Polar bears (Ursus maritimus) are among those species most susceptible to the rapidly changing arctic climate, and their survival is of global concern. Despite this, little is known about polar bear ...species history. Future conservation strategies would significantly benefit from an understanding of basic evolutionary information, such as the timing and conditions of their initial divergence from brown bears (U. arctos) or their response to previous environmental change.
We used a spatially explicit phylogeographic model to estimate the dynamics of 242 brown bear and polar bear matrilines sampled throughout the last 120,000 years and across their present and past geographic ranges. Our results show that the present distribution of these matrilines was shaped by a combination of regional stability and rapid, long-distance dispersal from ice-age refugia. In addition, hybridization between polar bears and brown bears may have occurred multiple times throughout the Late Pleistocene.
The reconstructed matrilineal history of brown and polar bears has two striking features. First, it is punctuated by dramatic and discrete climate-driven dispersal events. Second, opportunistic mating between these two species as their ranges overlapped has left a strong genetic imprint. In particular, a likely genetic exchange with extinct Irish brown bears forms the origin of the modern polar bear matriline. This suggests that interspecific hybridization not only may be more common than previously considered but may be a mechanism by which species deal with marginal habitats during periods of environmental deterioration.
► Polar bears and brown bears have been hybridizing throughout the last 100,000 years ► The current polar bear matriline descends from brown bears that lived near Ireland ► This matriline most likely originated prior to or during the last ice age ► The dynamics of bear matrilines have been driven by largely by climate change
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
Over 60% of the modern distribution range of brown bears falls within Russia, yet palaeoecological data from the region remain scarce. Complete modern Russian brown bear mitogenomes are abundant in ...the published literature, yet examples of their ancient counterparts are absent. Similarly, there is only limited stable isotopic data of prehistoric brown bears from the region. We used ancient DNA and stable carbon (δ
C) and nitrogen (δ
N) isotopes retrieved from five Pleistocene Yakutian brown bears (one Middle Pleistocene and four Late Pleistocene), to elucidate the evolutionary history and palaeoecology of the species in the region. We were able to reconstruct the complete mitogenome of one of the Late Pleistocene specimens, but we were unable to assign it to any of the previously published brown bear mitogenome clades. A subsequent analysis of published mtDNA control region sequences, which included sequences of extinct clades from other geographic regions, assigned the ancient Yakutian bear to the extinct clade 3c; a clade previously identified from Late Quaternary specimens from Eastern Beringia and Northern Spain. Our analyses of stable isotopes showed relatively high δ
N values in the Pleistocene Yakutian brown bears, suggesting a more carnivorous diet than contemporary brown bears from Eastern Beringia.
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IZUM, KILJ, NUK, PILJ, PNG, SAZU, UL, UM, UPUK
Human colonization of the New World is generally believed to have entailed migrations from Siberia across the Bering isthmus. However, the limited archaeological record of these migrations means that ...details of the timing, cause and rate remain cryptic. Here, we have used a combination of ancient DNA, 14C dating, hydrogen and oxygen isotopes, and collagen sequencing to explore the colonization history of one of the few other large mammals to have successfully migrated into the Americas at this time: the North American elk (Cervus elaphus canadensis), also known as wapiti. We identify a long-term occupation of northeast Siberia, far beyond the species’s current Old World distribution. Migration into North America occurred at the end of the last glaciation, while the northeast Siberian source population became extinct only within the last 500 years. This finding is congruent with a similar proposed delay in human colonization, inferred from modern human mitochondrial DNA, and suggestions that the Bering isthmus was not traversable during parts of the Late Pleistocene. Our data imply a fundamental constraint in crossing Beringia, placing limits on the age and mode of human settlement in the Americas, and further establish the utility of ancient DNA in palaeontological investigations of species histories.
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BFBNIB, NMLJ, NUK, PNG, SAZU, UL, UM, UPUK
The mandible size variability including sexual size dimorphism (SSD) of the cave lion (Panthera spelaea) in the Pleistocene of Northern Eurasia time has been studied basing on the univariate and ...multivariate statistical analyses of 76 specimens from 43 localities. It has been confirmed that SSD in adult P. spelaea, as well as in extant P. leo, is the dominant form of group variability of mandible and, to somewhat lesser extent, of variability of cheek teeth. The lowest degree of SSD has been found in a relatively small Beringian subspecies, P. spelaea vereshchagini. The geographical variability of the cave lion from Western to Eastern Eurasia was not a cline at least in the Late Pleistocene. Our results confirm a decrease in overall mandible size from the Middle Pleistocene to the Late Pleistocene over a large part of the species' range. We speculate that evolutionary changes in mandible size, lower canines or cheek teeth may have proceeded at different rates, allometry and probable heterochrony. Our results have added a new evidence to support the subspecies status of the Beringian lion (P. spelaea vereshchagini), but they are insufficient for other decisions on cave lion taxonomy at the subspecies level.
