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A Phylogenetic Approach Mgr. Pavel Duda

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A Phylogenetic Approach Mgr. Pavel Duda School of Doctoral Studies in Biological Sciences University of South Bohemia in České Budějovice Faculty of Science Human population history and evolution of culture: A phylogenetic approach Ph.D. Thesis Mgr. Pavel Duda Supervisor: prof. RNDr. Jan Zrzavý, CSc. Department of Zoology, Faculty of Science, University of South Bohemia České Budějovice 2017 This thesis should be cited as: Duda, P. 2017: Human population history and evolution of culture: A phylogenetic approach, Ph.D. Thesis. University of South Bohemia, Faculty of Science, School of Doctoral Studies in Biological Sciences, České Budějovice, Czech Republic, 263 pp. Annotation This thesis uses phylogenetic and phylogenetic comparative methods to investigate human population history and evolution of cross-cultural variation. Such research requires a robust phylogenetic hypothesis of human populations as a framework. This thesis uses a supertree approach to infer a composite phylogeny of human populations based on published phylogenetic trees based on genetic and linguistic data. It assesses the stability of the inferred supertree topology and identifies individual populations whose phylogenetic position is particularly unstable. It assesses the congruence between genetic and linguistic data and tests hypothesis about language relationships and coevolution between genes and languages on a global scale. The supertree is used to reconstruct the origin and evolution of religious beliefs and behaviors using a global sample of hunter-gatherer populations and a set of phylogenetic comparative methods. This thesis also describes evolution of Central African pygmies, a group of human populations that represents an interesting case of morphological and cultural adaptation in human species, and reviews the history and current developments of phylogenetic (tree building) approaches to cross-cultural variation. Declaration [in Czech] Prohlašuji, že svoji disertační práci jsem vypracoval samostatně pouze s použitím pramenů a literatury uvedených v seznamu citované literatury. Prohlašuji, že v souladu s § 47b zákona č. 111/1998 Sb. v platném znění souhlasím se zveřejněním své disertační práce, a to v nezkrácené podobě elektronickou cestou ve veřejně přístupné části databáze STAG provozované Jihočeskou univerzitou v Českých Budějovicích na jejích internetových stránkách, a to se zachováním mého autorského práva k odevzdanému textu této kvalifikační práce. Souhlasím dále s tím, aby toutéž elektronickou cestou byly v souladu s uvedeným ustanovením zákona č. 111/1998 Sb. zveřejněny posudky školitele a oponentů práce i záznam o průběhu a výsledku obhajoby kvalifikační práce. Rovněž souhlasím s porovnáním textu mé kvalifikační práce s databází kvalifikačních prací Theses.cz provozovanou Národním registrem vysokoškolských kvalifikačních prací a systémem na odhalování plagiátů. V Českých Budějovicích, 27.2.2017 …………………. Mgr. Pavel Duda This thesis originated at the Faculty of Science, University of South Bohemia, in the study programme Zoology. Financial support This thesis was supported by Grant Agency of the University of South Bohemia (GA JU 042/2013/P; GA JU 140/2013/P) and The Czech Science Foundation (GA ČR 16-26369S; GA ČR 14-36098G). Acknowledgements A special thank you goes to my supervisor Jan Zrzavý, who have been supervising me since I started working on my bachelor’s thesis. I am grateful for his interesting ideas and keen insights, his relentless enthusiasm and sense of humor. I especially appreciate that he enabled me to pursue my own research interests. He provided indispensable assistance and showed lots of patience while letting me do what I want, a decision he had to defend on a national radio. Thanks to David Storch for taking interest in my research and for inviting me to the Center for Theoretical Study (CTS). The time spent at the CTS was worthwhile and inspiring. Thanks to Vojtěch Novotný for his interest in my research and support. I am grateful to Olaf Bininda- Emonds for allowing me to visit him at the department Systematics and Evolutionary Biology at The Carl von Ossietzky University of Oldenburg. Our discussions were invaluable and I like to remember the time spent in Oldenburg. A big thank you goes to Hervey Peoples, who approached me at the conference of Human Behavior and Evolution Society in Montpellier and persuaded me to work on “The origins of religion” with her. The production of the paper was complicated to say the least but through countless of extensive emails, multiple re-analyses, rewritings, and resubmissions, we were able to produce a worthwhile piece of research. Thanks to Frank Marlowe for his contribution to the paper. Thanks to Jan Havlíček for inviting me