Declaration Dr. Thomas H. Pringle - Buffalo Field Campaign

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DEVELOPMENT OF FECAL DNA SAMPLING METHODS TO ASSESS GENETIC POPULATION STRUCTURE OF GREATER YELLOWSTONE BISON By Florence Marie Gardipee Associate of Science, Medical Laboratory Technology, Austin Community College, Austin, Texas, 1982 Bachelor of Science, Wildlife Biology, The University of Montana, Missoula, Montana, 2003 Thesis presented in partial fulfillment of the requirements for the degree of Master of Science Wildlife Biology The University of Montana Missoula, MT Spring 2007 Approved by: <strong>Dr</strong>. David A. Strobel, Dean Graduate School Fred W. Allendorf, Co-Chair Division of Biological Sciences Gordon Luikart, Co-Chair Division of Biological Sciences Mark Hebblewhite Department of Ecosystem and Conservation Sciences Richmond Clow Native American Studies
Gardipee, Florence, M.S., May 2007 Wildlife Biology Development of fecal DNA sampling methods to assess genetic population structure of Greater Yellowstone bison Co-Chairperson: Fred W. Allendorf Co-Chairperson: Gordon Luikart The bison (Bison bison) of Yellowstone National Park (YNP) and Grand Teton National Park (GTNP) represent two of only three remaining populations of plains bison that have no evidence of hybridization with cattle. Therefore, these bison are an important source for ecological and genetic restoration of wild bison. Little is known regarding genetic population structure and gene flow among the Greater Yellowstone Area (GYA) bison herds. I evaluated the feasibility of fecal DNA sampling for genetic analyses of wild bison populations. I used matched blood and fecal samples from eight radio-collared bison from Hayden Valley breeding group (YNP), and multiplex polymerase chain reaction (PCR) of four microsatellite loci to assess amplification success and genotyping error rates. The amplification success rate was 92% and the genotyping error rate was 12% on average across all individuals, and loci. Exclusion of two poor quality samples from data analyses increased amplification success to 97%, and reduced the genotyping error rate to 4%. I PCR amplified a 470 bp mitochondrial DNA (mtDNA) fragment for sequencing, and successfully identified haplotypes for120 individuals. The error rate for mtDNA sequencing was 0.0005 nucleotide mis-incorporations across all samples. Sequencing and RFLP analysis of mtDNA control region from 179 fecal samples collected over two consecutive seasons was conducted to evaluate population structure among YNP breeding groups, and between GTNP and YNP bison populations. I found significant genetic distinction between YNP and GTNP bison populations (FST = 0.191, p < 0.001). The differences in haplotype frequencies between Hayden Valley and Lamar Valley breeding groups were highly significant (FST = 0.367, p < 0.001), and nearly two times greater than between GTNP and YNP thus providing evidence for at least two genetically distinct breeding groups within YNP. Differences between breeding groups remained significant even though haplotype frequencies were different between years within Hayden Valley (FST = 0.054, p < 0.05). The techniques and protocols developed have allowed high amplification success, low genotyping and sequencing error rates. This study demonstrated that non-invasive fecal DNA sampling is feasible for bison, and detected fine-scale population genetic structure in among GYA bison, suggesting female philopatry. ii
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Page 10 and 11: • The mutation rate in mitochondr
Page 12 and 13: possibility of mitochondrial dysfun
Page 14 and 15: arginine R100 provides an essential
Page 16 and 17: inbreeding, small herd sizes and ge
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Page 20 and 21: Table 3. Bison non-sporadic mitocho
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Page 28 and 29: Table of Contents Abstract………
Page 30 and 31: List of Figures 1-1 Map of YNP show
Page 32 and 33: Dedication The work presented withi
Page 34 and 35: Preface Dale Lott grew up on the Na
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Page 38 and 39: within a possible third location (M
Page 40 and 41: samples. However, repeated genotypi
Page 42 and 43: population structure within YNP bre
Page 44 and 45: The highly differentiated populatio
Page 46 and 47: Figure 1-1. Map of YNP showing loca
Page 48 and 49: INTRODUCTION Wild bison are at risk
Page 50 and 51: sample was extracted twice using th
Page 52 and 53: Fragment analysis was carried out o
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Page 56 and 57: aligned with less than two out of t
Page 58 and 59: ears (Ursus americanus), and brown
Page 60 and 61: Figures: Figure 2-1. Flow diagram s
Page 62 and 63: Table 2-2. Amplification success (A
Page 64 and 65: Appendix 2-3. Allelic dropout (AD)
Page 66 and 67: strong fine scale genetic different
Page 68 and 69: fidelity to breeding areas may be h
Page 70 and 71: RFLP PCR amplification was carried
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Page 74 and 75: and Lamar Valley, in comparison to
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The differences in haplotype freque
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Figures: Figure 3-1. Approximate lo
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Literature Cited Allendorf, F.W., R
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Côté, S.D., F. Dallas, F. Marshal
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Luikart, G., S. Zundel, D. Rioux, C
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Tedford, S. Zimov, and A. Cooper. 2
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general approach using mtDNA marker
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2 K.C. Douglas et al. / Mitochondri
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mitochondrial genome is 16318-16323
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Bison Herd (bHap13 and bHap16), the
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spread distribution of bison prior
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Declaration Dr. Thomas H. Pringle - Buffalo Field Campaign

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