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Proquest Dissertations MAPPING THE HYPOTELMINORHEIC HABITAT BY STUDYING THE POPULATION STRUCTURE OF AMPHIPODS IN SEEPS By Karen Kavanaugh Submitted to the Faculty of the College of Arts and Sciences of American University in Partial Fulfillment of the Requirements for the Degree of Master of Science In Dean of the College of Arts and Sciences CUe~~~ ~ u;oq Date 2009 American University Washington, D.C. 20016 AMERICAN UNIVERSITY LIBRARY UMI Number: 1472764 All rights reserved INFORMATION TO ALL USERS The quality of this reproduction is dependent upon the quality of the copy submitted. In the unlikely event that the author did not send a complete manuscript and there are missing pages, these will be noted. Also, if material had to be removed, a note will indicate the deletion. UMI ......-=*Dissertation Publishing~ UMI 1472764 Copyright 2010 by ProQuest LLC. All rights reserved. This edition of the work is protected against unauthorized copying under Title 17, United States Code. Pro uesf --- ---· ProQuest LLC 789 East Eisenhower Parkway P.O. Box 1346 Ann Arbor, Ml48106-1346 MAPPING THE HYPOTELMINORHEIC HABITAT BY STUDYING THE POPULATION STRUCTURE OF AMPHIPODS IN SEEPS BY Karen Kavanaugh ABSTRACT The hypotelminorheic is a type of perched aquifer with an unknown geographic extent. Depending on the local topography, groundwater from one hypotelminorheic may flow to the surface forming a single seep, or to several surface locations forming multiple seeps. In order to infer the boundaries of the hypotelminorheic, I analyzed the population structure of a subterranean seep amphipod species. I analyzed a 628 bp region of mtDNA corresponding to the cytochrome oxidase c subunit I gene from 118 specimens of S. tenuis potomacus, collected from 9 seeps along the George Washington Memorial Parkway. Pairwise comparisons among sites (uncorrected "p" = 0.7- 12.7%) and the nested clade phytogeographic analysis suggested that hypotelminorheic habitats are fragmented. However, population subdivision (within site uncorrected "p" = 0- 13.06%) found at many ofthe sites suggests that hypotelminorheic habitats have a dynamic extent that fluctuates with the water table, forming temporary corridors between hypotelminorheics. 11 ACKNOWLEDGEMENTS Funding for this project was provided by American University and the U.S. National Park Service. Many thanks to my advisor, Dr. Dan Fong, and my committee, Dr. Dave Carlini and Dr. Dave Culver, for their patience, guidance, and support. Thanks to Ben Hutchins who mentored me both in the field and in the genetics laboratory. Special thanks to Katie 0' Neill and Bryan Adams for providing me with their friendship and much needed help collecting samples in the field. 111 TABLE OF CONTENTS ABSTRACT ........................................................................................ .ii ACKNOWLEDGEMENTS ....................................................................... iii LIST OF TABLES ................................................................................. vi LIST OF ILLUSTRATIONS ................................ ." .................................... vii Chapter 1. INTRODUCTION ...................................................................... 1 The Hypotelminorheic Habitat.. ................................................. 1 Amphipods ........................................................................ 4 COl: A Useful Molecular Marker for Studying Population Structure .................................................................. 6 Studying Gene Flow ............................................................. 8 Population Structure: The Island Model, Isolation by Distance, and Habitat Fragmentation ............................................. 9 Hypothesis and Predictions ................................................... 14 2. METHODS ............................................................................. l6 Sample Collection .............................................- .................. 16 DNA Extraction .................................................................20 PCR ............................................................................... 20 Gel Purification of the COl Gene .............................................21 lV Gene Sequencing ............................................................... 22 Analyses .......................................................................... 23 Sequence Characterization ............................................ 23 Phylogenetic Analysis ................................................. 24 Population Structure ................................................... 25 Nested Clade Phytogeographic Analysis ........................... 25 3. RESULTS ............................................................................. 