Washington University in St. Louis Washington University Open Scholarship Arts & Sciences Electronic Theses and Dissertations Arts & Sciences Spring 5-15-2017 Population Genomics of a Baboon Hybrid Zone in Zambia Kenneth Lyu Chiou Washington University in St. Louis Follow this and additional works at: https://openscholarship.wustl.edu/art_sci_etds Part of the Biological and Physical Anthropology Commons, and the Genetics Commons Recommended Citation Chiou, Kenneth Lyu, "Population Genomics of a Baboon Hybrid Zone in Zambia" (2017). Arts & Sciences Electronic Theses and Dissertations. 1094. https://openscholarship.wustl.edu/art_sci_etds/1094 This Dissertation is brought to you for free and open access by the Arts & Sciences at Washington University Open Scholarship. It has been accepted for inclusion in Arts & Sciences Electronic Theses and Dissertations by an authorized administrator of Washington University Open Scholarship. For more information, please contact [email protected]. WASHINGTON UNIVERSITY IN ST. LOUIS Department of Anthropology Dissertation Examination Committee: Jane Phillips-Conroy, Chair Amy Bauernfeind Clifford Jolly Allan Larson Amanda Melin Population Genomics of a Baboon Hybrid Zone in Zambia By Kenneth L. Chiou A dissertation presented to The Graduate School of Washington University in partial fulfillment of the requirements for the degree of Doctor of Philosophy May 2017 St. Louis, Missouri © Kenneth L. Chiou Contents List of Figures v List of Tables vii Acknowledgments ix Abstract xiv 1 Hybrid Zones and Papio: A Review 1 Introduction . 1 Hybridization . 2 Study animals . 5 Evolution of genus Papio ................................. 7 Hybridization in Papio ................................... 15 Zambian Papio: diversity and distribution . 23 Relevance to Homo ..................................... 35 Study site . 40 Research summary . 44 Overview of upcoming chapters . 50 References . 52 2 Noninvasive Population Genomics from Feces 70 Introduction . 71 ii Results . ............................................ 73 Discussion . 79 Methods . 82 Samples . 82 DNA enrichment . 83 Library preparation and sequencing . 85 Analysis . 86 Acknowledgments . 88 References . 88 3 Population Signatures of Selection between Parental Species 93 Introduction . 93 Methods . 95 Samples . 95 DNA isolation and library preparation . 95 Sequence alignment and variant identification . 96 Inference of ancestry . 97 Estimation of differentiation . 98 Functional enrichment analysis . 99 Results and Discussion . 100 Conclusion . 108 Acknowledgments . 109 References . 109 4 Population Genomic Analysis of the Hybrid Zone 119 Introduction . 120 Methods . 122 Samples . 122 DNA isolation, library preparation and sequencing . 123 iii Detecting introgression . 124 Local adaptation analysis . 124 Genomic cline analysis . 126 Functional enrichment analysis . 128 Results and Discussion . 128 Hybrid zone structure . 129 Signatures of local adaptation and extreme introgression . 135 Gene function and biological pathway analysis . 137 JAK/STAT signaling pathway . 138 FGF and TLR signaling pathways . 140 Other pathways with aberrant introgression . 141 Outer dense fiber protein 2 . 141 Conclusion . 144 Acknowledgments . 146 References . 146 5 Summary and Conclusions 154 Appendices 162 A Supplementary Figures 163 B Supplementary Tables 176 C Supplementary Protocol 214 D Supplementary Note 221 iv List of Figures 1.1 Baboon distribution map . 7 1.2 Baboon mitochondrial tree . 9 1.3 Baboon nuclear tree . 10 1.4 Anubis baboons . 16 1.5 Hamadryas baboons . 17 1.6 Yellow baboons . 22 1.7 Zambian national parks . 24 1.8 Zambian rivers . 25 1.9 Zambian ecoregions . 26 1.10 Zambian baboon distribution map . 27 1.11 Grayfoot baboons . 32 1.12 Kinda baboons . 33 1.13 Kinda × grayfoot baboon hybrids . 36 1.14 Kafue National Park map . 40 1.15 Kafue National Park rivers map . 41 1.16 Kafue National Park geological map . 42 1.17 Kafue National Park vegetation map . 43 1.18 Lake Itezhi Tezhi map . 45 1.19 Challenges of baboon trapping . 48 1.20 Project track log . 49 1.21 Sightings and photos map . 50 v 1.22 Samples map ........................................ 51 2.1 FecalSeq overview . 75 2.2 Comparison of enrichment magnitude . 77 2.3 Concordance with blood-derived genotype data . 78 3.1 Ancestry assignment . 97 3.2 FST gene scan distribution . 100 4.1 Genomic cline parameters . 127 4.2 Ancestry clustering . 129 4.3 Ancestry results map . 130 4.4 Nuclear and sex-linked ancestry comparisons . 131 S1 Alignment rate by starting host percentage . 163 S2 RADtag quality control plots . 164 S3 Comparison of genome mapping percentages . 165 S4 ADMIXTURE cross validation results . 165 S5 Multidimensional scaling results . 166 S6 MDS by ADMIXTURE results . 167 S7.