Genomes of Pleistocene Siberian Wolves Uncover Multiple Extinct Wolf Lineages

Abstract

Summary Extant Canis lupus genetic diversity can be grouped into three phylogenetically distinct clades: Eurasian and American wolves and domestic dogs. 1 Genetic studies have suggested these groups trace their origins to a wolf population that expanded during the last glacial maximum (LGM) 1 , 2 , 3 and replaced local wolf populations. 4 Moreover, ancient genomes from the Yana basin and the Taimyr peninsula provided evidence of at least one extinct wolf lineage that dwelled in Siberia during the Pleistocene. 3 5 Previous studies have suggested that Pleistocene Siberian canids can be classified into two groups based on cranial morphology. Wolves in the first group are most similar to present-day populations, although those in the second group possess intermediate features between dogs and wolves. 6 7 However, whether this morphological classification represents distinct 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 and 14 ka old, including samples from the two morphological categories. We found these specimens cluster with the two 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 Pleistocene Siberian canid 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 independent lineages similarly related to present-day wolves and dogs.

Genome-scale sequencing and analysis of human, wolf, and bison DNA from 25,000-year-old sediment

“…Previous studies have found that presentday wolf population structure has mostly formed after the LGM. 23,34,[36][37][38][39] Our results are consistent with this scenario because the SAT29 environmental genome harbored an Article ancestry that diverged from the ancestors of modern wolves and dogs before these diversified. Although Late Pleistocene wolves in the Caucasus were not closely related to those in Siberia, they thus had a similarly basal ancestry that has either gone extinct or been transformed by later population processes.…”

Dog domestication and the dual dispersal of people and dogs into the Americas

“…mtDNA analyses of these canids also showed that they belong to an ancient European wolf lineage that is genetically highly divergent from any dog haplogroup (30). Similarly, genetic analyses of proposed Paleolithic dogs from the sites of Ulakhan Sular (23), Tumat (46), Razboinichya (27), Berelekh (23), Kostenki 8 (23), and Eliseevichi (25) have shown these canids to be more closely related to ancient and modern wolves than they are to dogs (30,37,47).…”

Examining Natural History through the Lens of Palaeogenomics

“…However, mitochondrial data represent only a single maternally inherited non-recombining locus, meaning that they do not always reveal the nuances of past population processes. Consequently, it is possible that local populations of grey wolves in Eurasia still derive substantial nuclear genomic ancestry from much older Quaternary populations that remained in situ, though available palaeogenomic data suggest this is unlikely to be the case [96]. Conversely, palaeogenomic data from a 5000 year old giant panda (Ailuropoda melanoleuca) specimen, from outside the current range of the species, revealed a genetic contribution and connection with modern populations that are not reflected in the mitochondrial data [57].…”