Micropterus salmoides Largemouth bass p x x Esocidae Northern pike p x x Esox lucius 19
Table 2-L continued. Fundulidae Fwululus sciadicus Plains topminnow IN. I x Hiodontidae Hiodon a/osoides Goldeye IN. I x x Ictaluridac Ameiurus me/as Black bullhead IN. T x x A. 11atalis Yellow bullhead IN. T x lcwlurus punctatus Channel catfish p x x Pylodictis o/ivaris Flathead catfish p x Noturus jlavus Stonecat IN, I x x N. gyrinus Tadpole madtom IN x x Sciacnidae Aplodi110111s gr111111ie11s Freshwater drum 0 x Lepisosteidae Lepisosteus platostomus Shortnose gar p x Gasterosteidae Culaea i11co11sta11s Brook stickleback I x " X'' denotes species presence. a Trophic classes: P = Piscivore, H =Herbivore. 0 = Omnivore, FF= Filter feeder. G = Generalist. and IN = Insectivore. b Tolerance: In= Intolerant, T =Tolerant. 20 x l.2 m deep, 4.7 mm (bar-measure) mesh, or 9.1 m long x l.2 m deep, 4.7 mm (bar measure) mesh) was used as the primary sampling tool for each site. Several seine hauls of approximately similar length were made in a downstream direction until the entire stream reach was sampled. Length of seine haul and stream width were recorded to
2 determine area sampled (m ) for each reach.
All fish collected with seines, and those accumulated in the downstream block net were included in the sample. Fish were held in a holding pen placed in the stream.
Topeka shiners were immediately separated from other species and placed in water-filled
buckets. Total length (mm), weight (g), and sex (i.e., male, female, juvenile) were recorded for individual Topeka shiners before release. Other fishes were anesthetized
with carbon dioxide. Total length (mm) and weight (g) were recorded for the first 50
individuals of each species. after which additional fish were identified, enumerated, and
weighed in bulk. Fishes not used as voucher specimens were placed in a separate holding
pen to recover before being released.
Voucher specimens were collected according to standard guidelines of ASIH
( 1998) and according to the stipulations in the federal collecting permit (permit number
PRT-704930). Topeka shiners were not preserved as voucher specimens unless a) it was
an accidental mortality. in which case it would count toward the total of two voucher
specimens per stream, b) the species had not been previously reported from that stream,
or c) the specimen was found at a location that would significantly increase the range of
the species within its currently known dist1ibution within a watershed. 21
Fish community data were reported using species richness and Shannon' diversity index (H') (Lind 1985). Species richness was defined as the number of species (taxa) present at each site, and species diversity was used to describe relative abundance for each species (Allan 1995). Species diversity was calculated with Shannon's diversity index (H') where H' = - LPi(lnPi). Pi is the probability of each species present, and is defined as n/N, where ni is the number of individuals present for each species. and N is total number of species present (Lind 1985). Statistical analyses included analysis of variance (ANOV A) to determine differences in species diversity between the James,
Vermillion, and Big Sioux river basins, and stepwise logistic regression (SAS 1991) to determine fish species most commonly associated with Topeka shiner populations.
Relative abundance of each trophic class was determined for river basin tributaries. All species captured were assigned to one of six trophic classes (i.e., piscivore, omnivore, herbivore, insectivore, filter feeder, and generalist). Catch per unit
area (CPUA) of Topeka shiners was quantified as the number of Topeka shiners per 100
m2 of stream seined. Length-frequency histograms were plotted for Topeka shiners for
each river basin. The Fulton-type index of well being was used to compare condition
(weight at length) of Topeka shiners among each river basin. Condition (Kn.) was
calculated as follows:
3 KTL = W/L x 100,000
where W represents weight (g), Lis the length (cm) of the fish. and l00,000 is a standard
scaling constant. 22
Results
I collected 39.685 fishes from tributaries of the James. Vermillion. and Big Sioux river basins from 1999 to 2000. Cyprinids were usually the dominant family in number of species and number of individuals. Topeka shiners made up 0.4-5.4 % of cyprinids collected (Table 2-2).
Table 2-2. Total number of fish captured for t1ibutaries of the James, Vermillion, and Big Sioux 1ivers, and percentage of Topeka shiners captured 1999-2000. % Cyprinids % Topeka shiners among Cyprinids River Basin Total number fishes captured 1999 2000 1999 2000 James 6.850 77 33 5.4 l.l Vermillion 12.243 74 84 1.0 0.42 Big Sioux 20.592 84 91 1.6 3.2
James River Basin Tributaries
In 1999, I captured 3,925 individuals of 27 species representing seven families
(Appendix 1). Cyprinids were the most abundant family and composed about 77% of the
total catch. Topeka shiners constituted approximately 5% of cyprinids captured in 1999.
Centrarchids (10%) were second in abundance followed by lctalurids (9%), Catostomids
(2%), Clupeids(l %). Percids (< 1%). and Fundulids (< l %). In 2000, l captured 2.925
individuals of 18 species representing six families (Appendix 2). lctalurids were the most
abundant family and comprised 44% of the total catch. respectively. Cyprinids and
Centrarchids were the next two most abundant families representing 33% and 20% of the
total catch. respectively. These two families were followed by Catostomids (1%). 23
Perci Vermillion River Basin Tributaries ln 1999, I captured 5,764 individuals of 27 species representing seven families (Appendix 3). Cyprinids were the most abundant family and composed approximately 74% of the total catch. Topeka shiners constituted 1% of cyprinids captured in 1999. Centrarchids (18%) were second in abundance followed by Ictalurids (6%), Catostomids (1%), Percids (<1%), Esocids (<1%), andHiodontids (<1%). In 2000, I captured 6.479 individuals of 18 species representing five families (Appendix 4). Cyprinids dominated the fish community and comprised 84% of the total catch. Topeka shiners constituted approximately 0.4% of all cyprinids captured in 2000. lctalurids and Centrarchids were the next two most abundant families representing I 0% and 4% of the catch, while Catostomids and Percids constituted 1.5% and< 1% of the catch, respectively. For both years. Cyprinids were represented by 12 species, Centrarchids by six species. lctalurids by four species, Catostomids by three species, Percids by two species, Esocids by one species. and Hiodontids by one species. 24 Big Sioux River Basin Tributaries In 1999. I captured 8.641 individuals of 26 species representing six families (Appendix 5). Cyprinidae was the most abundant family and composed approximately 84% of the total catch. Topeka shiners constituted 1.5 % of all cyprinids captured in 1999. lctalurids (7%) were second in abundance followed by Catostomids (6% ). Centrarchids (1 %), Percids (< 1%), and Esocids (< 1%). In 2000, I captured I 1.951 individuals of 25 species representing six families (Appendix 6). Cyprinids dominated the fish community and composed 91 % of the total catch. Topeka shiners constituted 3.2% of all cyprinids captured in 2000. Catostomids and Ictalurids were the next two most abundant families representing 4% and 2% of the total catch, respectively, followed by Centrarchids (2%), Percids (1 %), and Esocids (< 1%). For both years, the family Cyprinids was represented by 12 species, Percids by five species. Centrarchids by four species, Ictalurids by four species, Catostomids by three species, and Esocids by one species. Trophic Classes Five trophic classes (Table 2-1) were present in each river basin (i.e .. piscivore, omnivore, herbivore, insectivore, and generalist). Insectivores dominated (50-60 %) fish communities in Big Sioux River tributaries, followed by omnivores, generalists, and piscivores for both sample years (Figure 2-1). Filter feeders were not present during either year. 70 60 ~- 50 -c 0 ·-...... VJ I 0 40 0.. ~ 6 u 30 CJ > ...... ('j 20 v e:::: I 10 ~ I 0 p H 0 FF G IN Trophic Class - 1999 c::::::J 2000 Figure 2-1. Relative abundance of six trophic classes sampled from Big Sioux River tributaries during 1999 and 2000. Trophic classes are as fol lows: P = Piscivore, H = Herbivore, 0 =Omnivore, IT= Filter Feeder. G =Generalist. and IN= Insectivore. 26 Insectivore was the predominant trophic class for both years in Vermillion River tributaries (Figure 2-2). Omnivores were the next most abundant trophic class (28-30 % ). Generalist species increased in abundance from 5 % (1999) to 15 % (2000). Pi sci vores were only present in 1999. while herbivores were only present in 2000. Filter feeders were not present during either year. In James River tributaiies insectivores were the dominant trophic class (Figure 2-3). Omnivores decreased in abundance from 36 % in 1999 to 30 % in 2000. Generalist species declined in abundance from 9% in 1999 to 3% in 2000: however, piscivores increased in relative abundance from < I% in 1999 to 11 % in 2000. Herbivores and filter feeders were only present in 1999. Community Measures Shannon's diversity index (H') was used to compare fish species diversity of tributaries in each river basin for James. Vermillion, and Big Sioux river basin tributaries (Tables 2-3, 2-4, 2-5). Species richness for James River tributaries ranged from 2 to 17 (median= 12, n = 18), while species diversity ranged from 0.13 to 2.22 (median= 1.61, n = 18). Species richness for Vermillion River tributaries ranged from 7 to 16 (median= 12, n = 18), while species diversity ranged from 0.90 to 2. I 2 (median= 1.72, n = 18). Species richness for Big Sioux River tributaries ranged from 4 to 21 (median= 13, n = 25). while species diversity ranged from 0. 13 to 2.25 (median= 1.77. n = 25). Analysis of variance indicated no significant differences in species diversity among river basin tributaries ( F = 0.35, df = 2, P = 0.7033). 17 70 60 ~--- '-' 50 c: 0 ...... rJJ 40 0a. E 0 u 30 v > ...... C<;l 20 v 0::: 10 0 p H 0 FF G IN Trophic Class - 1999 c:::::J 2000 Figure 2-2. Relative abundance or six trophic classes sampled from Vermillion River tributaries during 1999 and 2000. Trophic classes are as follows: P = Piscivore. H = Herbivore. 0 =Omnivore. FF= Filter Feeder. G =Generalist. and IN= Insectivore. 28 60--, I 50 -~ -c 40 _,0 VJ 0 0. E 30 u0 il) > ...... 20 ro -:.I ~ 10 p H 0 FF G IN Trophic Class - 1999 c:::::J 2000 Figure 2-3. Relative abundance or six trophic classes sampled from .lames River tributaries during 1999 and 2000. Trophic classes arc as follows: P == Piscivore. H = Herbivore. 0 =Omnivore. FF= filter Feeder. Ci =Generalist and IN= Insectivore. 29 Table 2-3. Species richness (number of taxa sampled per site) and species diversity (Shannon index, H') (Lind 1985) for James River tributaries during 1999 and 2000 sampling seasons. Subscripts indicate different sample sites on the same stream. Community composition Stream Shannon index (H') Number of taxa per site Twelve Mile Creek * 2.22 15 Enemy Creek * 2. 16 14 Middle Pearl Creek * 2.12 14 Redstone Creek * 2.08 12 Pearl Creek1 * 2.05 12 Elm River** 1.83 13 Firesteel Creek * 1.79 17 Pearl Creek2 * 1.76 15 Wolf Creek* 1.64 7 Rock Creek ** 1.59 12 Shue Creek* 1.56 12 West Firesteel Creek* 1.52 11 North Branch Dry Run Creek ** 1.32 5 Sand Creek ** 1.24 6 Redstone Tributary ** 1.06 7 Moccasin Creek ** 0.56 2 Redstone Creek ** 0.30 6 Snake Creek ** 0.13 3 *Site sampled during 1999 field season. ** Site sampled during 2000 field season. 30 Table 2-4. Species richness (number of taxa sampled per site) and species diversity (Shannon index, H') (Lind 1985) for Vermillion River tributaries during 1999 and 2000 sampling seasons. Subscripts indicate different sample sites on the same stream. Community composition Stream Shannon index (H') Number of taxa per site Camp Creek** 2.12 14 Little Vermillion River** 2.08 13 West Fork Vermillion River2 * 2.00 16 Blind Creek * 1.97 16 West Fork Vermillion River1* l.93 l l Long Creek1 ** 1.81 8 Turkey Ridge Creek2* 1.80 13 Ash Creek** 1.80 12 West Fork Vermillion River4 * 1.78 11 West Fork Vermillion River3 * 1.66 12 Turkey Ridge Creek1 * 1.63 14 East Fork Vermillion River, * 1.62 16 Outlet of Silver Lake** 1.47 12 East Fork Vermillion River** l.35 9 Turkey Ridge Creek ** 1.20 7 East Fork Vermillion River2 * l.18 14 Clay Creek Ditch** l.18 11 Long Creek2 ** 0.90 9 * Site sampled during 1999 field season. ** Site sampled during 2000 field season. 