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The grey wolf (Canis lupus) was the first species to give rise to a domestic population, and they remained widespread throughout the last Ice Age when many other large mammal species went extinct. Little is known, however, about the history and possible extinction of past wolf populations or when and where the wolf progenitors of the present-day dog lineage (Canis familiaris) lived1–8. Here we analysed 72 ancient wolf genomes spanning the last 100,000 years from Europe, Siberia and North America. We found that wolf populations were highly connected throughout the Late Pleistocene, with levels of differentiation an order of magnitude lower than they are today. This population connectivity allowed us to detect natural selection across the time series, including rapid fixation of mutations in the gene IFT88 40,000–30,000 years ago. We show that dogs are overall more closely related to ancient wolves from eastern Eurasia than to those from western Eurasia, suggesting a domestication process in the east. However, we also found that dogs in the Near East and Africa derive up to half of their ancestry from a distinct population related to modern southwest Eurasian wolves, reflecting either an independent domestication process or admixture from local wolves. None of the analysed ancient wolf genomes is a direct match for either of these dog ancestries, meaning that the exact progenitor populations remain to be located. © 2022, The Author(s). 8028-00005B; IP DKRVO 2019-2023, MK000094862; 220457/Z/20/Z, ERC-2013-StG-337574-UNDEAD, ERC-2019-StG-853272-PALAEOFARM; 075-15-2021-1069; European Molecular Biology Organization, EMBO: 217223/Z/19/Z; Vallee Foundation; Velux Fonden; Wellcome Trust, WT; Francis Crick Institute, FCI: FC001595; Horizon 2020 Framework Programme, H2020: 796877; Medical Research Council, MRC; Natural Environment Research Council, NERC: 210119/Z/18/Z, NE/K003259/1, NE/K005243/1, NE/S00078X/1, NE/S007067/1; Cancer Research UK, CRUK; European Research Council, ERC: 852558; Grantová Agentura České Republiky, GA ČR: 15-06446S; Svenska Forskningsrådet Formas: 2018-01640; Knut och Alice Wallenbergs Stiftelse; Vetenskapsrådet, VR: 681396, BELSPO B2/191/P2/ICHIE; Russian Science Foundation, RSF: 16-18-10265-RNF, 20-17-00033, 21-18-00457-RNF, 310763; Science for Life Laboratory, SciLifeLab; Narodowa Agencja Wymiany Akademickiej, NAWA: PPN/PPO/2018/1/00037 This work was supported by grants to P. Skoglund from the European Research Council (grant no. 852558), the Erik Philip Sörensen Foundation and the Science for Life Laboratory, Swedish Biodiversity Program, made available by support from the Knut and Alice Wallenberg Foundation. A.B., L.S., P. Swali and P. Skoglund were supported by Francis Crick Institute core funding (FC001595) from Cancer Research UK, the UK Medical Research Council and the Wellcome Trust. P. Skoglund was also supported by the Vallee Foundation, the European Molecular Biology Organisation and the Wellcome Trust (217223/Z/19/Z). Computations were supported by SNIC-UPPMAX. We also acknowledge support from Science for Life Laboratory, the Knut and Alice Wallenberg Foundation, the National Genomics Infrastructure funded by the Swedish Research Council and the Uppsala Multidisciplinary Center for Advanced Computational Science for assistance with massively parallel sequencing and access to the UPPMAX computational infrastructure. We thank the Yukon gold mining community and First Nations, including the Tr’ondëk Hwëch’in, for continued support of our palaeontology research in the Yukon Territories, Canada. We thank the Danish National High-Throughput Sequencing Centre and BGI-Europe for assistance in sequencing data generation and the Danish National Supercomputer for Life Sciences–Computerome ( https://computerome.dtu.dk ) for computational resources. We thank National Museum Wales for continued sampling support. M. Germonpré acknowledges support from the Brain.be 2.0 ICHIE project (BELSPO B2/191/P2/ICHIE). M.T.P.G. was supported by the European Research Council (grant no. 681396). M.-H.S.S. was supported by the Velux Foundations through the Qimmeq Project, the Aage og Johanne Louis-Hansens Fond and the Independent Research Fund Denmark (8028-00005B). L.D. acknowledges support from FORMAS (2018-01640). D.W.G.S. received funding for this project from the European Union’s Horizon 2020 research and innovation programme under Marie Skłodowska-Curie grant agreement no. 796877. M.P. was supported by the Polish National Agency for Academic Exchange–NAWA (grant no. PPN/PPO/2018/1/00037). V.J.S. was supported by the University of Zurich’s University Research Priority Program ‘Evolution in Action: From Genomes to Ecosystems’. This research was done with the participation of ZIN RAS (grant no. 075-15-2021-1069). We are grateful to the museum of the Institute of Plant and Animal Ecology UB RAS (Ekaterinburg, Russia) for provision of samples. R.P.J. and C.O’D. were supported by the Standing Committee for Archaeology of the Royal Irish Academy through the Archaeological Excavation Research Grant Scheme. E.Y.P., P.N. and V.V.P. are supported by the Russian Science Foundation (grant no. 16-18-10265-RNF and 21-18-00457-RNF). Y.V.K. was supported by the Russian Science Foundation (grant no. 20-17-00033). M.H. was supported by the European Research Council (consolidator grant GeneFlow no. 310763). M.L.-G. was supported by the Czech Science Foundation GAČR (grant no. 15-06446S) and institutional financing of the Moravian Museum from the Czech Ministry of Culture (IP DKRVO 2019-2023, MK000094862). L.S. is supported by the Sir Henry Wellcome fellowship (220457/Z/20/Z). We thank Staatliches Museum für Naturkunde Stuttgart for sample access. L.F. and G.L. were supported by European Research Council grants (ERC-2013-StG-337574-UNDEAD and ERC-2019-StG-853272-PALAEOFARM) and Natural Environmental Research Council grants (NE/K005243/1, NE/K003259/1, NE/S007067/1 and NE/S00078X/1). L.F. was also supported by the Wellcome Trust (210119/Z/18/Z). This research was funded in whole, or in part, by the Wellcome Trust (FC001595). For the purpose of open access, the author has applied a CC-BY public copyright licence to any author accepted manuscript version arising from this submission.

