The Cave Lion (Panthera spelaea and Panthera fossilis)

[Balam]

Turns out that the cave lion diversification from the modern lion happened later than previously thought, with some researches considering subspecies of Panthera leo (in case there remained any doubts on their positions as true lions), but this is debatable.

Lions are one of the world’s most iconic megafauna, yet little is known about their temporal and spatial demographic history and population differentiation. We analyzed a genomic dataset of 20 specimens: two ca. 30,000-y-old cave lions (Panthera leo spelaea), 12 historic lions (Panthera leo leo/Panthera leo melanochaita) that lived between the 15th and 20th centuries outside the current geographic distribution of lions, and 6 present-day lions from Africa and India. We found that cave and modern lions shared an ancestor ca. 500,000 y ago and that the 2 lineages likely did not hybridize following their divergence. Within modern lions, we found 2 main lineages that diverged ca. 70,000 y ago, with clear evidence of subsequent gene flow. Our data also reveal a nearly complete absence of genetic diversity within Indian lions, probably due to well-documented extremely low effective population sizes in the recent past. Our results contribute toward the understanding of the evolutionary history of lions and complement conservation efforts to protect the diversity of this vulnerable species.

Previous studies based on partial fragments of the mitochondrial genome have estimated that cave and modern lions diverged ca. 500,000 y ago, using the appearance in the fossil record of the ancestral cave lion Panthera fossilis (5, 6). More recently, the divergence time was estimated to be 1.89 million years ago using full mitochondrial sequences and multiple fossil constraints (8). To investigate these discrepancies among estimates, and to fully resolve the position of cave lions in the phylogeny, we applied three independent methods that leverage the power of whole-genome sequences and do not rely on fossil record calibrations to estimate the divergence time between cave and modern lions.

First, we investigated the split time between the ancestral populations by estimating the probability F (Aderived|Bheterozygous) (17) of an individual A (such as the Siberian or Yukon cave lion) carrying a derived allele discovered as a heterozygote in a modern lion individual B. This summary statistic was then used to estimate the divergence time of the cave lion lineage given a model of population history in modern lions inferred using the pairwise sequential Markovian coalescent (PSMC) (18). We estimated that F(Cave lion|Modern lion) averaged at ∼0.15 (Fig. 2A), meaning that cave lions carry the derived allele in ∼15% of the heterozygous sites detected in modern lions (14.7 to 16.4%; SI Appendix, Table S2). From a simulation of the expected distribution pattern of F(Cave lion|Modern lion), given the population history of modern lions, a mutation rate (µ) of 4.5 × 10−9 per generation (11), and a generation time of 5 y (19), 

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We further explored the divergence time between cave and modern lions by exploiting the fact that the Siberian cave lion was a male (SI Appendix, Table S5). Male X chromosomes can be used to construct synthetic pseudodiploid genomes and estimate rates of coalescence between their ancestral populations. Since the effective population size (Ne) is inversely correlated with the amount of coalescing events occurring at a particular point in time, the Ne inferred from a pseudodiploid chromosome of two diverged populations should suddenly increase around the time of their divergence, as no coalescent events can happen after this estimated time assuming reproductive isolation occurred after the split. Indeed, we inferred from the PSMC of cave and each modern lion combined X chromosomes that there was a sharp increase in Ne to an unmeasurably large size ca. 495,000 y ago (Fig. 2B; 460,000 to 578,000 y ago, SI Appendix, Table S6). However, we caution that there may be added uncertainty around this estimate due to the low depth of coverage in the X-chromosome of the Siberian cave lion (1.96-fold, SI Appendix, Table S5).

We also assessed estimates of sequence divergence (dxy), which should be directly related to the split time (T) and the Ne of the common ancestor (Neanc) (dxy = 2Tµ + 4Nanc µ). We found that the mismatch rate between the Siberian cave lion and modern lions using only transversions was an average dxy = 0.00067 (SI Appendix, Fig. S6). Assuming that µ = 4.5 × 10−9 per generation (11), a transition/transversion ratio of 1.9 (SI section 4), a branch shortening in the Siberian cave lion of 6,000 generations (SI Appendix, Table S1) and Neanc of 55,000 individuals (Fig. 3A), we obtained a split time of ca. 108,000 generations [540,000 y assuming a generation time of 5 y (19)]. Given the general congruence among our estimates, we conclude that the most likely split time between cave and modern lions is ca. 500,000 y ago. This estimate is also remarkably consistent with the early Middle Pleistocene appearance of P. fossilis in the European fossil record (5).

Full study: https://www.pnas.org/content/early/2020/04/28/1919423117 Reply