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 14 c 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. The cave lion (Panthera spelaea) was an apex predator across the Holarctic 1,2 until their extinction at the end of the Pleistocene 3 (last occurrence in the fossil record 14,219 ± 112 cal BP 4). Cave lions were larger than extant lions 5 , and Pleistocene cave art suggests that they did not have manes. However they may have shared several behavioural traits with their modern counterparts, such as group living and courtship rituals 6. Cave lion taxonomy has been contentious, being variously considered a subspecies of Panthera leo 7,8 , a sister species to extant lions (Panthera spelaea) 5,9 , or even being more closely related to the tiger (Panthera tigris spelaea) 10. In particular, the molecular estimate of the timing of the split between cave lions and extant lions has varied considerably between studies (~ 600 kya 8 ; 1.23-2.93 mya 11). Ersmark et al. 12 identified two major cave lion mitochondrial DNA haplogroups (based on ~ 348 bp of ATP8 and control region sequences) and showed that

Grey wolf genomic history reveals a dual ancestry of dogs

“…Samples ALAS_024, VAL_033, ALAS_016, VAL_008, HMNH_007, HMNH_011, VAL_050, VAL_005, DS04, VAL_037, VAL_012, VAL_011, VAL_18A, IN18_016 and IN18_005 were processed at the Swedish Museum of Natural History in Stockholm, Sweden, following previously described methods for permafrost bone and tooth samples 51 . In brief, this involved DNA extraction using the methodology of ref.…”

Geographic and temporal variability in Pleistocene lion-like felids: Implications for their evolution and taxonomy

“…The phylogenetic relationships of these felids and their taxonomic ranking are, however, still controversial and not well resolved. Morphological studies supplemented by molecular data in the past decades have provided support for both the species model (Terzea, 1965;Vereshchagin, 1971;Wiszniowska, 1978;Baryshnikov and Boeskorov, 2001;Sotnikova and Nikolskiy, 2006;Ovodov and Zaika, 2008;Barnett et al, 2009Barnett et al, , 2014Barnett et al, , 2016Christiansen and Harris, 2009;Mazák, 2010;Stuart and Lister, 2011;Ersmark et al, 2015;Chernova et al, 2020;Stanton et al, 2020) and the subspecies model Kurtén, 1968Kurtén, , 1985Hemmer, 1967Hemmer, , 1974Schütt, 1969;Schütt and Hemmer, 1978;Turner, 1984;Gross, 1992;Burger et al, 2004;Bona, 2006;Diedrich, 2008Diedrich, , 2009Diedrich, , 2011aDiedrich, , 2011cSchouwenburg et al, 2009;Baryshnikov and Tsoukala, 2010;Diedrich and Rathgeber, 2012;de Manuel et al, 2020). In addition, lions with their enormous Pleistocene geographic distribution from Africa through Eurasia up to America show relatively great morphological differences between regions.…”

The Preliminary Analysis of Cave Lion Cubs Panthera spelaea (Goldfuss, 1810) from the Permafrost of Siberia

“…In order to molecularly determine sex, we extracted DNA, built double-stranded Illumina libraries, and shotgun-sequenced the two cave lion samples of hair and skin following the approach of Stanton et al [11]. Briefly, the tissue was digested in a buffer optimised to digest keratin-rich tissues [12], before extracting DNA using the methodology of Yang et al [13].…”