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Neanderthals and Denisovans are extinct groups of hominins that separated from each other more than 390,000 years ago 1 , 2 . Here we present the genome of ‘Denisova 11’, a bone fragment from Denisova Cave (Russia) 3 and show that it comes from an individual who had a Neanderthal mother and a Denisovan father. The father, whose genome bears traces of Neanderthal ancestry, came from a population related to a later Denisovan found in the cave 4 – 6 . The mother came from a population more closely related to Neanderthals who lived later in Europe 2 , 7 than to an earlier Neanderthal found in Denisova Cave 8 , suggesting that migrations of Neanderthals between eastern and western Eurasia occurred sometime after 120,000 years ago. The finding of a first-generation Neanderthal–Denisovan offspring among the small number of archaic specimens sequenced to date suggests that mixing between Late Pleistocene hominin groups was common when they met. Genomic evidence of the offspring of a Neanderthal mother and a Denisovan father suggests that mixing among different hominin groups may have more been frequent than previously appreciated.

To date, the only Neandertal genome that has been sequenced to high quality is from an individual found in Southern Siberia. We sequenced the genome of a female Neandertal from ~50,000 years ago from Vindija Cave, Croatia, to ~30-fold genomic coverage. She carried 1.6 differences per 10,000 base pairs between the two copies of her genome, fewer than present-day humans, suggesting that Neandertal populations were of small size. Our analyses indicate that she was more closely related to the Neandertals that mixed with the ancestors of present-day humans living outside of sub-Saharan Africa than the previously sequenced Neandertal from Siberia, allowing 10 to 20% more Neandertal DNA to be identified in present-day humans, including variants involved in low-density lipoprotein cholesterol concentrations, schizophrenia, and other diseases.

Genetic similarity among late Neanderthals is predicted well by their geographical location, and although some of these Neanderthals were contemporaneous with early modern humans, their genomes show no evidence of recent gene flow from modern humans. Late Neanderthal relations Many questions remain about the relationship between populations of Neanderthals around the time of their final interactions with modern humans, and how this contributed to the evolution of modern humans. Janet Kelso, Svante Pääbo and colleagues sequenced the genomes of five Neanderthals that lived between 39,000 and 47,000 years ago, broadening the temporal and geographical range of available Neanderthal genomes. They analyse these genomes together with previously sequenced ancient genomes and find that relatedness among Neanderthals is related to geographic proximity. They find that the majority of gene flow into early modern humans originated from one or more Neanderthal populations that diverged from the late Neanderthals at least 70,000 years ago, but after their split from the Altai Neanderthal approximately 150,000 years ago. Although it has previously been shown that Neanderthals contributed DNA to modern humans 1 , 2 , not much is known about the genetic diversity of Neanderthals or the relationship between late Neanderthal populations at the time at which their last interactions with early modern humans occurred and before they eventually disappeared. Our ability to retrieve DNA from a larger number of Neanderthal individuals has been limited by poor preservation of endogenous DNA 3 and contamination of Neanderthal skeletal remains by large amounts of microbial and present-day human DNA 3 , 4 , 5 . Here we use hypochlorite treatment 6 of as little as 9 mg of bone or tooth powder to generate between 1- and 2.7-fold genomic coverage of five Neanderthals who lived around 39,000 to 47,000 years ago (that is, late Neanderthals), thereby doubling the number of Neanderthals for which genome sequences are available. Genetic similarity among late Neanderthals is well predicted by their geographical location, and comparison to the genome of an older Neanderthal from the Caucasus 2 , 7 indicates that a population turnover is likely to have occurred, either in the Caucasus or throughout Europe, towards the end of Neanderthal history. We find that the bulk of Neanderthal gene flow into early modern humans originated from one or more source populations that diverged from the Neanderthals that were studied here at least 70,000 years ago, but after they split from a previously sequenced Neanderthal from Siberia 2 around 150,000 years ago. Although four of the Neanderthals studied here post-date the putative arrival of early modern humans into Europe, we do not detect any recent gene flow from early modern humans in their ancestry.

The evolution and development of human mortuary behaviors is of enormous cultural significance. Here we report a richly-decorated young infant burial (AVH-1) from Arma Veirana (Liguria, northwestern Italy) that is directly dated to 10,211–9910 cal BP (95.4% probability), placing it within the early Holocene and therefore attributable to the early Mesolithic, a cultural period from which well-documented burials are exceedingly rare. Virtual dental histology, proteomics, and aDNA indicate that the infant was a 40–50 days old female. Associated artifacts indicate significant material and emotional investment in the child’s interment. The detailed biological profile of AVH-1 establishes the child as the earliest European near-neonate documented to be female. The Arma Veirana burial thus provides insight into sex/gender-based social status, funerary treatment, and the attribution of personhood to the youngest individuals among prehistoric hunter-gatherer groups and adds substantially to the scant data on mortuary practices from an important period in prehistory shortly following the end of the last Ice Age.

