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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.

BackgroundResolving the historical biogeography of the leopard(Panthera pardus)is a complex issue, because patterns inferred from fossils and from molecular data lack congruence. Fossil evidence supports an African origin, and suggests that leopards were already present in Eurasia during the Early Pleistocene. Analysis of DNA sequences however, suggests a more recent, Middle Pleistocene shared ancestry of Asian and African leopards. These contrasting patterns led researchers to propose a two-stage hypothesis of leopard dispersal out of Africa: an initial Early Pleistocene colonisation of Asia and a subsequent replacement by a second colonisation wave during the Middle Pleistocene. The status of Late Pleistocene European leopards within this scenario is unclear: were these populations remnants of the first dispersal, or do the last surviving European leopards share more recent ancestry with their African counterparts?ResultsIn this study, we generate and analyse mitogenome sequences from historical samples that span the entire modern leopard distribution, as well as from Late Pleistocene remains. We find a deep bifurcation between African and Eurasian mitochondrial lineages (∼710 Ka), with the European ancient samples as sister to all Asian lineages (∼483 Ka). The modern and historical mainland Asian lineages share a relatively recent common ancestor (∼122 Ka), and we find one Javan sample nested within these.ConclusionsThe phylogenetic placement of the ancient European leopard as sister group to Asian leopards suggests that these populations originate from the same out-of-Africa dispersal which founded the Asian lineages. The coalescence time found for the mitochondrial lineages aligns well with the earliest undisputed fossils in Eurasia, and thus encourages a re-evaluation of the identification of the much older putative leopard fossils from the region. The relatively recent ancestry of all mainland Asian leopard lineages suggests that these populations underwent a severe population bottleneck during the Pleistocene. Finally, although only based on a single sample, the unexpected phylogenetic placement of the Javan leopard could be interpreted as evidence for exchange of mitochondrial lineages between Java and mainland Asia, calling for further investigation into the evolutionary history of this subspecies.

The human skull of Rhunda in Central Germany is one of the rare human remains belonging to the cold episode of the Younger Dryas or GS-1 based on direct radiocarbon dating (10,200 ± 60 uncal BP GrA-15947). The return of periglacial conditions from northern France to northern Germany favoured the expansion of the reindeer herds, as testified by their numerous remains found at the Ahrensburgian sites. The isotopic composition of the collagen (δ 13 C coll and δ 15 N coll ) of the Rhunda individual provides insight into the relative dietary contribution of terrestrial ungulates, such as reindeer, compared to the intake of aquatic resources. The systematic higher δ 13 C coll values found for reindeer compared to horse during the Younger Dryas in northern Germany, the Ardennes and south-western England result from a different diet specialization, i.e. the high consumption of lichen by reindeer. The isotopic pattern evidenced in the Pleniglacial reflects such a niche partitioning, while the isotopic pattern of the Late-Glacial Interstadial reveals overlapping ranges in 13 C abundances in the different ungulates species, resulting most likely from a decrease in niche diversity. Despite their isotopic variability linked to trophic position and habitat, the freshwater fishes of the Belgian Ardennes show systematic higher δ 15 N coll values (6.6 to 11.7‰) than those of the terrestrial ungulates ( 15 N coll value of the Rhunda human (13‰) can thus be explained by an important consumption of freshwater resources, while the δ 13 C coll value (− 20.5‰) is too low to consider a significant input of anadromous fishes and their marine-influenced isotopic signature. The application of a Bayesian model confirms this pattern with a minimum contribution of 40% of aquatic resources as protein source for the human diet. In contrast, the input of protein of terrestrial origin hardly exceeded 40% of horse and 20% of reindeer meat consumption. Although existing archaeological and isotopic evidence already suggests a significant use of aquatic resources during the Late-Glacial, the human of Rhunda illustrates an intensive exploitation of the freshwater ecosystem at a time and latitude where the access to palatable plants must have been challenging.

Near the end of the Pleistocene epoch, populations of the woolly mammoth (Mammuthus primigenius) were distributed across parts of three continents, from western Europe and northern Asia through Beringia to the Atlantic seaboard of North America. Nonetheless, questions about the connectivity and temporal continuity of mammoth populations and species remain unanswered. We use a combination of targeted enrichment and high-throughput sequencing to assemble and interpret a data set of 143 mammoth mitochondrial genomes, sampled from fossils recovered from across their Holarctic range. Our dataset includes 54 previously unpublished mitochondrial genomes and significantly increases the coverage of the Eurasian range of the species. The resulting global phylogeny confirms that the Late Pleistocene mammoth population comprised three distinct mitochondrial lineages that began to diverge ~1.0–2.0 million years ago (Ma). We also find that mammoth mitochondrial lineages were strongly geographically partitioned throughout the Pleistocene. In combination, our genetic results and the pattern of morphological variation in time and space suggest that male-mediated gene flow, rather than large-scale dispersals, was important in the Pleistocene evolutionary history of mammoths.

Cave bears are among the most well known extinct Pleistocene mammals. Their biogeography and taxonomy, along with the factors that led to their extinction, have been subject to long-standing controversy. Here, we reconstruct the phylogeography as well as the temporal and spatial population dynamics of cave bears across their range using mitochondrial DNA control region sequences from 77 published as well as 65 new cave bear samples, Our analyses reveal a dramatic loss of genetic diversity in cave bear populations after 30,000 years before present and provide evidence for a range decline from east to west towards the onset of the last glacial maximum. Our results also suggest that the three major haplogroups within cave bears, which may correspond to distinct species, were previously more widespread, with relict populations in remote and alpine areas still harbouring haplotypes that have disappeared from most of their previous range. Applying a phylogenetic dating approach, we estimated the age of the oldest of our samples, originating from the Yana River region in north-eastern Siberia, to be around 178,000 years, which confirms a previous estimate of a Middle Pleistocene age based on its stratigraphic position. Our results extend our knowledge about the evolutionary history of cave bears, but they also show that to unravel the complexities of cave bear evolution future ancient DNA studies on this Pleistocene species will need to go beyond short mitochondrial DNA fragments, including full mitochondrial genomes as well as nuclear DNA sequences.

