UNIVERSITY OF COPENHAGEN STOCKHOLM UNIVERSITY PhD Thesis Tatiana Richtman Feuerborn Genomic Insights into the Population History of Circumpolar Arctic Dogs Supervisors: Anders J. Hansen Love Dalen Mikkel-Holger Strander Sinding Kerstin Liden Submitted: 29th February 2020 UNIVERSITY OF COPENHAGEN STOCKHOLM UNIVERSITY PhD Thesis Tatiana Richtman Feuerborn Genomic insights into the population history of circumpolar Arctic dogs Supervisors: Anders J. Hansen Love Dalén Mikkel-Holger Strander Sinding Kerstin Lidén Submitted: 29th February 2020 Cover Image: Tatiana Richtman Feuerborn / 1 / “In point of fact they [Canadian Inuit Dogs] are probably the purest bred dogs in the world, being so securely segregated from the rest of the canine world.” Lindsay 1935 2 / 3 / Table of Contents List of papers 5 Candidate’s Contributions 6 English Summary 7 Dansk abstract 8 Svensk sammanfattning 9 Introduction 10 Domestication of the Dog 10 The Role of Dogs in the Arctic 10 Human History in Siberia 11 Human History in the North American Arctic 12 Dogs in the Siberian/Eurasian Arctic 14 Dogs in the North American Arctic 15 Implications of Recent Contact Between the West and the Arctic on Arctic Dogs 16 Epidemics in Arctic Dogs 18 Relationship Between Wolves and Sled Dogs 19 Objectives 21 Methods and Materials 22 Materials 22 Palaeogenetics 22 DNA Extraction 25 Next Generation Sequencing (NGS) 25 Computational Methods 26 Results & Discussion 29 Mitochondrial Haplotype Frequency Shifts Associated Human Cultures 29 Identification and Dietary Stable Isotope Analysis of Mammal Fur in Arctic Clothing 30 Population Structure in Arctic Dogs 31 Gene Flow From Non-Arctic Dogs into Arctic Dogs 33 Introgression From Wolves into Arctic Dogs 35 Mitigation Against Human Contamination in Sequenced Faunal Libraries 36 Future Directions 3 8 References 39 Acknowledgements 48 4 / List of papers I. Ameen, C.*, Feuerborn, T. R. *, Brown, S.K.*, Linderholm, A.*, et al. (2019) ‘Specialised sledge dogs accompanied the Inuit dispersal across the North American Arctic’, Proceeding of the Royal Society B., 286, h ttps://doi.org/10.1098/rspb.2019.1929 II. Harris, A.* Feuerborn, T. R.*, Sinding, M.-H. S., Nottingham, J., Knudsen, R., Rey-Iglesia, A., Schmidt, A.-L., Appelt, M., Gronnøw, B., Alexander, M., Eriksson, G., Dalén, L., Hansen, A.J., and Lidén, K. (Submitted) ‘Archives of human-dog relationships: Genetic and stable isotope analysis of Arctic fur clothing’ III. Feuerborn, T. R ., Carmagnini, A ., Gopalakrishnan, S., Losey, R., Appelt, M., Grønnow, B., Schmidt, A.-L., Gilbert, M.T.P., Meldgaard, M., Larson, G., Dalen, L., Hansen, A.J.*, Sinding, M.-H.S* , Frantz, L.A* (Manuscript) ‘Gen omic insight into the population history of Siberian dogs’ IV. Feuerborn, T. R ., Gopalakrishnan, S., Fernández Díaz-Maroto, P., Appelt, M., Grønnow, B., Schmidt, A.-L., Rankin, L., Gilbert, M.T.P. , Dalen, L., Meldgaard, M., Sinding, M.-H.S.*, Hansen, A.J.* (M anuscript ) ‘Pre-contact Inuit dog genomes show a lost wealth of dog diversity in the North American Arctic’ V. Feuerborn, T. R , Pečnerová, P., Ersmark, E., Dehasque, M., Krzewinska, M., Lagerholm, V.K., Munters, A., Rodriguez, R., Ureña, I., von Seth, J., van der Valk, T., Götherström, A., Dalen, L., Díez-del-Molino, D. (Manuscript) ‘Competitive mapping allows to identify and exclude human DNA contamination in ancient faunal genomic datasets’ * These authors contributed equally to this work. The articles are reprinted with permission from the respective publishers. The following paper which I contributed to is included as an appendix: Sinding, M-H.S., Gopalakrishnan, S., Ramos-Madrigal, J., de Manuel Monter, M., Pitulko, V.V., Kuderna, L., Feuerborn, T.R. , Frantz, L.A.F., Vieira, F.G., Niemann, J., Samaniego Castruita, J.A., Carøe, C., Andersen-Ranberg, E.U., Skoglund, P., Jordan, P.D., Pavlova, E.Y., Nikolskiy, P.A., Kasparov, A.K., Ivanova, V.V., Willerslev, E., Fredholm, M., Wennerberg, S.E., Heide-Jørgensen, M.P., Dietz, R., Sonne, C., Meldgaard, M., Dalén, L., Larson, G., Petersen, B., Sicheritz-Pontén, T., Bachmann, L., Wiig, Ø., Marques-Bonet, T., Hansen, A.J., and Gilbert, M.T.P. (Submitted) ‘Emergence of Arctic-Adapted Dogs at Pleistocene-Holocene Transition’ I am an author on the following papers that were published during my PhD but are not included in this thesis: Pečnerová P., Díez-del-Molino D., Dussex N., Feuerborn T. , von Seth J., van der Plicht J., Nikolskiy P., Tikhonov A., Vartanyan S., Dalén L. (2017) Genome-based sexing provides clues about behavior and social structure in the woolly mammoth. Current Biology 27(22): 3505-3510. Rowan, B.A., Heavens, D., Feuerborn, T.R. , et al. (2019) ‘An Ultra High-Density Arabidopsis thaliana Crossover Map That Refines the Influences of Structural Variation