Ancient DNA of narrow-headed vole reveal common features of the Late Pleistocene population dynamics in cold-adapted small mammals.

The narrow-headed vole, collared lemming and common vole were the most abundant small mammal species across the Eurasian Late Pleistocene steppe-tundra environment. Previous ancient DNA studies of the collared lemming and common vole have revealed dynamic population histories shaped by climatic fluctuations. To investigate the extent to which species with similar adaptations share common evolutionary histories, we generated a dataset comprised the mitochondrial genomes of 139 ancient and 6 modern narrow-headed voles from several sites across Europe and northwestern Asia covering approximately the last 100 thousand years (kyr). We inferred Bayesian time-aware phylogenies using 11 radiocarbon-dated samples to calibrate the molecular clock. Divergence of the main mtDNA lineages across the three species occurred during marine isotope stages (MIS) 7 and MIS 5, suggesting a common response of species adapted to open habitat during interglacials. We identified several time-structured mtDNA lineages in European narrow-headed vole, suggesting lineage turnover. The timing of some of these turnovers was synchronous across the three species, allowing us to identify the main drivers of the Late Pleistocene dynamics of steppe- and cold-adapted species.

Large giraffids (Mammalia, Ruminantia) from the new late Miocene fossiliferous locality of Kemiklitepe-E (Western Anatolia, Turkey).

Kemiklitepe is a well-known locality with four recognised fossiliferous horizons, KTA to KTD, which have yielded a plethora of mammalian remains. Previous taxonomic studies indicate the presence of three giraffid taxa: Samotherium major and Palaeotragus rouenii from the uppermost three horizons, KTA, KTB and KTC, as well as Palaeotragus rouenii and Samotherium? sp. from the lowermost KTD horizon. In this study a new locality, Kemiklitepe-E, is presented for the first time. Kemiklitepe-E is located approximately 350 m NW of the classic Kemiklitepe locality. The fossiliferous sedimentary rocks at Kemiklitepe-E occur at the same stratigraphic level as localities KTA, KTB and KTC. The preliminary faunal list includes representatives of Proboscidea, Chalicotheriidae, Equidae, Bovidae and Giraffidae. Comprehensive descriptions and comparisons of the Kemiklitepe-E Giraffidae specimens suggest the co-occurrence of two large giraffids: Samotherium major and Helladotherium duvernoyi. Samotherium major, previously documented from this region, is the most common taxon at Kemiklitepe. Helladotherium duvernoyi is rare at Kemiklitepe and here reported for the first time. The two taxa coexisted during the middle Turolian in Greece and Western Anatolia. In addition, it is suggested that specimens of Samotherium? sp described from KTD possibly belong to Samotherium neumayri. Based on the stratigraphic position of fossiliferous rocks, as well as the faunal data presented herein, the newly discovered locality is considered to be of middle Turolian (MN12) age.

Palaeodietary traits of large mammals from the middle Miocene of Gracanica (Bugojno Basin, Bosnia-Herzegovina).

Recent excavations at the Gracanica coal mine (Bugojno Basin, Bosnia-Herzegovina) have unearthed numerous skeletal parts of fossil vertebrates, including a noteworthy collection of mammalian remains. Previous palaeoecological investigations of the Dinarides Lake System were established using stratigraphical, palaeofloral, and malacological data. However, large mammal remains have so far not been used to reconstruct the terrestrial palaeoenvironment of this important fossil ecosystem. Here, the palaeodietary preferences of large mammals were investigated, using a multiproxy approach by employing dental microwear and dental mesowear analysis, in order to provide new perspectives on the terrestrial palaeoecology of the Dinarides Lake System. The dental microwear of all available adult mammalian teeth was analysed. Dental mesowear analysis was employed for ungulate and proboscidean taxa, using mesowear scores and mesowear angles, respectively. The analysis reveals the presence of browsing, "dirty browsing", and mixed-feeding herbivorous taxa, with seasonal fruit, or even grass intake. Additionally, the analysis of the carnivores suggests the presence of hyaena- and cheetah-like hypercarnivores, as well as generalists. The palaeodietary traits of the fossil mammals suggest a closed canopy-like environment, which is supported by the fossil plant assemblage. Palaeopalynological data confirm the omnipresence of fleshy fruit-bearing plants, herbaceous taxa, as well as grasses, which justifies the seasonal fruit browsing, the common "dirty browsing", and the occasional grazing behaviour visualized for some of the fossil mammals from Gracanica.

