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Phylogenetic and Ecological Analysis of Two University of Texas at Tyler Scholar Works at UT Tyler Biology Theses Biology Spring 4-7-2017 Phylogenetic and ecological analysis of two populations of the Kitsatchie Painted Crayfish, Orconectes maletae (Decapoda: Cambaridae) Larrimy Beth Brown University of Texas at Tyler Follow this and additional works at: https://scholarworks.uttyler.edu/biology_grad Part of the Evolution Commons, and the Population Biology Commons Recommended Citation Brown, Larrimy Beth, "Phylogenetic and ecological analysis of two populations of the Kitsatchie Painted Crayfish, Orconectes maletae (Decapoda: Cambaridae)" (2017). Biology Theses. Paper 44. http://hdl.handle.net/10950/576 This Thesis is brought to you for free and open access by the Biology at Scholar Works at UT Tyler. It has been accepted for inclusion in Biology Theses by an authorized administrator of Scholar Works at UT Tyler. For more information, please contact [email protected]. Phylogenetic and ecological analysis of two populations of the Kitsatchie Painted Crayfish, Orconectes maletae (Decapoda: Cambaridae) by Larrimy B. Brown A thesis submitted in partial fulfillment of the requirements for the degree of Master of Science Department of Biology John S. Placyk Jr., Ph.D., Committee Chair College of Arts and Sciences University of Texas at Tyler April 2017 The University of Texas at Tyler Tyler, Texas This is the certify that the Master’s Thesis of Larrimy B. Brown has been approved for the thesis requirement on April 7, 2017 for the Master of Science degree Acknowledgments I would like to start by thanking my wonderful and loving husband for supporting me in every way through my journey into biology, as well as, my father and Aunt Robin for taking my phone calls every time I called them frustrated or bustling with excitement. No matter what the situation has been, they have always been there for me through all of this. I would also like to thank my twin sons, Parker and Colton, for being my inspiration and motivation throughout this process. Thank you to my committee members, Lance Williams and Josh Banta, who have offered me so much advice and guidance throughout this project. A special thanks to Marsha Williams and Kate Hertweck for taking time out of their busy schedules to teach me how to work with many of the statistical and other software packages. Thank you to my advisor, John Placyk, for giving me the opportunity to learn from him and offering me guidance throughout my time at the University of Texas at Tyler. I would like to thank my funding sources, Texas Parks and Wildlife and the Texas Academy of Sciences. Thank you to Brianna Ciara, Cynthia Ontiveros, Brenda Arras, and Edith Plants-Paris for all of the hard work they put into helping me with my field collections. Finally, I would like to thank Justin Hernandez for his contributions to the ecological niche modeling portion of this paper. Table of Contents List of Tables……………………………………………………………………………………….i List of Figures………………………………………………………………………………………ii Abstract……………………………………………………………………………………………...iii Chapter One: Introduction…………………………………………………………………………..1 Molecular Ecology Introduction..………………………………………….3 Ecological Niche Modeling Introduction..…………………………………5 Chapter Two: Materials and Methods………………………………………………………………6 2014 Texas Survey Methods……………………………………………….6 Molecular Ecology Methods……………………………………………….6 Ecological Niche Modeling Methods………………………………………7 Chapter 3: Results…………………………………………………………………………………12 2014 Texas Survey Results………………………………………………….12 Molecular Ecology Results………………………………………………….15 Ecological Niche Modeling Results…………………………………………21 Chapter 4: Discussion………………………………………………………………………………49 2014 Texas Survey Discussion……………………………………………….49 Molecular Ecology Discussion………………………………………………..49 Ecological Niche Modeling Discussion………………………………………51 Chapter 5: Conclusion………………………………………………………………………….……54 Literature Cited………………………………………………………………………………………56 i List of Tables Table 1. Presence points used in all Maxent models…………………………………………………...…15 Table 2. Shows the environmental layers used, the source and website from where the layers were obtained, the scale, and time period…………………………………………………………………..…...15 Table 3. Tissue sample collection information, including: collection site number, county, GPS coordinates, date of collection, and tissue sample names…………………………………….…..….