The causes of the late Pleistocene megafaunal extinctions are still enigmatic. Although the fossil record can provide approximations for when a species went extinct, the timing of its disappearance alone cannot resolve the causes and mode of the decline preceding its extinction. However, ancient DNA analyses can reveal population size changes over time and narrow down potential causes of extinction. Here, we present an ancient DNA study comparing late Pleistocene population dynamics of two closely related species, cave and brown bears. We found that the decline of cave bears started approximately 25,000 years before their extinction, whereas brown bear population size remained constant. We conclude that neither the effects of climate change nor human hunting alone can be responsible for the decline of the cave bear and suggest that a complex of factors including human competition for cave sites lead to the cave bear's extinction.

Lions were the most widespread carnivores in the late Pleistocene, ranging from southern Africa to the southern USA, but little is known about the evolutionary relationships among these Pleistocene populations or the dynamics that led to their extinction. Using ancient DNA techniques, we obtained mitochondrial sequences from 52 individuals sampled across the present and former range of lions. Phylogenetic analysis revealed three distinct clusters: (i) modern lions, Panthera leo; (ii) extinct Pleistocene cave lions, which formed a homogeneous population extending from Europe across Beringia (Siberia, Alaska and western Canada); and (iii) extinct American lions, which formed a separate population south of the Pleistocene ice sheets. The American lion appears to have become genetically isolated around 340,000 years ago, despite the apparent lack of significant barriers to gene flow with Beringian populations through much of the late Pleistocene. We found potential evidence of a severe population bottleneck in the cave lion during the previous interstadial, sometime after 48,000 years, adding to evidence from bison, mammoths, horses and brown bears that megafaunal populations underwent major genetic alterations throughout the last interstadial, potentially presaging the processes involved in the subsequent end-Pleistocene mass extinctions. Wiley Online Library

Caves are terrestrial depositories that preserve a large variety of organic and inorganic remains. These may contain important Quaternary climatic and ecological information. Most of the faunal remains, however, cannot be linked to any Interglacial or Glacial period exclusively. Reliable dating of such remains is therefore required. Experience has, however, shown that ESR dating of speleothems or 230 Th/U dating of bones are of disputable value. Only TIMS- 230 Th/U dating of speleothems appears to yield reliable ages. Dating the bottom and top of speleothem layers permit assigning Pleistocene faunal remains to the OIS chronology if the deposition of the speleothems and the faunal remains are clearly correlated. Care must be taken to consider the depositional situation of each site before interpreting any age dates. In this paper we present an overview of all numerically dated paleontological cave sites in Central Europe between OIS 5 and OIS 8. A total of 25 strata were dated from 13 sites, most of them deposited during OIS 5; the rest belonging to OIS 6 and 7. Numerically dated paleontological sites older than OIS 8 are not known.

The site of Hunas is a cave ruin, filled with bedded sediments up to the roof. About 20 m sediments from the top down were excavated and yielded Middle Paleolithic artifacts as well as numerous faunal remains, including Macaca. With a single human molar, the site is one of the rare Neanderthalian localities in Germany. New TIMS-U/Th dating of speleothems at the base of the profile indicate that the whole sequence was not deposited during the late Middle Pleistocene as previously thought, but during the last glacial. According to the new chronological results, Hunas is the only place which shows the coexistence of man and monkey in the Wurmian of Central Europe. The Macaca remains are the most recent evidence of magots in Central Europe so far.

Caves are among the most important sites preserving Quaternary fossils. Owing to the CaCO3-rich environment and the protection against erosion, even remains of early Pleistocene faunas are preserved in caves, while contemporaneous surface deposits have been lost. However, faunal remains cannot be linked to any interglacial or glacial period since no species exists which is characteristic of any specific period. Reliable dating of such remains is therefore required. This is now possible applying 230Th/U dating of speleothems. ESR dating of speleothems or 230Th/U dating of bones is, however, of disputable value. Dating of the base and top speleothem accretional layers permit assigning Pleistocene faunal remains to the MIS chronology. In this paper, we present for the first time an overview of all numerically dated palaeontological cave sites in Central Europe between MIS 5 and MIS 8. From twelve sites, a total of 31 strata were dated, most of them deposited during MIS 5; the rest belongs to MIS 6 and MIS 7; and only one sample representing MIS 8 provided reliable numerical dates. Numerically dated palaeontological cave sites older than MIS 8 are not known.

To reconstruct the phylogenetic position of the extinct cave lion (Panthera leo spelaea), we sequenced 1 kb of the mitochondrial cytochrome b gene from two Pleistocene cave lion DNA samples (47 and 32 ky B.P.). Phylogenetic analysis shows that the ancient sequences form a clade that is most closely related to the extant lions from Africa and Asia; at the same time, cave lions appear to be highly distinct from their living relatives. Our data show that these cave lion sequences represent lineages that were isolated from lions in Africa and Asia since their dispersal over Europe about 600 ky B.P., as they are not found among our sample of extant populations. The cave lion lineages presented here went extinct without mitochondrial descendants on other continents. The high sequence divergence in the cytochrome b gene between cave and modern lions is notable. © 2003 Elsevier Inc. All rights reserved.