Biology subjects

Bocherens, H.

Publications and source records attributed to Bocherens, H..

10 recordsLinked to original sources

bioRxiv2024

Ancient biomolecules suggest learned foraging strategy in extinct cave bears

Studying the behavioural ecology of long-extinct species is challenging due to the difficulty in measuring the behavioural phenotype and correlating this with genetic and environmental factors. However, a multidisciplinary approach integrating isotope analysis of diet and ancient DNA analysis of genetic relationships offers a potential framework to test the proximate causes of dietary preferences. Our study focuses on Late Pleistocene cave bears from the Romanian Carpathians. Stable isotope analysis of bone collagen reveals substantial lifetime variation in food plant preferences among individuals. We find that bears with similar diets do not cluster according to their population structure, sex, time period, climatic conditions, or location. This disconnect suggests that diet preference in cave bears is not genetically inherited, and instead that individuals adapted their diets based on foraging experience. This integrative approach opens new avenues for understanding Pleistocene animal behaviour, leveraging ancient biomolecules synergistically to reveal insights otherwise inaccessible.

evolutionary biology↗

bioRxiv2024

Trophic adaptation of large terrestrial omnivores to global change

Large omnivores at the top of food webs play a key role in ecosystems, as their ability to feed on multiple trophic levels stabilizes food-web dynamics and impacts ecosystem functioning. However, it is largely unexplored how large omnivores adapt their trophic interactions to altered resource availability under global change, particularly in terrestrial ecosystems. Here, we combine macroecological and paleoecological approaches and reveal that extant bears, the largest terrestrial omnivores, adapt their trophic position in food webs dynamically to net primary productivity and growing season length. Throughout their geographic ranges, extant bears occupy higher trophic positions in unproductive ecosystems with short growing seasons than in productive ecosystems with long growing seasons. Consistent with this geographic pattern, the trophic position of the brown bear sharply decreased at the transition from the Late Pleistocene to the Holocene, coinciding with an increase in net primary productivity and growing season length. These findings demonstrate that trophic interactions of omnivores are not static but change dynamically in response to environmental change. Our findings suggest that global change impacts on primary production and vegetation seasonality may trigger shifts in the functional role of omnivores, with consequences for food webs and ecosystem functions. Significance statementLarge omnivores play a key role in ecosystems, as they stabilize food-web dynamics and impact ecosystem functioning. However, how omnivores adapt their trophic interactions to changes in resource availability under global change remains unexplored. Combining macroecological and paleoecological approaches, we show that extant bears, the largest terrestrial omnivores, occupy lower trophic positions in food webs as net primary productivity and growing season length increase. This trophic adaptation is evident across the geographic ranges of all extant terrestrial bear species and for brown bears at the transition from the Late Pleistocene to the Holocene. Therefore, impacts of global change on primary production and vegetation seasonality may trigger shifts in the functional role of omnivores, with consequences for food webs and ecosystems. One sentence summaryGlobal changes in primary productivity and vegetation seasonality alter the functional role of large omnivores in terrestrial ecosystems.

ecology↗

bioRxiv2023

A late Neanderthal reveals genetic isolation in their populations before extinction

Neanderthal genomes have been recovered from sites across Eurasia, painting an increasingly complex picture of their populations structure, mostly indicating that late European Neanderthals belonged to a single metapopulation with no significant evidence of deep population structure. Here we report the discovery of a late Neanderthal individual, nicknamed "Thorin", from Grotte Mandrin in Mediterranean France, and his genome. These dentognathic fossils, including a rare example of distomolars, are associated with a rich archeological record of their final technological traditions in this region [~]50-42 thousand years ago. Thorins genome reveals a deep divergence with other late Neanderthals. Thorin belonged to a population with small group size that showed no genetic introgression with other known late European Neanderthals, revealing genetic isolation of his lineage despite them living in neighboring regions. These results have important implications for resolving competing hypotheses about causes of the Neanderthals disappearance. One Sentence SummaryA new French Neanderthal fossil and its genome reveal complex population dynamics during the past 100,000 years.