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BFBNIB, GIS, IJS, KISLJ, NUK, PNG, UL, UM, UPUK
Saber-toothed cats (Machairodontinae) are among the most widely recognized representatives of the now largely extinct Pleistocene megafauna. However, many aspects of their ecology, evolution, and ...extinction remain uncertain. Although ancient-DNA studies have led to huge advances in our knowledge of these aspects of many other megafauna species (e.g., mammoths and cave bears), relatively few ancient-DNA studies have focused on saber-toothed cats 1–3, and they have been restricted to short fragments of mitochondrial DNA. Here we investigate the evolutionary history of two lineages of saber-toothed cats (Smilodon and Homotherium) in relation to living carnivores and find that the Machairodontinae form a well-supported clade that is distinct from all living felids. We present partial mitochondrial genomes from one S. populator sample and three Homotherium sp. samples, including the only Late Pleistocene Homotherium sample from Eurasia 4. We confirm the identification of the unique Late Pleistocene European fossil through ancient-DNA analyses, thus strengthening the evidence that Homotherium occurred in Europe over 200,000 years later than previously believed. This in turn forces a re-evaluation of its demography and extinction dynamics. Within the Machairodontinae, we find a deep divergence between Smilodon and Homotherium (∼18 million years) but limited diversity between the American and European Homotherium specimens. The genetic data support the hypothesis that all Late Pleistocene (or post-Villafrancian) Homotherium should be considered a single species, H. latidens, which was previously proposed based on morphological data 5, 6.
•We present the first near-complete mitochondrial genomes from saber-toothed cats•Smilodon and Homotherium are estimated to have diverged ca. 18 million years ago•We find limited genetic divergence between American and European Homotherium•Late Pleistocene Homotherium should be considered a single species: H. latidens
Paijmans et al. present ancient DNA from some of the most recognized extinct Pleistocene megafauna: the saber-toothed cats. The results elucidate the evolutionary history of these iconic carnivores and provide genetic evidence that saber-toothed cats existed in Europe over 200,000 years later than previously believed.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
Museum collections are essential for reconstructing and understanding past biodiversity. Many museum specimens are, however, challenging to identify. Museum samples may be incomplete, have an unusual ...morphology, or represent juvenile individuals, all of which complicate accurate identification. In some cases, inaccurate identification can lead to false biogeographic reconstructions with cascading impacts on paleontological and paleoecological research. Here, we analyzed an unusual Equid mandible found in the Far North of the Taymyr peninsula that was identified morphologically as Equus hemionus, an ancestor of present‐day Asiatic wild asses. If correct, this identification represents the only finding of a putative Late Pleistocene hemione in the Arctic region, and is therefore critical to understanding wild ass evolution and paleoecology. To confirm the accuracy of this specimen's taxonomic assignment, we used ancient DNA and mitochondrial hybridization capture to identify and place this specimen in the larger equid phylogeny. We find that the specimen is actually a member of E. caballus, the ancestor of domestic horses. Our study demonstrates the utility of ancient DNA to validate morphological identification, in particular of incomplete, otherwise problematic, or taxonomically unusual museum specimens.