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

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.

Hyena paleogenomes reveal a complex evolutionary history of cross-continental gene flow between spotted and cave hyena.

The genus Crocuta (African spotted and Eurasian cave hyenas) includes several closely related extinct and extant lineages. The relationships among these lineages, however, are contentious. Through the generation of population-level paleogenomes from late Pleistocene Eurasian cave hyena and genomes from modern African spotted hyena, we reveal the cross-continental evolutionary relationships between these enigmatic hyena lineages. We find a deep divergence (~2.5 Ma) between African and Eurasian Crocuta populations, suggesting that ancestral Crocuta left Africa around the same time as early Homo. Moreover, we find discordance between nuclear and mitochondrial phylogenies and evidence for bidirectional gene flow between African and Eurasian Crocuta after the lineages split, which may have complicated prior taxonomic classifications. Last, we find a number of introgressed loci that attained high frequencies within the recipient lineage, suggesting some level of adaptive advantage from admixture.

Historical biogeography of the leopard (Panthera pardus) and its extinct Eurasian populations.

BACKGROUND: 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? RESULTS: 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. CONCLUSIONS: 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.

Mesopithecus pentelicus from the Turolian locality of Kryopigi (Kassandra, Chalkidiki, Greece).

New material of the Mio-Pliocene colobine Mesopithecus from the Turolian locality of Kryopigi (Greece) is described here. It includes a complete skull with the atlas attached and other dental and postcranial elements representing at least five individuals (four males and one female). The material is compared with Mesopithecus delsoni, Mesopithecus pentelicus, Mesopithecus monspessulanus and intermediate forms from more than a dozen Turolian localities of the Greco-Iranian province. These comparisons support the attribution of the Kryopigi material to M. pentelicus. The chronostratigraphic distribution of Mesopithecus species and intermediate forms suggests that the Kryopigi fauna could be dated as younger than the Perivolaki locality with M. delsoni/pentelicus (7.1-7.3 Ma, MN12) and older than the Dytiko localities with M. aff. pentelicus, M. cf. pentelicus and M. cf. monspessulanus (?middle MN13). The dimensions of the atlas are within the distribution of extant colobines. The skull shows bite-marks, probably caused by the hyaena Adcrocuta eximia.

Evolutionary History of Saber-Toothed Cats Based on Ancient Mitogenomics.

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].

Functional morphological adaptations of the bony labyrinth in marsupials (Mammalia, Theria).

Diprotodontia represents the largest and ecologically most distinct order of marsupials occurring in Australasian being highly divers in size, locomotion, habitat preferences, feeding, and activity pattern. The spatial orientation in the habitat and therefore the three-dimensional space is detected by the vestibular system of the inner ear, more precisely by the three semicircular canals. In this study, we investigated the bony labyrinth of diprotodontian and selected non-diprotodontian marsupial mammals of almost all genera with noninvasive micro-CT scanning and 3D-reconstructions. In principal component analyses, the subterranean taxon can be separated from gliding and saltatorial taxa, whereas arboreal species can be separated from saltatorial specimens. The highest PCA loadings of this functional distinction are clearly found in the diameter of the semicircular canals, whereas the overall shape (height, width, length) of the semicircular canals is less important. Additionally, the investigated arboreal and fossorial species of South America are nested in the morphospace of the Australasian taxa. Even if a phylogenetic signal in the anatomy of the bony labyrinth cannot be excluded entirely, the main functional morphological signal of the vestibular system is found in the diameter of the semicircular canals. With the large dataset of extant marsupial mammals analysed here, the locomotion mode of extinct taxa can be inferred in future studies independent of any evidence of postcranial material.

Palaeobiology of Hyaenodon exiguus (Hyaenodonta, Mammalia) based on morphometric analysis of the bony labyrinth.

Species of the extinct genus Hyaenodon were among the largest carnivorous mammals from the Late Eocene through Early Miocene in North America, Europe and Asia. The origin, phylogeny and palaeobiology of Hyaenodonta are still ambiguous. Most previous studies focused on teeth and dental function in these highly adapted species, which might be influenced by convergent morphologies. The anatomy of the bony labyrinth in vertebrates is generally quite conservative and, additionally, was used in functional-morphological studies. This study provides the first anatomical description of the bony labyrinth of the extinct European species Hyaenodon exiguus in comparison to selected extant carnivoran taxa discussed from a functional-morphological perspective. Hyaenodon exiguus may have occupied a hyaena-like dietary niche with a semi-arboreal lifestyle, based on the relative height, width and length of the semicircular canals of the inner ear. However, this contradicts previous functional-morphological studies focusing on the diameter of the canals, which presumably represent the signal of locomotion mode.