genomics↗

bioRxiv2021

Late Pleistocene palaeoecology and phylogeography of woolly rhinoceroses

The woolly rhinoceros (Coelodonta antiquitatis) was a cold-adapted herbivore, widely distributed from western Europe to north-east Siberia during the Late Pleistocene. Previous studies associate the extinction of the species ~14,000 years before present to climatic and vegetational changes, and suggest that later survival of populations in north-east Siberia may relate to the later persistence of open vegetation in that region. Here, we analyzed carbon ({delta}13C) and nitrogen ({delta}15N) stable isotopes and mitochondrial DNA sequences to elucidate the evolutionary ecology of the species. Our dataset comprised 286 woolly rhinoceros isotopic records, including 192 unpublished records, from across the species range, dating from >58,600 14C years to ~14,000 years before present. Crucially, we present the first 71 isotopic records available to date of the 15,000 years preceding woolly rhinoceros extinction. The data reveal ecological flexibility and geographical variation in woolly rhinoceros stable isotope compositions through time. In north-east Siberia, we detected{delta} 15N stability through time. This could reflect long-term environmental stability, and might have enabled the later survival of the species in the region. To further investigate the palaeoecology of woolly rhinoceroses, we compared their isotopic compositions with that of other contemporary herbivores. This analysis suggests possible niche partitioning between woolly rhinoceros and both horse (Equus spp.) and woolly mammoth (Mammuthus primigenius), and isotopic similarities between woolly rhinoceros and both musk ox (Ovibos moschatus) and saiga (Saiga tatarica) at different points in time. To provide phylogeographical context to the isotopic data, we analyzed 61 published mitochondrial control region sequences. The data show a lack of geographic structuring; we found three haplogroups with overlapping distributions, all of which show a signal of expansion during the Last Glacial Maximum. Furthermore, our genetic findings support the notion that environmental stability in Siberia had an impact on the paleoecology of woolly rhinoceroses in the region. Our study highlights the utility of combining stable isotopic records with ancient DNA to advance our knowledge of the evolutionary ecology of past populations and extinct species.

evolutionary biology↗

bioRxiv2019

Ancient RNA from Late Pleistocene permafrost and historical canids shows tissue-specific transcriptome survival

While sequencing ancient DNA from archaeological material is now commonplace, very few attempts to sequence ancient transcriptomes have been made, even from typically stable deposition environments such as permafrost. This is presumably due to assumptions that RNA completely degrades relatively quickly, particularly when dealing with autolytic, nuclease-rich mammalian tissues. However, given the recent successes in sequencing ancient RNA (aRNA) from various sources including plants and animals, we suspect that these assumptions may be incorrect or exaggerated. To challenge the underlying dogma, we generated shotgun RNA data from sources that might normally be dismissed for such study. Here we present aRNA data generated from two historical wolf skins, and permafrost-preserved liver tissue of a 14,300-year-old Pleistocene canid. Not only is the latter the oldest RNA ever to be sequenced, but also shows evidence of biologically relevant tissue-specificity and close similarity to equivalent data derived from modern-day control tissue. Other hallmarks of RNA-seq data such as exon-exon junction presence and high endogenous ribosomal RNA content confirms our datas authenticity. By performing independent technical replicates using two high-throughput sequencing platforms, we show not only that aRNA can survive for extended periods in mammalian tissues, but also that it has potential for tissue identification, and possibly further uses such as in vivo genome activity and adaptation, when sequenced using this technology.

genomics↗

bioRxiv2018

Integrative isotopic Paleoecology (δ13C, δ18O) of a Late Pleistocene vertebrate community from Sergipe, NE Brazil

Isotopes are one of the best tools to reconstruct the Paleoecology of extinct taxa, yielding insights about their diet (through carbon; C3 and C4 plants), niche breadth (BA) and the environment in which they lived. In the present work we go deeper in the use of isotopes and explore a mathematical mixing model with the stable isotopes of two elements (carbon and oxygen) to (1) suggest the relative contribution of four types of food resources (leaves, fruits, roots and C4 grass) for meso- and megaherbivores (weight > 100 kg) that lived in the Late Pleistocene of Poco Redondo, Sergipe, Brasil, and (2) evaluate which of these herbivores could be the potential prey for the carnivores Smilodon populator and Caiman latirostris. To explore the intra/interspecific competition of these fauna, we generate weight estimation, standardized niche breadth (BA) for the meso-megamammals from Sergipe and compare with data from the meso-megaherbivores from Africa, concluding that Eremotherium laurillardi and Toxodon platensis were the best resource competitors in the Late Pleistocene of Sergipe, and reinforcing their importance as key species in this extinct community. Finally, we reconstructed the paleoenvironment in which the vertebrate community of Sergipe lived, estimating Mean Annual Temperature ({degrees}C), Mean Annual Precipitation, Biomass and Energy Expendidure, noting that environments in the Late Pleistocene of Sergipe were similar to those of Africa nowadays, but hotter and with more energy expenditure for these meso-megamammals.

