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The high-quality genome sequence of a 45,000-year-old modern human from Siberia reveals that gene flow from Neanderthals into the ancestors of this individual had already occurred about 7,000 to 13,000 years earlier; genomic comparisons show that he belonged to a population that lived close in time to the separation of populations in east and west Eurasia and that may represent an early modern human radiation out of Africa that has no direct descendants today.

Here, the authors present mtDNA and chronological data for sediments from excavations in the South Chamber of Denisova Cave, from which they construct a timeline of hominin and faunal occupation that fills stratigraphic gaps in other parts of the cave.

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.

High-coverage and low-coverage genomic data for some of the earliest modern humans in Europe provide insights into recent admixture with Neanderthals and familial relationship links with distant communities approximately 45,000 years ago.

With the generation of large pan-cancer whole-exome and whole-genome sequencing projects, a question remains about how comparable these datasets are. Here, using The Cancer Genome Atlas samples analysed as part of the Pan-Cancer Analysis of Whole Genomes project, the authors explore the concordance of mutations called by whole exome sequencing and whole genome sequencing techniques.

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.

A non-destructive DNA isolation method for the stepwise release of DNA trapped in ancient tooth and bone artefacts is developed.

Sequencing of the bonobo genome shows that more than three per cent of the human genome is more closely related to either the bonobo genome or the chimpanzee genome than those genomes are to each other.

Genetic data for 13 Neanderthals from 2 Middle Palaeolithic sites in the Altai Mountains of southern Siberia presented provide insights into the social organization of an isolated Neanderthal community at the easternmost extent of their known range.

Identifying Neanderthal and Denisovan bone fragments using collagen peptide mass fingerprinting and mitochondrial DNA analysis at Denisova Cave, the authors are able to date the earliest secure Denisovan presence at the cave to c. 200 ka. The stratigraphic association with lithics and faunal remains allows the authors to explore the behavioural and environmental adaptations of these elusive hominins.

Genome-wide data for the three oldest known modern human remains in Europe, dated to around 45,000 years ago, shed light on early human migrations in Europe and suggest that mixing with Neanderthals was more common than is often assumed.

Ancient mitochondrial DNA from sediments reveals the sequence of Denisovan, Neanderthal and faunal occupation of Denisova Cave, and evidence for the appearance of modern humans at least 45,000 years ago.

Analysis of ancient genomic data of 51 humans from Eurasia dating from 45,000 to 7,000 years ago provides insight into the population history of pre-Neolithic Europe and support for recurring migration and population turnover in Europe during this period.

Modern human genomes contain Neanderthal sequences, but it is unclear whether these were selected. Here, Khrameeva et al.show that Neanderthal sequences associated with lipid catabolism are three times more frequent in Europe, suggesting that these sequences might have been beneficial to Europeans.

Deep whole-genome sequencing of 300 individuals from 142 diverse populations provides insights into key population genetic parameters, shows that all modern human ancestry outside of Africa including in Australasians is consistent with descending from a single founding population, and suggests a higher rate of accumulation of mutations in non-Africans compared to Africans since divergence.

Using DNA from a finger bone, the genome of an archaic hominin from southern Siberia has been sequenced to about 1.9-fold coverage. The group to which this individual belonged shares a common origin with Neanderthals, and although it was not involved in the putative gene flow from Neanderthals into Eurasians, it contributed 4–6% of its genetic material to the genomes of present-day Melanesians. A tooth whose mitochondrial genome is very similar to that of the finger bone further suggests that these hominins are evolutionarily distinct from Neanderthals and modern humans.

A complete genome sequence is presented of a female Neanderthal from Siberia, providing information about interbreeding between close relatives and uncovering gene flow events among Neanderthals, Denisovans and early modern humans, as well as establishing substitutions that became fixed in modern humans after their separation from the ancestors of Neanderthals and Denisovans.

Populations from North-eastern Europe, in particular those speaking Uralic languages, carry additional ancestry in similarity with modern East Asian populations. Here, the authors analyse ancient genomic data from 11 individuals from Finland and Northwest Russia, and identify genomic signals of migrations from Siberia that began at least 3500 years ago.

Bayesian modelling of chronometric, stratigraphic and genetic data from Denisova Cave provides a chronological framework for understanding Neanderthal and Denisovan presence at the site, as well as interactions between these groups.

A sequencing study comparing ancient and contemporary genomes reveals that most present-day Europeans derive from at least three highly differentiated populations: west European hunter-gatherers, ancient north Eurasians (related to Upper Palaeolithic Siberians) and early European farmers of mainly Near Eastern origin.

Ancient DNA studies over the past decade have yielded a plethora of insights into the Denisovan archaic hominin group. The authors review our understanding of Denisovan population history and their interactions with other human groups, insights from studies of Denisovan ancestry in modern humans, what we know about the Denisovan phenotype and their impact on our own evolutionary history.

In this Perspective, a group representing a range of stakeholders makes the case for a set of five proposed globally applicable ethical guidelines for ancient human DNA research.

Analysis of DNA from a 37,000–42,000-year-old modern human from Romania reveals that 6–9% of the genome is derived from Neanderthals, with the individual having a Neanderthal ancestor as recently as four to six generations back.

Nuclear DNA sequences from Middle Pleistocene Sima de los Huesos hominins show they were more closely related to Neanderthals than to Denisovans, and indicate a population divergence between Neanderthals and Denisovans that predates 430,000 years ago.

In the modern human genome, elevated Neanderthal ancestry is found at genes affecting keratin filaments, suggesting that gene flow with Neanderthals helped modern humans to adapt to non-African environments; deficiencies of Neanderthal ancestry are also found, particularly on the X chromosome and in genes expressed highly in testes, suggesting that some Neanderthal mutations were not tolerated on a modern human genetic background as they reduced male fertility.

A risk haplotype for type 2 diabetes is identified with four amino acid substitutions in SLC16A11, which is present at ∼50% frequency in Native American samples and ∼10% in east Asian samples, but is rare in European and African samples; SLC16A11 may alter hepatic lipid metabolism, causing an increase in triacylglycerol levels.