31 Table 2-5. Species richness (number of taxa sampled per site) and species diversity (Shannon index, H') (Lind 1985) for Big Sioux River tributaties during 1999 and 2000 sampling seasons. Subscripts indicate different sample sites on the same stream. Community composition Stream Shannon index (H') Number of taxa per site Six Mile Creek1 ** 2.2S lS Pipestone Creek * 2.16 18 Six Mile Creek2 * 2.07 16 1 Medary Creek2 2.06 IS Willow Creek* 1.91 13 Squaw Creek1 * 1.90 12 Spring Creek ** 1.85 9 Six Mile Creek2*** 1.84 15 North Deer Creek*** 1.82 14 Indian River ** 1.81 13 Squaw Creek2 * 1.80 12 Medary Creek*** 1.79 21 West Pipestone Creek * 1.77 10 Hidewood Creek ** l.7S 14 Split Rock Creek * 1.61 15 Brule Creek ** I.SS s 1 Medary Creek1 1.47 14 West Branch Skunk Creek ** 1.47 11 Six Mile Creek1 * 1.40 10 Beaver Creek ** 1.33 4 Skunk Creek ** 1.30 IS Flandreau Creek ** 1.14 16 Gravel Creek ** 0.94 9 Inlet Lake Tetonkaha * 0.41 s South Fork North Deer Creek * 0.13 s * Site sampled during 1999 field season. ** Site sampled during 2000 field season. ***Sites sampled by East Dakota Water Development Disttict, Brookings, South Dakota during summer 2000. 1 Sites sampled by Craig Milewski. Ph.D. candidate. South Dakota State University, Brookings, South Dakota. 32 Topeka shiner Abundance Topeka shiners are relatively widespread throughout the James, Vermillion, and Big Sioux river tributaries, but catch rates per 100 m2 were relatively low. For 61 sites sampled over two years, overall mean catch per unit area (CPUA) of Topeka shiners was 6.29 ± 1.82 fish/ l 00 m2 and ranged from 0.2/ l 00 m2 to 46.6/ 100 m2 (Tables 2-6 through 2-9). Distribution of CPUA was< l at five sites,~ 1-10 at 20 sites, and> IO at three sites. Basin mean CPUA of Topeka shiners in Vermillion River tributaries during 1999 was 5.2 ± 2.28 (SE) fish/100 m2 (Table 2-6), while sample sites the following year had a 2 mean CPUA of 4.8 ± 2.71 (SE) fish/100 m . Only two sites sampled during the 2000 field season contained Topeka shiners. James River tributmies also exhibited a decline in Topeka shiner abundance between sample years. Basin mean CPUA was 7.6 ± 3.41 (SE) fish/100 m2 in 1999 (Table 2-7), while it was 4.6 ± 3.65 (SE) fish I lOO m2 in 2000. James River tributaries were similar to Vermillion River tributaries during 2000, in that only two sites sampled contained Topeka shiners. Basin mean CPUA of Topeka shiners in Big Sioux River tributaries during 1999 was 2.8 ± 0.99 (SE) fish/ 100 m2 (Table 2-8), while in 2000 it was 13.3 ± 11.12 (SE) ftsh/100 m2 (Table 2-9). Catch rates for both sample years ranged from 0.5 fish/100 m2 2 to 46.6 fish/100 m . 33 Table 2-6. Total number of and catch per unit area CPUA for Topeka shiners captured in Vermillion River tributaries during 1999. Catch per unit area is expressed as fish/100 m2 per seine haul. Subscripts indicate different sites sampled on the same stream. Number of Site Mean stream width (m) ±SE CPUA Topeka shiners West Fork Vermillion River1 7.8 ± 0.55 7.3 8 West Fork Vermillion River2 4.9 ± 0.64 8.2 21 West Fork Vermillion River3 11.6 ± 1.76 1.0 6 West Fork Vermillion River4 12.6 ± 1.63 0.3 3 Turkey Ridge Creek1 9.1±0.25 0.4 Blind Creek 2.5 ± 0.09 14.l 6 Basin Mean 5.2 ± 2.28 xx 34 Table 2-7. Total number of and catch per unit area CPUA for Topeka shiners captured in James River tributaries during 1999. Catch per unit area (CPUA) is expressed as fish/ 100 m2 per seine haul. Subscripts indicate different sites sampled on the same stream. Number of Site Mean stream width (m) ± SE CPUA Topeka shiners Middle Pearl Creek 3.6 ± 1.09 26.5 85 Shue Creek 7.2 ± 0.54 1.7 5 Pearl Creek1 3.1±0.41 9.6 17 Pearl Creek2 2.8 ± 0.30 4.5 15 Enemy Creek 7.2 ± 0.80 8.6 39 Twelve Mile Creek 3.6 ± 0.48 2.2 3 Firesteel Creek 18.6 ± 0.93 0.2 3 Basin Mean 7.6 ± 3.41 xx 35 Table 2-8. Total number of and catch per unit area CPUA for Topeka shiners in Big Sioux River tributaiies during 1999. Catch per unit area is expressed as fish/100 m2 per seine haul. Subscripts indicate different sites sampled on the same stream. Number of Site Mean stream width (m) ±SE CPUA Topeka shiners Six Mile Creek1 3.4 ± 0.20 1.4 2 Six Mile Creek2 3.6 ± 0.18 3.3 3 West Pipestone Creek 4.7 ± 0.48 1.0 4 Pipestone Creek 6.9 ± 0.43 7.3 98 Split Rock Creek 26.6 ± 2.41 0.7 7 Medary Creek, 5.7 ± 0.27 0.5 Medary Creek2 5.1±0.18 5.3 3 Basin Mean 2.8 ± 0.99 xx 36 Table 2-9. Total number of and catch per unit area CPUA for Topeka shiners in tributaries to the James, Vermillion, and Big Sioux River Basins during 2000. Catch per unit area is expressed as fish/100 m2 per seine haul. Subscripts indicate different sites sampled on the same stream. Topeka abundance Mean stream width Basin Site (m2 ±SE CPUA Number 1 Vermillion River Outlet of Silver Lake 2.7 ± 0.35 2.1 4 Camp Creek 3.9 ± 0.31 7.5 19 James River2 Rock Creek 8.4 ± 1.38 l.O 8 North Branch Dry Run Creek 4.1±0.52 8.3 3 3 Big Sioux River Six Mile Creek1 5.3 ± 0.50 4.1 35 Medary Creek 8.3 ± 0.66 l.O 2 North Deer Creek 6.8 ± 1.03 l.5 Six Mile Creek2 9.2 ± 0.87 46.6 311 1 Basin mean CPUA ±SE= 4.8 ± 2.71. 2 Basin mean CPUA ±SE= 4.6 ± 3.65. 3 Basin mean CPUA ±SE= 13.3 ± 11.12. 37 Length and Condition o,fTopeka shiners Topeka shiner total length for Vermillion River tributaries ranged from 37 mm to 61 mm, with a mean of 49.5 ± 0.63 (SE) mm: Topeka shiner total length for James River tributaries ranged from 38 mm to 68 mm. with a mean of 52.1 ± 0.52 (SE) mm: and finally Topeka shiner total length for Big Sioux River tributaries ranged from 34 mm to 73 mm, and had an average length of 51.5 ± 0.33 (SE) mm. Analysis of variance indicated no significant differences in mean total length of Topeka shiners among river basin tributaries (df = 2, P = 2.15). Mean length of shiner males was 56.1 ± .05 (SE) and mean length of shiner females was 49 .1 ± 0.04 (SE); however, analysis of variance indicated that there was no significant difference is lengths of males versus females (F = 2.34, df =l, p = 0.126). Fulton's condition index for Topeka shiners was similar for each river basin. Mean K for Vermillion River basin Topeka shiners was 1.09 ± 0.07 (SE), and ranged from 0.42 to 1.92. Topeka shiners in the James River basin had a mean K of 1.14 ± 0.04 (SE), and ranged from 0.43 to 1.76. Finally. Big Sioux River basin Topeka shiner condition averaged 0.92 ± 0.02 (SE), and ranged from 0.40 to 2.14. Analysis of variance showed that there was no significant difference for Topeka shiner condition among river basin tributaries (F = 56.49, df = 2, P = 1.41). Species Associated with Topeka shiners Two individual models were created with stepwise logistic regression to determine fish community associations with Topeka shiners. The first model was based 38 2 on number of fish collected for each species at each site (abundance; number/ 100 m ). The second model was based on presence or absence of other species (regardless of abundance) at each site in relation to Topeka shiner presence. Abundance Model The model for number of fish collected for each species and their relationship with Topeka shiners is as follows: Log (p/1-p) = -1.0396 + 0.0289 (OSF) + 1.7212 (TPM) where p is the probability of Topeka shiners being present, OSF is orangespotted sunfish, and TPM is tadpole madtom. The two variables for this model indicate that Topeka shiners are more likely to be present in streams when orangespotted sunfish (P = 0.054) and tadpole madtoms (P = 0.048) are also present. Values for concordant, discordant, and ties were 74.0. 18.8. and 7.3 %. respectively. Concordance values are the probability that 0.74 of the observations were greater than zero, and the model will correctly predict Topeka shiner presence 74.0 % of the time. Discordance is the probability that 0.188 of the observations were Jess than zero. Ties are the probability that 0.073 of the observations are equal to one another, and do not aid in correctly or incorrectly predicting Topeka shiner presence. Presence/ Absence Model The model based on presence/absence for other species at each sample site is as follows: Log (p/ 1-p) = -7.10 + 1.69 (BIG)+ 2.55 (BBH) + 4.15 (RES)+ 2.55 (TPM) 39 where pis the probability of Topeka shiners being present, BIG is bigmouth shiner, BBH is black bullhead. RES is red shiner. and TPM is tadpole madtom. These four variables show that Topeka shiners are more likely to be present in streams when bigmouth shiners (P =0.034). black bullheads (P =0.004) . red shiners (P =0 .006). and tadpole madtoms (P = 0.021) are also present. Values for concordant, discordant, and ties were 83.5, 7.5, and 9.0%. respectively. Discussion Fish community composition for tributaries of the James. Vermillion, and Big Sioux rivers appear to be relatively diverse for this region. Previous studies have shown that fish communities in midwestem streams may have low species richness because they are unstable (e.g .. fluctuating flow and temperature conditions) (Matthews 1988). Despite prairie streams having unstable environments, species diversity (H') values for the majority of tributaries sampled in eastern South Dakota had a value greater than 1.0. Allan (1995) noted that species diversity values indicate that richness (number of taxa) is high (> 1.0), and most species are equally abundant for that site. Most tributaries that I sampled in 1999-2000 followed this trend, however six sites had a species diversity value less than 1.0. These low values could be linked to lack of in-stream habitat heterogeneity (e.g .. lack of pool-riffle complexes, absence of large woody deb1is, uniform substrate types) found at each of these sites. Mackay and Kalff ( 1969) found that species richness was lower in more physically uniform stream habitats. These six sites were all characterized by channelized run habitat with steep stream banks. and had silt as the 40 dominant substrate type. Sites where species richness and diversity were higher had several substrate types present throughout the sample reach, pool-riffle complexes were more common, and run habitats had a somewhat uneven channel shape. Trophic gui Ids for tributaries in each basin indicated that fish communities in all three river basins were dominated mainly by insectivores, while piscivores usually composed less than 10% of the fish community present. Predation on Topeka shiners is most likely from black bullheads, channel catfish, creek chubs. and northern pike, species that are native to each river basin. It has been hypothesized that Topeka shiners are negatively impacted by largemouth bass introduced into small impoundments constructed on tributaries containing Topeka shiners (Mammoliti 1995; Tabor 1998). Largemouth bass have become fairly common throughout much of Kansas, Nebraska, Missouri, and Iowa as a result of extensive construction and stocking of impoundments and farm ponds (Winston 2000). Schrank et al. (200 I) found that the number of impoundments within a watershed, and catch per unit effort of largemouth bass were significantly higher in locations where Topeka shiners have been extirpated than in sites with fish. In eastern South Dakota, small tributary impoundments are not numerous, and I found few largemouth bass in streams so it is less likely that largemouth bass or other introduced predators are having a substantial impact on Topeka shiner populations. Topeka shiners were relatively widespread throughout tributaiies in South Dakota, but were not abundant. Fryda (2001) found that sturgeon chubs Macrhybopsis gelida were widespread in the White River, South Dakota. but catch rates were low (0.1 - 2 1.9 fish/ 100 m ). Topeka shiners have traditionally comprised a small portion of the total 41 fish community caught during a sampling effort (Nickum and Sinning 1971; Braaten 1993; Cunningham and Hickey 1999). Low catch rates could be attributed to lack of precipitation causing several streams to become intennittent, therefore forcing fish populations to become trapped into isolated pools. Several tributaries sampled during 2000 consisted of isolated pools, and had only one or two Topeka shiners present for the entire reach. Gear efficiency did not appear to contribute to low catch rates of Topeka shiners. In addition to seining, block nets were used at the beginning and end transects of each sample reach. Dauble and Gray (1980) found that seining was most efficient when sampling streams with even substrates and low flow. Most tributaries that I sampled contained silt, sand, or gravel substrates, and had minimal or low flow velocities. Little information has been collected on