paleontology↗

bioRxiv2018

Untangling the Evolutionary History of European Bison (Bison bonasus)

European bison (Bison bonasus) are the largest endemic vertebrates in Europe, and one of the few megafaunal species to have survived the mass megafaunal extinction during the Pleistocene/Holocene transition (12-9 thousand years ago). Untangling their evolutionary history would provide valuable information about the response of European megafauna to periods of rapid environmental change. However, a severe and recent population bottleneck obscures much of the population history that could be inferred from the genomes of modern individuals. While several studies have attempted to analyse ancient European bison populations directly using ancient DNA, their datasets were limited in temporal and geographic range. In this study we present the most comprehensive dataset of ancient European bison mitochondrial genomes to date, with 131 ancient bison samples from across the Eurasian continent covering over 50 thousand years. We reveal patterns of bison distribution and concurrent environmental changes across a broad geographical and temporal range. In particular, population expansions following periods of extensive forest reduction combined with a decrease in anthropogenic pressures suggest that European bison remain preferentially adapted to an open steppe environment through to the present day.

evolutionary biology↗

bioRxiv2018

Out of Africa by spontaneous migration waves

Hominin evolution is characterized by progressive regional differentiation, as well as migration waves, leading to anatomically modern humans that are assumed to have emerged in Africa and spread over the whole world. Why or whether Africa was the source region of modern humans and what caused their spread remains subject of ongoing debate. We present a spatially explicit, stochastic numerical model that includes ongoing mutations, demic diffusion, assortative mating and migration waves. Diffusion and assortative mating alone result in a structured population with relatively homogeneous regions bound by sharp clines. The addition of migration waves results in a power-law distribution of wave areas: for every large wave, many more small waves are expected to occur. This suggests that one or more out-of-Africa migrations would probably have been accompanied by numerous smaller migration waves across the world. The migration waves are considered \"spontaneous\", as the current model excludes environmental or other factors. Large waves preferentially emanate from the central areas of large, compact inhabited areas. During the Pleistocene, Africa was the largest such area most of the time, making Africa the statistically most likely origin of anatomically modern humans, without a need to invoke additional environmental or ecological drivers.

evolutionary biology↗

bioRxiv2018

Modern wolves trace their origin to a late Pleistocene expansion from Beringia

Grey wolves (Canis lupus) are one of the few large terrestrial carnivores that maintained a wide geographic distribution across the Northern Hemisphere throughout the Pleistocene and Holocene. Recent genetic studies have suggested that, despite this continuous presence, major demographic changes occurred in wolf populations between the late Pleistocene and early Holocene, and that extant wolves trace their ancestry to a single late Pleistocene population. Both the geographic origin of this ancestral population and how it became widespread remain a mystery. Here we analyzed a large dataset of novel modern and ancient mitochondrial wolf genomes, spanning the last 50,000 years, using a spatially and temporally explicit modeling framework to show that contemporary wolf populations across the globe trace their ancestry to an expansion from Beringia at the end of the Last Glacial Maximum - a process most likely driven by the significant ecological changes that occurred across the Northern Hemisphere during this period. This study provides direct ancient genetic evidence that long-range migration has played an important role in the population history of a large carnivore and provides an insight into how wolves survived the wave of megafaunal extinctions at the end of the last glaciation. Moreover, because late Pleistocene grey wolves were the likely source from which all modern dogs trace their origins, the demographic history described in this study has fundamental implications for understanding the geographical origin of the dog.

evolutionary biology↗

bioRxiv2017

The Genomic History Of Southeastern Europe

Farming was first introduced to southeastern Europe in the mid-7th millennium BCE - brought by migrants from Anatolia who settled in the region before spreading throughout Europe. To clarify the dynamics of the interaction between the first farmers and indigenous hunter-gatherers where they first met, we analyze genome-wide ancient DNA data from 223 individuals who lived in southeastern Europe and surrounding regions between 12,000 and 500 BCE. We document previously uncharacterized genetic structure, showing a West-East cline of ancestry in hunter-gatherers, and show that some Aegean farmers had ancestry from a different lineage than the northwestern Anatolian lineage that formed the overwhelming ancestry of other European farmers. We show that the first farmers of northern and western Europe passed through southeastern Europe with limited admixture with local hunter-gatherers, but that some groups mixed extensively, with relatively sex-balanced admixture compared to the male-biased hunter-gatherer admixture that prevailed later in the North and West. Southeastern Europe continued to be a nexus between East and West after farming arrived, with intermittent genetic contact from the Steppe up to 2,000 years before the migration that replaced much of northern Europes population.

genetics↗