Dogs are known to be the oldest animals domesticated by humans. Although many studies have examined wolf domestication, the geographic and temporal origin of this process is still being debated. To address this issue, our study sheds new light on the early stages of wolf domestication during the Magdalenian period (16–14 ka cal BP) in the Hegau Jura region (Southwestern Germany and Switzerland). By combining morphology, genetics, and isotopes, our multidisciplinary approach helps to evaluate alternate processes driving the early phases of domestication. The isotope analysis uncovered a restricted, low δ15N protein diet for all analyzed Gnirshöhle specimens, while morphological examinations and phylogenetic relationships did not unequivocally assign them to one or the other canid lineage. Intriguingly, the newly generated mitochondrial canid genomes span the entire genetic diversity of modern dogs and wolves. Such high mitochondrial diversity could imply that Magdalenian people tamed and reared animals originating from different wolf lineages. We discuss our results in light of three ecological hypotheses and conclude that both domestication and the existence of a specialized wolf ecomorph are highly probable. However, due to their proximity to humans and a restricted diet, we propose domestication as the most likely scenario explaining the patterns observed herein.

Mammoth (Mammuthus primigenius) is one of the main game species during the Upper Palaeolithic in the Swabian Jura. Procurement and exploitation of this mega mammal shows quantitative differences and qualitative changes between the Aurignacian and the Gravettian periods. The raw material ivory in the Aurignacian became replaced by mammoth ribs in the Gravettian accompanied by technological changes concerning points as well as cultural changes concerning jewelry. Although some signs of climatic deterioration from the Aurignacian to the Gravettian are evident and the ecological niche of mammoth is partly occupied by horses in both periods, the habitat of the mammoth populations does not seem to have been endangered. From the point of view of the organic artefact industry, we argue for a clear cultural break, in contrast to a degree of continuity observed in the lithic industry.