length and condition of Topeka shiners. Barber (1986) developed criteria based on total length of Topeka shiners to assess population structure in Kansas streams. Individuals< 42 mm were considered juveniles, and individuals> 42 mm were considered adults, however age groups were not distinguished from one another (e.g., age-0, age-1, age-2). Dahle and Hatch (2000) conducted several mark-recapture studies to estimate population size in Minnesota. but did not distinguish age groups or create length-frequency distributions to show recruitment patterns because of lack of quantitative criteria. Fish community associations for Topeka shiners were based on two logistic models, number of fish for each species at each site (abundance) and presence or absence of a species at each site (regardless of abundance). The two models suggested an 42 association between Topeka shiners and six other species (Table 2-10). Tadpole madtom appeared in each model as a positive association. All six species are classified as tolerant or intermediately tolerant to turbid, watm water, and hypoxic conditions in prairie streams. All are associated with small streams with low to moderate flow; however, some are associated with intermittency. Pflieger (1997) also included red shiners and bigmouth shiners in his Topeka shiner assemblage. Four species in my association list use clean gravel for nests. Topeka shiners have been known to spawn with red shiners and two other shiners in sunfish nests, such as those of orangespotted sunfish and green sunfish (Pflieger 1997). Creek chubs build gravel-mound nests, while black bullheads sometimes excavate nests over gravel. Topeka shiners could possibly be using nests created by these species in the absence of sunfish species, although I have no evidence to support this theory. Winston (2000) found that Topeka shiners were associated with fathead minnows and black bullheads, and Michl and Peters (1993) found that bigmouth shiners, red shiners, fathead minnows, and creek chubs were part of the fish community sampled with Topeka shiners in Nebraska. Katula ( 1998) suggested that Topeka shiners are "quite hardy," while Minckley and Cross (1959) found them to have the greatest spawning success during drought conditions. Fathead minnows are tolerant of high temperatures and low dissolved oxygen thus, they are able to withstand harsh environmental conditions common in prairie streams (Pflieger 1997). Black bullheads are found in pools of small intermittent creeks and backwaters, and are highly tolerant to extremes in temperatures (Campbell and Branson 1978; Pflieger 1997). The species associated with Topeka 43 Table 2-10. Fishes associated with the Topeka shiner in eastern South Dakota. Ecological traits are summarized from Pfleiger (1997), Lee et al. (1980), Harlan and Sipea ker (l 987) Pl a fki net a.I ( 1989) ' Common Tolerance and Ecological traits related to Topeka Model and troghic scientific shiner (with caveats) assignment name Presence- red shiner intermediate pioneer species in disturbed habitats, absence omnivore spawn on sunfish nests with Topeka native shiners; regional distribution same as Topeka shiner bigmouth intermediate associates with sand and red shiners in shiner insectivore small, low flow streams with unstable bottoms; broadcast spawner. more common in permanent streams; scarce in middle Missouri River basin, especially West creek chub tolerant found in small, sometimes intermittent generalist headwater creeks where few fish native present; constructs gravel mound nests male guards nest and drives off mm nows tadpole intermediate found in quiet, slow moving, muddy madtom insectivore streams native secretive, lays eggs in clusters in cavities and beneath ledges, uncommon except in eastern Missouri River tributaries black intermediate pools of small intermittent creeks and bullhead omnivore muddy oxbows and backwaters, native excavates saucer-shaped nest nest fanned and guarded, black bullhead widespread and common 44 Table 2-10, continued. Abundance tadpole intermediate found in quiet, slow moving, muddy madtom insectivore streams native secretive, lays eggs in clusters in cavities and beneath ledges, uncommon except in eastern Missouri River tributaries orangespott- intermediate streams with low to intermediate flow, ed sunfish insectivore prai1ie creek pools, builds nests on clean native gravel (as do green sunfish); red shiner, redfin shiner and Topeka shiner spawn over nests absent in extreme headwaters with green sunfish 45 shiners in my study thus are tolerant to harsh environmental conditions common in prairie streams. Because habitat availability is continually changing with seasonal and temporal variations in flow and temperature, it has been advantageous for prairie stream fishes to become well adapted to a wide variety of habitats instead of specializing on particular habitat types to persist (Braaten and Berry 1997). Conclusion The goal of this portion of the study was to determine fish species associations with Topeka shiners. Two models suggest that Topeka shiners are associated with six other species. This finding helps to satisfy one of several research needs and objectives identified in the draft Topeka shiner recovery plan. My model predicted an association between orangespotted sunfish and Topeka shiners; however, no observations were made witnessing Topeka shiners using sunfish nests for spawning. Several questions still exist regarding obligate spawning relationships for Topeka shiners. Future studies are needed to determine if obligate spawning relationships exist throughout the entire Topeka shiner range or for only certain portions of the range. My study also indicated that Topeka shiners are widespread, but not abundant throughout South Dakota. Catch per unit area, and length and weight data collected from this study will be a useful tool to help establish baseline criteria for future studies that may be targeting reproduction and age-class structure of Topeka shiner populations in eastern South Dakota and southwestern Minnesota. 46 Chapter 3 Habitat preferences and distribution of the Topeka shiner Introduction Stream surveys are necessary tools to describe and characterize habitat features. and determine factors influencing biotic communities (Meador et al. 1993). Layher et al. (1987) suggested that in-stream habitat is a major factor regulating fish communities in warmwater prairie streams. Several factors linked to in-stream habitat and landscape habitat deterioration have led to an 80% decline in occurrence of Topeka shiners throughout their historical range (Tabor 1993). Reduced water quality from non-point source pollution. unmanaged livestock access to streams and riparian areas. channel incision. and sedimentation are factors contributing to the decline of this species (Gelwicks and Bruenderman 1996: Tabor 1998) Topeka shiners are widespread in the James. Vermillion, and Big Sioux river basins in eastern South Dakota. but they have not been found in abundant numbers. Topeka shiners typically inhabit intermittent and unstable prairie streams (Minckley and Cross 1959: Cross and Collins 1995: Pflieger 1997: Tabor 1998). and natural abiotic factors in each watershed may influence their abundance (Poff and Ward 1989). Limited studies have been concluctecl on South Dakota streams (Cunningham and Hickey 1997: Cunningham and Hickey 1999). but no comprehensive survey of habitat requirements for Topeka shiners exists in South Dakota. A better understanding of the structural and furn.:tional habitat processes influencing Topeka shiner presence is needed in South 47 Dakota. GIS models created to address habitat requirements at the \Vatershed or landscape scales shmved that Topeka shiner presence \Vas related to increased stream size. stable !low regime. increased groundwater delivery. decreased stream gradient, and increased stream size discrepancy (\Vall et al. 2001 ). This portion or my research deals with documentation of habitat conditions at the reach (local) scale. A reach is typically defined as any specified length of stream that maintains its average channel shape. flO\v. and physical. chemical. and biological characteristics (Bain and Stevenson 1999). Habitat associations with Topeka shiner presence Yvere identified to coiled baseline data to allow temporal comparisons of fish populations and habitat change, and to help define critical habitat and guide habitat restoration efforts. i\kthods Physical habitat and hydrological features were measured at 61 tributary and mainstem sites of the James. Vermillion. and Big Sioux rivers from .lune-September during 1999 and 2000 (Table 3-1. Table 3-2). Sample sites visited in 1999 \Vere based on historic Topeka shiner locations recorded in the South Dakota Natural Heritage Database (Doug Backlund. South Dakota Department of Game. Fish an Parks. personal communication). Sample sites visited in 2000 were determined from a preliminary GIS model that identified potential Topeka shiner habitat as high. medium. and low probability. Fish sampling was done in reaches representing each probability class. Physical habitat sampling procedures followed transect methodologies outlined by Simonson ct al. ( 1994) and Platts et al. (1983). Ten preliminary stream widths \Vere 48 Table 3-1. Legal description (township, range. section) of South Dakota streams sampled during June through September 1999. number of Topeka shiners sampled in each stream. and Universal Transverse Mercator (UTM) coordinates for each sample site. Subscripts indicate different sample ~i_!es l~I~ the sam_e strea_1_n_. __ Stream (abbreviation) Coordinates 4819940 N West Fork Vermillion River (WfV 1) IOlN 54W 30 8 14 0633430 E 4843319 N West Fork Vermillion River (WfV2) 103N 55\V JO 21 14 0627125 E 4839949 N West fork Vermillion River (\VFVJ 103N 55\V 27 14 0627804 E 4823200 N East Fork Vermillion River (EFV i) IOIN 53W 14 0 14 0648464 E 4903656N Middle Pearl Creek (MPL) 1 JON 60\V 34 85 14 0577673 E 4921970 N Shue Creek (SHU) lllN 60\'-/ 6 5 14 0572268 E 4902214 N Pearl Creek (PRL 1) 109N 60W 4 17 14 0575859 E Pearl Creek (PRL 2) 109N 60W 8 15 4910991 N Six Mile Creek (SIXi) llON 50\V 14 2 14 0676285 E 4923122 N Inlet Lake Tetonkaha (IL T) lllN 52\V 0 14 0658179 E Squaw Creek (SQW 1) 106N 49\V 3 0 4875571 N Squaw Creek (SQW ) 2 106N 49\V 2 0 14 0685362 E 4918867 N Six Mile Creek (SIX ) 'Y) 2 I llN 49W 4 14 0682637 E 4916792 N South Fork No11h Deer Creek (SFD) lllN 50W 34 0 140673215E 4831457 N Enemy Creek (ENY) 102N 60W 16 39 145765041 E West Pipestone Creek (WPIP) 102N 48W 3 4 4837541 N 14 0695606 E 49 Table 3-1 continued. ------·----.·. ------· 4825231 N Willow Creek (WIL) 10\N 50\V JO () 14 0675672 E 4823383 N ... Twelve Mile Creek (TLV) IOIN 59W 8 .) 14 0585497 E 4871528 N Pipestone Crei.:k (Pl P) 106N 47\V 22 98 14 0703 896 F. 4803216 N Wolf Creek (WOL) 99N 57Vv' 20 () 14 0613251 E 4807154 N West Fork Vermillion River (WFV 4 ) 99N 53W 7 3 14 0650331 E 4847645 N Split Rock Creek (SPL T) 103N 47\V 4 7 14 0701947 E ... Firesteel Creek (FIR) 104N 62\V 26 .) 4784744 N Turkey Ridge Creek (TRK 1) 97N 53W 26 14 0656889 E 4777135 N Turkey Ridge Creek (TRKJ 96N 52\V 16 0 14 0663706 E 4816713 N East Fork Vermillion River (EFV,) IOON 53\V 17 () 14 0650847 E ..,_ _,... 4850300 N West Firesteel Creek {WFIR) 104N 63W 0 14 0551456 E 4880651 N Redstone Creek (RED) 107N 60\V 14 0 14 0580724 E 4777152 N Blind Creek (BLN) 96N 51 \V 16 6 14 0673005 E Medary Creek (MED 1)** 109N 49W 10 Medary Creek (MED2)** I ION 48W 33 3 ------.. - ...... _ ..... ____ ,...... ,,_.,_____ .. ,, __ ._.. ,,. ------.,--.,,.,.,,. _____ "_,_.--- **Sites sampled by Craig Milewski. Ph.D. candidate. South Dakota State University. Brookings, South Dakota. 50 Table 3-2. Legal description (township. range, section) of South Dakota streams sampled during June through August 2000. number of Topeka shiners sampled in each stream, and Universal Transverse rv1ercator (lJTtv1) coordinates for each sample site. Subscripts indicate different sample_site_s__ ~~1~ ~~~ame_ ~!rea~ll_:______----~--- ·- Stream (abbreviation) Township Range Coordinates 4925075 N Six Mile Creek (SIX,) I 12N 48\V 35 14 688864 E 4896814 N Spring Creek (SPR) 109N 47\V 0 14 699772 E 4919403 N Redstone tributary' (TRED) lllN 57 'VI' 15 0 14 607037 E Redstone Crel:k (RED) IIIN 57\V 5 () 4870650 N East Fork Vermillion River (EFV) 106N 54\V () 14 636806 E Gravel Creek (GRV) I 18N 52\V 19 0 4861612 N Rock Creek (RCK) 105N 57W 15 14 606933 E 5004065 N Indian River (IND) 120N 52\V 15 0 14 644497 E 4889393 N Sand Creek (SAN) 1081\ 62W 24 () 14 584300 E 4744763 N Brule Creek (BRU) 93N 50\V 27 () 14 685432 F 4855800 N Skunk Creek (SKU) 104N sow 0 14 674462 E 4840829 N West Branch Skunk Creek (WSK) 103N 51W 29 () 14 662362 E 4824204 N ~ Beaver Creek (BVR) IOIN 48W I -' () 14 696159 E 4770629 N Ash Creek (ASH) 95N 51\V 8 0 14 672676 E 4754839 N Clay Creek Ditch (CLY) 94N 53W 30 () 14 650061 E North Branch Dry Run Creek (NDR) 99N 60\V 20 3 4802364 N 14 583276 E 51 Table 3-2 continued. 