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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 study in Nature characterizes the genome of Denisova 11 and reveals her to be a first-generation offspring of Neanderthal and Denisovan parents, thereby providing direct evidence of genetic mixing between genetically distinct groups of archaic hominins.

Genetic analysis uncovers a direct descendant of two different groups of early humans.

A comprehensive search for super-archaic introgression in >400 modern human genomes, including >200 from Island Southeast Asia, corroborates widespread Denisovan ancestry in ISEA populations but fails to detect any substantial super-archaic admixture signals compatible with the endemic fossil record.

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.

Analysis of Icelandic genomes reveals chromosome fragments of Neanderthal and Denisovan origin, the latter of which occurred through Denisovan gene flow either into ancestors of the Neanderthals or directly into humans.

Existing methods to identify the presence of DNA from other hominin species can be limited in the ability to accurately estimate introgression waves, or can only be applied to specific populations. Here, the authors have developed a generalizable method to identify introgression in multi-wave situations.

It is known that there was gene flow from Neanderthals to modern humans around 50,000 years ago; now, analysis of a Neanderthal genome from the Altai Mountains in Siberia reveals evidence of gene flow 100,000 years ago in the other direction—from early modern humans to Neanderthals.

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Evidence for the presence of Homo during the Middle Pleistocene is limited in continental Southeast Asia. Here, the authors report a hominin molar from Tam Ngu Hao 2 (Cobra Cave), dated to 164–131 kyr. They use morphological and paleoproteomic analysis to show that it likely belonged to a female Denisovan.

How traits specific to modern humans have evolved is difficult to study. Here, Gokhman et al. compare measured and reconstructed DNA methylation maps of present-day humans, archaic humans and chimpanzees and find that genes that affect vocal tract and facial anatomy show methylation changes between archaic and modern humans.

Photos of missing fossil show these ancient hominins had slimmer digits than their Neanderthal relatives.

Jawbone from China reveals that the ancient human was widespread across the world — and lived at surprising altitude.

A20, encoded by TNFAIP3, is a negative-feedback inhibitor of NF-κB. Grey and colleagues identify natural human variants of TNFAIP3, which lower A20 activity and increase autoinflammatory responses. These alleles were inherited by descendants of Denisovans who crossed the Wallace Line to inhabit Oceania.

The ancient human remains were found using a method that can scan thousands of bones relatively quickly.

Introgression of Neanderthals and Denisovans left genomic signals in anatomically modern human after Out-of-Africa event. Here, the authors identify a third archaic introgression common to all Asian and Oceanian human populations by applying an approximate Bayesian computation with a Deep Learning framework.

Genomic analyses of human populations in the Pacific provide insights into the peopling history of the region and reveal episodes of biological adaptation relating to the immune system and lipid metabolism through introgression from archaic hominins and polygenic adaptation.

Studying the asymmetry in the pattern of Neanderthal introgression in modern human genomes between individuals of East Asian and European ancestry, the authors show recurrent gene flow from Neanderthals into modern humans.

Ancient DNA keeps expanding our understanding of complex genetic relationships between Pleistocene hominins. Here, Posth and colleagues analyse the mitochondrial genome of an archaic human that diverged from other Neanderthals ∼270,000 years ago, providing the minimum age for an African introgression into Neanderthals.

Organoids that contain an ancient version of a gene that influences brain development are smaller and bumpier than those with human genes.

This study presents a method to identify divergent gene regulation between archaic hominin and anatomically modern human sequences, and shows differences in gene regulatory architecture between the two groups.

Nature asked the pioneer of ancient-DNA research about some of his greatest discoveries.

The authors use machine learning to characterize the splicing landscape of archaic hominins. Archaic-specific splice-altering variants might have contributed to phenotypic differences among hominins and were under negative selection.

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.

Ancient DNA from closely related individuals offers fresh insight into Neanderthals’ lives and social structures.

Epigenetic maps help to explain how archaic humans differed from modern ones despite having very similar DNA sequences.

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.

Admixture with other hominin species helped humans to adapt to high-altitude environments; the EPAS1 gene in Tibetan individuals has an unusual haplotype structure that probably resulted from introgression of DNA from Denisovan or Denisovan-related individuals into humans, and this haplotype is only found in Denisovans and Tibetans, and at low frequency among Han Chinese.

Fossil evidence indicates that Denisovans occupied the Tibetan Plateau in the Middle Pleistocene epoch and successfully adapted to this high-altitude hypoxic environments long before the regional arrival of modern Homo sapiens.

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.

Analysing archaic and modern human genomes, the authors show that Neanderthal introgression reintroduced thousands of lost ancestral variants with gene regulatory activity and that these reintroduced alleles are more tolerated by modern humans than introgressed Neanderthal-derived alleles.

The analysis of whole-genome sequence data from both modern and ancient humans has provided evidence for archaic adaptive introgression. Here, the authors provide an overview of the statistical methods used and the supporting evidence for reported examples of archaic introgression, which may have driven the acquisition of beneficial variants that enabled adaptation and survival in new environments.

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.

Thirty years after the study of ancient DNA began, it promises to upend our view of the past.

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.

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.

A genetic analysis reveals that some people who have severe reactions to the SARS-CoV-2 virus inherited certain sections of their DNA from Neanderthals. However, our ancestors can’t take all the blame for how someone responds to the virus.

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.

Population differences in immune responses to SARS-CoV-2 can be explained by environmental exposures, but also by local adaptation acting through genetic variants acquired after admixture with archaic hominin forms.

Historical interbreeding between Neanderthals and humans should leave signatures of historical demographics in modern human genomes. Analysing the size distribution of Neanderthal fragments in non-African genomes suggests consistent differences in the generation interval across Eurasia, and that this could explain mutational spectrum variation.

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 genome-wide association study and fully automatic landmarking approach on frontal 2D face photographs of >6000 Latin Americans identifies novel genomic regions influencing facial features and implicates Neanderthal introgression in nasal shape.

People who have inherited nerve-altering mutations from the ancient hominins tend to experience more pain.

A Review describes the three key phases that define the origins of modern human ancestry, and highlights the importance of analysing both palaeoanthropological and genomic records to further improve our understanding of our evolutionary history.

Whole-genome sequence data for 108 individuals representing 28 language groups across Australia and five language groups for Papua New Guinea suggests that Aboriginal Australians and Papuans diverged from Eurasian populations approximately 60–100 thousand years ago, following a single out-of-Africa dispersal and subsequent admixture with archaic populations.