The evidence of modern and complex behavior is a key debate in human evolution. Neanderthals have been excluded from this debate from many years, until new insight have provided a new conception of the Neanderthal behavior. Nevertheless, although archaeological data of complex and modern behavior has been inferred, this is not a generalized scenario in Middle Paleolithic sites. In the present paper, we point taphonomical issues as the responsible for this misconservation of cognitive markers. Furthermore, we highlight the action of ursids as one of the agents that has most modified the archaeological record. Nevertheless, bears not just erase behavioral evidences, their action may also generate material realities that can be misinterpreted by archaeologist as Neanderthal behavioral markers. In the present paper we analyze issues related to organized use of space and symbolic behavior such as inhumation practices and graphical expression. We approach this issue from a multidisciplinary research based mainly in actualistic, experimental, paleontological and ethological observations.

The cave bear (Ursus spelaeus) is one of the Late Pleistocene megafauna species that faced extinction at the end of the last ice age. Although it is represented by one of the largest fossil records in Europe and has been subject to several interdisciplinary studies including palaeogenetic research, its fate remains highly controversial. Here, we used a combination of hybridisation capture and next generation sequencing to reconstruct 59 new complete cave bear mitochondrial genomes (mtDNA) from 14 sites in Western, Central and Eastern Europe. In a Bayesian phylogenetic analysis, we compared them to 64 published cave bear mtDNA sequences to reconstruct the population dynamics and phylogeography during the Late Pleistocene. We found five major mitochondrial DNA lineages resulting in a noticeably more complex biogeography of the European lineages during the last 50,000 years than previously assumed. Furthermore, our calculated effective female population sizes suggest a drastic cave bear population decline starting around 40,000 years ago at the onset of the Aurignacian, coinciding with the spread of anatomically modern humans in Europe. Thus, our study supports a potential significant human role in the general extinction and local extirpation of the European cave bear and illuminates the fate of this megafauna species. © 2019, The Author(s). Introduction Results - Sample collection and processing - Phylogenetic analysis - Population size analysis Discussion - Phylogeography and population dynamics - Extinction Material and Methods - Sample collection - DNA extraction - Sequence processing - Data from other studies - Alignment and model selection - Inferring phylogenetic relationships - Comparison of D-Loop and Mitogenome Tree Topology Differences - Bayesian phylogenetic inference and demographic reconstruction - Accession numbers

Fox (Vulpes vulpes and Vulpes lagopus), wolf (Canis lupus) and dog (Canis lupus familiaris) remains are commonly found in the faunal assemblages of Magdalenian sites in Central Europe. However, little is known about their ecology in terms of food preference and niche partitioning. We hypothesize that domestication leads to a new trophic niche for dogs and even for commensal animals, such as foxes, compared to their wild counterparts (i.e. wolves and wild non-commensal foxes). To test our hypothesis, we used stable isotope analysis (δ13C, δ15N) of bone collagen extracted from canid bones from several Magdalenian sites in southwestern Germany and Switzerland (between 17,000 and 13,000 years ago). We then ran Bayesian statistic systems (SIBER, mixSIAR) to reconstruct the trophic niches and diets of Magdalenian canids. We conclude that a significant niche partitioning of canids is reflected in their carbon and nitrogen isotopic composition. Furthermore, we were able to distinguish between the niche of dogs and individual commensal foxes on the one hand, and wolves on the other hand. We suggest that while wolves had permanent, unrestricted access to all types of dietary resources coming from a diversity of prey species, the diet of dogs was controlled by humans. Most of the foxes built their own niche with a diet primarily comprised of small mammals. However, some red foxes showed commensal relationships in their reconstructed diet to dogs and wolves.

