Whole-genome sequencing data generated for the remains of four Pleistocene wolf specimens from sites in Northeast Siberia.

Extant Canis lupus genetic diversity can be grouped into three phylogenetically distinct clades: Eurasian grey wolves, American grey wolves, and domestic dogs. Genetic studies have suggested these three groups trace their origins to a wolf population that expanded during the Last Glacial Maximum (LGM), and potentially replaced local wolf populations. In addition, ancient genomes from the Yana basin and the Taimyr peninsula have provided evidence of at least one extinct wolf lineage that dwelled in Siberia during the Pleistocene. Previous studies have suggested that Pleistocene Siberian canids can be classified in two groups based on cranial morphology. Wolves in the first group are most similar to present-day populations, while those in the second group possess intermediate morphological features between domesticated dogs and wolves. However, whether this morphological classification represents distinct Pleistocene Siberian canid genetic groups remains unknown. To investigate this question, and the relationships between Pleistocene canids, present-day wolves and dogs, we resequenced the genomes of four Pleistocene canids from Northeast Siberia, dated between >50 to 14 thousand years old (ka), including samples from the two distinct morphological categories. When analysed alongside the genomes of ancient and present-day canids, we found that these four specimens cluster with two other previously sequenced Pleistocene wolves, which are genetically more similar to Eurasian wolves. Our results show that, though the four specimens represent extinct wolf lineages, they do not form a monophyletic group. Instead, each of the Pleistocene Siberian canids branched off the lineage that gave rise to present-day wolves and dogs. Finally, our results suggest the two previously described morphological groups could represent lineages derived from a large population of wolves, of which numerous lineages are now extinct.