Paleogenomics, also known as genome-wide ancient DNA analysis, is transforming our understanding of the human past, but has been much less intensively used to understand the history of other species. ...However, paleogenomic studies of non-human animals and plants have the potential to address an equally rich range of evolutionary, paleoecological, paleoenvironmental, and archaeological research questions. Three recent case studies of cave bears, horses, and maize provide examples of the ways that paleogenomics can be used to examine potential causes of extinctions and dynamic processes of domestication. Much more research in these areas is needed, and we conclude by highlighting key future directions.
To date, genome-wide analyses of ancient organisms have primarily focused on humans, despite the fact that there are millions of living and extinct plant and animal species that also can be studied with these techniques.
Natural history museums, archives, and archaeological collections harbor abundant sources of ancient DNA for studying past plant and animal genetic diversity around the world.
Ancient DNA provides access to genomic data covering hundreds of thousands of years, allowing for the investigation of evolutionary, ecological, social, and environmental questions in deep time, especially regarding the ways that humans have interacted with other species and modified past ecosystems and environments.
Case studies of cave bears, horses, and maize highlight the power of paleogenomic data to shed light on extinctions, admixture between domestic and wild animals, and the gradual selection for domestication genes during plant and animal domestication.
It is time to apply the power of genome-wide ancient DNA analysis to non-humans as ambitiously as it has been applied to our own species, making sure to treat ancient specimens in an ethical way that preserves them for future generations.
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The Cave Bear, Ursus spelaeus (sensu lato), was one of many megafaunal species that became extinct during the Late Pleistocene in Europe. With new data we revisit the debate about the extinction and ...paleoecology of this species by presenting new chronometric, isotopic and taphonomic evidence from two Palaeolithic cave bear sites in northeastern Italy: Paina Cave and Trene Cave. Two direct radiocarbon dates on well-preserved collagen have yielded ages around 24,200-23,500 cal yr BP, which make them the latest known representatives of the species in Europe. The carbon (δ
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C) and nitrogen (δ
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N) isotopic values of bone collagen exhibit values similar to those of older cave bears from Swabian Jura and France, suggesting that the feedings preferences of cave bears remained unchanged until the disappearance of this species in Europe. Several bear remains preserved traces of human modification such as cut marks, which enables a reconstruction of the main steps of fur recovery and the butchering process. The broad range of plant types available and the favorable location of Berici Hills may have played an important role in the range expansion of cave bears and their interaction with the Paleolithic hunters settled the same area.
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Cave bear (Ursus spelaeus), brown bear (Ursus arctos), and Neanderthals were potential competitors for environmental resources (shelters and food) in Europe. In order to reinforce this view and ...contribute to the ongoing debate on late Neanderthal behavior, we present evidence from zooarchaeological and taphonomic analyses of bear bone remains discovered at Rio Secco Cave and Fumane Cave in northeast Italy, an extended geographic area north of the Adriatic Sea. The remains from both caves come from layers dated to 49-42 ky cal. BP, and suggest close interactions between humans and bears, with data not only limited to the association of Mousterian lithic artifacts with numerous bear remains, but also the detection of clearly preserved traces of human modification such as cut and percussion marks, which enable a reconstruction of the main steps of fur recovery and the butchering process. Examples of Neanderthal bear exploitation are extremely sporadic in Europe, and Grotta Rio Secco and Grotta Fumane can be considered rare cases of remain accumulations generated by the human predation of bears of varied age classes during or near the end of hibernation. All of this evidence suggests that bears had a strategic role in the nomadic economy of Neanderthal hunting groups.
•Cave bear, brown bear and Neanderthals were potential competitors for environmental shelters and food.•Examples of Neanderthal bear exploitation are extremely sporadic in Western Eurasia.•Bone taphonomy from caves in Southern Alps suggests Neanderthals hunted cave and brown bears.•Ongoing debate on late Neanderthal behavior is feeded.