The prevalence of contaminant microbial DNA in ancient bone samples represents the principal limiting factor for palaeogenomic studies, as it may comprise more than 99% of DNA molecules obtained. Efforts to exclude or reduce this contaminant fraction have been numerous but also variable in their success. Here, we present a simple but highly effective method to increase the relative proportion of endogenous molecules obtained from ancient bones. Using computed tomography (CT) scanning, we identify the densest region of a bone as optimal for sampling. This approach accurately identifies the densest internal regions of petrous bones, which are known to be a source of high-purity ancient DNA. For ancient long bones, CT scans reveal a high-density outermost layer, which has been routinely removed and discarded prior to DNA extraction. For almost all long bones investigated, we find that targeted sampling of this outermost layer provides an increase in endogenous DNA content over that obtained from softer, trabecular bone. This targeted sampling can produce as much as 50-fold increase in the proportion of endogenous DNA, providing a directly proportional reduction in sequencing costs for shotgun sequencing experiments. The observed increases in endogenous DNA proportion are not associated with any reduction in absolute endogenous molecule recovery. Although sampling the outermost layer can result in higher levels of human contamination, some bones were found to have more contamination associated with the internal bone structures. Our method is highly consistent, reproducible and applicable across a wide range of bone types, ages and species. We predict that this discovery will greatly extend the potential to study ancient populations and species in the genomics era.

Evidence of hunting and exploitation of cave bears (Ursus spelaeus, sensu lato) are recently documented in western and eastern sites of its former European distribution in Middle and Upper Palaeolithic contexts. Human hunting and exploitation has always been accepted for brown bears (Ursus arctos) but not for cave bears. Recently in Hohle Fels (Swabian Jura), a vertebrae was found with an embedded flint projectile. Furthermore, cut and impact marks document processing of this game. Alongside cave bear, small numbers of coeval brown bears are always present in caves. In open-air sites, both bear species are recorded in low but equal numbers. The question why U. arctos survived the Last Glacial Maximum (LGM) still remains open. In this respect, the Gravettian is the crucial period for these questions, as the latest dates for cave bears fall into this time span. The question of whether hunting by Neanderthals or Anatomically Modern Humans (AMH) had an impact on the demise and final extinction of cave bears is discussed, considering ecological and behavioural parameters. In this context, Hohle Fels Cave from the Swabian Jura (Germany), and Deszczowa Cave in the Krakowsko-Czestochowska Upland (Poland), as well as five open air sites in the Czech Republic and one from Poland are discussed.

The population dynamics of the Pleistocene woolly mammoth (Mammuthus primigenius) has been the subject of intensive palaeogenetic research. Although a large number of mitochondrial genomes across Eurasia have been reconstructed, the available data remains geographically sparse and mostly focused on eastern Eurasia. Thus, population dynamics in other regions have not been extensively investigated. Here, we use a multi-method approach utilising proteomic, stable isotope and genetic techniques to identify and generate twenty woolly mammoth mitochondrial genomes, and associated dietary stable isotopic data, from highly fragmentary Late Pleistocene material from central Europe. We begin to address region-specific questions regarding central European woolly mammoth populations, highlighting parallels with a previous replacement event in eastern Eurasia ten thousand years earlier. A high number of shared derived mutations between woolly mammoth mitochondrial clades are identified, questioning previous phylogenetic analysis and thus emphasizing the need for nuclear DNA studies to explicate the increasingly complex genetic history of the woolly mammoth.

