Publications by authors named "Hervé Bocherens"

55 Publications

A refined proposal for the origin of dogs: the case study of Gnirshöhle, a Magdalenian cave site.

Sci Rep 2021 Mar 4;11(1):5137. Epub 2021 Mar 4.

Institute for Archaeological Sciences, University of Tübingen, Rümelinstraße 23, 72070, Tübingen, Germany.

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 δN 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.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41598-021-83719-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7933181PMC
March 2021

Genomes of Pleistocene Siberian Wolves Uncover Multiple Extinct Wolf Lineages.

Curr Biol 2021 Jan 29;31(1):198-206.e8. Epub 2020 Oct 29.

Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark; Center for Evolutionary Hologenomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark; Bioinformatics, Department of Health Technology, Technical University of Denmark, Lyngby, Denmark. Electronic address:

Extant Canis lupus genetic diversity can be grouped into three phylogenetically distinct clades: Eurasian and American wolves and domestic dogs. Genetic studies have suggested these groups trace their origins to a wolf population that expanded during the last glacial maximum (LGM) and replaced local wolf populations. Moreover, ancient genomes from the Yana basin and the Taimyr peninsula provided evidence of at least one extinct wolf lineage that dwelled in Siberia during the Pleistocene. Previous studies have suggested that Pleistocene Siberian canids can be classified into two groups based on cranial morphology. Wolves in the first group are most similar to present-day populations, although those in the second group possess intermediate features between dogs and wolves. However, whether this morphological classification represents distinct genetic groups remains unknown. To investigate this question and the relationships between Pleistocene canids, present-day wolves, and dogs, we resequenced the genomes of four Pleistocene canids from Northeast Siberia dated between >50 and 14 ka old, including samples from the two morphological categories. We found these specimens cluster with the two previously sequenced Pleistocene wolves, which are genetically more similar to Eurasian wolves. Our results show that, though the four specimens represent extinct wolf lineages, they do not form a monophyletic group. Instead, each Pleistocene Siberian canid branched off the lineage that gave rise to present-day wolves and dogs. Finally, our results suggest the two previously described morphological groups could represent independent lineages similarly related to present-day wolves and dogs.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.cub.2020.10.002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7809626PMC
January 2021

Author Correction: Heavy reliance on plants for Romanian cave bears evidenced by amino acid nitrogen isotope analysis.

Sci Rep 2020 Oct 28;10(1):18805. Epub 2020 Oct 28.

Department of Geosciences, Biogeology, University of Tübingen, Hölderlinstraße 12, 72074, Tübingen, Germany.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41598-020-75177-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7591857PMC
October 2020

Rapid adaptive evolution to drought in a subset of plant traits in a large-scale climate change experiment.

Ecol Lett 2020 Nov 27;23(11):1643-1653. Epub 2020 Aug 27.

Plant Ecology Group, Institute of Evolution and Ecology, University of Tübingen, Tübingen, Germany.

Rapid evolution of traits and of plasticity may enable adaptation to climate change, yet solid experimental evidence under natural conditions is scarce. Here, we imposed rainfall manipulations (+30%, control, -30%) for 10 years on entire natural plant communities in two Eastern Mediterranean sites. Additional sites along a natural rainfall gradient and selection analyses in a greenhouse assessed whether potential responses were adaptive. In both sites, our annual target species Biscutella didyma consistently evolved earlier phenology and higher reproductive allocation under drought. Multiple arguments suggest that this response was adaptive: it aligned with theory, corresponding trait shifts along the natural rainfall gradient, and selection analyses under differential watering in the greenhouse. However, another seven candidate traits did not evolve, and there was little support for evolution of plasticity. Our results provide compelling evidence for rapid adaptive evolution under climate change. Yet, several non-evolving traits may indicate potential constraints to full adaptation.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1111/ele.13596DOI Listing
November 2020

Pre-extinction Demographic Stability and Genomic Signatures of Adaptation in the Woolly Rhinoceros.

Curr Biol 2020 Oct 13;30(19):3871-3879.e7. Epub 2020 Aug 13.

