Institut für Zoo- und Wildtierforschung Evolutionsgenetik Coat colours and mitochondrial lineages of ancient horses to document domestication Dissertation zur Erlangung des akademischen Grades „doctor rerum naturalium“ (Dr. rer. nat.) eingereicht am Fachbereich für Biologie, Chemie und Pharmazie der Freien Universität Berlin vorgelegt von Dipl.-Biologe Michael Cieslak Berlin, Juni 2011 Die experimentellen Arbeiten zur vorliegenden Dissertation wurden in der Zeit von Juni 2007 bis April 2011 im Institut für Zoo- und Wildtierforschung (Evolutionsgenetik), Department für Nutzpflanzen- und Tierwissen- schaften der Humboldt-Universität zu Berlin und im Deutschen Archäologischen Institut durchgeführt. Die Dissertation wurde am Fachbereich Biologie, Chemie, Pharmazie der Freien Universität Berlin eingereicht. 1. Gutachter: Prof. Dr. Heribert Hofer (Leibniz-Institut für Zoo- und Wildtierforschung, Berlin) 2. Gutachter: Prof. Dr. Stephan Sigrist (Institut für Biologie, Freie Universität Berlin) Tag der Disputation: 06.02.2012 ACKNOWLEDGEMENTS I. ACKNOWLEDGEMENTS First of all, I would like to acknowledge and express my deep gratitude to Prof. Dr. Heribert Hofer for supervising me at the end of my doctoral studies and for serving as the chair of my doctoral examination and dissertation committee. Moreover, I would like to thank the further member of the dissertation committee, Prof. Dr. Stephan Sigrist. In particular, I am truly indebted and thankful to PD Dr. Arne Ludwig who supervised me throughout the years of my doctoral studies. This dissertation would not have been possible without his advice, feedback, input, perspectives, and critical insights that helped focus my efforts. Moreover, I am sincerely and heartily grateful to Dr. Melanie Pruvost. She introduced me to the work of ancient DNA research and her support, kindness, and helpful suggestions have been invaluable. I would also like to thank the past and present members of the Institute for Zoo- and Wildlife Research (IZW) for their help and support and for the profitable time I could spend there. This applies particularly to the Research Group of Evolutionary Genetics under the supervision of Prof. Dr. Simone Sommer. I would also like to take this opportunity to thank Dr. Monika Reissmann and the members of her group at the Department of Breeding Biology and Molecular Genetics (Humboldt University Berlin) and Prof. Dr. Norbert Benecke at the German Archaeological Institute (Berlin) in whose labs I could work. I would also like to thank my parents, Gisela and Richard Cieslak. Their faith and confidence in me has shaped me to be the person I am today. And finally, I would like to thank Dung Tieu Thi Phuong, Siti Mariam, Manuel Arnegger, Benjamin Ott and Christoph Rothmeier for the support and motivation that I received from them. The research conducted in this study was supported by the DFG (Deutsche Forschungs- gemeinschaft) requested by Arne Ludwig (LU 852/6-2; LU 852/7-3). i CONTENTS II. CONTENTS I. ACKNOWLEDGEMENTS................................................................................................................................................................. i II. CONTENTS ...................................................................................................................................................................................... ii III. ABBREVIATIONS ........................................................................................................................................................................ iii IV. SUMMARY ................................................................................................................................................................................... iv V. ZUSAMMENFASSUNG ................................................................................................................................................................. v 1. INTRODUCTION ............................................................................................................................................................................. 1 1.1 Domestication of animals ........................................................................................................................................................... 1 1.1.1 Origin of species domestication ......................................................................................................................................... 1 1.1.2 Purpose of studying domesticates ...................................................................................................................................... 2 1.2 Genetic documenting of domestication ...................................................................................................................................... 4 1.2.1 Documenting of domestication and lineages ..................................................................................................................... 5 1.2.1.1 Question of molecular markers for optimal lineage classification ............................................................................ 5 1.2.1.2 Signature of domestication on lineage diversity and geographic lineage distribution .............................................. 6 1.2.1.3 Documenting place and time of domestication using lineages .................................................................................. 6 1.2.2 Documenting of domestication and selected phenotypic character ................................................................................... 9 1.2.2.1 Signature of domestication on variation of a selected phenotypic character. ........................................................... 9 1.2.2.2 Documenting place and time of domestication using a selected phenotypic character ........................................... 10 1.3 Identification of a genetic background of a phenotypic trait .................................................................................................... 11 1.4 Coat colouration as phenotypic character under breeding ........................................................................................................ 11 1.4.1 Coat colour phenotypes ................................................................................................................................................... 11 1.4.2 Coat-colour-associated genes .......................................................................................................................................... 12 1.5 Background and techniques for ancient DNA .......................................................................................................................... 15 2. AIMS OF THE STUDY .................................................................................................................................................................. 18 3. TAXONOMIC CLASSIFICATION ................................................................................................................................................ 21 4. SUMMARY OF PAPERS ............................................................................................................................................................... 24 4.1 Summary of paper I .................................................................................................................................................................. 24 4.2 Summary of paper II ................................................................................................................................................................ 26 4.3 Summary of paper III ............................................................................................................................................................... 29 4.4 Summary of paper IV ............................................................................................................................................................... 31 5. DISCUSSION .................................................................................................................................................................................. 33 5.1 Benefits of ancient DNA approaches to document horse domestication .................................................................................. 33 5.2 Mitochondrial HVR1 part for the equine lineage classification ............................................................................................... 36 5.3 Lineage diversity and geographic lineage distribution of ancient wild horses .......................................................................... 37 5.4 Lineage diversity and geographic lineage distribution under domestication ............................................................................ 39 5.5 Coat colour variation of ancient wild horses ............................................................................................................................ 42 5.6 Coat colour variation under domestication and early breeding ................................................................................................. 43 5.7 Chronological appearance of investigated coat colour phenotypes .......................................................................................... 45 5.8 Conclusion about origin of horse domestication ...................................................................................................................... 46 5.9 Outlook