We report here a new discovery of a cave bear left metatarsal 3 from Rochedane, an archaeological site near Montbeliard (French Jura) that yielded only Lateglacial and Holocene material, with no evidence of pre-LGM deposits, a context that made this bone a possible candidate for being a post-LGM cave bear in western Europe. To test this hypothesis, this bone was analyzed for mitochondrial DNA, which confirmed its attribution to cave bear of the Ursus spelaeus lineage, and a direct radiocarbon AMS dating on well preserved collagen (%C, %N and C/N well in the range of fresh collagen) yielded an age of 23,900 +110 -100 BP (28,730-28,500 cal BP, one sigma range). Its carbon and nitrogen isotopic values were similar to those of slightly older cave bears from the Swabian Jura, around 300 km to the East, suggesting that the ecological preferences of cave bears remained unchanged until the extirpation of this species in western Europe. Interestingly, the genetic type U. spelaeus was replaced by Ursus ingressus around 28,000 C-14 BP in the Swabian Jura. In contrast, the older type U. spelaeus apparently persisted in France ca. 3000 years longer. Traces left on the cave bear metapodium have been left by human activity on this bone, as it was the case for older cave bear bones from the Swabian Jura. This case study shows that cave bear remains found in post-LGM sites or layers may be candidates to be late survivors of this extinct species, but without direct radiocarbon AMS dated on well-preserved collagen (demonstrated by actual chemical composition results) and ancient DNA confirmation of the species attribution, such evidence can only be considered dubious. (C) 2013 Elsevier Ltd and INQUA. All rights reserved.

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.

Here we describe the variability of projectile points made from bone, antler, and ivory recovered from cave sites in the Ach and Lone Valleys (Swabian Jura), focusing on Aurignacian and Gravettian assemblages. Based on the faunal provenience of the points, we recognize a distinctive change in raw material use from the Aurignacian to the Gravettian: during the Aurignacian antler was used for the small split-base points, bone for highly variable points, and ivory for the comparatively large and unstandardized points. During the Gravettian hardly any antler points have been found and bone points were manufactured from mammoth ribs. The raw materials tend to be associated with a specific type of point and chaine operatoire.

Sub-fossilised remains may still contain highly degraded ancient DNA (aDNA) useful for palaeogenetic investigations. Whether X-ray computed [micro-] tomography ([μ]CT) imaging of these fossils may further damage aDNA remains debated. Although the effect of X-ray on DNA in living organisms is well documented, its impact on aDNA molecules is unexplored.Here we investigate the effects of synchrotron X-ray irradiation on aDNA from Pleistocene bones. A clear correlation appears between decreasing aDNA quantities and accumulating X-ray dose-levels above 2000 Gray (Gy). We further find that strong X-ray irradiation reduces the amount of nucleotide misincorporations at the aDNA molecule ends. No representative effect can be detected for doses below 200 Gy. Dosimetry shows that conventional μCT usually does not reach the risky dose level, while classical synchrotron imaging can degrade aDNA significantly. Optimised synchrotron protocols and simple rules introduced here are sufficient to ensure that fossils can be scanned without impairing future aDNA studies.

The vast majority of information about the Middle Paleolithic of the Swabian Jura in southwestern Germany comes from the well-known cave sites of the Ach and Lone Valleys. The Neanderthal occupations of Swabia show a wide range of assemblage types. Lithic technologies varied over time and space and include assemblages defined as belonging to the Swabian Mousterian, the Keilmessergruppe and the Blattspitzengruppe. Organic artifacts include bone retouchers and a small number of bone points. Human bones are rare, and there is no indication that the sites were used as cemeteries. Anthropogenic features in the form of combustion features with numerous fragments of burnt bone are documented at several of the sites. Game species vary from site to site, but in general horses and reindeer are the most common hunted game. Seasonality data usually point to the use of the caves in the colder times of the year. Spatial analyses are hampered by the small size and the small number of the excavations conducted with modern techniques. The overall archaeological pattern suggests a settlement system with relatively few people living in the landscape and using a “low impact” subsistence pattern that allowed Neanderthals to coexist with cave bears without driving their populations to extinction. Mobility was high and social units were generally small and presumably contained small groups of kin. The low density of finds at most Swabian sites points to their sporadic but repeated use by Neanderthals and an average occupation intensity and population density an order of magnitude lower than that of the subsequent Aurignacian period.