Previous dating of the Vi-207 and Vi-208 Neanderthal remains from Vindija Cave (Croatia) led to the suggestion that Neanderthals survived there as recently as 28,000–29,000 B.P. Subsequent dating yielded older dates, interpreted as ages of at least ∼32,500 B.P. We have redated these same specimens using an approach based on the extraction of the amino acid hydroxyproline, using preparative high-performance liquid chromatography (Prep-HPLC). This method is more efficient in eliminating modern contamination in the bone collagen. The revised dates are older than 40,000 B.P., suggesting the Vindija Neanderthals did not live more recently than others across Europe, and probably predate the arrival of anatomically modern humans in Eastern Europe. We applied zooarchaeology by mass spectrometry (ZooMS) to find additional hominin remains. We identified one bone that is Neanderthal, based on its mitochondrial DNA, and dated it directly to 46,200 ± 1,500 B.P. We also attempted to date six early Upper Paleolithic bone points from stratigraphic units G₁, Fd/d+G₁ and Fd/d, Fd. One bone artifact gave a date of 29,500 ± 400 B.P., while the remainder yielded no collagen. We additionally dated animal bone samples from units G₁ and G₁–G₃. These dates suggest a co-occurrence of early Upper Paleolithic osseous artifacts, particularly split-based points, alongside the remains of Neanderthals is a result of postdepositional mixing, rather than an association between the two groups, although more work is required to show this definitively.

Extinct lineages of Yersinia pestis , the causative agent of the plague, have been identified in several individuals from Eurasia between 5000 and 2500 years before present (BP). One of these, termed the ‘LNBA lineage’ (Late Neolithic and Bronze Age), has been suggested to have spread into Europe with human groups expanding from the Eurasian steppe. Here, we show that the LNBA plague was spread to Europe’s northwestern periphery by sequencing three Yersinia pestis genomes from Britain, all dating to ~4000 cal BP. Two individuals were from an unusual mass burial context in Charterhouse Warren, Somerset, and one individual was from a single burial under a ring cairn monument in Levens, Cumbria. To our knowledge, this represents the earliest evidence of LNBA plague in Britain documented to date. All three British Yersinia pestis genomes belong to a sublineage previously observed in Bronze Age individuals from Central Europe that had lost the putative virulence factor yapC . This sublineage is later found in Eastern Asia ~3200 cal BP. While the severity of the disease is currently unclear, the wide geographic distribution within a few centuries suggests substantial transmissibility. An extinct prehistoric plague lineage of Yersinia pestis has been documented from Central Europe to Asia during the Late Neolithic and Bronze Age. Here, Swali et al. show that this lineage spread to Europe’s northwestern periphery by sequencing three ~4000 year-old Yersinia pestis genomes from Britain.

The Troisième caverne of Goyet has yielded the largest assemblage of Neandertal remains in Northern Europe with clear evidence of anthropogenic modifications. However, its skeletal fragmentation has long limited detailed morphological and behavioural study on the assemblage. In this study, we integrate palaeogenetic, isotopic, morphometric, and structural analyses of the long bones to assess the biological profiles of the Neandertals from Goyet and explore whether they present particularities that could shed light on the formation of this unique cannibalised assemblage. We identify a minimum of six individuals, including four adult or adolescent females. Compared to Homo sapiens and Neandertals—including regional specimens—the females from Goyet display short statures and reduced diaphyseal robusticity of their long bones. They lack skeletal markers associated with high mobility despite isotopic evidence for non-local origins. The overrepresentation of short, morphologically gracile, non-local females, alongside two immature individuals, suggests a strong selection bias in the individuals present at the site. Dated between 41,000 and 45,000 years ago, a period marked by Neandertal cultural diversity, biological decline and the arrival of Homo sapiens in Northern Europe, the cannibalised female and juvenile Neandertals from Goyet indicate exocannibalism, possibly linked to inter-group conflict, territoriality, and/or specific treatment of outsiders.

[This corrects the article DOI: 10.1371/journal.pone.0324911.].

The Micoquian is the broadest and longest enduring cultural facies of the Late Middle Palaeolithic that spread across the periglacial and boreal environments of Europe between Eastern France, Poland, and Northern Caucasus. Here, we present new data from the archaeological record of Stajnia Cave (Poland) and the paleogenetic analysis of a Neanderthal molar S5000, found in a Micoquian context. Our results demonstrate that the mtDNA genome of Stajnia S5000 dates to MIS 5a making the tooth the oldest Neanderthal specimen from Central-Eastern Europe. Furthermore, S5000 mtDNA has the fewest number of differences to mtDNA of Mezmaiskaya 1 Neanderthal from Northern Caucasus, and is more distant from almost contemporaneous Neanderthals of Scladina and Hohlenstein-Stadel. This observation and the technological affinity between Poland and the Northern Caucasus could be the result of increased mobility of Neanderthals that changed their subsistence strategy for coping with the new low biomass environments and the increased foraging radius of gregarious animals. The Prut and Dniester rivers were probably used as the main corridors of dispersal. The persistence of the Micoquian techno-complex in South-Eastern Europe infers that this axis of mobility was also used at the beginning of MIS 3 when a Neanderthal population turnover occurred in the Northern Caucasus.