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Brigham Young University GENETIC CONSIDERATIONS FOR THE CONSERVATION AND MANAGEMENT OF YELLOWSTONE CUTTHROAT TROUT (ONCORHYNCHUS CLARKII BOUVIERI) IN YELLOWSTONE NATIONAL PARK by David Joel Janetski A thesis submitted to the faculty of Brigham Young University in partial fulfillment of the requirements for the degree of Master of Science Department of Integrative Biology Brigham Young University December 2006 BRIGHAM YOUNG UNIVERSITY GRADUATE COMMITTEE APPROVAL of a thesis submitted by David Joel Janetski This thesis has been read by each member of the following graduate committee and by majority vote has been found to be satisfactory. ______________________ _____________________________________ Date Dennis K. Shiozawa, Chair ______________________ _____________________________________ Date R. Paul Evans ______________________ _____________________________________ Date Jerald B. Johnson ______________________ _____________________________________ Date Keith A. Crandall ii BRIGHAM YOUNG UNIVERSITY As chair of the candidate’s graduate committee, I have read the thesis of David Joel Janetski in its final form and have found that (1) its format, citations, and bibliographical style are consistent and acceptable and fulfill university and department style requirements; (2) its illustrative materials including figures, tables, and charts are in place; and (3) the final manuscript is satisfactory to the graduate committee and is ready for submission to the university library. ________________________ _____________________________________ Date Dennis K. Shiozawa Chair, Graduate Committee Accepted for the Department ________________________ _____________________________________ Date Jack W. Sites Acting Department Chair Accepted for the College ________________________ _____________________________________ Date Rodney J. Brown Dean, College of Biology and Agriculture iii ABSTRACT GENETIC CONSIDERATIONS FOR THE CONSERVATION AND MANAGEMENT OF YELLOWSTONE CUTTHROAT TROUT (ONCORHYNCHUS CLARKII BOUVIERI) IN YELLOWSTONE NATIONAL PARK David Joel Janetski Department of Integrative Biology Master of Science A key component to conservation is an accurate understanding of genetic subdivision within a species. Despite their ecological and economic importance, relatively little is understood about the genetic structuring of Yellowstone cutthroat trout in Yellowstone National Park. Here, we use traditional (Fst, Rst, Nm, and AMOVA) and modern (Bayesian assignment tests, coalescent theory, and nested clade analysis) analytical approaches to describe the population genetic subdivision of cutthroat trout spawning populations in Yellowstone Lake and to identify genetically distinct population segments throughout Yellowstone National Park. Evidence for restricted gene flow between spawning populations within Yellowstone Lake was detected using nested clade analysis. This is the first molecular evidence for restricted gene flow iv between spawning populations in Yellowstone Lake. In contrast, traditional methods such as Fst and Rst as well as the Bayesian clustering program STRUCTURE v2.0 failed to detect evidence for restricted gene flow. Across our sampling range within Yellowstone National Park, eleven genetically distinct cutthroat trout population segments were detected. These showed a general pattern of small, isolated populations with low genetic diversity in headwater streams and wide- spread, genetically diverse populations in higher-order rivers. We recommend populations be managed to maintain current levels of genetic diversity and gene flow. Based on the recent decline of and distinct morphological, behavioral, and genetic nature of cutthroat trout in Yellowstone Lake, we recommend the Yellowstone Lake spawning populations collectively be recognized as an evolutionarily significant unit. v ACKNOWLEDGEMENTS I would like to thank Dennis Shiozawa and Paul Evans for always being willing to share their time by discussing ideas, offering suggestions, and reviewing manuscripts. Thanks also to Jerry Johnson and Keith Crandall for their helpful reviews. Special thanks to Andrew Johnson, Becky Miller, Matt Pyne, and Rebecca Scholl for assistance with sample collecting, lab work, map creation, and data analysis. Also thanks to all those who helped catalogue samples, isolate DNA, and keep the lab running. I thank Matt Campbell of the Idaho Fish and Game who kindly assisted in developing primers. I am also grateful to Dan Mahony, Todd Koel, Kerry Gunther, and Kristine Smith of the National Park Service, who were responsible for collecting tissue samples and organizing collecting trips. I also thank to Yellowstone Park Foundation for partially funding this project. Thanks also to all of my family members, who have always supported and encouraged my interest