Palaeogenetic investigations in three geographically close caves (Hohle Fels, Geisenklosterle, and Sirgenstein) in the Ach Valley near Blaubeuren (Swabian Jura) document the sudden replacement of Ursus spelaeus by Ursus ingressus around 28,000 14 C BP. New radiocarbon dates suggest an earlier immigration of Ursus ingressus and at least a partial coexistence with Ursus spelaeus some 4500 years before the ultimate replacement. These two genetic types of cave bears used the same caves for hibernation and had the same herbivorous diet, as shown by the stable isotope results. In contrast, sympatric brown bears (Ursus arctos) exhibited a clearly different ecology, as shown by the carnivorous pattern of their isotopic signatures, and probably did not use the caves as dens before the Last Glacial Maximum (LGM). Once established, the younger cave bear (Ursus ingressus) remained the only cave bear for only another circa 2000 years after the last appearance of the classical cave bear (Ursus spelaeus) in the Ach Valley and elsewhere. The final appearance of cave bear (sensu lato) is now dated to 25,560 � 130 BP, disproving a refuge area of this species in the Swabian Jura. After the extinction of cave bears (sensu lato), brown bears took over their cave dens and their nutritional niche as they shift to a diet dominated by plant food. 2011 Elsevier Ltd and INQUA.

Intra-individual variations in carbon (δ13C) and nitrogen (δ15N) isotope measurements of dentine collagen in ungulate teeth can be related to diet and environmental changes at different periods during the life of the animal. A protocol of serial sampling of first, second and third molar roots was applied to modern caribou (17–27 months old) of the Qamanirjuaq herd (Rangifer tarandus groenlandicus), Canada. Based on a previous study, we predicted that M2 would reflect winter, M3 summer and M1 a complete year in terms of the isotopic record. Relatively high δ15N values (ca. 6 to 8‰), previously attributed to winter stress, were found in different molars of different specimens, reflecting a period of growth between April 1966 to April 1967. Previous results on other teeth from the same population confirmed that a high δ15Ncoll value signal corresponded to the winter of 1966/67. This temporary increase in δ15N value was probably linked to diet and/or environmental change. Collagen from M1 reflects the first winter whereas M2 and M3 reflect the second winter of life of young caribou. A longer time record including summer is represented by the bone collagen of the mandible. Results obtained on molar roots and mandible bone of the modern caribou of Banks Island herd (Rangifer tarandus pearyi) confirmed this seasonal record. Such collagen isotopic analysis on M1, M2 and M3 roots and jawbone can be applied to reindeer found in archaeological sites. Mandibles retaining deciduous premolars are preferable to avoid the possible loss of the winter tooth signal observed in animals older than 2 years. Copyright © 2010 John Wiley & Sons, Ltd.

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.

Considerable debate surrounds claims for early evidence of music in the archaeological record. Researchers universally accept the existence of complex musical instruments as an indication of fully modern behaviour and advanced symbolic communication but, owing to the scarcity of finds, the archaeological record of the evolution and spread of music remains incomplete. Although arguments have been made for Neanderthal musical traditions and the presence of musical instruments in Middle Palaeolithic assemblages, concrete evidence to support these claims is lacking. Here we report the discovery of bone and ivory flutes from the early Aurignacian period of southwestern Germany. These finds demonstrate the presence of a well-established musical tradition at the time when modern humans colonized Europe, more than 35,000 calendar years ago. Other than the caves of the Swabian Jura, the earliest secure archaeological evidence for music comes from sites in France and Austria and post-date 30,000 years ago.

