The Asiatic wild dog (Cuon alpinus), restricted today largely to South and Southeast Asia, was widespread throughout Eurasia and even reached North America during the Pleistocene. Like many other species, it suffered from a huge range loss towards the end of the Pleistocene and went extinct in most of its former distribution. The fossil record of the dhole is scattered and the identification of fossils can be complicated by an overlap in size and a high morphological similarity between dholes and other canid species. We generated almost complete mitochondrial genomes for six putative dhole fossils from Europe. By using three lines of evidence, i.e., the number of reads mapping to various canid mitochondrial genomes, the evaluation and quantification of the mapping evenness along the reference genomes and phylogenetic analysis, we were able to identify two out of six samples as dhole, whereas four samples represent wolf fossils. This highlights the contribution genetic data can make when trying to identify the species affiliation of fossil specimens. The ancient dhole sequences are highly divergent when compared to modern dhole sequences, but the scarcity of dhole data for comparison impedes a more extensive analysis.

Department of Biological Sciences University at Albany 1400 Washington Avenue Albany NY 12222 USA

Department of Genetics and Genome Biology University of Leicester Leicester LE1 7RH UK

Department of Geology Faculty of Geology and Geophysics University of Bucharest 1 Nicolae Bălcescu Avenue 010041 Bucharest Romania

Department of Paleozoology Faculty of Biological Sciences University of Wrocław Sienkiewicza 21 50 335 Wrocław Poland

Emil Racoviţă Institute of Speleology Romanian Academy 31 Frumoasă Street 010986 Bucharest Romania

Institute for Biochemistry and Biology University of Potsdam Karl Liebknecht Str 24 25 14476 Potsdam Germany

Moravian Museum Anthropos Institute Zelný trh 6 65937 Brno Czech Republic

Research Institute of the University of Bucharest Earth Environmental and Life Sciences Division Panduri 90 92 050663 Bucharest Romania

School of Science and Technology Nottingham Trent University Clifton Lane Nottingham NG11 8NS UK

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