Centre for Palaeogenetics, Svante Arrhenius väg 20C, Stockholm 10691, Sweden; Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Box 50007, Stockholm 10405, Sweden; Department of Zoology, Stockholm University, Stockholm 10691, Sweden. Electronic address:

Ancient DNA has significantly improved our understanding of the evolution and population history of extinct megafauna. However, few studies have used complete ancient genomes to examine species responses to climate change prior to extinction. The woolly rhinoceros (Coelodonta antiquitatis) was a cold-adapted megaherbivore widely distributed across northern Eurasia during the Late Pleistocene and became extinct approximately 14 thousand years before present (ka BP). While humans and climate change have been proposed as potential causes of extinction [1-3], knowledge is limited on how the woolly rhinoceros was impacted by human arrival and climatic fluctuations [2]. Here, we use one complete nuclear genome and 14 mitogenomes to investigate the demographic history of woolly rhinoceros leading up to its extinction. Unlike other northern megafauna, the effective population size of woolly rhinoceros likely increased at 29.7 ka BP and subsequently remained stable until close to the species' extinction. Analysis of the nuclear genome from a ∼18.5-ka-old specimen did not indicate any increased inbreeding or reduced genetic diversity, suggesting that the population size remained steady for more than 13 ka following the arrival of humans [4]. The population contraction leading to extinction of the woolly rhinoceros may have thus been sudden and mostly driven by rapid warming in the Bølling-Allerød interstadial. Furthermore, we identify woolly rhinoceros-specific adaptations to arctic climate, similar to those of the woolly mammoth. This study highlights how species respond differently to climatic fluctuations and further illustrates the potential of palaeogenomics to study the evolutionary history of extinct species.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.cub.2020.07.046DOI Listing
October 2020

Fox dietary ecology as a tracer of human impact on Pleistocene ecosystems.

PLoS One 2020 22;15(7):e0235692. Epub 2020 Jul 22.

Institute for Scientific Archaeology, University of Tübingen, Tübingen, Germany.

Nowadays, opportunistic small predators, such as foxes (Vulpes vulpes and Vulpes lagopus), are well known to be very adaptable to human modified ecosystems. However, the timing of the start of this phenomenon in terms of human impact on ecosystems and of the implications for foxes has hardly been studied. We hypothesize that foxes can be used as an indicator of past human impact on ecosystems, as a reflection of population densities and consequently to track back the influence of humans on the Pleistocene environment. To test this hypothesis, we used stable isotope analysis (δ13C, δ15N) of bone collagen extracted from faunal remains from several archaeological sites located in the Swabian Jura (southwest Germany) and covering a time range over three important cultural periods, namely the Middle Palaeolithic (older than 42,000 years ago) attributed to Neanderthals, and the early Upper Palaeolithic periods Aurignacian and Gravettian (42,000 to 30,000 years ago) attributed to modern humans. We then ran Bayesian statistic systems (SIBER, mixSIAR) to reconstruct the trophic niches and diets of Pleistocene foxes. We observed that during the Middle Palaeolithic period, when Neanderthals sparsely populated the Swabian Jura, the niches occupied by foxes suggest a natural trophic behavior. In contrast, during the early Upper Palaeolithic periods, a new trophic fox niche appeared, characterized by a restricted diet on reindeer. This trophic niche could be due to the consumption of human subsidies related to a higher human population density and the resulting higher impact on the Pleistocene environment by modern humans compared to Neanderthals. Furthermore, our study suggests that, a synanthropic commensal behavior of foxes started already in the Aurignacian, around 42,000 years ago.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0235692PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7375521PMC
September 2020

Ancestors of domestic cats in Neolithic Central Europe: Isotopic evidence of a synanthropic diet.

Proc Natl Acad Sci U S A 2020 07 13;117(30):17710-17719. Epub 2020 Jul 13.

Senckenberg Centre for Human Evolution and Palaeoenvironment, University of Tübingen, 72076 Tübingen, Germany.

Cat remains from Poland dated to 4,200 to 2,300 y BCE are currently the earliest evidence for the migration of the Near Eastern cat (NE cat), the ancestor of domestic cats, into Central Europe. This early immigration preceded the known establishment of housecat populations in the region by around 3,000 y. One hypothesis assumed that NE cats followed the migration of early farmers as synanthropes. In this study, we analyze the stable isotopes in six samples of Late Neolithic NE cat bones and further 34 of the associated fauna, including the European wildcat. We approximate the diet and trophic ecology of Late Neolithic felids in a broad context of contemporary wild and domestic animals and humans. In addition, we compared the ecology of Late Neolithic NE cats with the earliest domestic cats known from the territory of Poland, dating to the Roman Period. Our results reveal that human agricultural activity during the Late Neolithic had already impacted the isotopic signature of rodents in the ecosystem. These synanthropic pests constituted a significant proportion of the NE cat's diet. Our interpretation is that Late Neolithic NE cats were opportunistic synanthropes, most probably free-living individuals (i.e., not directly relying on a human food supply). We explore niche partitioning between studied NE cats and the contemporary native European wildcats. We find only minor differences between the isotopic ecology of both these taxa. We conclude that, after the appearance of the NE cat, both felid taxa shared the ecological niches.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1073/pnas.1918884117DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7395498PMC
July 2020

Buried in water, burdened by nature-Resilience carried the Iron Age people through Fimbulvinter.