28 Collection and Sequencing ................................................... .28 Sequence Characterization .................................................... .29 Phylogenetic Analysis ......................................................... 32 Population Structure ........................................................... .44 Nested Clade Phytogeographic Analysis .................................... .47 4. DISCUSSION ........................................................................ 47 Lack of an Overall Isolation by Distance Pattern Among the Ingroup Seeps Suggests that the Hypotelminorheic is Discontinuous .......................................................... .4 7 Evidence that Hypotelminorheic Habitats are Fragmented ............... .48 The Extent of the Hypotelminorheic is Dynamic ........................... 51 Implications for the Conservation of Rare Species of Stygobromus in Seeps .................................................. 59 Conclusions ....................................................................... 60 APPENDIX ......................................................................................... 63 REFERENCES ..................................................................................... 64 v LIST OF TABLES 1. Number of Specimens Collected and Sequenced from Each Site ..................... 30 2. Number of Sequences from Each Site Where Stop Codons Were Present in All 6 Reading Frames ......... : .............................................................. 31 3. Number of Sequences from Each Site that Were Used in the Analyses .............. 31 4. Results of the Tajima's D Test for Selective Neutrality ................................ 32 5. Distribution ofHaplotypes .................................................................. 34 6. Average Uncorrected PercentPairwise Distances Within Each S. tenuis potomacus Site, Within Each Cluster, and Among Clusters ....................... 35 7. Average Uncorrected Percent Pairwise Distances Within Outgroup Sites and Between Outgroup and Ingroup Sites ................................._ ............... 37 8. Average Uncorrected Percent Pairwise Distances Between Each Site ............... 38 9. Results of an AMOVA Constructed for S. tenuis potomacus ......................... .40 A 1. Significant Results of the Nested Clade Phytogeographic Analysis ................ 63 Vl LIST OF ILLUSTRATIONS 1. Map of Collection Sites for Stygobromus tenuis potomacus, S. pizzinii, and Crangonyx shoemakeri .................................................................. 17 2. Map of S. pizzinii Collection Sites in C&O Geographic Cluster ...................... 18 3. Map of S. tenuis potomacus Collection Sites in Northern GWMP Cluster. ........ .18 4. Map of S. tenuis potomacus Collection Sites in Central GWMP Cluster. ........... 19 5. Map of S. tenuis potomacus Collection Sites in Southern GWMP C1uster. ......... 19 6. Map of the Geographic Distribution of Haplotypes Shared Among Multiple S. tenuis potomacus Sites ................................................................. 33 7. Phylogram of S. tenuis potomacus Estimated Using the Maximum Likelihood Criterion with C. shoemakeri as the Root of the Tree ............................. .41 8. Phylogram of S. tenuis potomacus Estimated Using the Maximum Likelihood Criterion with S. pizzinii as the Root of the Tree ................................... .42 9. Graph ofFst Values, an Estimate of Genetic Diversity, vs. the Geographic Distance Between Sites ............................................................................. 44 10. Unrooted Haplotype Network Estimated for S. tenuis potomacus Using the Maximum Parsimony Criterion ....................................................... .46 Vll CHAPTER 1 INTRODUCTION The Hypotelminorheic Habitat In 1962, the Croatian biologist, Milan Mestrov, defined a new freshwater habitat that he called the hypotelminorheic (1962). The hypotelminorheic is a shallow, subterranean aquifer that is perched above a water impermeable clay layer, usually within close proximity to the surface. Where the water table of the hypotelminorheic intersects the ground surface in an area with a slight depression or gradual slope, groundwater from the hypotelminorheic exits to the surface, forming a seep (Culver, Pipan, and Gottstein 2006). Depending on the local topography, the groundwater from one hypotelminorheic habitat may exit to the surface at a single seep, or to several surface locations at multiple seeps. In this scenario, a seep is a point of exit of the hypotelminorheic groundwater to the surface. The surface habitat associated with a seep may be a localized wet spot or a shallow pool if the seep is situated in a depression, or a small rill if the seep
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