4955490 N Hidewood Crct!k (I IDW) I 15N 49\V 35 () 14 684022 E () Long Creek (LNG 1) 97N 51W 20 4793251 N ~., Long Creek ( l.NGJ 98N 51w -'- 0 14671288E 5056737 N Elm River (FUvl) 125N 64\V 3 () 14 537495 E 5019820 N Moccasin Creek (MOC) 11'.!N 64\\1 34 0 14 537882 E 4841T22N Little Vermillion River (LY) 103N 53\V 21 0 14 644265 E 4882979 N Flandreau Creek (FLD) 107N 47W 15 0 14 702985 E 4802493 N Camp Creek (CMP) 99N 52W 32 19 14 661310 E 4816023N Outlet of Silver Lake (OSI.) IOON 55\V 19 4 14633150 E 4793284 N Turkey Ridge! Creek (TRK) 98N 55W 26 () 14 637821 E 5002270 N Snake Creek (SNK) 120N 65 \\! 28 0 14 526821 E North Deer Creek (NDC)** llON sow 28 Six Mile Creek, (SIXJ** lllN 48\V 6 311 Medary Creek (MED)** 109N 49\V 19 2 1Unnamed tributary. **Sites sampled by East Dakota Water Development District. Brookings. South Dakota. taken using a Sokkia/SK lcvding bedrod to determine mean stream ·width, and then reach length was determined. Each sample reach included 1 ~ transects placed three mean stream widths apart to ensure that all in-stream habitat types (pool. riffle, run) were sampled within the designated reach (Simonson et al. 1994 ). When access was limited (e.g .. fence line indicating different ownership rights). transect numbers \Vere reduced. Universal Transverse Mercator (UTM) coordinates \Vere taken at the first and thirteenth transects using a Magellan Global Positioning System (CiPS) unit. Coordinates \Vere used to determine position location and stream gradient for GIS maps. Several variables used to describe channel morphology were measured or visually estimated at each transect (lab le 3-3 ). A I 00-m CAM-line fiberglass measuring tape with 1-m im:rements \Vas stretched from left top-of-bank (I .TB) to right top-of-bank (RTI3) with LTB located at 0.0 m on the tape. Top-of-bank was defined as the point where the stream bank joins the floodplain (Harrelson ct al. 1994). The Sokkia/SK leveling bedrod was used for vertical measurements. and the CAM tape was used for horizontal measurements across each transect. Horizontal and vertical measurements w·ere taken to the nearest 0.1 m. Features measured across each transect. moving !cit to right included L TB. left hankfull (LI3F). left edge \Valer (LEW). 0.25 stream width (STRl). 0.50 stream \Vidth (STR2). 0.75 stream width (STR3), right edge water (REW). right bankfull (RUF). and RTR (Figure 3-1 ). In-stream habitat types (pools. riilles. runs) were measured to the nearest meter to determine what percentage or each habitat type characterized the sample reach. Other stream bank and riparian features measured included bank angle. stream bank length. 53 Table 3-3. Habitat variables measured at tributary sample sites throughout the James Ve~1~1il)io1\.~~~- §_i_g_Sioux river basins i!1 I ?99 and 20_00_: ____ . ____ ·---- Habitat variable Category or measurement Stream \vidth m Bankfull \Vidth 111 Bankfull height 111 Top-of-bank \vidth 111 Rank height m Bank angle degrees Stream bank kngth 111 Vegetated stream bank 111 Eroded stream bank m Deposited stream bank 111 Stream bank vegetation type sedge/rush. grasslrorb, willows. shrubs. cottonwoods. green ash. silver maple. other Age class of trees seedling/sprout sapling, mature. decadent dead. other Riparian buffer width >10 111 . <10 Ill Riparian land use crops. pasture, prairie, shrub, \\etland. forested. other Animal vegetation use none. low·. moderate, high. very high Bank sl u111page present, absent Overhanging vegetation 111 Undercut bank m Submerged macrophytes 111 Emergent macrophytes 111 Large vvoody debris present. absent Stream depth 111 Habitat type pool. riffle. run , pool -run. riffle-run 54 Len bank Right bank To -of-bank width 13 ankfull \Vidth RBF Stream width LF.\:V Figure 3-1. Horizontal measurements taken at transects in streams of the James, Vermillion. and Big Sioux Rivers. 55 length of stn.:am bank vegetated. length of stream bank eroded, length or stream bank deposition. overhanging vegetation. undercut bank. submerged macrnphytes. and emergent macrophytes. All variables were measured to the nearest 0.1 m, with the exception of bank angle. \Vhich was measured in degrees. Visually estimated teatures included dominant stream bank vegetation type, age class of trees (if present). riparian buffer width, surrounding landuse practices, animal vegetation use. bank stumpage, large woody debris. and percent canopy cover. Substrate composition for each site was characterized by taking three samples from each bank (upper, mid. and lower), and a minimum of eight samples of bottom sediment across the \Vetted portion of each transect at equally spacccl distances. Substrate samples \Vere measured and categorized according to Harrelson et al. ( 1994) (Table 3-4). Water quality measurements were taken mid-morning immcdiatcly upon arrival at each sample site (Table 3-5). Turbidity (percent transmittance, NTU) and dissolved oxygen (mg/L) were measured using a portable Hach kit. Water temperature (°C) and conductivity (JtSll:m) \Vere measured with a YSI meter. Air temperature (0 C) was measured with a hand-held thermometer. Water clarity was measun:cl with a secchi disk to the nearest centimeter. Vdm:ity was measured at each transect for the entire sample reach across three evenly sp~1c<.:d points (STR 1. STR2. and STRJ. figure 3-2). \Vhcn lhl\ving water was present. ivh.~ asurements were taken using a top-set wading rod and a lVlarsh-McBirney tlmv meter unit at 0.6 stream depth in portions of the stream less than 0.76 min depth, and at 0.2 and 0.8 stream depth in portions or the stream greater than 0. 76 111. Discharge 56 Type Abbreviation Description Detritus DET sticks. wood. coarse plant material (CPOM) Muck-mud MUCK black. very fine organic (FPOM) Clay CL <0.004 111111 (slick) Silt SI 0.001-0.062 111111 Sand Si\ 0.062-2 111111 (gritty) Very fine gravel VFG >2-4 mm Fine gravel FG >4-8 mm Medium gravel rv1G >8-16 111111 Coarse gravel CG >16-32 111111 Very coarse gravel VCG >32-64 mm Cobble co >64-128 mm Large cobble LC > 128-256 111111 Boulder BO > 256-512 111111 Large boulder LB >512 111111 57 Table 3-5. Water characteristics measured at transects along sites sampled throughout the James. Vermillion. and Big Sioux River basins in I 999 and 2000. Water characteristic variable Category or measurement Air temperature oc Water temperature oc Conductivity ~1S/cm Dissolve oxygen mg/L Turbidity percent transmittance. NTU Secchi disk depth (cm) Discharge m3/s Vdocity mis 58 RT!:;B~---- Stream bank kngth Bankfull height \\!at er surfac1.: STRI STR2 Figure 3-2 . Vertical measurements taken at transects in streams of the .lames, Vermillion. and Big Sioux rivers. 59 \Vas measunxl for each study site at the transect with the most uniform stream tlO\v. Water depth and flow were measured at 20 equidistant points across the wetted portion of each transect (Platts et al. 1983 ). Discharge was calculated for each site using Qcalc soft\vare. Photographs were taken in both upstream and downstream directions at transects I. 6. and 13. A hand held chalkboard within the frame of each photograph included transect number. date. county. stream name. site number. and legal description of the site (township. range. and section). These photographs are archived in the Department of \Vildlite and Fisheries Sciences at South Dakota State University. Data analyse for physical habitat characteristics. substrate composition. and water quality parameters \Vere calculated using stepwise logistic regression in SAS (SAS Institute 1991 ). Logistic regression procedures for physical habitat. substrate composition. and wah:r quality \Vere based on presence/absence data Ii.Jr Topeka shiners at each study site. Variables measured by category (e.g .. vegetation type. Table 3-3) were further analyzed using Chi-square analysis. Results Photographic documentation indicated that Topeka shiners \Vere found in relatively varied habitats (Appendix 7). Fc\v streams sampled had severe erosion problems due to animal use (livestock): most streams had low animal use. Riparian 3 vegetation consisted primarily of grasses and forbs. Discharge was usually< 1.0 111 /s and velocity \Vas usually< 0.2 m/s. Dissolved oxygen ranged from 4.0-9.0 mg/Land \Valer temperatures were between 17 and 27 °C from June through August. Substrate 60 types consisted mainly of very fine gravel. fine gravel. medium gravel, and cobble: however, Topeka shiners \Vere also found over silt and sand substrates. Primary macrohabitat \vhere Topeka shiners were collected was runs. Physical Habitat Model The data set used for the physical habitat model included 302 presence observations and 335 absence observations: Log (p/1-p) = 4.64 - 0.66 (Bl-I) - 0.23 (STRBD) - 0.77 (ANVG)- 0.39 (VEG) - 0.45 (AGE) - 0.83 (OVG) - 0.43 (SUB) - 0.48 (HABTYP) + 0.45 (RIVER)- 2.49 (YEAR) where pis the probability of Topeka shiners being present. BH is stream bank height. STRl3D is length of stream bank deposition. ANVG is animal vegetation use. VEG is dominant stream bank vegetation type, AGE is age class of trees present OVG is overhanging stream bank vegetation. SUB is submerged rnacrophytes. I lABTYP is in stream habitat type. RIVER is river basin in \Vhich each tributary is located. and YEAR is the year a stream reach was sampled. Values for concordant. discordant, and ties were 82.2. 17.7. 0.2 %, respectively. Concordance values are the probability that 0.822 of the observations were greater than zero. and the model will correctly associate Topeka shiner presence \Vi th habitat variables in the model 82.2 % of the time. Discordance is the probability that 0.177 of the observations \Vere less than zero. Tics arc the probability that 0.002 of the observations are equal to one another. and do not aid in correctly or incorrectly associating Topeka shiner presence with habitat variables in the model. 61 Animal vegetation use was evaluated as none. low. moderate, high. or very high. No animal use indicated that no grazing from livestock was evident. and the riparian vegetation was intact. LO\v animal use indicated that minimal grazing had occurred on the riparian veg1...~ tation , and there was little or no erosion on the stream bank. Ivloderate animal use indicated that less than half of the riparian vegetation had been grazed. and that the stream bank was somewhat degraded due to soil compaction. High animal use indicated that at least half of the riparian vegetation had been grazed or disturbed. and the stream bank \Vas lacking vegetation (e .g .. bare ground was present) due to soil compaction. Very high animal use indicated that over half of the riparian vegetation had been grazc (15.9%). moderate animal vegetation use I 13.7 %). high animal vegetation use (5.0 %). and very high animal vegetation use (0.55 %). Dominant stream bank vegetation was classified into eight categories including sedges/rushes. grasses/forbs. shrubs, willows Salix spp .. cottonwoods J>o1)!{/11s deltoides. green ash Fi·axi11us penmyfrannica. silver maple Acer sacchari1111111, and other. Chi square analysis indicated that Topeka shiners were associated with streams that had stream bank vegetation comprised primarily of grasses/forbs (P=0.00Ld1'=7) (54.2 %), followed by sedges/rushes (J6.6 %). Cottonwoods (4.5 %). other ( 1.4 1Y.1) . willows 62 (l .3%). shrubs (0.86 %). and silver maple (0.39 %) are stream bank vegetation types least likely to be associated with Topeka shiner populations. Age class of trees was classified into five categories including no trees present, seedling/sprout. young/sapling. mature. and decadent/dead. Chi-square analysis indicated that Topeka shiners were associated with sites \Vhere trees were not located directly along the stream bank (P=0.0Cl3. df=4) (89.1 %). Topeka shiners were least likely to be present in streams where seedling/sprout (4.0 %). young/sapling (3.4 %), mature (2.9 %), and decadent/dead (0.55 % ) trees \Vere present. In-stream habitat type was classified into three categories: pools. rinles, and runs. Run habitats were characterized as having uniform width. depth. and flow. and having variable substrate types. Riffle habitats were characterized as having shallow depth with swift flow, and partially exposed substrate. usually cobble or gravel. Pool habitats \Vere characterized by skrn· moving. deeper and wider sections of the stream channel. and low gradient. usually less than I % (l'vlcMahon et al. 1996: Armantrout 1998). Chi-square analysis showed that runs were the dominant habitat type associated \Vith Topeka shiner presence (P=0.075. clf=2) (68.2 %). followed by pool and rime habitats at 23.2% and 8.5 %, respectively. River and year variables were classified according to sample year ( 1999. 