to co-write books Pygmejové and Biologické a evoluční teorie kultury and for introducing me to University Research Center (UNCE), Nature and culture working group at Charles University of Prague. Thanks to Linda Hroníková, Zuzana Schierová, and Lenka Ovčáčková for their editorial assistance. I am grateful to all my colleagues and friends at the Department of Zoology. František Sedláček was always helpful and benevolent as chair of the specialist board of the Ph.D. study programme Zoology. I was lucky to have shared the office with Honza Robovský, Míša Másílková, Terka Holicová, and others, to whom I am grateful for pleasant working environment, engaging discussions, and an occasional welcome distraction. I would like to thank my family, especially to my stepfather František, who enabled me to study. I am immensely grateful to my wife Pavla, who was with me during the whole Ph.D. study, and who I give most credit for the fact that the past five years was, overall, the happiest, most fulfilling time of my life. List of publications and author’s contribution This thesis is based on the following publications (listed chronologically): I. Duda, P., & Zrzavý, J. (2016). Human population history revealed by a supertree approach. Scientific Reports, 6, 10. doi:10.1038/srep29890 (IF 2015 = 5.228) Pavel Duda is the first and corresponding author of the study. He conceived and designed the study with J. Zrzavý, analyzed the data, created the artworks and co-wrote the paper with J. Zrzavý. II. Peoples, H. C., Duda, P., & Marlowe, F. W. (2016). Hunter-gatherers and the origins of religion. Human Nature-an Interdisciplinary Biosocial Perspective, 27(3), 261-282. doi:10.1007/s12110-016-9260-0 (IF 2015 = 1.895) Pavel Duda designed the study with H. Peoples, analyzed the data, created the artworks and co-wrote the paper with H. Peoples. III. Duda, P. (2015). Pygmejové pohledem evoluční biologie. In: Hroníková, L., Schierová, Z. (Eds.). Pygmejové: nejmenší lidé pohledem antropologie & Šebestova sbírka v Hrdličkově muzeu člověka PřF UK (pp. 18-48). Praha: Academia. Pavel Duda searched the literature, created the artworks and wrote the manuscript. IV. Duda, P. (in press). Kulturní fylogenetika - Využití fylogenetických metod ke studiu Evoluční historie jazyka a kultury. In: Ovčáčková, L. (Ed.), Biologické a evoluční teorie kultury. Praha: Academia. Pavel Duda searched the literature, created the artworks and wrote the manuscript. Co-author agreement Jan Zrzavý, the supervisor of this Ph.D. thesis and co-author of the paper “Human population history revealed by a supertree approach”, fully acknowledges the major contribution of Pavel Duda to the presented paper. …………………………………………. prof. RNDr. Jan Zrzavý, CSc., co-author Hervey Peoples, the first and corresponding author of the paper “Hunter-gatherers and the origins of religion”, fully acknowledges the major contribution of Pavel Duda to the presented paper. ….....…………………………. Hervey C. Peoples, first author Contents Introduction ............................................................................................................................ 1 1. Evolution of culture .................................................................................................. 1 2. Phylogenetic comparative methods .......................................................................... 4 3. Human population history ........................................................................................ 5 3.1 Phylogenies based on genetic data ......................................................................... 5 3.2 Phylogenies based on linguistic data ...................................................................... 7 4. Cultural phylogenetics ............................................................................................ 10 4.1 Building phylogenies ............................................................................................ 10 4.2 Using phylogenies ................................................................................................ 11 5. Phylogenies as a framework for studying evolution of culture .............................. 12 6. Supertree approach .................................................................................................. 14 7. Aims and scope of the thesis .................................................................................. 15 Chapter I ............................................................................................................................... 34 Duda, P., & Zrzavý, J. (2016). Human population history revealed by a supertree approach. Scientific Reports, 6, 10. Chapter II .............................................................................................................................. 46 Peoples, H. C., Duda, P., & Marlowe,
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