Abstract
The cave lion is an extinct felid that was widespread across the Holarctic throughout the Late Pleistocene. Its closest extant relative is the lion (Panthera leo), but the timing of the divergence between these two taxa, as well as their taxonomic ranking are contentious. In this study we analyse 31 mitochondrial genome sequences from cave lion individuals that, through a combination of 14C and genetic tip dating, are estimated to be from dates extending well into the mid-Pleistocene. We identified two deeply diverged and well-supported reciprocally monophyletic mitogenome clades in the cave lion, and an additional third distinct lineage represented by a single individual. One of these clades was restricted to Beringia while the other was prevalent across western Eurasia. These observed clade distributions are in line with previous observations that Beringian and European cave lions were morphologically distinct. The divergence dates for these lineages are estimated to be far older than those between extant lions subspecies. By combining our radiocarbon tip-dates with a split time prior that takes into account the most up-to-date fossil stem calibrations, we estimated the mitochondrial DNA divergence between cave lions and lions to be 1.85 Million ya (95% 0.52– 2.91 Mya). Taken together, these results support previous hypotheses that cave lions existed as at least two subspecies during the Pleistocene, and that lions and cave lions were distinct species.
Highlights
The cave lion is an extinct felid that was widespread across the Holarctic throughout the Late Pleistocene
Cave lions were larger than extant lions[5], and Pleistocene cave art suggests that they did not have manes
Morphological analysis of skulls and mandibles has shown that cave lions from Yakutia, Alaska and the Yukon Territory are smaller than those from Europe, and led to the conclusion that Beringian lions should be recognised as a distinct subspecies “Panthera spelaea vereshchagini n.subsp"[13]
Summary
Sequencing reads from all samples were mapped to the cave lion mitochondrial genome (genbank accession number KX258452), and duplicates were removed using a custom perl script that removes reads with identical start and end positions, keeping the first observed such read. It has been known for some time that the Panthera genus has undergone a large translocation of mtDNA into the nuclear genome (numt)[29]. The samples were obtained with permission from all sample providers
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