The woolly mammoth (Mammuthus primigenius) was an emblematic and key species of the so-called mammoth steppe ecosystem between ca. 110,000 and 12,000 years ago. Its contribution to human subsistence during the Gravettian period as source of raw material was documented in southwestern France and southwestern Germany, with some evidence of active hunting in the latter region. However, decreasing genetic diversity and increasing indications of nutritional stress point to a likely decline of this megaherbivore. The specificity of the ecological niche occupied by the woolly mammoth is clearly reflected by their collagen 13C and 15N abundances (δ13Ccoll and δ15Ncoll), measured on skeletal remains of the typical mammoth steppe. The abundances of carbon-13 in mammoth collagen are comparable to those of other grazers like horse (Equus sp.), while the nitrogen-15 abundances are significantly higher (about 3‰) than in the other herbivores, either horse or reindeer (Rangifer tarandus). During the Aurignacian and Gravettian occupation at Geißenklösterle in the Ach Valley (Germany), the mammoths had the expected stable isotope signature, but the nitrogen-15 of horses showed an unexpected overlap with those of the mammoth. This unusual pattern was already occurring during the Aurignacian, while the oxygen-18 abundances in bone phosphate (δ18Obp) of horse and reindeer were unchanged between Aurignacian and Gravettian periods, which rules out significant change in environmental and climatic conditions. Thus, we hypothesize that during the Aurignacian and Gravettian, the ecological niche of mammoth was intact but not occupied intensively by mammoths due to a decline in their population. This decline could be tentatively explained by human pressure through hunting. In Dordogne (France), decreasing horse and reindeer δ15Ncoll values coeval to decreasing horse δ18Obp values between the Aurignacian and the Early Gravettian periods reflected a clear change in the environment, while no contrast in δ15Ncoll values was observed between the Early and Final Gravettian at the Abri Pataud. The mammoth of Dordogne yielded slightly higher δ15Ncoll values than expected, probably as a consequence of the nursing effect since all the analyzed samples were ivory instead of bone. The direct dating and sulphur-34 measurement on the ivory of the Early Gravettian at Pataud showed that almost all of them were of contemporaneous and local origin. Significant contrasts in δ34Scoll values were found between the Dordogne and the Ach Valley for the same herbivores species, which confirms the potential of sulphur-34 in collagen as a mobility tracker.

The giant deer Megaloceros giganteus is among the most fascinating Late Pleistocene Eurasian megafauna that became extinct at the end of the last ice age. Important questions persist regarding its phylogenetic relationship to contemporary taxa and the reasons for its extinction. We analyzed two large ancient cervid bone fragments recovered from cave sites in the Swabian Jura (Baden-Württemberg, Germany) dated to 12,000 years ago. Using hybridization capture in combination with next generation sequencing, we were able to reconstruct nearly complete mitochondrial genomes from both specimens. Both mtDNAs cluster phylogenetically with fallow deer and show high similarity to previously studied partial Megaloceros giganteus DNA from Kamyshlov in western Siberia and Killavullen in Ireland. The unexpected presence of Megaloceros giganteus in Southern Germany after the Ice Age suggests a later survival in Central Europe than previously proposed. The complete mtDNAs provide strong phylogenetic support for a Dama-Megaloceros clade. Furthermore, isotope analyses support an increasing competition between giant deer, red deer and reindeer after the Last Glacial Maximum, which might have contributed to the extinction of Megaloceros in Central Europe.

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.

This paper examines the faunal assemblages from Middle Palaeolithic cave sites in the Ach Valley and views them in a broader chronological context along with the Upper Palaeolithic assemblages of the region. We present data from the key Middle Palaeolithic sites of Geisenklosterle, Sirgenstein, Grose Grotte and Kogelstein. Except Kogelstein, which is a hyena den, the other three sites served as cave bear hibernation dens, where cave bear is the most abundant species. The most frequent game species during the Upper Palaeolithic are horse, mammoth and reindeer. But these animals are mainly represented by specific skeletal elements, which were important as raw material for the production of organic tools. The large variety of organic tools made from bone, antler, and ivory, and the refuse resulting from their production in Upper Palaeolithic layers stands in contrast to the extreme rarity of organic tools and production debris in Middle Palaeolithic layers. The faunal assemblages in the Ach Valley document continuity in the seasonal use of the landscape and the preferred game, but reflect changes in the use of sites and organic technology between the Middle and the Upper Palaeolithic. Based on the faunal and lithic assemblages from the caves of the Ach Valley, most of the sites were used more intensively in the Upper Palaeolithic than in the Middle Palaeolithic. If these assemblages provide representative samples, the available data suggest lower population densities and greater mobility of Neanderthals during the Middle Palaeolithic than of modern humans during the Upper Palaeolithic. Copyright © 2004 John Wiley & Sons, Ltd.