PLoS One 2020 21;15(4):e0231787. Epub 2020 Apr 21.

Department of Cultures, Archaeology, University of Helsinki, Helsinki, Finland.

Levänluhta is a unique archaeological site with the remains of nearly a hundred Iron Age individuals found from a water burial in Ostrobothnia, Finland. The strongest climatic downturn of the Common Era, resembling the great Fimbulvinter in Norse mythology, hit these people during the 6th century AD. This study establishes chronological, dietary, and livelihood synthesis on this population based on stable carbon and nitrogen isotopic and radiocarbon analyses on human remains, supported by multidisciplinary evidence. Extraordinarily broad stable isotopic distribution is observed, indicating three subgroups with distinct dietary habits spanning four centuries. This emphasizes the versatile livelihoods practiced at this boundary of marine, freshwater, and terrestrial ecosystems. While the impact of the prolonged cold darkness of the 6th century was devastating for European communities relying on cultivation, the broad range of livelihoods provided resilience for the Levänluhta people to overcome the abrupt climatic decline.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0231787PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7173937PMC
July 2020

Heavy reliance on plants for Romanian cave bears evidenced by amino acid nitrogen isotope analysis.

Sci Rep 2020 04 20;10(1):6612. Epub 2020 Apr 20.

Department of Geosciences, Biogeology, University of Tübingen, Hölderlinstraße 12, 72074, Tübingen, Germany.

Heavy reliance on plants is rare in Carnivora and mostly limited to relatively small species in subtropical settings. The feeding behaviors of extinct cave bears living during Pleistocene cold periods at middle latitudes have been intensely studied using various approaches including isotopic analyses of fossil collagen. In contrast to cave bears from all other regions in Europe, some individuals from Romania show exceptionally high δN values that might be indicative of meat consumption. Herbivory on plants with high δN values cannot be ruled out based on this method, however. Here we apply an approach using the δN values of individual amino acids from collagen that offsets the baseline δN variation among environments. The analysis yielded strong signals of reliance on plants for Romanian cave bears based on the δN values of glutamate and phenylalanine. These results could suggest that the high variability in bulk collagen δN values observed among cave bears in Romania reflects niche partitioning but in a general trophic context of herbivory.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41598-020-62990-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7170912PMC
April 2020

Divergent mammalian body size in a stable Eocene greenhouse climate.

Sci Rep 2020 03 4;10(1):3987. Epub 2020 Mar 4.

Department of Geosciences, University of Tübingen, Hölderlinstraße 12, D-72074, Tübingen, Germany.

A negative correlation between body size and the latitudinal temperature gradient is well established for extant terrestrial endotherms but less so in the fossil record. Here we analyze the middle Eocene site of Geiseltal (Germany), whose record is considered to span ca. 5 Myrs of gradual global cooling, and generate one of the most extensive mammalian Paleogene body size datasets outside North America. The δO and δC isotopic analysis of bioapatite reveals signatures indicative of a humid, subtropical forest with no apparent climatic change across Geiseltal. Yet, body mass of hippomorphs and tapiromorphs diverges rapidly from a respective median body size of 39 kg and 124 kg at the base of the succession to 26 kg and 223 kg at the top. We attribute the divergent body mass evolution to a disparity in lifestyle, in which both taxa maximize their body size-related selective advantages. Our results therefore support the view that intrinsic biotic processes are an important driver of body mass outside of abrupt climate events. Moreover, the taxonomy previously used to infer the duration of the Geiseltal biota is not reproducible, which precludes chronological correlation with Eocene marine temperature curves.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41598-020-60379-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7055232PMC
March 2020

Ancient West African foragers in the context of African population history.

Nature 2020 01 22;577(7792):665-670. Epub 2020 Jan 22.

Department of Genetics, Harvard Medical School, Boston, MA, USA.

Our knowledge of ancient human population structure in sub-Saharan Africa, particularly prior to the advent of food production, remains limited. Here we report genome-wide DNA data from four children-two of whom were buried approximately 8,000 years ago and two 3,000 years ago-from Shum Laka (Cameroon), one of the earliest known archaeological sites within the probable homeland of the Bantu language group. One individual carried the deeply divergent Y chromosome haplogroup A00, which today is found almost exclusively in the same region. However, the genome-wide ancestry profiles of all four individuals are most similar to those of present-day hunter-gatherers from western Central Africa, which implies that populations in western Cameroon today-as well as speakers of Bantu languages from across the continent-are not descended substantially from the population represented by these four people. We infer an Africa-wide phylogeny that features widespread admixture and three prominent radiations, including one that gave rise to at least four major lineages deep in the history of modern humans.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41586-020-1929-1DOI Listing
January 2020

Ancient DNA suggests modern wolves trace their origin to a Late Pleistocene expansion from Beringia.