Effects of late quaternary climate change on Palearctic shrews.

The Late Quaternary was a time of rapid climatic oscillations and drastic environmental changes. In general, species can respond to such changes by behavioral accommodation, distributional shifts, ecophenotypic modifications (nongenetic), evolution (genetic) or ultimately face local extinction. How those responses manifested in the past is essential for properly predicting future ones especially as the current warm phase is further intensified by rising levels of atmospheric carbon dioxide. Here, we use ancient DNA (aDNA) and morphological features in combination with ecological niche modeling (ENM) to investigate genetic and nongenetic responses of Central European Palearctic shrews to past climatic change. We show that a giant form of shrew, previously described as an extinct Pleistocene Sorex species, represents a large ecomorph of the common shrew (Sorex araneus), which was replaced by populations from a different gene-pool and with different morphology after the Pleistocene Holocene transition. We also report the presence of the cold-adapted tundra shrew (S. tundrensis) in Central Europe. This species is currently restricted to Siberia and was hitherto unknown as an element of the Pleistocene fauna of Europe. Finally, we show that there is no clear correlation between climatic oscillations within the last 50 000 years and body size in shrews and conclude that a special nonanalogous situation with regard to biodiversity and food supply in the Late Glacial may have caused the observed large body size.

Influence of climate warming on arctic mammals? New insights from ancient DNA studies of the collared lemming Dicrostonyx torquatus.

BACKGROUND: Global temperature increased by approximately half a degree (Celsius) within the last 150 years. Even this moderate warming had major impacts on Earth's ecological and biological systems, especially in the Arctic where the magnitude of abiotic changes even exceeds those in temperate and tropical biomes. Therefore, understanding the biological consequences of climate change on high latitudes is of critical importance for future conservation of the species living in this habitat. The past 25,000 years can be used as a model for such changes, as they were marked by prominent climatic changes that influenced geographical distribution, demographic history and pattern of genetic variation of many extant species. We sequenced ancient and modern DNA of the collared lemming (Dicrostonyx torquatus), which is a key species of the arctic biota, from a single site (Pymva Shor, Northern Pre Urals, Russia) to see if climate warming events after the Last Glacial Maximum had detectable effects on the genetic variation of this arctic rodent species, which is strongly associated with a cold and dry climate. RESULTS: Using three dimensional network reconstructions we found a dramatic decline in genetic diversity following the LGM. Model-based approaches such as Approximate Bayesian Computation and Markov Chain Monte Carlo based Bayesian inference show that there is evidence for a population decline in the collared lemming following the LGM, with the population size dropping to a minimum during the Greenland Interstadial 1 (Bølling/Allerød) warming phase at 14.5 kyrs BP. CONCLUSION: Our results show that previous climate warming events had a strong influence on genetic diversity and population size of collared lemmings. Due to its already severely compromised genetic diversity a similar population reduction as a result of the predicted future climate change could completely abolish the remaining genetic diversity in this population. Local population extinctions of collared lemmings would have severe effects on the arctic ecosystem, as collared lemmings are a key species in the trophic interactions and ecosystem processes in the Arctic.

First DNA sequences from Asian cave bear fossils reveal deep divergences and complex phylogeographic patterns.

Until recently, cave bears were believed to have only inhabited Europe. However, recent morphological evidence suggests that cave bears' geographic range extended as far east as Transbaikalia, Eastern Siberia. These Asian cave bears were morphologically distinct from European cave bears. However, how they related to European lineages remains unclear, stressing the need to assess the phylogenetic and phylogeographic relationship between Asian cave bears and their European relatives. In this work, we address this issue using a 227 base-pair fragment of the mitochondrial control region obtained from nine fossil bone samples from eight sites from the Urals, Caucasus, Altai Mountains, Ukraine and Yana River region in Eastern Siberia. Results of the phylogenetic analyses indicate that (i) the cave bear from the Yana River is most closely related to cave bears from the Caucasus region; (ii) the Caucasus/Yana group of bears is genetically very distinct from both European cave bears and brown bears, suggesting that these bears could represent an independent species; and (iii) the Western European cave bear lineage reached at least temporarily to the Altai Mountains, 7000 km east of their known centre of distribution. These results suggest that the diversity of cave bears was greater than previously believed, and that they could survive in a much wider range of ecological conditions than previously assumed. They also agree with recent studies on other extinct and extant species, such as wolves, hyenas and steppe bison, which have also revealed higher genetic and ecological diversity in Pleistocene populations than previously known.

