Microstratigraphic preservation of ancient faunal and hominin DNA in Pleistocene cave sediments

Ancient DNA recovered from Pleistocene sediments represents a rich resource for the study of past hominin and environmental diversity. However, little is known about how DNA is preserved in sediments and the extent to which it may be translocated between archaeological strata. Here, we investigate DNA preservation in 47 blocks of resin-impregnated archaeological sediment collected over the last four decades for micromorphological analyses at 13 prehistoric sites in Europe, Asia, Africa, and North America and show that such blocks can preserve DNA of hominins and other mammals. Extensive microsampling of sediment blocks from Denisova Cave in the Altai Mountains reveals that the taxonomic composition of mammalian DNA differs drastically at the millimeter-scale and that DNA is concentrated in small particles, especially in fragments of bone and feces (coprolites), suggesting that these are substantial sources of DNA in sediments. Three microsamples taken in close proximity in one of the blocks yielded Neanderthal DNA from at least two male individuals closely related to Denisova 5, a Neanderthal toe bone previously recovered from the same layer. Our work indicates that DNA can remain stably localized in sediments over time and provides a means of linking genetic information to the archaeological and ecological records on a microstratigraphic scale

Compound-specific radiocarbon dating and mitochondrial DNA analysis of the Pleistocene hominin from Salkhit Mongolia

A skullcap found in the Salkhit Valley northeast Mongolia is, to our knowledge, the only Pleistocene hominin fossil found in the country. It was initially described as an individual with possible archaic affinities, but its ancestry has been debated since the discovery. Here, we determine the age of the Salkhit skull by compound-specific radiocarbon dating of hydroxyproline to 34,950 – 33,900 Cal. BP (at 95% probability), placing the Salkhit individual in the Early Upper Paleolithic period. We reconstruct the complete mitochondrial genome (mtDNA) of the specimen. It falls within a group of modern human mtDNAs (haplogroup N) that is widespread in Eurasia today. The results now place the specimen into its proper chronometric and biological context and allow us to begin integrating it with other evidence for the human occupation of this region during the Paleolithic, as well as wider Pleistocene sequences across Eurasia

Compound-specific radiocarbon dating and mitochondrial DNA analysis of the Pleistocene hominin from Salkhit Mongolia

A skullcap found in the Salkhit Valley in northeast Mongolia is, to our knowledge, the only Pleistocene hominin fossil found in the country. It was initially described as an individual with possible archaic affinities, but its ancestry has been debated since the discovery. Here, we determine the age of the Salkhit skull by compound-specific radiocarbon dating of hydroxyproline to 34,950–33,900 Cal. BP (at 95% probability), placing the Salkhit individual in the Early Upper Paleolithic period. We reconstruct the complete mitochondrial genome (mtDNA) of the specimen. It falls within a group of modern human mtDNAs (haplogroup N) that is widespread in Eurasia today. The results now place the specimen into its proper chronometric and biological context and allow us to begin integrating it with other evidence for the human occupation of this region during the Paleolithic, as well as wider Pleistocene sequences across Eurasia

Denisovan ancestry and population history of early East Asians

International audienc

The earliest Denisovans and their cultural adaptation

Since the initial identification of the Denisovans a decade ago, only a handful of their physical remains have been discovered. Here we analysed ~3,800 non-diagnostic bone fragments using collagen peptide mass fingerprinting to locate new hominin remains from Denisova Cave (Siberia, Russia). We identified five new hominin bones, four of which contained sufficient DNA for mitochondrial analysis. Three carry mitochondrial DNA of the Denisovan type and one was found to carry mtDNA of the Neanderthal type. The former come from the same archaeological layer near the base of the cave’s sequence and are the oldest securely dated evidence of Denisovans at 200 ka (thousand years ago) (205–192 ka at 68.2% or 217–187 ka at 95% probability). The stratigraphic context in which they were located contains a wealth of archaeological material in the form of lithics and faunal remains, allowing us to determine the material culture associated with these early hominins and explore their behavioural and environmental adaptations. The combination of bone collagen fingerprinting and genetic analyses has so far more-than-doubled the number of hominin bones at Denisova Cave and has expanded our understanding of Denisovan and Neanderthal interactions, as well as their archaeological signatures.Results - ZooMS. - microCT analysis. - mtDNA analysis. Discussion Method

Past climate changes, population dynamics and the origin of Bison in Europe

International audienceBackground: Climatic and environmental fluctuations as well as anthropogenic pressure have led to theextinction of much of Europe’s megafauna. The European bison or wisent (Bison bonasus), one of the last wildEuropean large mammals, narrowly escaped extinction at the onset of the 20th century owing to hunting andhabitat fragmentation. Little is known, however, about its origin, evolutionary history and population dynamicsduring the Pleistocene.Results: Through ancient DNA analysis we show that the emblematic European bison has experienced severalwaves of population expansion, contraction, and extinction during the last 50,000 years in Europe, culminatingin a major reduction of genetic diversity during the Holocene. Fifty-seven complete and partial ancient mitogenomesfrom throughout Europe, the Caucasus, and Siberia reveal that three populations of wisent (Bison bonasus) andsteppe bison (B. priscus) alternately occupied Western Europe, correlating with climate-induced environmentalchanges. The Late Pleistocene European steppe bison originated from northern Eurasia, whereas the modernwisent population emerged from a refuge in the southern Caucasus after the last glacial maximum. A populationoverlap during a transition period is reflected in ca. 36,000-year-old paintings in the French Chauvet cave. Bayesiananalyses of these complete ancient mitogenomes yielded new dates of the various branching events during theevolution of Bison and its radiation with Bos, which lead us to propose that the genetic affiliation betweenthe wisent and cattle mitogenomes result from incomplete lineage sorting rather than post-speciation gene flow.Conclusion: The paleogenetic analysis of bison remains from the last 50,000 years reveals the influence ofclimate changes on the dynamics of the various bison populations in Europe, only one of which survived intothe Holocene, where it experienced severe reductions in its genetic diversity. The time depth and geographicalscope of this study enables us to propose temperate Western Europe as a suitable biotope for the wisentcompatible with its reintroduction

Earliest Known Human Burial in Africa

The origin and evolution of hominin mortuary practices are topics of intense interest and debate1–3. Human burials dated to the Middle Stone Age (MSA) are exceedingly rare in Africa and unknown in East Africa1–6. Here we describe the partial skeleton of a roughly 2.5- to 3.0-year-old child dating to 78.3 ± 4.1 thousand years ago, which was recovered in the MSA layers of Panga ya Saidi (PYS), a cave site in the tropical upland coast of Kenya7,8. Recent excavations have revealed a pit feature containing a child in a flexed position. Geochemical, granulometric and micromorphological analyses of the burial pit content and encasing archaeological layers indicate that the pit was deliberately excavated. Taphonomical evidence, such as the strict articulation or good anatomical association of the skeletal elements and histological evidence of putrefaction, support the in-place decomposition of the fresh body. The presence of little or no displacement of the unstable joints during decomposition points to an interment in a filled space (grave earth), making the PYS finding the oldest known human burial in Africa. The morphological assessment of the partial skeleton is consistent with its assignment to Homo sapiens, although the preservation of some primitive features in the dentition supports increasing evidence for non-gradual assembly of modern traits during the emergence of our species. The PYS burial sheds light on how MSA populations interacted with the dead. The earliest known human burial in Africa, that of a young child, is dated to around 78,000 years ago