Mol Ecol 2020 05 2;29(9):1596-1610. Epub 2020 Jan 2.

Department of Zoology, University of Cambridge, Cambridge, UK.

Grey wolves (Canis lupus) are one of the few large terrestrial carnivores that have maintained a wide geographical 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 geographical origin of this ancestral population and how it became widespread remain unknown. Here, we used a spatially and temporally explicit modelling framework to analyse a data set of 90 modern and 45 ancient mitochondrial wolf genomes from across the Northern Hemisphere, spanning the last 50,000 years. Our results suggest that contemporary wolf populations trace their ancestry to an expansion from Beringia at the end of the Last Glacial Maximum, and that this process was most likely driven by Late Pleistocene ecological fluctuations that occurred across the Northern Hemisphere. 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 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.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1111/mec.15329DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7317801PMC
May 2020

Large-scale mitogenomic analysis of the phylogeography of the Late Pleistocene cave bear.

Sci Rep 2019 08 15;9(1):10700. Epub 2019 Aug 15.

Institute for Archaeological Sciences, University of Tübingen, Tübingen, Germany.

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.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41598-019-47073-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6695494PMC
August 2019

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

PLoS Biol 2019 07 30;17(7):e3000166. Epub 2019 Jul 30.

Section for Evogenomics, The Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.

While sequencing ancient DNA (aDNA) 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 it also shows evidence of biologically relevant tissue specificity and close similarity to equivalent data derived from modern-day control tissue. Other hallmarks of RNA sequencing (RNA-seq) data such as exon-exon junction presence and high endogenous ribosomal RNA (rRNA) content confirms our data's authenticity. By performing independent technical library 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. aRNA also has possible further potential, such as identifying in vivo genome activity and adaptation, when sequenced using this technology.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1371/journal.pbio.3000166DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6667121PMC
July 2019

Adapt or die-Response of large herbivores to environmental changes in Europe during the Holocene.

Glob Chang Biol 2019 09 12;25(9):2915-2930. Epub 2019 Jul 12.

Mammal Research Institute, Polish Academy of Sciences, Białowieża, Poland.

Climate warming and human landscape transformation during the Holocene resulted in environmental changes for wild animals. The last remnants of the European Pleistocene megafauna that survived into the Holocene were particularly vulnerable to changes in habitat. To track the response of habitat use and foraging of large herbivores to natural and anthropogenic changes in environmental conditions during the Holocene, we investigated carbon (δ C) and nitrogen (δ N) stable isotope composition in bone collagen of moose (Alces alces), European bison (Bison bonasus) and aurochs (Bos primigenius) in Central and Eastern Europe. We found strong variations in isotope compositions in the studied species throughout the Holocene and diverse responses to changing environmental conditions. All three species showed significant changes in their δ C values reflecting a shift of foraging habitats from more open in the Early and pre-Neolithic Holocene to more forest during the Neolithic and Late Holocene. This shift was strongest in European bison, suggesting higher plasticity, more limited in moose, and the least in aurochs. Significant increases of δ N values in European bison and moose are evidence of a diet change towards more grazing, but may also reflect increased nitrogen in soils following deglaciation and global temperature increases. Among the factors explaining the observed isotope variations were time (age of samples), longitude and elevation in European bison, and time, longitude and forest cover in aurochs. None of the analysed factors explained isotope variations in moose. Our results demonstrate the strong influence of natural (forest expansion) and anthropogenic (deforestation and human pressure) changes on the foraging ecology of large herbivores, with forests playing a major role as a refugial habitat since the Neolithic, particularly for European bison and aurochs. We propose that high flexibility in foraging strategy was the key for survival of large herbivores in the changing environmental conditions of the Holocene.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1111/gcb.14733DOI Listing
September 2019

Prey-to-fox isotopic enrichment of S in bone collagen: Implications for paleoecological studies.

Rapid Commun Mass Spectrom 2019 Aug;33(16):1311-1317

Senckenberg Centre for Human Evolution and Palaeoenvironment (HEP) at Tuebingen University, Hölderlinstr. 12, 72074, Tübingen, Germany.

Rationale: The trophic enrichment factor (TEF) is a parameter reflecting the difference in isotopic ratio between a consumer's tissues and diet, used in isotopic ecology and paleoecology to track dietary habits. The TEF of sulfur is believed to be low, but was, until now, only documented in a limited number of taxa. In this study we use a subfossil accumulation of bones from a red fox (Vulpes vulpes) den to verify the TEF for sulfur in fox bone collagen.