2000). and river basin (.lames. Vermillion. and Dig Sioux). Chi-square analysis by sample year indicated that 1999 data were more successful in determining the likelihood of Topeka shiner presence (P=0.001.clt~l) (57. I %) than were data from 2000 (42.8 %). This may be attributed to higher water levels during I 999 than in 2000. Streams sampled during 63 1999 were perenniaL while several streams sampled during 2000 \Vere intermittent. Chi squan: analysis by river basin indicated that the Big Sioux River basin contained the greatest number of streams with Topeka shiners present (P=0.001 . df=2) ( 41.4 %), followed by the Vermillion River basin (30.5 %). and finally the .James River basin (28.1 %). 5'11bstrate Composition Model The data set used for this model included 25 presence observations. and 29 absence observations: Log (p/1-p) = -1 .06 + 0.08 (VFG) + 0.09 (CO) where pis the probability of Topeka shiners being present. VFCi is very line gravel. and CO is cobble. The two variables for the substrate composition model indicate that Topeka shiners are associated \Vith streams that have some gravel and cobble substrates present. Values for concordant. discordant, and ties were 70.2, 28.4, and J .4 Topeka shiners than sites without Topeka shiners. One class of gravel substrate (very fine gravel) was signi ticantly different bel\veen presence and absence sites according to the model. as was thl'. percentage or cobble. Streams sampkJ during summer 2000 exhibited similar stn:am substrate characteristics to those sampled in 1999 where Topeka shiners were present (Table 3-7). Table 3-8 shows that Topeka shiners \Vere absent from Table 3-6. Substrate composition ('Yo) at Topeka shiner presence sites for James, Vermillion, and Big Sioux River tributaries, 1999. (CL= clay. SI= silL SA= sand, VFG= very fine gravel. FG= fine gravel. MG= medium gravel, CG= course gravel, yc_Q= very~9-urscgravd. CO=_<.:_o_b~le ]_,_~_=_largecob~le.BQ~ boulder. L~:lar~e boulder) 2 ------·····-··-- Substrate Classification ·------h------Stream CL SI SA VFG FG MG CG VCG co LC BO LB 1 Six Mile Creek 1 (BSR ) 0 1 21 35 22 18 1 2 0 0 0 0 Six Mile Creek2 (BSR) 0 22 37 8 7 7 6 5 8 0 0 0 ...... West Pipestone Creek (BSR) 0 .) 60 6 .) 10 6 8 4 0 0 0 Pipestone Creek (BSR) 2 I 59 16 1"'-' 9 0 0 0 0 0 0 ..,') ... Split Rock Creek (BSR) 0 8 .) .... 14 .) 4 1 I 7 () 30 0 .., .., Medary Creek1** (BSR) 0 7 14 29 30 14 .) _1 0 0 0 0 Medary Creek2** (BSR) 1 38 61 () () () () () () () () 0 2 .., West Fork Vermillion River 1(VMR ) I 6 5 30 26 7 2 0 0 0 .) 0 ... West Fork Vermillion River2 (VMR) 0 2 25 10 19 16 13 2 .) 7 2 West Fork Vermillion River3 (VMR) I 36 16 4 19 10 I 1 4 0 8 0 ")'"'_.) .)"'") _ West Fork Vermillin River4 (VMR) 0 13 2 8 10 2 2 4 4 0 ')..,__, .., Turkey Ridge Crcek 1(VMR) 8 63 2 0 0 0 0 .) I 0 0 Blind Creek (VMR) 56 21 13 () () () 1 1 5 2 1 0 3 ., Middle Pearl Creek (.IMR ) 0 34 36 .1 24 1 1 () 1 0 0 0 .., .., Shue Creek (JMR) 0 4 46 20 12 6 5 .) .) 1 0 0 Pearl Creek 1 (.IMR) 0 5 _)r 12 9 18 10 2 6 0 1 I 2 , ,,, ___,_,4·--->'<- _,_...,_,_,,_._.._,.._.,,...... _...... __ .. ______,_,_"''-"'°' - ______. - ·----. - ---- __..,. - ______°'+- Table 3-6 continued. - ·------Pearl Creck2 (JMR) 4 4 5 24 24 29 7 2 1 0 0 () Enemy Creek (JMR) 70 15 0 2 6 7 0 0 0 0 0 0 Twelve Mile Creek (Hv1R) 44 9 21 9 12 5 () 0 0 0 0 0 , ,., Firesteel Creek (JMR) () 5 42 .) JO 20 .) 0 17 0 () 0 ------· ------·---.------. ------** Sites sampled by Craig 1Vfilev,·ski. Ph. D. candidate, South Dakota State University, Brookings, South Dakota. 1 Big Sioux River basin. 2 Vermillion River basin. 3 James River basin. 0--, Vl Table 3-7. Substrate composition(%) at Topeka shiner prest.:nce sites for James. Vermillion. and Big Sioux River tributaries. 2000. (CL= clay. SI= silt. SA= sand, VFG= very fine gravel. FG= fine gravel. MG= medium gravel. CG= course gravel, VCG~~ ~cr~-~l~~-~-rscgravel. CQ= cobl:i~..:...~C=_largcc~)bl2!~:BO= boulde!. LB= large hould'?_!:_)_ _ _- ·- - ··- ., Substrate Classifications - - .. Stream CL SI SA VFG FG MG CG VCG co LC BO LB . . . ------1 - . . -·- . . ------. - ----·- -·· - Six Mile Creek 1 (BSR) 0 28 15 2 5 14 13 12 10 0 () 2 Outlet of Silver Lake (VMR) 0 7 17 5 18 22 9 7 8 0 7 0 .., Camp Creek (VMR) 6 48 6 7 .) 21 2 0 6 0 0 .., 3 () () Rock Creek (.TMR) I 49 15 -' 0 0 16 12 4 0 .., North Branch Dry Run Creek (JMR) 30 37 11 0 13 6 0 0 -' () () 0 Six Mile Crcek2 (BSR)** () I I I 16 14 9 8 13 2 () North Deer Creek (f3SR)** 0 18 60 20 2 0 0 0 0 0 0 0 Medary Creek (BSR)** () _)"'_, 16 25 24 12 0 0 0 0 0 0 - ----.·-- -- ...... ··" - ·- ·-·-·-··---- ___,, ______,. ______.. _ ..______------Big Sioux River basin. 2 Vennillion River basin. 3 James River basin. ** Sites sampled by East Dakota Water Development District. Brookings, South Dakota. °'°" Tabk 3-8. Substrate composition(%) at Topeka shiner absence sites for James. Vermillion, and Big Sioux River tributaries. 1999. (CL= clay. SI= silt. SA= sand. VFG= very fine gravt.:L FG= fin1.: gravel. MG= medium graveL CG= course gravel, VCG= ycry cour:~~-~ravcLC'O=_ C(~J)Ic. LC= lar~e-~o~~le,~5)= boulder. LI:~= I~_!]_~ boulder) -··------Substrate Classification -- Stream CL SI SA VFG FG MG CG VCG co LC BO LB - - East Fork Vermillion Rivcr 1 (VMR) 0 9 29 () 10 25 14 4 5 0 4 0 Turkey Ridge Creek2 (VMR) 0 39 35 2 5 10 2 6 I 0 () () East Fork Vermillion River2 (VMR) 0 0 67 10 4 13 2 0 2 0 2 0 ., ., ., Lake Tetonkaha Inlet (BSl~.)2 51 ) 0 38 -' I I -' 0 0 0 0 Squaw Creek 1 (BSR) 0 15 14 4 8 10 6 25 8 10 0 0 ..,.., Squav1· Creek2 (BSR) 0 27 ..:u 7 6 10 6 0 10 0 I 0 South Fork North Deer Creek (BSR) 29 30 40 I 0 0 () 0 0 0 () 0 .., Willmv Creek (BSR) 0 62 21 4 6 1 .) 1 1 0 1 0 3 Wolf Creek (.JMR) 0 I 63 11 4 6 6 () 8 () 1 0 Redstone Creek (JMR) 0 12 ')..,__, 5 6 4 5 I 24 5 15 0 West Firesteel Creek (JMR) 4 25 45 6 9 6 2 I 2 () 0 0 ------·----··.-----~- ---~------·------Vermillion River basin. 2 Big Sioux River basin. 3 Ja1;1es River basin. °'-..J 68 streams \Vith a high percentage of finer substrates. Streams sampled during summer 2000 also showt:d similar trends where clay. silt. and sand substrates were dominant in streams where Topeka shiners were absent (Table 3-9). Wa1er Quality Model Stepwise logistic regression did not indicate any variables (air temperature, water temperature, wnductivity, dissolved oxygen, turbidity. secchi depth. discharge. and velocity) playing a significant role in predicting Topeka shiner presence. P-values for each variabk (air temperature. P=0.434: water temperature, P=0.893: conductivity, P=0.540: dissolved oxygen. P=0.723: turbidity. P=0.482; secchi depth. P=0.915; discharge, P=0.613: and average velocity, P=0.899) showed no detectable influences to determine associations between the water quality model and Topeka shiner presence. Turbidity \Vas measured in percent transmittance in 1999: ho\vever. in 2000 turbidity was measured in NTU. Mean percent transmittance for streams sampled during 1999 was 63.2% (SE± 6.3 ). Sites with Topeka shiners present had a mean percent transmittance of 57.6% (SE± 9.1 ), and a range from 3 to 96%. Streams sampled during 2000 had a mean NTU of 38.4 (SE± 5.28). Streams with Topeka shiners present ranged from 11.2 to 94.5 NTU. and had a mean of 44.1 (SE± 13.0). Dissolved oxygen averaged 7.27 mg/L (SE± 0.33) in 1999. and 5.91 mg/L (SE± 0.49) in 2000. JVkan dissolved oxygen for sites with Topeka shiners present in 1999 was 7.0 mg/L (SE± 0.38). and ranged from 4.1 to 9.9 mg/L. Mean dissolved oxygen for sites Table 3-9. Substrate composition(%) at Topeka shiner absence sites for .lames. Vermillion. and Big Sioux River tributaries. 2000. (CL= clay, SJ= silt. SA= sand. VF V~G~very course !:2.~vel.C<2:=:cobbk. LC= lar~e~~bble. BO= bo~1lder. LB= large boul~er)____ Substrate Classification ------Stream CL SI SA VFG FG MG CG VCG co LC BO LB ------I ..,., ------.------~ Spring Creek (BSR ) 1 0 .) .) 18 13 26 8 I 0 0 0 0 ., Hidewood Creek (BSR) 29 17 0 30 20 1 () 0 ·' 0 0 0 Gravel Creek (BSR) () 100 0 0 0 0 () () () 0 0 0 Indian River (BSR) 2 _?"_, 26 8 19 21 1 () 0 () 0 0 Brule Creek (BSR) 23 0 44 8 16 4 () 0 () 0 5 0 Skunk Creek (BSR) 11 28 15 11 18 13 3 0 1 0 () 0 West Branch Skunk Creek (BSR) I 66 16 0 10 7 () () () 0 0 0 ., Beaver Creek (BSR) I () 85 5 .) 5 () 0 () 0 1 0 ., Flandreau Creek (BSR) 4 5 21 7 11 28 17 4 0 .) 0 0 East Fork Vennillion River ., ., 23 () 67 0 4 .) .) 0 0 () 2 0 0 (VMR ) ., Turkey Ridge Creek (VMR) I 26 15 21 34 .) 0 () 0 0 0 0 Long Creek2 (VMR) 2 35 58 5 0 0 0 0 0 0 0 0 Clay Creek Ditch (VMR) u 38 62 0 0 () 0 () 0 0 0 0 Ash Creek (VMR) 0 73 19 I 5 2 0 0 0 0 0 0 ., Little Vermillion River (VMR) 3 40 4 .) 12 28 7 1 2 () () 0 - ""------·-c ,. ··-----'·'· ...... ,.,_ ,<·.·c-''--·--·-·.··.·.· ------'°°" Tahlc 3-9. continued. - ~-.--.··--·-.------... - - -··------··------.,,., ------·----- () Redstone tributary (.IMR-') -' .... 62 0 0 0 0 0 0 0 4 0 Sand Creek (JMR) 0 0 100 0 0 () () 0 0 () 0 0 Redstone Creek (.JMR) () 100 0 0 () () () 0 0 () () 0 r"i.1!occasinCreek (.JMR) 35 65 0 0 0 0 () () 0 0 () 0 Snake Creek (JMR) () 100 0 0 () () 0 0 0 0 0 0 ,., Elm River (JMR) 2 () 38 0 16 9 7 4 21 1 () -·-·-----·------1 Big Sioux Ri~~~b-;sin. 2 Vermillion River basin. J .fal!les River basin. -....J 0 71 with Topeka shiners present in 2000 was 6.4 mgll (SE± 0.89), and ranged from 3.9 to 10.8 mg/L. Appendix 8 and Appendix 9 summarize all water quality measurements. All 1,vater quality variables had odds ratios equal to or near 1.0. 1,vith the exception of discharge and velocity. Discharge had an odds ratio of 0.349. and velocity had an odds ratio of 0.696. indicating some other interaction may be taking place between these two variables. PROC PLOT \Vas used in SAS to further determine whether these two variables were influencing Topeka shiner presence. Data output of presence versus discharge indicated that at lower disl:harge levels 3 (< 1.0 m /s) there was an equally likely chance Topeka shiners would be present, while at higher discharge kvels (> 2.0 nr'ls) the likelihood of Topeka shiner presence decreased. PROC PLOT of · presence versus velocity indicated that at velocities less than 0.20 m/s. there was an equally likely chance that Topeka shiners would be present at a site. HO\vev1.:r. the like I ihood or Topeka shiner presence in streams decreased as velocities surpassed 0.20 mis. ~vlean velocity for all sites sampled in 1999 was 0.11 m/s (SE± 0.01 ). and mean velocity for all sites sampled in 2000 was 0.08 mis (SF± 0.01 ). Sites where Topeka shiners were present in 19 1)9 had a mean vel0<.:ity of 0.10 mis (SE± 0.01 ). and ranged from 0.05 mis to 0.34 mis. All sites where Topeka shiners were present had flowing water in 1999. J-lo,vever. several sites \Vhere Topeka shiners wcrl: sampled in 2000 had intermittent tlO\\' and fish were found in isolated pools most likely supplied by groundvv·ater recharge. Mean velocity at sample sites where flowing \Nater was present was 0.04 mis (SE± 0.02). 72 Mean discharge in 1999 was 0.43 m·'/s (SE± 0.18). and mean discharge in 2000 was 0.14 nY1/s (SE± 0.03 ). During 1999. mean discharge for streams \Vi th Topeka shiners present \Vas 0.21 nY'/s (SE± 0.04). and ranged from 0.009 m3/s to 0.64 m3/s. 3 During 2000. mean discharge for streams with Topeka shiners present was 0.05 111 /s (SE ± 0.04). and ranged from 0.0009 m3/s to 0.18 111 3/s. Tables 3-10 and 3-11 show velocity and discharge values recorded for each site sampled during 1999 and 2000. The majority 3 or sites where Topeka shiners YVere found had discharge< 1.0 111 /s. and velocity< 0.20 111/s. Discussion GIS habitat models for my study were created to predict Topeka shiner distribution. and statistical models were created to determine which habitat variables were influencing shiner presence. Physical habitat characteristics influence fish occunence. abundance. and production (Hubert et al. 1989: Leftwich ct al. 1997). and help explain water quality. tlow regime. and energy inputs (Kan· and Dudley 1981 ). Hydrologic data help to explain short-term factors influencing fish abundance and also to expbin habitat degradation. whereas morphological data (i.e .. physical habitat) measure long-term factors influencing channel shape and availability of in-stream habitat. The physical habitat model contained I 0 variables that indicated habitat associations for Topeka shiner presence. Bank height was low at most sites \vherc Topeka shiners \Vere found. Low bank height is generally an indicator that a stream is not highly incised or channclizccl. l\lost streams in the .lames and Big Sioux river basins 73 Table 3-10. Discharge (nr1/s) and mean velocity (m/s) ±SE for each site sampled during June through September 1999 in eastern South Dakota. Stream. ------Me~e~,-(";;,l0±·~5E -[)i~~h;~{;3/s). 