Early Pleistocene origin and extensive intra-species diversity of the extinct cave lion

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.

Figure 1

Phylogeny based on 7,929 bp of the mitochondrial genome. Priors used for the TMRCA split between lions and cave lions were from Barnett et al. (2.08 mya, standard deviation of 0.52 mya). Branch thickness corresponds to posterior support (values given in Figure S5), with any values less than 0.5 shown by a hash). The eleven oldest splits all have posterior support > 0.95. Tip numbers correspond to sample IDs in Table S1, the x-axis scale is in ¹⁴C years before present.

Figure 2

Location of all specimens included in this study (see Table S1 for detailed sample information). Red and blue dots correspond to clades B and C respectively, and the white dot corresponds to the single representative of “Lineage A” (Fig. 1) Numbers correspond to sample number (in parentheses) and radiocarbon years before present, unless suffixed by an asterisk, in which case they were estimated by BEAST (see Methods; 95% credibility intervals given in Table S2). Map created using QGIS v2.12.1-Lyon (https://qgis.org/en/site/).