Ancient DNA Analysis of the Oldest Canid Species from the Siberian Arctic and Genetic Contribution to the Domestic Dog

May Ancient DNA Analysis of the Oldest Canid Species from the Siberian Arctic and Genetic Contribution to the Domestic Dog Esther J. Lee 0 1 2 D. Andrew Merriwether 0 1 2 Alexei K. Kasparov 0 1 2 Pavel A. Nikolskiy 0 1 2 Marina V. Sotnikova 0 1 2 Elena Yu Pavlova 0 1 2 Vladimir V. Pitulko 0 1 2 0 Current address: Department of Sociology , Anthropology, and Social Work , Texas Tech University , Lubbock, TX , United States of America 1 1 Department of Anthropology, Binghamton University , Binghamton, NY , United States of America, 2 Department of Sociology , Anthropology, and Social Work , Texas Tech University , Lubbock, TX , United States of America, 3 Institute for the History of Material Culture, Russian Academy of Sciences , St. Petersburg , Russia , 4 Geological Institute, Russian Academy of Sciences , Moscow , Russia , 5 Arctic and Antarctic Research Institute , St. Petersburg , Russia 2 Academic Editor: David Caramelli, University of Florence , ITALY - Modern Arctic Siberia provides a wealth of resources for archaeological, geological, and paleontological research to investigate the population dynamics of faunal communities from the Pleistocene, particularly as the faunal material coming from permafrost has proven suitable for genetic studies. In order to examine the history of the Canid species in the Siberian Arctic, we carried out genetic analysis of fourteen canid remains from various sites, including the well-documented Upper Paleolithic Yana RHS and Early Holocene Zhokhov Island sites. Estimated age of samples range from as recent as 1,700 years before present (YBP) to at least 360,000 YBP for the remains of the extinct wolf, Canis cf. variabilis. In order to examine the genetic affinities of ancient Siberian canids species to the domestic dog and modern wolves, we obtained mitochondrial DNA control region sequences and compared them to published ancient and modern canid sequences. The older canid specimens illustrate affinities with pre-domestic dog/wolf lineages while others appear in the major phylogenetic clades of domestic dogs. Our results suggest a European origin of domestic dog may not be conclusive and illustrates an emerging complexity of genetic contribution of regional wolf breeds to the modern Canis gene pool. It is widely accepted that the domestic dog (Canis lupus familiaris) descended from the gray wolf (Canis lupus), but the process of domestication as well as geographical origin and approximate date of first domestication is still debated [1,2,3]. Genetic studies of modern dog and wolf populations have shown divergent views, from a single origin in East/South Asia [4,5] or the Near East [6] to multiple areas of domestication and/or hybridization with regional wolf breeds Competing Interests: The Ford Motor Company aided in the research of the Aachim Lighthouse site. There are no patents, products in development or marketed products to declare. This does not alter the authors' adherence to all the PLOS ONE policies on sharing data and materials. [6,7]. Furthermore, the possibility of admixture with other canid species has also been previously suggested [8,9]. On the other hand, recent mitochondrial genome analysis of ancient canids has suggested a European origin of domestic dogs [10]. Archaeological evidence is not always straightforward for the morphological identification of domestic dogs, especially as the earliest dogs were essentially the same size as wolves [11,12,13], but advanced morphometric analyses have improved the efforts [14,15,16]. The oldest archaeological evidence of domestic dog has been identified in western Europe and the Near East, dating to at least 14,000 cal BC [17,18]. Some have argued that domesticated dogs were present prior to the Last Glacial Maximum, but this is currently disputed [13,19,20,21,22]. Archaeological and paleontological research conducted in the Arctic Siberia within past couple of decades have yielded a large amount of bone material suitable for genetic studies, as they mostly come from permafrost deposits that are common in the area. Many ancient DNA studies have focused on extinct Pleistocene or wild species that occupied Siberia [23,24,25,26], but here we focus on the oldest domesticated species Canis. Different Canidae species, such as the arctic fox and wolf, were among the Pleistocene arctic fauna that continued into the present [27,28]. Within the region, studies have claimed the presence of dogs in the Russian Plain and Kamchatka by 13,000 cal BC [29,30]. A recent study has suggested the presence of a domestic dog in southern Siberia dated to ca. 33,300 cal BC, which predates the oldest evidence from western Europe and the Near East [22]. However, the Siberian canid remain was morphologically most similar to dogs from Greenland and unlike ancient and modern wolves and putative dogs from central Russia [22]. Sablin and Khlopachev [29] have argued that the presence of Pleistocene dog in the central Russian plain at Elis (...truncated)