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The archaeological site of Payre (South-eastern France) has yielded a remarkable Early Middle Palaeolithic sequence with mixed occupations of Neanderthal and large carnivore occupations ranging from ...MIS 8 to 6. Recent discoveries during the reassessment of collections brought to light at least a dozen cave (Ursus spelaeus) and brown bear (Ursus arctos) remains bearing cut marks, indicating the in situ carcass processing (skinning, evisceration, dismembering, defleshing) of these large carnivores by early Neanderthals. This is just one of an increasing number of such examples throughout Europe, highlighting once again the diversity of food and non-food resources exploited by these hominins. Furthermore, so far, these discoveries are the sole evidence of large carnivore exploitation by Neanderthal in the western part of the middle Rhône basin, where Palaeolithic sites and Pleistocene bone accumulations are abundant. These new discoveries are put into context with the other known occurrences in Europe.
•Large carnivores exploitation played a part in the dietary and cultural behavior of early Neanderthal populations.•Several species of Ursids have been exploited.•Early Neanderthals took advantage of a wide range of resources from these animals.•These practices occurred occasionally on a wide time span covering the Middle Palaeolithic.•Large carnivores exploitation is a Europe-wide phenomenon.
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Palaeogenomes provide the potential to study evolutionary processes in real time, but this potential is limited by our ability to recover genetic data over extended timescales.1 As a consequence, ...most studies so far have focused on samples of Late Pleistocene or Holocene age, which covers only a small part of the history of many clades and species. Here, we report the recovery of a low coverage palaeogenome from the petrous bone of a ∼360,000 year old cave bear from Kudaro 1 cave in the Caucasus Mountains. Analysis of this genome alongside those of several Late Pleistocene cave bears reveals widespread mito-nuclear discordance in this group. Using the time interval between Middle and Late Pleistocene cave bear genomes, we directly estimate ursid nuclear and mitochondrial substitution rates to calibrate their respective phylogenies. This reveals post-divergence mitochondrial transfer as the dominant factor explaining their mito-nuclear discordance. Interestingly, these transfer events were not accompanied by large-scale nuclear introgression. However, we do detect additional instances of nuclear admixture among other cave bear lineages, and between cave bears and brown bears, which are not associated with mitochondrial exchange. Genomic data obtained from the Middle Pleistocene cave bear petrous bone has thus facilitated a revised evolutionary history of this extinct megafaunal group. Moreover, it suggests that petrous bones may provide a means of extending both the magnitude and time depth of palaeogenome retrieval over substantial portions of the evolutionary histories of many mammalian clades.
•The oldest genome sequence from a non-permafrost environment.•A revised phylogeny of cave bears based on nuclear genomes.•Direct estimation of ursid nuclear and mitochondrial substitution rates.•Shows importance of climatic changes on species evolution.
Barlow et al. present the oldest published genome from a non-permafrost environment: from a 360,000-year-old cave bear that inhabited the Southern Caucasus during the Middle Pleistocene. Using this and other cave bear genomes, they determine nuclear and mitochondrial substitution rates and revise the evolutionary history of the extinct cave bear.
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The study of fossil bone assemblages has brought up evidence of the existence in the Pleistocene of faunal communities with no modern analogues. This is notably the case for Palaeolithic ...archaeological sites that have yielded, in the same stratigraphic layers, remains of species that are rarely sympatric in present-day ecosystems. The Mousterian – layer C – and Châtelperronian – layer B – of Grotte XVI (Dordogne, France) provide examples of such “composite” faunas: high proportions of Red deer (21 % and 34 % of the total number of identifiable remains of ungulates, respectively), Roe deer (17 % and 14 %) and Reindeer (42 % and 26 %) have been described in the same assemblages. In order to better interpret these no-analog communities, large mammal remains from layers B and C of Grotte XVI are reanalysed here. Taxonomic identifications, taphonomic data (cortical surface states, anthropic marks, evidences of carnivore activity, etc.), season-of-death estimates and bone refits (intra- and inter-layers) are combined and analysed as part of a three-dimensional spatial study of the faunal assemblages.The results obtained support the hypothesis that the noanalog mammal communities of Grotte XVI do not represent true past species associations (i.e., the “composite” faunas of the site do not document the past existence of no-analog ecosystems), but rather to the combined effect of publication error and intense post-depositional mixing of distinct bone assemblages. This study underlines once again the usefulness, if not the necessity, of a complete taphonomic and spatial analysis that critically revises field stratigraphic units prior to any archaeological or paleo-environmental interpretation