……18 Table 4. Percent sequence divergence of all three genes, comparing the Texas populations and Louisiana populations both within and between populations………………………………………………………...21 Table 5. AMOVA results obtained from the COI gene segment…………………………………………21 Table 6. Pairwise Fst obtained from the COI AMOVA…………………………………………………..22 Table 7. Matrix of significant P-values obtained from the COI AMOVA………………………………..22 Table 8. AMOVA results obtained from the 16s gene segment………………………………………….23 Table 9. Pairwise Fst obtained from the 16s AMOVA…………………………………………………...23 Table 10. Matrix of significant P-values obtained from the 16s AMOVA……………………………….24 Table 11. AUC values obtained from all 3 niche models used in this study……………………………...27 Table 12. Estimates of relative contributions of the environmental variables to the Texas as an individual species Maxent model……………………………………………………………………………………..29 Table 13. Estimates of relative contributions of the environmental variables to the Louisiana as an individual species Maxent model………………………………………………………………………….38 ii List of Figures Figure 1. All 25 historical sites sampled in Cypress Creek in East Texas. Samples were not obtained in 14 of the 25 sites sampled (blue). Samples were collected in 11 of the 25 sites (red)……………………17 Figure 2. Haplotype network comparing the unique haplotypes of the Texas and Louisiana subpopulations…………………………………………………………………………………………….24 Figure 3. Habitat suitability map highlighting the areas for each population with the highest habitat suitability for each population of O. maletae with niche overlap…………………………………………28 Figure 4. The logistic response to mean temperature of the driest quarter by the Texas population……..30 Figure 5. The logistic response to stream order by the Texas population………………………………...31 Figure 6. The logistic response to precipitation during the driest quarter by the Texas population……...32 Figure 7. The logistic response to precipitation during the wettest month by the Texas population……..33 Figure 8. Shows the logistic response to soil type (gSSURGO) by the Texas population……………….34 Figure 9. The logistic response to USGS Geology by the Texas subpopulation…………………………35 Figure 10. The logistic response to cumulative square drainage area by the Texas subpopulation………36 Figure 11. The logistic response to the mean temperature during the wettest quarter by the Texas subpopulation……………………………………………………………………………………………...37 Figure 12. The logistic response to the mean temperature during the wettest quarter by the Louisiana subpopulation……………………………………………………………………………………………...39 Figure 13. The logistic response to soil type (gSSURGO) by the Louisiana subpopulation……………..40 Figure 14. The logistic response to cumulative square drainage area by the Louisiana subpopulation….41 Figure 15. The logistic response to stream order by the Louisiana subpopulation……………………….42 Figure 16. The logistic response USGS Geology by the Louisiana subpopulation………………………43 Figure 17. The logistic response to precipitation during the driest quarter by the Louisiana subpopulation……………………………………………………………………………………………..44 Figure 18. The logistic response to precipitation during the wettest month by the Louisiana subpopulation……………………………………………………………………………………………..45 Figure 19. The logistic response to the mean temperature during the driest quarter by the Louisiana subpopulation……………………………………………………………………………………………..46 Figure 20. Test gain for the model run with Texas-Louisiana as a combined species…………………..47 Figure 21. Probability distribution map from the model run with Texas-Louisiana as a combined species…………………………………………………………………………………………………….48 Figure 22. Test gain for the model run with Texas as an individual species…………………………….49 Figure 23. Probability distribution map from the model run with Texas as an individual species………50 Figure 24. Probability distribution map from the model run with Louisiana as an individual species…..51 Figure 25. Test gain for the model run with Louisiana as an individual species…………………………52 iii Abstract Phylogenetic and ecological analysis of two populations of the Kitsatchie Painted Crayfish, Orconectes maletae (Decapoda: Cambaridae) Larrimy Brown Thesis Chair: John S. Placyk, Jr., Ph.D. The University of Texas at Tyler May 2017 The primary aim of this study was to assess the conservation status of the East Texas population of the Kistachie Painted Crayfish, Orconectes maletae. Orconectes maletae has been given a Global Heritage Ranking of G2, or imperiled, because of population declines in the Kisatchie Bayou drainage in Louisiana; however, similar data for Texas is lacking. For the current study, surveys of 25 historical sites in Texas were conducted in the Cypress Creek and Caddo Lake drainage from June to August 2014 and revealed that O. maletae was either absent or in low enough abundance to evade detection at close to 60% of these sites. Because of the lack of natural history data available for O. maletae, very little is known about the optimal habitat requirements and the population biology of this organism. The current distribution of the species in Texas and Louisiana is disjunct. As such, the current study used molecular genetic techniques
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