in nature and in fisheries. Finally, I would like to express my gratitude to my wife Amanda for her encouragement, patience, and unwavering support through this whole process. vi TABLE OF CONTENTS Page TABLE OF CONTENTS.............................................................................................................. vii LIST OF TABLES.......................................................................................................................viii LIST OF FIGURES ....................................................................................................................... xi INTRODUCTION .......................................................................................................................... 1 MATERIALS AND METHODS.................................................................................................... 6 RESULTS ..................................................................................................................................... 17 DISCUSSION............................................................................................................................... 23 CONCLUSIONS........................................................................................................................... 35 LITERATURE CITED ................................................................................................................. 37 TABLES........................................................................................................................................ 49 FIGURES ..................................................................................................................................... 72 APPENDIX................................................................................................................................... 91 vii LIST OF TABLES Table 1. Number of samples (N) per location throughout YNP (including Yellowstone Lake), BYU numbers, GPS coordinates (UTM,WGS84/NAD83), and date collected. Although only one set of GPS coordinates is listed for each location, Heart River, Sickle Creek, Crooked Creek, Snake River, and Forest Creek were sampled in a number of locations, which are available upon request. Table 2. Internal primer pair sequences used for amplifying ND1, ND2, and ITS-2. Table 3. Sequences of six microsatellite primer sets, their annealing temperatures (Ta), and references. Table 4. Percentage of native YCT genes from ten sampling locations and species designations for each gene for each individual. (N = number sequenced, RT = rainbow trout, WCT = westslope cutthroat trout, YCT = Yellowstone cutthroat trout, het = heterozygote). Table 5. Phylogeographical inferences based on nested clade analysis. Only the haplotypes and clades for which clade distance (Dc) and/or nested clade distance (Dn) were significantly large (L) or small (S) are listed. Chain of inference refers to the steps taken in Templeton’s (2004) inference key to arrive at the given conclusion. Table 6. Summary of genetic diversity for each microsatellite locus for all populations (AR = Allelic richness, NA = Number of alleles, GD = Genetic diversity; FSTAT). viii Table 7. Observed and Expected heterozygosities locus by locus for all populations (* = p<0.05, ** = p<0.01, NA = locus is monomorphic; ARLEQUIN). Table 8. Pairwise Fst values (mtDNA) for Yellowstone Lake spawning populations (Bold = 0.01<p<0.05; ARLEQUIN). Table 9. Number of effective migrants (Nm) between Yellowstone Lake spawning populations based on Fst (ARLEQUIN). Table 10. Pairwise Rst values (microsatellites) for Yellowstone Lake spawning populations (Bold = 0.01<p<0.05, Bold = p<0.01; ARLEQUIN). Table 11. Number of effective migrants (Nm) between Yellowstone Lake spawning populations based on Rst (ARLEQUIN). Table 12. Pairwise Fst from mtDNA for all YNP populations (Bold = p>0.01; p<0.01 for all other values; ARLEQUIN). Table 13. Number of effective migrants (Nm) between all YNP populations based on Fst (ARLEQUIN). Table 14. Pairwise Rst from microsatellite data for all YNP populations (Bold = p>0.01; all other values p<0.01; ARLEQUIN). Table 15. Number of effective migrants (Nm) between all YNP populations based on Rst (ARLEQUIN). Table 16. Theta (ș), effective population size (Ne), and effective number of females (Nf) for two population sets (LAMARC). Table 17. Migration rates (M), standard deviations, and effective number of migrants (Nm, calculated according to the equation [Nm = M/(4șrecipient population)]; LAMARC) compared to Nm using Fst = 1/(4Nm + 1) (ARLEQUIN) for population set 1. ix Table 18. Migration rates (M), standard deviations, and effective number of migrants (Nm, calculated according to the equation [Nm = M/(4șrecipient population)]; LAMARC) compared
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