Methods: Collagen was extracted from 30 samples of subfossil bones, including foxes and their prey. The δ S values of the bone collagen samples were measured with an elemental analyzer connected to an isotope ratio mass spectrometer. The TEF was calculated as [Δ S = (mean δ S in predator) - (mean δ S in prey)], using taphonomic indices to estimate the mean diet, and calculated separately for different age classes of the predator.

Results: We modeled 12 variants of TEF for different estimations of the diet composition and for three fox age classes (adult, subadult, and juvenile). The estimated TEF values range from -0.54 to +0.03‰ and are similar to TEFs known for other mammals. Absolute TEF values are nearly equal to or lower than the analytical error, which is ±0.4‰.

Conclusions: For the first time, we present direct δ S data for the bone collagen of a free-living predator and its naturally selected prey. Our results indicate very low or even slightly negative TEF values for sulfur. Furthermore, according to our results, the δ S value should not be considered a reliable indicator of trophic position in terrestrial food webs but rather, it should be used to disentangle different food webs based on different primary producers.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1002/rcm.8471DOI Listing
August 2019

Out of Africa by spontaneous migration waves.

PLoS One 2019 23;14(4):e0201998. Epub 2019 Apr 23.

Department of Geosciences, Eberhard Karls University Tübingen, Tübingen, Germany.

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 extrinsic 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.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0201998PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6478371PMC
December 2019

Evolutionary history and palaeoecology of brown bear in North-East Siberia re-examined using ancient DNA and stable isotopes from skeletal remains.

Sci Rep 2019 03 14;9(1):4462. Epub 2019 Mar 14.

Natural History Museum of Denmark, University of Copenhagen, DK-1350, Copenhagen K, Denmark.

Over 60% of the modern distribution range of brown bears falls within Russia, yet palaeoecological data from the region remain scarce. Complete modern Russian brown bear mitogenomes are abundant in the published literature, yet examples of their ancient counterparts are absent. Similarly, there is only limited stable isotopic data of prehistoric brown bears from the region. We used ancient DNA and stable carbon (δC) and nitrogen (δN) isotopes retrieved from five Pleistocene Yakutian brown bears (one Middle Pleistocene and four Late Pleistocene), to elucidate the evolutionary history and palaeoecology of the species in the region. We were able to reconstruct the complete mitogenome of one of the Late Pleistocene specimens, but we were unable to assign it to any of the previously published brown bear mitogenome clades. A subsequent analysis of published mtDNA control region sequences, which included sequences of extinct clades from other geographic regions, assigned the ancient Yakutian bear to the extinct clade 3c; a clade previously identified from Late Quaternary specimens from Eastern Beringia and Northern Spain. Our analyses of stable isotopes showed relatively high δN values in the Pleistocene Yakutian brown bears, suggesting a more carnivorous diet than contemporary brown bears from Eastern Beringia.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41598-019-40168-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6418263PMC
March 2019

Stable isotopes reveal patterns of diet and mobility in the last Neandertals and first modern humans in Europe.

Sci Rep 2019 03 14;9(1):4433. Epub 2019 Mar 14.

Department of Geosciences, Biogeology, University of Tübingen, Hölderlinstrasse 12, 72074, Tübingen, Germany.

Correlating cultural, technological and ecological aspects of both Upper Pleistocene modern humans (UPMHs) and Neandertals provides a useful approach for achieving robust predictions about what makes us human. Here we present ecological information for a period of special relevance in human evolution, the time of replacement of Neandertals by modern humans during the Late Pleistocene in Europe. Using the stable isotopic approach, we shed light on aspects of diet and mobility of the late Neandertals and UPMHs from the cave sites of the Troisième caverne of Goyet and Spy in Belgium. We demonstrate that their diet was essentially similar, relying on the same terrestrial herbivores, whereas mobility strategies indicate considerable differences between Neandertal groups, as well as in comparison to UPMHs. Our results indicate that UPMHs exploited their environment to a greater extent than Neandertals and support the hypothesis that UPMHs had a substantial impact not only on the population dynamics of large mammals but also on the whole structure of the ecosystem since their initial arrival in Europe.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41598-019-41033-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6418202PMC
March 2019

The genomic history of southeastern Europe.