L'étude d'ensembles osseux fossiles conclut parfois à l'existence d'associations fauniques pléistocènes sans analogues actuels. Par exemple, certains sites paléolithiques ont délivré, dans les mêmes couches, les vestiges d'espèces aujourd'hui rarement sympatriques. Les couches moustériennes et châtelperroniennes de la Grotte XVI (Dordogne, France) sont un exemple de telles faunes "composites" : toutes deux associent de fortes proportions de Cerf (21%-34%), de Chevreuil (14%-17%) et de Renne (26%-42%). Afin d'aider à l'interprétation de ces communautés nonanalogues, les vestiges de grands mammifères des couches B et C de la Grotte XVI sont ici ré-analysés. Déterminations taxonomiques, données taphonomiques, indices de saisonnalité et remontages osseux sont combinés et analysés dans le cadre d'une étude spatiale tridimensionnelle des nappes de vestiges. Les résultats obtenus permettent de proposer que les associations fauniques "composites" de la Grotte XVI ne représentent pas une réalité passée (i.e. l'existence d'écosystèmes passés non-analogues), mais sont le résultat, d'une part, d'une erreur de publication (inversion des décomptes de Chevreuil et de Bouquetin dans la publication princeps) et, d'autre part, du mélange de plusieurs assemblages osseux suite à d'intenses perturbations post-dépositionnelles d'origines multiples (dont notamment l'action de l'Ours des cavernes). Certains secteurs mieux préservés de la Grotte semblent enregistrer une succession d'associations fauniques plus homogènes et cohérentes d'un point de vue paléo-environnemental. Cette étude souligne de nouveau l'utilité voire la nécessité d'une analyse taphonomique et spatiale complète, avec critique et redéfinition des découpages stratigraphiques opérés à la fouille, avant toute interprétation archéologique ou paléoenvironnementale.
Ohne Schwanz bis zu 3,50 Meter lang, maximal 1,75 Meter hoch und bis zu 1200 Kilogramm schwer - das war der Hohlenbar (Ursus spelaeus) des Eiszeitalters. Obwohl diese ausgestorbene Barenart bereits ...1794 wissenschaftlich dokumentiert wurde, gibt sie uber 200 Jahre spater immer noch zahlreiche Ratsel auf. Wann ist der Hohlenbar entstanden? War er ein Einzelganger? Hat er einen Winterschlaf oder eine Winterruhe gehalten? Gab es eine Hohlenbarenjagdkultur und einen Hohlenbarenkult? Wann und warum ist er ausgestorben? Antworten auf diese und andere Fragen gibt das Taschenbuch Der Hohlenbar" des Wiesbadener Wissenschaftsautors Ernst Probst. Der Hohlenbar gilt als das grote Tier, das die Gebirge des Eiszeitalters jemals bewohnt hat. Erstaunlicherweise war er ein pflanzenfressendes Raubtier, das sich wahrend der kalten Jahreszeit wehrlos in Hohlen zuruckzog. Dennoch mussten Steinzeitmenschen um ihr Leben furchten, wenn sie ihm zur falschen Zeit begegneten.
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.
Studies on fossil bone microbial communities are scarce; even fewer studies were performed in cave deposits. For our research, sediments and fossil bones were sampled, and the whole community 16S ...rRNA gene-based metabarcoding analyses were performed on samples from Muierilor and Ursilor caves, some of Romania's most important archaeological and paleontological sites. Most of the identified taxa belong to Bacteria, with Proteobacteria, Acidobacteriota, Bacteroidota, and Actinobacteriota amongst the most abundant phyla in bone samples from both caves. The sediment samples presented similar composition, with Proteobacteria and Acidobacteriota being the most abundant phyla. The inferred bacteriomes indicated the presence of environment-specific bacteria, typical bone colonizers, and bacteria found in soils and decomposing human remains or archaeological profiles as well as phosphate-solubilizing and organotrophic bacteria. Diversity indices indicated a higher diversity in bone samples from Muierilor Cave than in Ursilor Cave samples and sediment samples from both caves. Environmental conditions, especially air relative humidity, were also considered in explaining the bacteriome diversity in different cave settings. These findings help to understand fossil bones' deposition and degradation in various environmental conditions. Furthermore, this is the first attempt to relate microenvironments and bacteria to preserving fossil bones from caves.
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