1 Six ivlile Cn.:ek 1 (8SR) (+) 0.34 ± 0.034 0.428 Inlet Lake Telonkaha (BSR) 0.02 ± ().005 0.039 Squaw Creek 1 (BSR) (J.07±0.013 0.029 Squaw Creek2( BS R) * * Six Mile Creck1(BSR) (+) 0.05 ± 0.008 0.074 South Fork North Deer Creek (BSR) 0.05 ± 0.007 0.048 Willow Creek (BSR) 0.03 ± 0.004 0.063 \Vest Pipestone Creek (BSR) (+) 0.11±0.012 0.142 Pipestone Creek (BSR) (+) 0.09 ± 0.011 0.218 Split Rock Creek (BSR) (+) 0.08 ± 0.023 0.644 Medary Creek 1 (BSR)** (+) 0.17±0.016 0.148 :vtedary CreC'k2 ( BSR)** 0.16 ± 0.013 0.066 2 West Fork Vermillion River1 (VMR) (+) 0.09 ± 0.016 * West Fork Vermillion River 2 (V\ilR) (+) (J.09±0.019 0.080 West Fork Vermillion River; (VIVIR) (+) 0.05 ± 0.006 0.241 - ') - East Fork Vermillion RivC'r1 (Vi\IR) 0.35 ± 0.049 )._) \Vest l·ork Vermillion Riwr.i (Vl\IR) (+) 0.10 ± 0.023 0.494 Turke')' Ridge Creek 1 (Vl'vlR) (+) 0.02 ± 0.002 0.089 Turkey Ridge Creek2 {Vl\IR) 0.06 ± 0.006 0.116 East Fork Vermillion Rivcrb (Vl\1R) 0.30 ± 0.037 1.45 Blind Creek (VMR) (+) 0.01 ± (J.001 0.009 1 ~vliddle Pearl Creek (Ji\l[{.)" (+) 0.09 ± 0.015 0.025 Shue Creek (JMR) (+) 0.07 ± 0.013 0.201 Pearl Creek 1 (Jl'v!R) (+) 0.10±0.017 0.033 Pearl Creek, (.li'vlR) (+) 0.11 ± 0.020 0.036 Enemy Creek (J !'vi R) ( +) 0.14±0.021 0.594 T\\elve l'vlik Creek (.IMR) (+) 0.19±0.021 0.192 74 Table 3-10. continued. Wolf Creek (JtvlR) 0.28 ± 0.029 1.37 Firesteel Creek (.li'v1R) (+) 0.04 ± 0.007 0.088 Redstone Creek (.IMR) 0.02 ± 0.003 0.334 West Fi rcstee I Creek ( Jiv!R) 0.06 ± 0.011 0.247 - ,--···------· * Values not measured because equipment was not functioning properly, no flow conditions. or water depth too shallow. **Sites sampled by Craig Mile\vski. Ph.D. candidate. South Dakota State University. Brookings, South Dakota. 1 Big Sioux River basin. 2 Vermillion River basin. -'.lames River basin. (+)Denotes sites when.: Topeka shiners were present. 75 Table 3-11. f\-1ean velocity (m/s) and discharge (nY'/s) fix each site sampled during .lune through August 2000 in eastern South Dakota. --'::--'::...... -···---·------·'----··---·-· ---~------Stream Mean Velocity± SE Discharge 1 Six Mile Creek 1 (BSR) (+) 0.132±0.021 0.179 Spring Creek (BSR) 0.235 ± 0.018 0.104 !Iide\vood Creek ( BSR) 0.092 ± 0.012 0.065 Gravd Crei.:k (BSR) * * Indian River (BSR) 0.019 ± 0.002 0.029 Brule Creek (BSR) 0.263 ± 0.021 0.625 Skunk Creek (BSR) 0.073 ± 0.015 0.089 West Branch Skunk Creek (BSR) 0.056 ± 0.015 0.023 Beaver Creek (BSR) 0.272 ± 0.015 0.290 Flandreau Creek ( BSR) 0.081±0.013 0.077 Medary Creek (BSR)** (+) * * North Deer Creek (BSR)** (+) * * * Six Mile Creek2 (BSR)** (+) * East Fork Vermillion River (VMR} 0.214 ± 0.007 0.340 Turkey Ridge Creek (VJ'vlR) 0.099 ± 0.008 0.031 Outlet Silver Lake (VIV1R) (+) * * Camp Creek (VMR) (+) * * Long Creek 1 (Vtv'IR) * * Long Creek2 (V~lR) * * Clay Creek (VMR) 0.(>31 ± 0.145 (J.()4() Ash Creek (VivlR) 0.022 ± 0.006 0.002 Little Vermillion River (VMR) * * Redstone Tributary (.liv1R}' * * Rock Creek (.TI'v!R) (+) 0.012 ± 0.001 * Sand Creek (JTVIR) * * -.·.·. ··-·------·---- -·------76 Table 3-1 L continued. ---- Moccasin Creek (.IMR) 0.039 ± 0.006 0.464 Snake Creek (.ll'v!R) 0.066 ± 0.012 0.191 Elm River (.l!VIR) 0.042 ± 0.008 0.118 North Branch Dry Run Creek (.IMR) (+) * * ' ------··--·--- ,___ ., ______,, ___ _ * Valw: not measured becaust: equipment was not functioning properly. no flow conditions. or water depth too shallow. ** Sites sampled by East Dakota Water Development District. Brookings. South Dakota. 1 Rig Sioux River basin. 2 Ve~·rnillion River basin. 3 James River basin. (+)Denotes sites where Topeka shiners were present. 77 did not shLnv signs of channelization or high bank heights. Johnson and l-1 iggi ns ( 1997) noted that only 3% of streams in eastern South Dakota have been excavated or modified. Ho\vever, streams in the lower reaches of the Vermillion River basin near Centerville. SD have been modified and Topeka shiners were absent at these sites. Channelized streams lack several physical habitat characteristics that provide in-stream diversity. Stream reaches that are channelized are uniform in water depth, have higher current velocity. have little or no in-stream cover (i.e., deep pools. large woody debris). and have steep eroding banks (Bulkley et al. 1976). Paragamian ( 1987) found that channelized streams in Iowa had substantially lower standing stock of iish than natural reaches. Stream bank depositional zones were minimal at sites where Topeka shiners were found. Streams with high stream bank deposition zones usually carry high loads of fine sediment. When sediment is deposited on substrate and stream banks. pools fill resulting in loss of in-stream habitat heterogeneity (pool-rit1le complexes). and riffles become covered in fine sediment. Rit1lcs are important components of stream systems because they typically have larger substrates that are more conducive for aquatic invertebrate production (Schlosser 1987: Foltz 1990). Riffles may serve as a major source of aquatic invertebrates. in addition to other substrate types that contain aquatic invertebrates, for Topeka shiners to incorporate into their diet. Hatch and Besaw· ( 1998) found that Topeka shiners are opportunistic omnivores, and that chironomids were an important food source as they made up a considerable portion of shiner diets. In lotic systems. substrate composition plays a major role in the life history of many fish. Fish species usually require several habitat types for survival throughout their 78 lite cycle. For example. age-0 and smaller fish may use interstitial spaces bctween rocks and course gravel substrate for re!'uge and protection from predators. The substrate model predicted that Topeka shim:rs were associated \Vith very fine gravel and cobble substrates. The lack of other substrate types (i.e. sand. medium gravel. coarse gravel) not found to be significant in the model may be attributed to variability in the data. The geology of eastern South Dakota is predominantly glacial till over shale. which explains the appearance of approximately 27% coarse substrates in streams. Substrate type is also known to play an important role in the reproductive life history of several fish species. Several other cyprinid species known to use gravel substrates for spawning include common shiners. red shiners. and creek chubs (Cross and Collins l 995). Topeka shiners use other sill-free substrates for spawning. but have been observed spawning over or near orangespotted sunfish and green sunfish nests constructed of gravel substrates (Kerns 1983: Barber 1986: PJlieger 1997: Tabor 1998). Sunfish species prepare spawning nests by clearing away silt to expose gravel or firm clay to form the base of the nest (Cross and Collins 1995). Loss of gravel substrates due to excessive sedimentation caused by intensive agricultural practices (Rabeni and Jacobsen 1999) may cause Topeka shiners to shilt from independently spawning over silt-fn.:c substrates. and rely exclusivdy on sunfish nests for spawning. This exclusive relationship could potentially become harmful to Topeka shiner populations if sunfish species abundance were to also dedine in response to degradation or Joss of in-stream habitat (pool-riffle complexes), or substantial changes in water quality conditions occur. 79 Animal use or vegetation also plays an important role in predicting Topeka shiners. Streams that have low animal use or vegetation usually do not have highly degraded stn:am banks. Streams that have moderate or high vegetation use arc usually inlensivdy grazed and have compacted stream banks. Detrimental effects from intensive cattle grazing cause reduced groundwater storage, which can lead to lower late-season base tlO\vs (Schramm and Hubert 1999). Loss of vegetation that contributes to stream bank stability may cause streams to erode more quickly by widening stream banks and decreasing \Valer depth. therefore resulting in decreased in-stream habitat heterogeneity (Platts I 981 : 1lauer and Lamberti 1998). Stream bank vegetation loss may also decrease the probability of sediment from row crop fields and overland runoff from being filtered out. thcrei"orc causing sediment loads and turbidity to increase (Platts et al. 1987). Decreased in-stream habitat heterogeneity will most likely result in loss of available spawning habitat for Topeka shiner populations, as previously mentioned. while increased turbidities may cause changes in feeding ecology and behavior patterns in Topeka shiners leading to possible increased declines in abundance. The stream bank vegetation type showing an association for Topeka shiner presence in m~ · study was grasses/forbs. Stream banks consisting of grasses/forbs acid to stream bank stability and control channel morphology because of their strong root systems (\Vesche and Isaak 1999). They also can serve as a better catchment for pesticides. !\:rt i Ii zers. and other overland runoff, preventing con tarn inan ls from entering the stream and leading to improved \Valer qua Iity . Grasses and forbs nvcrhangi ng the stream bank are important for associations of Topeka shiner presence, because they may 80 be an alternate source for shade along stream margins in the absence of trees. Shade produced from overhanging vegetation may provide areas of thermal refuge. and serve as a food source for aquatic invertebrates attached to vegetation extending into the water. Submerged macrophytes. another variable predicting Topeka shiner presence. may be found along channel margins or in areas of slower moving water. Areas containing submerged macrophytes may provick refuge from predators. in addition lo providing an extra food source of aquatic invertebrates attached to this vegetation. The variable age dass of trees indicated that Topeka shiners wi.:re likely to be present in streams where no trees were found directly along the stream bank. Prairie headwater streams experience great seasonal variations in tlow. with abiotic factors determining presence or species (Poff and \Varel 1989). The amount of grounchvatcr available to trees and other riparian vegetation species along stream banks could be the result of the degree of annual flooding (e.g., variability). and may play a role in abundance and type of riparian vegetation present along the stream bank. Additionally. tree seedlings may be more susceptible to grazing, therefore they may not be as abundant along the stream bank. In-stream habitat types most likely to predict Topeka shiner presence were runs, but I found some of the highest shiner densities in pools. This finding contrasts with that of other authors who usually found Topeka shiners in pool habitat (Braaten 1993; Hatch 2001. Professor. University of l'vlinnesota. ivlinncapolis. personal communication). Most streams sampled in my study could be classified as having a pool/run habitat type clue to slo\v velocitii.:s. Hov·iever. these streams were classified as runs because of rclativdy 81 uniform depths across the transect. in contrast to pool habitats that \Vere characterized as having deep holes and negative velocities. Braaten ( 1993) stated that Topeka shiners collected in tributaries tn the Vermillion River were found in five of seven pool habitats sampled. Results from a study on Topeka shim.:r populations in southwestern Minnesota streams (Hatch 2001. Professor, University of tvlinnesota. Minneapolis. personal communication) suggest that Topeka shin~rs select off-channel oxbow and closed-basin ponds instead of main-channel pool and run habitats. During my study. high numbers (e.g .. > 85 individuals) of Topeka shiners were observed in pool habitats. However. most streams sampkd consist<.:d of predominantly run habitat where Topeka shiners were found. Although the model