and Epigenetic Features’, GENETICS; https://doi.org/10.1534/genetics.119.302406 5 / Candidate’s Contributions Candidate contributions to thesis articles* I II III IV V Conceived the study Significant Significant Substantial Substantial Significant Designed the study Significant Substantial Substantial Substantial Significant Collected the data Significant Substantial Substantial Substantial Significant Analysed the data Substantial Substantial Substantial Substantial Significant Manuscript preparation Significant Significant Substantial Substantial Significant *Contribution Explanation: Minor: contributed in some way, but contribution was limited. Significant: provided a significant contribution to the work. Substantial: took the lead role and performed the majority of the work. 6 / English Summary The Siberian and North American Arctic have both borne witness to numerous migrations of humans and with them their dogs. This PhD thesis is based on whole genome data from 22 Siberian dogs and 72 North American Arctic dogs, in addition to 186 mitochondrial genomes Siberian and North American Arctic dogs. Mitochondrial genome data allowed for the identification of migration events that introduced distinct dog populations to North America, associated with different cultural complexes arriving to the region. A novel mitochondrial clade was also identified in dogs from eastern Siberia and Alaska. Genetic analysis was performed to confirm the macroscopic identification of fur used to make clothing in the Arctic in conjunction with stable isotope analyses to explore dietary differences of dog populations across the circumpolar region. The whole genome data generated for this PhD also detected and explored evidence for several gene flow events from West Eurasian dogs into the dogs of Siberia starting 10,900 BP. There was an additional gene flow event that introduced Near East related ancestry to the dogs of the Siberian Steppe before the Late Bronze Age. Dogs carrying this West Eurasian ancestry spread throughout Siberia, reaching northwestern Siberia by the Iron Age, by 2,000 BP. Further gene flow was detected later in Siberia from West Eurasia a thousand years later. North American Arctic dogs universally carry the Near East related ancestry that is seen in Siberian dogs starting in the Bronze Age, showing it had reached the Bering Strait before the ancestors of the Inuit departed Siberia for Alaska. Once in North America Inuit dogs experienced several other gene flow events from pre-contact subarctic dogs, modern European dogs, and wolves. The population structure seen in North American Arctic dogs reflects geography and the subsequent isolation as well as population turnover events associated with catastrophic epidemics in the dog populations. Finally, a simple method was developed to evaluate and remove human contamination from ancient DNA datasets originating from faunal taxa. All together this thesis has compiled genomic information from 94 Arctic dogs to shed light upon the genetic history of these dogs from the early Holocene through to the present day. This dataset has been able to provide insight not only into past dynamics of Arctic dogs but also a much needed resource for understanding and preserving the indigenous dog populations still present in the Arctic that face continued challenges of globalisation and climate change. 7 / Dansk abstract Det Sibiriske og Nordamerikanske Arktis har være vidne til talrige folkevandringer af historiske kulture og med disse vandringer fulgte folks hunde. Denne afhandling bygger på fuld-genom-data fra 22 Arktisk Sibiriske og 72 Arktisk Nordamerikanske hunde, samt 186 mitokondrielle genomer fra Arktiske hunde fra Sibirien og Nordamerika. Det mitokondrielle genom data tydeliggøre de individuelle folkevandringer, hvormed ny hunde populationer indførtes til Nordamerika i forbindelse med indvandring af nye kulture. Yderligere viser data en hidtil ukendt mitokondriel klade i hunde fra Østsibirien og Alaska. Genetiske undersøgelser blev brugt til at bekræfte makroskopiske artsbestemmelser af pels, brugt i klædedragter af Arktiske folk. Pels bestemt som hund, blev brugt til stabilisotopiske undersøgelser, der viser forskellige i diæt hos forskelig hunde populationer cirkumpolært i Arktis. Data fra fulde genomer, tydeliggøre adskillige bølger af genetisk diversitet fra Vesteurasiske hunde der bliver indblandet i Sibiriske hunde, allerede fra for 10,900 år siden. Der ses opblanding med Mellemøstlig hundediversitet i hunde fra den Sibiriske steppe før sen bronzealder. Denne opblandede diversitet spredes op igennem Sibirien og når Nordvestsibirien i jernalderen, hvorefter yderligere Vesteurasiske hundediversitet optræder i Sibirien efter jernalderen. Alle hunde i det Nordamerikanske Arktis,