Leibniz Institut für Zoo und Wildtierforschung Abteilung Evolutionsgenetik Deciphering evolutionary histories of Southeast Asian Ungulates: Comparative phylogeography in a Biodiversity Hotspot Publikationsbasierte DISSERTATION zur Erlangung des akademischen Grades “doctor rerum naturalium” (Dr. rer. nat.) in der Wissenschaftsdisziplin “Evolutionsgenetik” eingereicht an der Mathematisch-Naturwissenschaftlichen Fakultät der Univesität Potsdam von Renata Filipa Ribeiro Martins Potsdam, Juni 2017 Published online at the Institutional Repository of the University of Potsdam: URN urn:nbn:de:kobv:517-opus4-404669 http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-404669 This dissertation is based in the following manuscripts: 1 Renata F. Martins, Jörns Fickel, Minh Le, Thanh van Nguyen, Ha. M. Nguyen, Robert Timmins, Han Ming Gan, Jeffrine J. Rovie-Ryan, Dorina Lenz, Daniel W. Förster & Andreas Wilting (2017) Phylogeography of red muntjacs reveals three distinct mitochondrial lineages. BMC Evolutionary Biology, 17 (34). DOI: 10.1186/s12862-017-0888-0 2 Renata F. Martins, Anke Schmidt, Dorina Lenz, Andreas Wilting & Jörns Fickel. Human mediated introduction of introgressed deer across Wallace’s line: historical biogeography of Rusa unicolor and R. timorensis. Under review in Journal of Biogeography 3 Renata F. Martins, Dorina Lenz, Daniel W. Förster, Johanna von Seth, Love Dalén, Sen Nathan, Benoît Goossens, Peter van Coeverden de Groot, Jörns Fickel & Andreas Wilting. The lost genetic legacy of Sumatran and Javan rhinoceros: phylogeography and genetic diversity of historical populations. In preparation (formatted for submission) Contents Acknowledgments ............................................................................................................................. i List of Abbreviations ....................................................................................................................... iii Summary ......................................................................................................................................... iv Zusammenfassung ........................................................................................................................... vi General Introduction ......................................................................................................................... 1 1 General Introduction ................................................................................................................. 2 2 Aims of this study ................................................................................................................... 14 Manuscript I ................................................................................................................................... 15 Manuscript II .................................................................................................................................. 39 Manuscript III ................................................................................................................................. 63 General Discussion ......................................................................................................................... 85 1 Comparative phylogeography ................................................................................................ 86 2 Taxonomic and conservation implications of this study ........................................................ 92 3 Suitability of the methodology ............................................................................................... 93 4 Concluding Remarks and Outlook ......................................................................................... 94 Bibliography ................................................................................................................................... 97 Appendix ...................................................................................................................................... 105 Selbstständigkeitserklärung .......................................................................................................... 115 Acknowledgments This dissertation would not exist without help and support of many people whom I wish to thank first of all. I would like to start by thanking Prof. Dr. Jörns Fickel for the opportunity of conducting this research project under his supervision at the Leibniz Institute for Zoo and Wildlife Research (IZW). I greatly appreciate his guidance, support and time throughout the entire duration of my work. Likewise, I would like to thank Dr. Andreas Wilting for his invaluable involvement and extraordinary knowledge about all parts of this project. Also, I thank him for the opportunity to participate in his ongoing collaborations. In consequence, I would like to thank both Dr. Douglas Yu from the Center for Evolution and Ecology of Kunming, in Kunming, China and Dr. Minh Le from the Center for Resources and Ecological Studies in Hanoi, Vietnam. I deeply appreciated the opportunity to visit their labs and museums during the course of this doctoral thesis, which have inspired me more than I anticipated. I am also thankful to Prof. Dr. Heribert Hofer for allowing me to conduct my PhD project at the IZW. I want to thank as well collaborators to whom I am very grateful, which either provided samples or advice and, in many cases, both. Robert J. Timmins was an incredible teacher about the world of muntjacs. I thank also Peter J. von Coeverden de Groot for his precious help. Likewise, to all other co-authors who have made the manuscripts presented here possible I thank you from my heart. Finally, everyone from the museum collections, listed throughout the manuscripts, I wish to thank for allowing me to visit and sample, but especially for all the quick answers to all those urgent questions I had while analyzing the data. At this time I would like to thank all the colleagues at the Department of Evolutionary Genetics, for their support throughout the years. I would specially like to thank Dr. Daniel W. Förster for all his input and ideas and for the help with the laboratory methodologies and manuscripts. Also, I would like to thank Riddhi Patel, my office mate, with whom I learned so much. Likewise, I thank both Anke Schmidt and Ramona Taubert for their precious help in the lab. To Dorina Lenz, thank you for the help with the bioinformatics, it would have been harder without you. I would also like to thank Dr. Marie-Louise Kampmann for all she has taught me, especially what a good lab book looks like. I thank the people who sat in the office(s) close to me throughout the last years for their patience with my random outbursts, you will not miss them. Special thanks go to Tanja Noventa, who more than a big help was a needed friend during this all process. And finally to Saskia Wutke, thank you for all the experiences and all the moments during this time, you are on your way to great things. i I want to extend thanks to all the PhD students at the IZW, Berlin - the seminars; the parties; our symposium, were a great influence to get inspired and a way of sharing the joys and sorrows of completing a PhD. However, a special thanks is also needed to Sónia Fontes without whom life in Berlin wouldn't have been what it was. And to David Lehmann whom I dearly missed in those last PhD moments. A big thank you is owed to my family and my friends back home. Ten years (or more) of friendship cannot be summarized in a few sentences, as I cannot summarize what your friendship and support meant for the completion of this work. Sofia, Adriana, João, Susana, Francisco, Marta and Pio – thank you for everything. Our little emigrant moments in Portugal do more for my mental health than you can imagine and it is also because you believed in me that this work got done. To Ingo, thank you for entering my life when you did; for your support with my work and with my daily complaints. You did much more than you think. Lastly, obrigada mãe e pai por me encorajarem sempre a seguir em frente e a ir onde fosse preciso para atingir os meus objectivos. Obrigada pela força e inspiração, o vosso suporte foi e será sempre essencial. To all, a heartfelt thank you, Renata ii List of Abbreviations aDNA archival/ancient DNA bp base pairs BPP Bayesian Posterior Probability DNA Deoxyribonucleic acid gDNA genomic DNA HTS High Throughput Sequencing kb kilobases (1000 bp) kya Thousand years ago m meters MCMC Markov Chain Monte Carlo mtDNA mitochondrial DNA My million years Mya Million years ago nuDNA nuclear DNA NUMTs Nuclear copies of mitochondrial DNA NGS Next Generation Sequencing PCR Polymerase chain reaction iii Summary During the course of millions of years, evolutionary forces have shaped the current distribution of species and their genetic variability, by influencing their phylogeny, adaptability and probability of survival. Southeast Asia is an extraordinary biodiverse region, where past climate events have resulted in dramatic changes in land availability and distribution of vegetation, resulting likewise in periodic connections between isolated islands and the mainland. These events have influenced the way species are distributed throughout this region but, more importantly, they influenced the genesis of genetic diversity. Despite the observation that a shared paleo-history resulted in very diverse species phylogeographic patterns, the mechanisms behind these patterns are still poorly understood. In this thesis, I investigated and contrasted the