The population history of extant and extinct hyenas.

We have analyzed partial DNA sequences of the mitochondrial cytochrome b gene from extant striped, brown, and spotted hyenas as well as from Pleistocene cave hyenas. Sequences of the Pleistocene cave hyenas from Eurasia and modern spotted hyenas from Africa are intermixed in phylogenetic analyses, questioning any taxonomic delineation between the two groups. Contrary to cave hyenas in Eurasia, spotted hyenas in Africa show a phylogeographic pattern with little geographical overlap between two mitochondrial DNA (mtDNA) clades, suggesting two Pleistocene refugia in the north and south of Africa. Our results, furthermore, suggest three waves of migration from Africa to Eurasia for spotted hyenas, around 3, 1, and 0.3 MYA. A recent emigration of striped hyenas from Africa to Eurasia took place less than 0.1 MYA, resulting in a dramatic expansion of the geographical range of striped hyenas. In striped hyenas and within the geographical range of mtDNA clades in spotted hyenas, we found identical sequences several thousand kilometers apart, indicating a high rate of migration during the Pleistocene as well as the Holocene. Both striped and brown hyenas show low amounts of genetic diversity, with the latter ones displaying just a single haplotype.

Lack of phylogeography in European mammals before the last glaciation.

In many extant animal and plant species in Europe and North America a correlation exists between the geographical location of individuals and the genetic relatedness of the mitochondrial (mt) DNA sequences that they carry. Here, we analyze mtDNA sequences from cave bears, brown bears, cave hyenas, and Neandertals in Europe before the last glacial maximum and fail to detect any phylogeographic patterns similar to those observed in extant species. We suggest that at the beginning of the last glacial maximum, little phylogeographic patterns existed in European mammals over most of their geographical ranges and that current phylogeographic patterns are transient relics of the last glaciation. Cycles of retreat of species in refugia during glacial periods followed by incomplete dispersal from one refugium into other refugia during interglacial periods is likely to be responsible for the deep genetic divergences between phylogeographic clusters of mtDNA seen today.

Evidence for reproductive isolation between cave bear populations.

The European cave bear (Ursus spelaeus), which became extinct around 15,000 years ago, had several morphologically different forms. Most conspicuous of these were small Alpine cave bears found at elevations of 1,600 to 2,800 m. Whereas some paleontologists have considered these bears a distinct form, or even a distinct species, others have disputed this. By a combination of morphological and genetic methods, we have analyzed a population of small cave bears from Ramesch Cave (2,000 m altitude) and one of larger cave bears from Gamssulzen Cave (1,300 m), situated approximately 10 km apart in the Austrian Alps (Figure 1A). We find no evidence of mitochondrial gene flow between these caves during the 15,000 years when they were both occupied by cave bears, although mitochondrial DNA sequences identical to those from Gamssulzen Cave could be recovered from a site located about 200 km to the south in Croatia. We also find no evidence that the morphology of the bears in the two caves changed to become more similar over time. We suggest that the two cave bear forms may have represented two reproductively isolated subspecies or species.

Ancient DNA analyses reveal high mitochondrial DNA sequence diversity and parallel morphological evolution of late pleistocene cave bears.

Cave bears (Ursus spelaeus) existed in Europe and western Asia until the end of the last glaciation some 10,000 years ago. To investigate the genetic diversity, population history, and relationship among different cave bear populations, we have determined mitochondrial DNA sequences from 12 cave bears that range in age from about 26,500 to at least 49,000 years and originate from nine caves. The samples include one individual from the type specimen population, as well as two small-sized high-Alpine bears. The results show that about 49,000 years ago, the mtDNA diversity among cave bears was about 1.8-fold lower than the current species-wide diversity of brown bears (Ursus arctos). However, the current brown bear mtDNA gene pool consists of three clades, and cave bear mtDNA diversity is similar to the diversity observed within each of these clades. The results also show that geographically separated populations of the high-Alpine cave bear form were polyphyletic with respect to their mtDNA. This suggests that small size may have been an ancestral trait in cave bears and that large size evolved at least twice independently.