Authors:
Iain Mathieson Songül Alpaslan-Roodenberg Cosimo Posth Anna Szécsényi-Nagy Nadin Rohland Swapan Mallick Iñigo Olalde Nasreen Broomandkhoshbacht Francesca Candilio Olivia Cheronet Daniel Fernandes Matthew Ferry Beatriz Gamarra Gloria González Fortes Wolfgang Haak Eadaoin Harney Eppie Jones Denise Keating Ben Krause-Kyora Isil Kucukkalipci Megan Michel Alissa Mittnik Kathrin Nägele Mario Novak Jonas Oppenheimer Nick Patterson Saskia Pfrengle Kendra Sirak Kristin Stewardson Stefania Vai Stefan Alexandrov Kurt W Alt Radian Andreescu Dragana Antonović Abigail Ash Nadezhda Atanassova Krum Bacvarov Mende Balázs Gusztáv Hervé Bocherens Michael Bolus Adina Boroneanţ Yavor Boyadzhiev Alicja Budnik Josip Burmaz Stefan Chohadzhiev Nicholas J Conard Richard Cottiaux Maja Čuka Christophe Cupillard Dorothée G Drucker Nedko Elenski Michael Francken Borislava Galabova Georgi Ganetsovski Bernard Gély Tamás Hajdu Veneta Handzhyiska Katerina Harvati Thomas Higham Stanislav Iliev Ivor Janković Ivor Karavanić Douglas J Kennett Darko Komšo Alexandra Kozak Damian Labuda Martina Lari Catalin Lazar Maleen Leppek Krassimir Leshtakov Domenico Lo Vetro Dženi Los Ivaylo Lozanov Maria Malina Fabio Martini Kath McSweeney Harald Meller Marko Menđušić Pavel Mirea Vyacheslav Moiseyev Vanya Petrova T Douglas Price Angela Simalcsik Luca Sineo Mario Šlaus Vladimir Slavchev Petar Stanev Andrej Starović Tamás Szeniczey Sahra Talamo Maria Teschler-Nicola Corinne Thevenet Ivan Valchev Frédérique Valentin Sergey Vasilyev Fanica Veljanovska Svetlana Venelinova Elizaveta Veselovskaya Bence Viola Cristian Virag Joško Zaninović Steve Zäuner Philipp W Stockhammer Giulio Catalano Raiko Krauß David Caramelli Gunita Zariņa Bisserka Gaydarska Malcolm Lillie Alexey G Nikitin Inna Potekhina Anastasia Papathanasiou Dušan Borić Clive Bonsall Johannes Krause Ron Pinhasi David Reich

Nature 2018 03 21;555(7695):197-203. Epub 2018 Feb 21.

Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA.

Farming was first introduced to Europe in the mid-seventh millennium bc, and was associated with migrants from Anatolia who settled in the southeast before spreading throughout Europe. Here, to understand the dynamics of this process, we analysed genome-wide ancient DNA data from 225 individuals who lived in southeastern Europe and surrounding regions between 12000 and 500 bc. We document a west-east cline of ancestry in indigenous hunter-gatherers and, in eastern Europe, the early stages in the formation of Bronze Age steppe ancestry. We show that the first farmers of northern and western Europe dispersed through southeastern Europe with limited hunter-gatherer admixture, but that some early groups in the southeast mixed extensively with hunter-gatherers without the sex-biased admixture that prevailed later in the north and west. We also show that southeastern Europe continued to be a nexus between east and west after the arrival of farmers, with intermittent genetic contact with steppe populations occurring up to 2,000 years earlier than the migrations from the steppe that ultimately replaced much of the population of northern Europe.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1038/nature25778DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6091220PMC
March 2018

Genetic diversity, genetic structure and diet of ancient and contemporary red deer (Cervus elaphus L.) from north-eastern France.

PLoS One 2018 5;13(1):e0189278. Epub 2018 Jan 5.

Senckenberg Center for Human Evolution and Palaeoenvironment (HEP), University of Tübingen, Tübingen, Germany.

In north-eastern France, red deer (Cervus elaphus L.) populations were rebuilt from a few hundred individuals, which have subsisted in remote valleys of the Vosges mountains, and to a lesser extent from individuals escaped from private enclosures; at present times, this species occupies large areas, mainly in the Vosges Mountains. In this study, we examined the population dynamics of red deer in the Vosges Mountains using ancient and contemporary mitochondrial DNA (mtDNA) from 140 samples (23 ancient + 117 modern) spanning the last 7'000 years. In addition, we reconstructed the feeding habits and the habitat of red deer since the beginning of agriculture applying isotopic analyses in order to establish a basis for current environmental management strategies. We show that past and present red deer in the Vosges Mountains belong to mtDNA haplogroup A, suggesting that they originated from the Iberian refugium after the last glacial maximum (LGM). Palaeogenetic analysis of ancient bone material revealed the presence of two distinct haplotypes with different temporal distributions. Individuals belonging to the two haplotype groups apparently occupied two different habitats over at least 7'000 years. AM6 correlates with an ecological type that feeds in densely forested mountain landscapes, while AM235 correlates with feeding in lowland landscapes, composed of a mixture of meadows and riverine, herb-rich woodlands. Our results suggest that red deer of north-eastern France was able to adapt, over the long term, to these different habitat types, possibly due to efficient ethological barriers. Modern haplotype patterns support the historical record that red deer has been exposed to strong anthropogenic influences as a major game species.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0189278PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5755736PMC
January 2018