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.

This paper reports the results of the first systematic attempt to compile diachronic, quantitative data on the abundance of small mammals, birds and fish in the diets of the Paleolithic inhabitants of the Swabian Jura. Here we examine diet breadth and the use of small game and show that faunal assemblages from the Middle Paleolithic, Aurignacian and Gravettian reflect a high degree of continuity in the use of large game accompanied by increases in the use of small mammals, birds and fish.

International audience; The prey choice of extinct cave lions Panthera spelaea was determined using bone collagen isotopic signatures in the Belgian Ardennes and the Swabian Jura between 40,000 and 25,000 years ago as well as in the Late-glacial of the northwestern Alp foreland and of the Paris Basin. More than 370 specimens of large carnivorous and herbivorous mammals from 25 sites coeval with cave lion were analyzed. The isotopic results point to an individualistic prey choice for cave lions, with some individuals more oriented on reindeer and others on young cave bears. The isotopic signatures and therefore dietary choice of cave lions did not overlap with those of cave hyenas, indicating competitive exclusion between the large predators. The most recent western European cave lions seem to have been consuming mainly reindeer until the local extirpation of this prey species, which coincides chronologically with their own extinction. This restricted prey choice may be involved in the extinction of this large predator in Western Europe. Ó 2011 Elsevier Ltd and INQUA.

Several types of bears lived in Europe during the Late Pleistocene. Some of them, such as cave bears (Ursus s. spelaeus and Ursus ingressus), did not survive after about 25,000 years ago, while others are still extant, such as brown bear (Ursus arctos). Our article aims at a better understanding of the palaeoecology of these large “carnivores” and focuses on two regions, the Ach valley in the Swabian Jura (SW-Germany) with Geisenklosterle and Hohle Fels, and the Totes Gebirge (Austria) with Ramesch and Gamssulzen caves. Both regions revealed two genetically distinct cave bear lineages, and previous studies suggest behavioural differences for the respective bears in these two regions. In the Ach valley, irrespective of the cave site, U. s. spelaeus was replaced by U. ingressus around 28 ka uncal BP with limited chronological overlap without recognizable dietary changes as documented by the isotopic composition (13C, 15N) of the bones. Furthermore, the present study shows that the dental microwear pattern was similar for all bears in both caves, however with a larger variability in Geisenklosterle than in Hohle Fels. In contrast, the two Austrian caves, Gamssulzen (U. ingressus) and Ramesch (Ursus s. eremus), show considerable differences in both palaeodietary indicators, i.e., stable isotopes, and dental microwear, over at least 15,000 years. The oxygen and carbon analysis of the tooth enamel combined with the dental microwear of the same molars provide an extremely diversified picture of the feeding behaviour of these fossil bears. The already known differences between these two study areas are confirmed and refined using the new approaches. Moreover, the differences between the two cave bear lineages in the Totes Gebirge became even larger. Some niche partitioning between both types of cave bears was supported by the present study but it does not seem to be triggered by climate. This multi-disciplinary approach gives new insights into the palaeobiology of extinct bears.

In the absence of interaction with genetically distinct populations, changes in frequencies of distinct mitochondrial DNA (mtDNA) sequences (haplotypes) within a population are caused by mutations and genetic drift, both of which are comparatively slow processes. By contrast, interactions between populations may lead to rapid changes in haplotype frequencies [1–3], for instance through extinction and recolonialisation. So far, the only case of a direct replacement of mtDNA sequences within a continuous population has been described in historical mouse populations [2].