predicted runs had the most suitable habitat for Topeka shiners. it is wry likely that pools also contain suitable habitat conditions. especially pools containing groumhvater flow (Pflieger 1997). The physical habitat model also included associations for Topeka shiner presence by year sampled. Topeka shiner were more likdy to present in 1999 than in 2000. pt:rhaps because more frL·quent precipitation events prevented streams from becoming interminent in 1999, \Vhcreas streams in 2000 experienced extended periods of intermittency. These conditions caused Topeka shiners, in addition lo other fish species. to become trapped in isolated pools. most likely being supplied by groundwater recharge. Capone and Cushlan (I 991) indicated that species abundance in intermittent pools is influenced by both predation risk and the severity of environmental conditions in drying pools. Competition for limited food resources in isolated pools. and predation by black 82 bullheads (personal observation) may have contributed to a lower likdihood of Topeka shiners being present in 2000. The final variable in my physical habitat model that shows an association for Topeka shiner presence is river basin. particularly the Big Sioux Rivn basin. Streams in this basin contained the highest number of Topeka shiners sampled and most streams had cobble and gravel substrate. likely due to previous glacial events. The GIS model predicting Topeka shiner presence showed that the Big Sioux River basin contained the highest amount of ground\vater available in eastern South Dakota (\Vall et al. 200 I). Groundwater appears to be a primary variable predicting Topeka shiner presence because it provides areas of thermal refuge for streams experiencing die! changes in water temperature, and also prevents streams from experiencing intermittent conditions during the summer. Sampling efforts were easier and more efficient in this basin, probably due to lack of isolated pools associated with groundwater potential and stream permanency. Several studies have shown that physical habitat conditions influence presence of a species in lotic environments. Leftwich ct al. ( 1997) used stepwise logistic regression to generate three models predicting tangerine darter Percina aurantiaca occurrence in stream habitat units at t\vo scales. regional and local. The presence ol' tangerine darters was influcnccd by regional rather than local variablcs. Other studies have shO\vn that regional and local effects ma~' function independently or interact in relation to fish populations (Dunham and Vinyard 1997), but most evidence shows that broad landscape variables affecting fish populations arc specific and can be measured at the reach scale. Irwin ct al. ( 1997) found that distribution of age-0 largemouth bass was positively related 83 to landscape l'eatures at a localiz1:d (reach) scale. Ross et al. (1990) reported that local scale features (i.e. microhabitat) in11uence the distribution of bayou darters Etheostoma rubrum. All of these studies indicate that physical habitat at a landscape scale (regional or local) is the main feature influencing or predicting fish species abundance. Physical habitat variables that \Vere positively associated with Topeka shiner presence in South Dakota are consistent with the literature. and most likely were influenced by land use practices within each watershed at a local scale. Relationships between population characteristics and habitat variables are probably not cause and effect. but instead serve as indicators of overall stream or ecosystem condition (Tillma and Guy 1998). Water quality parameters were not associated with Topeka shiner presence. This may be due to samples being taken at one time during the day versus monitoring dicl changes in physicochcmical variables. The variability between habitat conditions in 1999 and 2000 may have reduced the predictability of the water quality model. Although physicochemical parameters did not predict Topeka shiner presence. other studies suggest that \vater quality conditions can affect fish populations in warm water prairie streams. Yu ( 1992) found that the presence of several cyprinid species in the Platte River. Nebraska were significantly affected by temperature. Temperature was found to influence fish physiology. causing lish species to switch preferred habitats. Fish species may also develop survival strategies in response to physicochemica\ variability in prairie streams including evolving wide limits of tolerance under stressful conditions. or evolving selective responses to changes in water quality and frequently occupying 84 different habitat patches containing optimal water quality conditions (ivlatthews and Hill 1980: ivlatthi.?ws 1987). Dcspitc Topeka shiners being absent from several sample sites, this does not ne<.:essarily indi<.:ale that they are completely extirpated \Vithin the entire stream reach. Habitat rnnditions (physical and hydrological) were probably not suitable in that particular area of the stream sampled. but Topeka shiners may have migrated upstream or downstream in search of more suitable conditions. Environmental fo<.:tors causing changes in these systems. and the response of Topeka shiners to these changes may have affected their presence within a stream reach. Pool/riffle complexes change between years and in-stream habitat dynamics can change throughout the year \Vithin a single stream reach. thus affecting species distribution (Frissell et al. 1986). An cxamplc of this \Vould be Turkl:~' Ridge Creek. I sampled three sites on this creek: on1.· site near Turkey Ridge. SD in the upper reach. and t\VO sites in the 10\ver reach near Vihorg and Centervilk, SD. Topeka shiners were not found near the Turkey Ridgc and Centerville sites: hO\vcvcr. shiners were sampled near the Viborg site. Discharge and velocity have also been linked directly to abundann: of fish species. Bain d al. ( 1988) found that changes in stream tlov.: directly modi tied physical habitat and that streams \Vith highly variable 110\vs provide unstable aquatic habitats. This is especially true for prairie streams that undergo extreme fluctuations in flow during one season . ~ · 1ost streams where Topeka shiners were found had velocities at or near 0.1 m/s. but recent evidence indicates that Topeka shiners ma~' b1: abk lo tolerate velocities of 0.30 tn 0.50 m/s, but only for short periods of time (Adams d al. 2000). If 85 Topeka shiners can tolerate these higher velocities for short time periods. the possibility exists that they may be able to migrate upstream to areas of potentially suitable habitat or invade previously uninhabited streams containing suitable habitat conditions. Although Topeka shiners may he able to tolerate high velocities for short time periods. high velocities may also pose some potential problems for upstream migration. Projects such as stream channelization or wetland drainage can substantially alter channel shape. therefore creating increased velocities over extended periods of time. Culverts can also create barriers to upstream migration. Steep slopes may be a problem because stream velocities may be so great as 10 prevent upstream movement. Additionally, excessive drops from a culve11 outlet are a height barrier that most fish spccics. including Topeka shiners. may not be able to overcome while moving upstream during critical spmvning periods or in search of more suitable habitat conditions (Cunningham 2000). Conclusion The goal of my study was to assess habitat conditions where Topeka shiners were historically found . Streams throughout eastern South Dakota were l'ound to have relatively good habitat conditions that can and do support Topeka shiner populations. and several new sites \Vere recorded for this species. adding to the overall distribution in South Dakota. Additionally. habitat conditions at the reach scale helped to identit)r where conservation effo11s should be focused for streams in South Dakota. This portion of my study helped to provide valuable infrmnation to fulfill several objectives identified in the draft Topeka shiner recovery plan (U.S. Fish and Wildlife Service 2001 ): identify 86 potential habitat determine and quantify habitat characteristics (physical and chemical) across the species range. and identify water quality impacts to the species and define levels of tolerance. Habitat conservation and landscape stewardship by private landowners is the key to the survival of this species throughout its entire range. Because the majority or optimum Topeka shiner habitat is located on private land. every effort should be made to work cooperatively with willing landowners to preserve these stream ecosystems. Cost share programs or conservation easements could be utilized and implemented by state and federal agencies to ensure that habitat is preserved. while still providing an economic incentive to private landowners. ivty study primarily focused on habitat requirements and distribution: however. more research is needed on population trends. l'vly study only provided a limited assessment Ii.ff Topeka shiners. and the data collected for this study do not indicate if these populations are increasing. decreasing. or stable. A more in-depth study encompassing a time frame greater than two years is needed to determine and monitor the health and status of these populations. and to aid in the conservation and recovery of this species. 87 Literature Cited Adams. S.R .. .I. J. Hoover. and K ..J. Killgore. 2000. Swimming performance of the Topeka shiner (Notropis topcka) an endangered mid\vestern minnow. American ivlidland Naturalist 144: 178-186. Allan. J.D. 1995. 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Total number or individuals sampled by species for sites located within the James River basin sampled during !_~1~cthrou~J1 Septcn~l:~_r !999 in castcn~- Sout~1_!~akota.Subscripts indicate differ~nl~~~1:!1plc-~t~s o_n_!.~e same strcan~._ Streams 1 .MPL SllU PRL ENY TLV WFIR se~cies_~rn- - -- - 1 P~L_: - _\\'QI:. -- - f:"IR .. ---~~12 Bigmouth shiner 2 () 9 14 5 8 8 I I 0 0 Black bullhead 45 43 3 ?"...... ) I 63 0 84 38 53 Black crappie 0 0 0 0 0 0 0 5 () 0 Blacknose daci.: 0 () 0 0 0 0 () () () () Blackside darter () 0 () 0 0 0 0 0 0 0 131ucgill 0 0 () 0 () 0 0 0 () 0 Bluntnose minnow 0 0 0 JO () 0 () () () () Brassy minnow 190 2 7 4 0 36 () 0 5 0 Central stonerollcr 9 I 2 5 20 12 () 0 () () Channel catfish 0 () () 0 () () 0 8 0 20 ., Common carp () I () () 25 18 0 4 I J Common shiner 19 0 I 33 25 66 0 0 I 0 Creek chub 59 47 39 91 2 30 () 3 0 49 Emerald shiner 0 0 0 0 0 0 12 0 0 0 Fathead minnow 106 I 11 17 34 8 5 7 97 6 ')"__, Gizzard shad 0 0 0 0 0 0 30 0 I 0 Goldeye () 0 0 0 0 0 0 0 () 0 Green suntish 13 () JO 11 0 0 0 12 4 .Iohnny darter 3 0 () 0 () I 0 0 0 3 Largemouth bass 0 () 0 0 0 0 () 0 0 0 Longnosc dace 0 () 0 0 12 0 () 0 0 0 - -- ·- -·-·--·---- -0 °' ~Pl~~~1~ix_l; c<:~tinu_<:9. --· ------.....---- Northern pike 0 0 (} 0 0 (} 0 () 0 0 Orangespolled sunfish -"..,.) 18 35 32 3 3 0 135 12 49 Plains minnow 0 0 0 0 2 0 0 () 0 () Plains topminnow 0 0 () 0 () 7 0 0 0 () Red shiner 4 152 21 146 6 49 4 203 63 13 River carpsucker () 0 0 0 0 0 6 () () 7 Sand shiner 41 298 60 347 36 47 3 11 4 32 Shorthead redhorse 0 0 0 0 0 0 0 5 0 8 Stonecat 0 0 0 0 0 0 () I () 0 .., Tadpole madtom 0 I () .) 0 0 0 () () 0 Topeka shiner 85 5 17 15 39 3 0 3 0 0 \Valleye () 0 () 0 0 0 0 I 0 0 White crappie 0 0 0 0 0 0 0 4 0 0 ..,.., White sucker ...,._, 9 0 4 I 3 0 2 I 0 Yellow perch 0 0 0 0 0 0 0 () 0 0 , .....,, .. ______,, ______,.____ ,.. ___,_,_,__ ,_.___ .._.... ------1 Abbreviations defined in Table 3-1. -.....]'° Appendix 2. Total number of individuals sarnpkd by species for sites (Oi.:all:dwithin the .lames River basin sampled from June through August 2000 in eastern South Dakota. Stn:arns 1 ?pec_ies TRED RCK SAN RED MOC SNK ELM NDR ------Bigmouth shiner () () () 0 () () 0 0 Black bullhead 193 214 94 498 I 184 24 29 Black crappie 0 () () 0 0 () 169 0 Blacknose dace 0 () () 0 0 () 0 0 l3luntnose minnow () () 0 0 () () 0 0 "I l3rassy minnow .) 43 24 0 0 () 0 0 Central stonerol ler {) 0 0 0 0 0 () () Channel catfish () () () () () () 73 0 Common carp 18 0 2 1 3 () 53 () Common shiner () 13 () 0 0 () 0 0 Creek chub () 8 () 0 0 0 0 () Fathead minnow 245 12 0 ") 0 () 0 69 Green sunfish 6 I I 0 4 0 4 0 64 Iowa darter () () 0 0 0 0 0 0 Johnnv darter () I 0 0 0 0 5 0 Largemouth bass 0 0 0 0 0 0 75 0 Northern pike () 0 0 0 0 0 3 0 Orangespotted sun fish 22 184 6 30 () () I 19 Red shiner 0 47 162 () () I 0 () .. -- •+-- - -- ___,______------., --·------. ------··------00'° 0r.e_~r~di._~_3.:_con~~~d.