Stable isotope signatures of large herbivore foraging habitats across Europe.

PLoS One 2018 2;13(1):e0190723. Epub 2018 Jan 2.

Mammal Research Institute, Polish Academy of Sciences, Białowieża, Poland.

We investigated how do environmental and climatic factors, but also management, affect the carbon (δ13C) and nitrogen (δ15N) stable isotope composition in bone collagen of the two largest contemporary herbivores: European bison (Bison bonasus) and moose (Alces alces) across Europe. We also analysed how different scenarios of population recovery- reintroduction in bison and natural recovery in moose influenced feeding habitats and diet of these two species and compared isotopic signatures of modern populations of bison and moose (living in human-altered landscapes) with those occurring in early Holocene. We found that δ13C of modern bison and moose decreased with increasing forest cover. Decreasing forest cover, increasing mean annual temperature and feeding on farm crops caused an increase in δ15N in bison, while no factor significantly affected δ15N in moose. We showed significant differences in δ13C and δ15N among modern bison populations, in contrast to moose populations. Variation in both isotopes in bison resulted from inter-population differences, while in moose it was mainly an effect of intra-population variation. Almost all modern bison populations differed in δ13C and δ15N from early Holocene bison. Such differences were not observed in moose. It indicates refugee status of European bison. Our results yielded evidence that habitat structure, management and a different history of population recovery have a strong influence on foraging behaviour of large herbivores reflected in stable isotope signatures. Influence of forest structure on carbon isotope signatures of studied herbivores supports the "canopy effect" hypothesis.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0190723PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5749876PMC
February 2018

Central European Woolly Mammoth Population Dynamics: Insights from Late Pleistocene Mitochondrial Genomes.

Sci Rep 2017 12 18;7(1):17714. Epub 2017 Dec 18.

Institute for Archaeological Science, University of Tübingen, Rümelinstraße 23, 72070, Tübingen, Germany.

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.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41598-017-17723-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5735091PMC
December 2017

Reply to "Comment on "Ecological niche of Neanderthals from Spy Cave revealed by nitrogen isotopes of individual amino acids in collagen." [J. Hum. Evol. 93 (2016) 82-90]" [J. Hum. Evol. 117 (2018) 53-55].

J Hum Evol 2018 04 10;117:56-60. Epub 2017 Oct 10.

Fachbereich Geowissenschaften, Paläobiologie (Biogeologie), Universität Tübingen, Hölderlinstraße 12, 72074 Tübingen, Germany; Senckenberg Centre for Human Evolution and Palaeoenvironment (HEP), Universität Tübingen, Hölderlinstraße 12, 72074 Tübingen, Germany.

View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.jhevol.2017.09.008DOI Listing
April 2018

Comparative performance of the BGISEQ-500 vs Illumina HiSeq2500 sequencing platforms for palaeogenomic sequencing.

Gigascience 2017 08;6(8):1-13

Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark.

Ancient DNA research has been revolutionized following development of next-generation sequencing platforms. Although a number of such platforms have been applied to ancient DNA samples, the Illumina series are the dominant choice today, mainly because of high production capacities and short read production. Recently a potentially attractive alternative platform for palaeogenomic data generation has been developed, the BGISEQ-500, whose sequence output are comparable with the Illumina series. In this study, we modified the standard BGISEQ-500 library preparation specifically for use on degraded DNA, then directly compared the sequencing performance and data quality of the BGISEQ-500 to the Illumina HiSeq2500 platform on DNA extracted from 8 historic and ancient dog and wolf samples. The data generated were largely comparable between sequencing platforms, with no statistically significant difference observed for parameters including level (P = 0.371) and average sequence length (P = 0718) of endogenous nuclear DNA, sequence GC content (P = 0.311), double-stranded DNA damage rate (v. 0.309), and sequence clonality (P = 0.093). Small significant differences were found in single-strand DNA damage rate (δS; slightly lower for the BGISEQ-500, P = 0.011) and the background rate of difference from the reference genome (θ; slightly higher for BGISEQ-500, P = 0.012). This may result from the differences in amplification cycles used to polymerase chain reaction-amplify the libraries. A significant difference was also observed in the mitochondrial DNA percentages recovered (P = 0.018), although we believe this is likely a stochastic effect relating to the extremely low levels of mitochondria that were sequenced from 3 of the samples with overall very low levels of endogenous DNA. Although we acknowledge that our analyses were limited to animal material, our observations suggest that the BGISEQ-500 holds the potential to represent a valid and potentially valuable alternative platform for palaeogenomic data generation that is worthy of future exploration by those interested in the sequencing and analysis of degraded DNA.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1093/gigascience/gix049DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5570000PMC
August 2017