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BFBNIB, FZAB, GIS, IJS, KILJ, NLZOH, NUK, OILJ, SAZU, SBCE, SBMB, UL, UM, UPUK
Prior to the Holocene, the range of the saiga antelope (Saiga tatarica) spanned from France to the Northwest Territories of Canada. Although its distribution subsequently contracted to the steppes of ...Central Asia, historical records indicate that it remained extremely abundant until the end of the Soviet Union, after which its populations were reduced by over 95%. We have analysed the mitochondrial control region sequence variation of 27 ancient and 38 modern specimens, to assay how the species’ genetic diversity has changed since the Pleistocene. Phylogenetic analyses reveal the existence of two well‐supported, and clearly distinct, clades of saiga. The first, spanning a time range from >49 500 14C ybp to the present, comprises all the modern specimens and ancient samples from the Northern Urals, Middle Urals and Northeast Yakutia. The second clade is exclusive to the Northern Urals and includes samples dating from between 40 400 to 10 250 14C ybp. Current genetic diversity is much lower than that present during the Pleistocene, an observation that data modelling using serial coalescent indicates cannot be explained by genetic drift in a population of constant size. Approximate Bayesian Computation analyses show the observed data is more compatible with a drastic population size reduction (c. 66–77%) following either a demographic bottleneck in the course of the Holocene or late Pleistocene, or a geographic fragmentation (followed by local extinction of one subpopulation) at the Holocene/Pleistocene transition.
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BFBNIB, FZAB, GIS, IJS, KILJ, NLZOH, NUK, OILJ, SAZU, SBCE, SBMB, UL, UM, UPUK
Cementum and dentine increment analysis was used for the first time to study the remains of cave bears from European Russia, the Urals and the Caucasus. This study analysed 12 canines belonging to 12 ...different individuals (five males and seven females) from genetically different lineages of cave bears. The increment analysis showed that all studied cave bears belong to the categories adults and old animals (from 10 to 32.5 years). The enamel crowns of all 12 canines were broken and/or had wear facets. Seven canines studied were severely broken (more than one‐third of a canine crown missing). Significant damage to dental crowns may indicate old age, conflict between males and/or high food abrasion. The absence of significant differences in the extent of canine breakage between the youngest and the oldest animals, as well as between the males and the females, may indicate a significant role of food abrasiveness in the process of the grinding of canines. Until now, the question of whether these animals visited caves year‐round or stayed there mainly for overwintering remained open. The increment analysis showed different seasons of the bears’ death. Six individuals died in the warm season and four individuals died in the cold season. In all of the studied caves (excluding Medvezhiya Cave) the animals died in the warm season as well as in the cold season. All of the studied females perished either during the cold season or at the very beginning of the warm season. On the contrary, almost all of the examined males perished in the warm season. Thus, the cave bears visited the caves year‐round. This study raises new questions in the study of the ecology of cave bears from different parts of their range.
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FZAB, GIS, IJS, KILJ, NLZOH, NUK, OILJ, SAZU, SBCE, SBMB, UL, UM, UPUK
Morphological and molecular data suggest the existence of several taxa of cave bears, which were found to belong to three major mitochondrial haplogroups: kudarensis (
kudarensis), spelaeus (
...ladinicus, eremus, spelaeus), and ingressus (
uralensis, ingressus,
kanivetz). An analysis of craniometrical variability was carried out based on 20 measurements of 279 skulls from 40 European, Ural, and Caucasian localities, in order to investigate morphological similarity/dissimilarity of these taxa in a multivariate approach. The craniometrical analysis divides cave bears into two groups: small cave bears and large cave bears. The group of small bears consists of
rossicus/
uralensis and
ladinicus. In some skull proportions, these taxa display intermediate position between brown and cave bears, i.e. presumably possessing archaic characters of their common ancestor. The group of large bears includes taxa with more specialized skulls. An early radiation within this group is demonstrated by
kudarensis which probably ranged across Asia, and
deningeri which occupied Europe east to the Ural Mountains. In its craniometrical characters,
kanivetz from the Late Pleistocene of the Urals resembles
deningeri. Other taxa of large cave bears (
spelaeus, ingressus and
eremus) reveal further evolution of cranial characters, being similar in the skull proportions. The level of difference between
spelaeus and
ingressus does not exceed that between subspecies of the recent brown bear, such as
Ursus arctos beringianus and
U. a. piscator. The examined isolated population of large cave bears from Volga River region (Zhiguli Hills) is similar to
ingressus. Thus, based on the craniometrical data, the following species of cave bear are recognized:
Ursus kudarensis (with the subspecies
U. k. praekudarensis and
U. k. kudarensis),
U. deningeri (several subspecies),
U. rossicus (with subspecies
U. r. rossicus and
U. r. uralensis),
U. ladinicus,
U. spelaeus (with subspecies
U. s. spelaeus, U. s. eremus, U. s. ingressus, and, provisionally,
U. s. kanivetz,).
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UL, UM, UPCLJ, UPUK
Resolving 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?
In 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.
The 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.
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DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
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