-.·.··--··- __ --······-·... - -·· -··· - ·-·-·-·- - -···-- - River carpsucker () 0 0 () 0 0 6 0 Sand shiner () .)" 45 () () () 7 0 Shorthcad redhorsc () 0 0 0 () 0 ')"--' () Stonccat 0 0 0 0 0 0 0 () Tadpole madtom 0 0 0 0 0 0 0 () Topeka shiner 0 8 0 0 0 0 0 .)" White sucker () 8 () I 0 () 201 0 Yellow perch () 0 0 () 0 0 () () - --- ·------,- -,-~--· Abbreviations arc defined in Table 3-2. ·..o ·-.a Appendix 3. Total number of individuals sampled by species for sites located within the Vermillion River watershed sampled during .June through September 1999 in eastern South Dakota. Subscripts indicate different sample sites on the same stream. - - ·------Strcamsi--- - ·------~---- Speci~s \VFY~ WFV~ EFY TRK TRK ... \VFV1 1 \Y'YY1 1 2 i::F.:Y2.. BU-J l~igmouthshiner 0 I 0 I 4 0 () 45 64 Black bullhead 21 246 67 0 0 6 I 0 11 Black crappie 0 0 0 165 0 () 3 0 0 Blacknose dace 0 0 0 0 0 0 0 0 0 Blackside daner 0 0 () 0 0 0 0 0 0 Bluegill 0 I 0 452 0 0 0 0 5 Bluntnosc minnow 0 0 0 0 0 0 0 0 0 Brassy minnow () 0 0 66 0 3 36 6 53 Central stonerol ler () () 0 0 () 0 0 0 5 Channel catfish () 0 0 0 0 0 7 5 0 Common carp I 3 () I 0 3 2 0 Common shiner 3 64 184 45 22 0 3 8 47 Creek chub 7 73 16 0 3 0 0 2 182 Emerald shiner 0 0 () 0 0 I 0 0 () Fathead minnow 42 138 177 -.>'.)' 21 6 12 10 202 Gizzard shad 0 0 0 0 0 0 0 0 0 Goldeye () 0 0 I 0 0 0 0 0 Green sunfish () 7 I 0 0 2 0 2 28 Johnny darter 0 4 () () 2 4 ') 0 0 Largemouth bass 0 0 0 31 I 0 4 4 2 Longnosc dace () 0 0 0 0 0 0 0 0 ,_, .,._.,.,., ______... -~----- •..., ,.. ,_. ·---·"------·------______0 0 Appendix 3_ continue~!._ ...---· ··- -·---- ·--~------··-----·-·---·· -- () () Northern pike I 2 I 0 2 0 0 Ora11gespo11c White sucker 20 16 8 4 4 10 0 IO I~ Yellow perch 0 0 () 2 0 0 0 0 0 1 Abbreviations---· defined in Table 3-1. 0 Appendix 4. Total number of individuals sampled by species for sites located \vithi11 the Vermillion River basin sampled from June through August 2000 in eastern South Dakota. Subscripts indicate different sample sites on the same stream. ·------·------·------·------s; . -- - - . trearns-, ----- ~ecies ITV TRK o~L__ S~LP LNG1 -_-.:.LN(I, CLY ASH LY Bigmouth shiner 0 121 0 4 0 34 324 111 0 Black bullhead 120 0 234 26 0 0 92 178 Black crappie 0 () 0 () 0 0 0 () 0 Blacknose dace 0 0 0 0 0 0 0 0 Bluntnose minnow 0 0 0 0 () () 0 () () ..,_., Brassy minnow I 0 () 2 34 0 () JO _,_ 18 .., .., .., Central stoncroller () _, 0 () () JO _, 0 Channel catfish () 0 0 0 2 () 0 0 () Common carp 0 21 () 5 6 () 0 Common shiner 12 () 7 27 0 () 54 55 Creek chub 7 198 14 14 2 148 289 133 Fathead minnow 165 5 49 104 5 1148 12 7 9 Green sunfish () .., 65 0 10 2 4 66 Iowa darter 0 0 0 0 0 0 0 0 0 .., Johnnv darter 0 () 5 0 6 0 0 _, 6 Largemouth bass 0 0 0 0 0 () 0 0 0 Northern pike 0 0 0 0 0 () () 0 0 Orangespotted sunfish 0 () 4 60 0 () 0 60 _.,.., () Red shiner 17 0 "'--' 4 0 4 2 20 0 1-J ~_ppendix4-' conti~~1._1_i:_d_. ______-··------·-- - - - ·-··- R ivcr carpsucker 0 () () () 0 () () 0 () .., Sand shiner 254 40 40 7 -' 656 898 181 25 Shorthead redhorsc 0 () 0 0 0 0 0 0 0 Sto111.:cat 0 0 0 0 0 0 0 0 JO Tadpole madtom 0 0 0 0 0 () 0 0 () Topeka shiner 0 0 4 19 0 0 0 0 0 \Vhite sucker () 0 0 3 0 0 91 1 9 Ycllmv perch () 0 0 0 0 0 0 0 0 ------·- 1 ------·- - -· Abbr;~iaiions-;~~-d~ftned in TaN~3-2 ~ 0 \.;J Appcndix 5. Total number of individuals sampled by spccics for sites located within the Big Sioux River watershed sampled during June through September 1999 in eastcrn South Dakota. Subscripts indicate di ffcrcnt sample sites on the same stream. -·--· ------~s~~a~n~i- -~- -~------·---- Species SIX1 ILT ~Q:!Y1.S..QW2~ SIX~ SFD WIL WPIP r..!f SPLT MED ~ 1 MED2* -···-·· ..--- ..-·----- Bigmouth shiner 17 0 62 0 51 0 11 34 30 () 945 173 Black bullhead 0 92 24 5 180 0 0 104 '-8') 28 0 Rlack aappic 0 0 0 0 0 0 0 0 0 () 0 0 Blacknosc dac<.: 0 0 0 0 0 0 0 0 0 0 0 Blacksidc darter 0 0 0 0 0 0 0 0 () 0 0 Bluegill 0 () 0 () () 0 () () () 0 () () Bluntnose minnow 0 () () () () 0 28 18 28 67 39 100 Brassy minnow 0 0 () 0 2 0 0 0 0 0 0 Central stoncroller 0 0 12 15 -''"' 0 () () 0 0 () 39 Channel catfish 0 0 () () 0 0 0 () () 0 0 Common carp 0 0 0 0 0 0 4 0 0 Common sh in er 45 0 162 98 84 0 25 4 88 197 153 266 Creek chub 8 0 216 41 53 II 5 159 4 126 321 Emerald shiner 0 0 0 0 0 0 0 0 0 0 0 0 Fathead minnow 8 0 292 52 41 0 99 0 II 64 22 341 Gizzard shad 0 0 () 0 () 0 0 0 0 0 0 () Goldcyc 0 0 () () 0 0 0 0 0 0 0 () Green sunfish 0 0 4 () 0 0 3 0 0 () Johnny darter 0 0 10 2 0 0 0 2 18 36 Largemouth bass 0 0 () 0 0 () 0 0 () 0 0 Longnose dace 0 0 0 0 0 () () () () () () 0 0 +. Appendix 5, con_ti~rne~:______--· ··------··· -- ---·"-- ·-- . - -- No11hern pike 0 3 0 2 0 I 4 0 9 4 ----- I -----3 Orangespotted sunfish () 3 11 3 2 I 9 0 26 22 0 () Plains minnow 0 0 0 0 0 () 0 0 0 0 () 0 Plains topminnow 0 0 0 0 0 0 0 0 () 0 0 0 Red shiner 103 0 39 15 31 0 9 29 77 777 5 14 River carpsucker 0 0 0 () () () 0 () () 44 0 0 Sand shiner 169 0 163 38 25 0 46 59 273 305 217 181 Shorthead redhorse 2 0 () 0 I () I 0 0 I 3 6 Stonecat 0 0 0 0 () () () 0 3 () 9 0 Tadpole madtom I 0 0 0 0 0 0 0 I () 0 7 Topeka shiner 2 0 0 0 4 0 () 4 98 7 I 3 Walleye 0 0 0 0 0 0 0 0 0 0 () 0 White crappie () (l () () {) () () 0 0 0 0 () White sucker 5 I 25 9 72 0 13 7 77 24 108 142 Yellow perch 0 2 0 0 0 0 I 0 0 0 0 0 1 -~------Abb1:cviations-~l-~f~~1ed-TnTable 3~1.--- - - * Sites sampled by Craig Milewski. Ph.D. candidate, South Dakota State University. Brookings, South Dakota. 0v. Appendi;-.; 6. Total numhcr of individuals sampled by species for sites located within the Big Sioux River basin sampled during .lune through August 2000 in eastern South Dakota. Subscripts indicate different sample sites on the same stream. ------·------...___ __ . - ··-·------. -·-- -· ------Streams ------·-- ··-·-·-- - - .. - - - Species 5-1~!5-P _R I-g:>\\ _g~_yIND BRU SKU WSK _!3_yR FLD ND<::; SIX ' _ 2 _rvl~~ Bigmouth shiner 76 27 89 88 468 35 12 0 45 32 4"?-'- 7 387 {) ') Black bullhead 19 0 24 0 15 0 115 I 0 7 8 .:.. Black crappie 0 0 0 0 0 0 5 0 0 () () () () Blacknose dace 11 13 I 0 14 0 0 0 () 60 0 0 0 ..., Bluntnose minnow 0 0 0 0 0 0 0 0 0 -' 0 () 40 Brassy minnow 0 1 1 0 0 () 0 0 () 14 0 I I 4 ..., Central stoncroller 60 5 8 -' 7 0 () 0 0 2 6 29 9 Channel catfish 0 0 0 0 0 0 2 () 0 0 () 0 0 ') ..., Common carp 0 0 0 0 () () 22 14 0 I () -' ..., Common shiner 167 9 9 600 110 0 I -' 0 772 169 179 70 ')..., Creek chub 42 14 27 50 29 0 ..__, 93 0 81 222 11 336 Fathead minnow 62 4 180 37 70 22 353 13 17 7 63 359 5 ..., Green sunfish 1 0 2 0 0 0 I -' 0 0 2 9 17 Iowa darter 0 0 0 2 1 0 0 0 () () () () 0 ..., ., () () .Johnny dar1cr 5 0 -' -' I 0 2 I 30 7 59 Largemouth bass 0 0 0 0 () 0 () () () () 0 () () () ..., Northern pike 0 0 0 0 0 0 0 0 0 0 0 -' -~~- ·--·- .. · - - · - · .. - - " ~------··--- - - ·- · ------· -- - - 0 C\ (\pp~}~dix6. co}1ti~~~-ed. Orangespotted sunfish 21 0 0 0 6 0 50 0 0 0 0 61 8 ..,.., Red shiner I I 0 0 0 0 30 986 4 _,_, 63 37 43 93 River carpsucker () 0 0 0 0 0 0 0 0 0 () 0 0 Sand shiner 30 I 48 2 213 48 1548 70 41 41 113 7 849 Shorthead rcdhorse 0 0 0 () 0 () 0 0 () 1 0 0 I 5 Stonecat 0 () () 0 0 () 0 () 0 5 0 0 Tadpole madtom 4 0 1 0 I 0 0 0 0 0 () 1 2 Topeka shiner _))..,- () () () 0 0 () () 0 () 1 311 2 Wh i tc sucker 45 10 26 26 4 19 24 1 () 1 58 99 178 Yellov.. • perch 0 0 8 () 0 0 2 0 0 0 7 0 5 ------·--·---·--·-·-·------··--.-. ,..___ ,___ ,._,._ ...____ -· 1 ·------'"-·----- Abbreviations arc defin~di1~-T;blc 3~2. * Sites sampled by East Dakota Water Development District. Brookings. South Dakota. 0 -.J 108 Appendix 7. Photographs taken at various sites where Topeka shiners were captured throughout eastern South Dakota from 1999-2000. Camp Creek- Vermillion River Basin, Turner County (near Chancellor, South Dakota) Rock Creek- James River Basin, Miner County (near Howard, South Dakota) 109 Appendix 7, continued. Six Mile Creek- Big Sioux River Basin, Brookings County (near White, South Dakota) Pearl Creek- James River Basin, BeadJe County (near Cavour, South Dakota) Appendix 8. Water temperature (°C), air tcmperatun..: (°C), turbidity (percent transmittance), secchi depth (cm). dissolved oxygen (mg/I). :ind condw.:tivity (~tS/cm)for 31 streams sampled l'rom .lune through September 1999 in eastern South Dakota. Subscripts indicate di ffi:rcnt sample sites on the same st~e~m. Water Air Secchi Dissolved Stream Turbiditv Conductivitv tempt:_r: Squaw Creek 1 (BSR) 30.0 34.0 88 12.0 Squaw Creek2 (BSR) 23.1 32.0 80 6.1 1448 South Fork No1th Deer Creek (BSR) 20.6 35.0 30 25.0 4.2 818 Six Mile Creek2 (BSR) 22.6 27.0 29 21.0 6.8 831 Willow Creek (BSR) 21.5 33.0 30 21.0 8.9 754 West Pipestone Creek (BSR) 24. I 30.0 96 9.1 864 Pipestone Creek (BSR) 17.5 32.0 48 7.1 961 Split Rock Creek (BSR) 23.0 25.0 5 21.5 8.6 565 Medary Creek 1 (BSR)** 19.0 21.0 86 8.2 650 l\fodary Creek 2 (BSR)** 19.0 21.0 81 30.0 9.9 610 2 West Fork Vermillion River 1 (VMR) 17.0 28.0 87 32.0 9.2 1597 \Vest Fork Vermillion River2 (VMR) 26.0 23.5 21.0 9.9 1800 West Fork Vermillion River, (VMR) 20.0 28.0 55 35.0 6.0 1600 East Fork Vermillion River 1 (Vl'vlR) 22.0 30.0 98 45.0 7.1 1400 West Fork Vermillion River4 (VMR) 25.0 33.0 95 28.5 4.1 l412 Turkey Ridge Creek 1 (VMR) 20.0 23.0 40 22.0 6.4 1944 Turkey Ridge Creek (VMR) 22.0 31.0 63 30.0 8.0 1870 2 ~ -·---.,.,__ ,___ ,_.____ ---- - ___,_,_.,.,."."""'·-- , ._._.____ "'''"'~ 0 0._ppendix 8,_con_t i 11~1ed__. --·-·*"" ______ East Fork Vermillion River2 (VMR) 22.0 29.0 90 8.1 1406 Blind Creek (VMR) 17.0 27.0 77 7.4 1900 Middle Pearl Cre<.:k(JMR); 17.0 24.0 89 5.9 1752 Shue Creek (.IM R) 21.0 24.0 9.1 Pearl Creek, (.IMR) 22.2 26.0 8.0 1880 Pearl Creek2 (.IMR) 25.0 24.1 20.0 6.5 Enemy Creek (JMR) 27.0 34.0 30.0 5.2 Twelve Mile Creek (JMR) 24.0 30.0 3 19.0 4.2 1832 Wolf Creek (.IMR) 25.0 J 1 0 84 32.0 7.2 1648 Firesteel Creek (JMR) 25.0 31.0 19.0 7.0 1080 ,., West Firesteel Creek (JMR) 23.0 27.0 86 25.5 8·-' 1425 Redstone Creek (JMR) 23.0 26.0 92 36.0 6.0 2200 .,.__ , ___ -· ------"'~------···-·------·------···--·- -- * Values not measured because equipment was not functioning properly, no now conditions. or shallow \vater depth. ** Sites sampled by Craig J'vlilewski. Ph.D. candidate. South Dakota State University, Brookings, South Dakota. 1 Big Sioux River basin. 2 Vc~millionRiver basin. 3 James R ivcr basin. Appendix 9. Water temperature (°C). air temperature (°C). turbidity (NTU), secchi depth (cm). dissolved oxygen (mg/I). and conductivity (pS/cm) for 28 streams sampled from June through August 2000 in eastern South Dakota. Subscripts indicate dilTcr~nt_:;amp_~e:_si~'=~?.!..1_t!1esame stream...... --·····--············-·--· _ --···--- ____ _ Vv'ater Air Secchi Dissolved Conductivit Stream Turbiditv te111pcrature temperature ili1lth_ Oxvgen y 17.0 23.0 11.3 30.0 10.8 860 Spring Creek (BSR) 17.0 25.0 0.30 33.0 12.0 660 I lide\vood Creek (BSR) 20.0 26.0 18.9 14.0 4.0 740 Gravel Creek (BSR) * Indian River (BSR) 15.5 23.0 8.5 823 Brule Creek (BSR) 20.0 28.0 27.2 17.0 7.7 1197 Skunk Creek (BSR) 24.0 29.0 77.4 16.2 1280 West Branch Skunk Creek (BSR) 18.8 31.0 14.2 12.0 1140 Beaver Creek (BSR) 21.7 25.0 41.3 6.1 880 Flandreau Creek (BSR) 22.5 28.0 14.3 30.0 5.1 984 North Deer Creek (BSR)** 30.7 36.0 22.0 8.6 448 .,., Six Mile Creek2 (BSR)** 22.7 25.0 11.2 50.0 3.9 8.).) Medary Creek (BSR)** 26.8 30.0 44.0 7.2 774 East Fork Vermillion River (VMRi 18.0 16.0 66.5 16.0 5.9 1490 Turkey Ridge Creek (ViV1R) 25.4 34.0 52.3 15.0 5.1 1525 Outlet of Silver Lake (VMR) 24.0 30.0 87.8 16.0 4.1 1530 Camp Creek (VMR) 18.3 25.0 94.5 17.5 4.1 750 tv Appendix 9_co!1li!1ll~~-__ 1 Long Creek (VMR) 25.8 30.0 17.2 I 5.0 7.6 1240 Clay Creek Ditch (VMR) 25.0 29.0 15.3 16.0 4.0 1750 Ash Creek (VMR) 27.0 28 .0 554 16.0 7.5 1599 ')")., Littl e Vermillion River (VMR) -- --' 30.0 41 .3 17.0 3.0 1068 Redstone Tributary (JM Rt; 18.0 26.0 35 .6 20.0 6.5 1990 Rock Creek (JMR) 22.3 27.5 38.1 23.0 5.3 1998 Sand Creek (.IMR) Moccasin Creek (.IMR) 24.8 32.0 20.1 27.0 2.2 1990 Snake Creek (JMR) 23 .7 27.0 16.8 21.0 3.9 1718 Elm River (JMR) 20.4 24.0 13.9 36.5 1546 North Branch Dry Run Creek (.IMR) 22.5 30.0 - 11.0 7.8 1316 ...... -·- - ·- ....__ _,,___ -- - ..- · ····--···-··--- -···· - - ·····-- ··-- ·------·····-·--·- ·-- ·····- ---- * Values not measured because equipment \Vas not functio11i11gproperly. no flow conditions, or shallow \Valer depth. ** Sites were sampled by East Dakota \Vater Development District, Brookings. South Dakota. 1 l3ig Sioux River basin. 2 Ve~·millionRiver basin. 3 .James River basin. (.,.>