Isotopic analyses suggest mammoth and plant in the diet of the oldest anatomically modern humans from far southeast Europe.

Sci Rep 2017 07 28;7(1):6833. Epub 2017 Jul 28.

Fachbereich Geowissenschaften, Forschungsbereich Paläobiologie, AG Biogeologie, Universität Tübingen, Hölderlinstr. 12, 72074, Tübingen, Germany.

Relatively high N abundances in bone collagen of early anatomically modern humans in Europe have often been interpreted as a specific consumption of freshwater resources, even if mammoth is an alternative high N prey. At Buran-Kaya III, access to associated fauna in a secured archaeological context and application of recently developed isotopic analyses of individuals amino acids offer the opportunity to further examine this hypothesis. The site of Buran-Kaya III is located in south Crimea and has provided a rich archaeological sequence including two Upper Palaeolithic layers, from which human fossils were retrieved and directly dated as from 37.8 to 33.1 ka cal BP. Results from bulk collagen of three human remains suggests the consumption of a high N prey besides the contribution of saiga, red deer, horse and hare, whose butchered remains were present at the site. In contrast to bulk collagen, phenylalanine and glutamic acid N abundances reflect not only animal but also plant protein contributions to omnivorous diet, and allow disentangling aquatic from terrestrial resource consumption. The inferred human trophic position values point to terrestrial-based diet, meaning a significant contribution of mammoth meat, in addition to a clear intake of plant protein.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41598-017-07065-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5533724PMC
July 2017

Deeply divergent archaic mitochondrial genome provides lower time boundary for African gene flow into Neanderthals.

Nat Commun 2017 07 4;8:16046. Epub 2017 Jul 4.

Institute for Archaeological Sciences, University of Tübingen, Rümelin Strasse 23, Tübingen 72070, Germany.

Ancient DNA is revealing new insights into the genetic relationship between Pleistocene hominins and modern humans. Nuclear DNA indicated Neanderthals as a sister group of Denisovans after diverging from modern humans. However, the closer affinity of the Neanderthal mitochondrial DNA (mtDNA) to modern humans than Denisovans has recently been suggested as the result of gene flow from an African source into Neanderthals before 100,000 years ago. Here we report the complete mtDNA of an archaic femur from the Hohlenstein-Stadel (HST) cave in southwestern Germany. HST carries the deepest divergent mtDNA lineage that splits from other Neanderthals ∼270,000 years ago, providing a lower boundary for the time of the putative mtDNA introgression event. We demonstrate that a complete Neanderthal mtDNA replacement is feasible over this time interval even with minimal hominin introgression. The highly divergent HST branch is indicative of greater mtDNA diversity during the Middle Pleistocene than in later periods.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1038/ncomms16046DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5500885PMC
July 2017

Neandertal cannibalism and Neandertal bones used as tools in Northern Europe.

Sci Rep 2016 07 6;6:29005. Epub 2016 Jul 6.

Institute for Archaeological Sciences, Archaeo- and Palaeogenetics, University of Tübingen, Rümelinstr. 23, 72070 Tübingen, Germany.

Almost 150 years after the first identification of Neandertal skeletal material, the cognitive and symbolic abilities of these populations remain a subject of intense debate. We present 99 new Neandertal remains from the Troisième caverne of Goyet (Belgium) dated to 40,500-45,500 calBP. The remains were identified through a multidisciplinary study that combines morphometrics, taphonomy, stable isotopes, radiocarbon dating and genetic analyses. The Goyet Neandertal bones show distinctive anthropogenic modifications, which provides clear evidence for butchery activities as well as four bones having been used for retouching stone tools. In addition to being the first site to have yielded multiple Neandertal bones used as retouchers, Goyet not only provides the first unambiguous evidence of Neandertal cannibalism in Northern Europe, but also highlights considerable diversity in mortuary behaviour among the region's late Neandertal population in the period immediately preceding their disappearance.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1038/srep29005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4933918PMC
July 2016