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The 2022 Nobel Prize in Physiology or Medicine was awarded to Svante Pääbo "for his discoveries concerning the genomes of extinct hominins and human evolution". Svante Pääbo pioneered the study of ancient DNA from archaeological samples and extinct species including hominins. His work changed how we understand human evolution and has implications for modern-day human physiology. To celebrate the award, Nature Portfolio presents a Collection of publications from Svante Pääbo as well as reviews and opinion from the field of ancient DNA including ethical concerns and future directions.
Determining the precise identity or origin of fragmentary fossils can be difficult. Here, mitochondrial DNA sequences are used to confirm that the skeleton of a child recovered in Uzbekistan in the 1930s was of Neanderthal origin and that remains from the Altai region of Siberia, much further east, are also Neanderthal, extending the Neanderthal range 2,000 km further east than previously assumed.
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.
Ancient mitochondrial DNA from a hominin individual who lived in the mountains of Central Asia between 48,000–30,000 years ago has been sequenced. Comparative genomics suggest that this mitochondrial DNA derives from an out-of-Africa migration distinct from the ones that gave rise to Neanderthals and modern humans. It also seems that this hominin lived in close spatio-temporal proximity to Neanderthals and modern humans.
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.
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.
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.
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 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.
A full mitochondrial genome from a 400,000-year-old Middle Pleistocene hominin from Spain unexpectedly reveals a close relationship to Denisovans, a sister group to the Neanderthals, raising interesting questions about the origins of Neanderthals and Denisovans.
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.
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.
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.
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.
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.
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.
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.
Direct dates for human remains found in association with Initial Upper Palaeolithic artefacts at Bacho Kiro Cave (Bulgaria) demonstrate the presence of Homo sapiens in the mid-latitudes of Europe before 45 thousand years ago.
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.
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.
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.
Chen et al. found that Foxp2 interacts with Mef2c to wire synaptic circuits linking neocortex to basal ganglia. The study analyzes the basics of circuit wiring underlying vocal communication.
Species comparisons using single-cell transcriptomics and accessible chromatin profiling in stem cell-derived cerebral organoids are used to map dynamic gene-regulatory changes that are unique to humans.
Risk of severe COVID-19 is conferred by a genomic segment that is inherited from Neanderthals and is carried by around 50% and 16% of people in south Asia and Europe, respectively.
Our evolutionary history has resulted in highly complex and sophisticated human physiology. Yet evolutionary footprints have also left us prone to diseases. In this Review, the authors discuss how events from the earliest history of life on Earth through to modern human evolution influence many disease traits and outcomes. They describe how an understanding and application of evolutionary frameworks can inform precision medicine initiatives.
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.
This Primer outlines the best ways to find, handle and analyse ancient DNA from various sources. The authors summarize ethical considerations and the importance of working closely with all stakeholders, including archaeologists, curators and descendant communities.
This PrimeView highlights important experimental and analytical aspects of conducting ancient DNA analysis, with a focus on collaboration and sample preservation.
Here the authors describe an updated protocol for single-stranded sequencing library preparation suitable for highly degraded DNA from ancient remains or other sources. The procedure can be performed manually or in an automated fashion.
With the increasing availability of ancient genomes from the same region or locality, the field of human history has started to address sociocultural aspects of human behaviour. The authors review recent case studies reconstructing the social consequences of past human migrations and advocate that this complex enterprise should be addressed by multidisciplinary teams.
This article reviews recent advances in ancient pathogen genomics, from methodological improvements in retrieving whole genomes to evolutionary analyses of ancient pathogens that remain relevant to public health. Focusing on the evolutionary history of the plague pathogen Yersinia pestis, the authors present unique insights afforded by the study of ancient pathogen genomes.
This protocol update describes silica-based approaches for purification of DNA from ancient bone, tooth and sediment samples. The optimized buffers yield short DNA fragments compatible with high-throughput sequencing library preparation.
Ancient genomes can inform our understanding of the history of human adaptation through the direct tracking of changes in genetic variant frequency across different geographical locations and time periods. The authors review recent ancient DNA analyses of human, archaic hominin, pathogen, and domesticated animal and plant genomes, as well as the insights gained regarding past human evolution and behaviour.
Sequencing genomes of ancient specimens, including human ancestors, can provide rich insights into evolutionary histories. However, ancient DNA samples are frequently degraded, damaged and contaminated with ancient and modern DNA from various sources. This Review describes the methodological and bioinformatic advances that allow these challenges to be overcome in order to process and sequence ancient samples for genome reconstruction, as well as recent progress in characterizing ancient epigenomes.
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.
There continues to be active debate about the timings, locations and details of various events in human population history. This Review describes how whole-genome sequencing of modern and ancient humans has complemented more traditional methods to provide valuable historical insights.
Next-generation sequencing has now been used to produce the first ancient hominin genome sequences and is also being used to sequence modern humans from many different populations. Together with SNP genotyping, these data are transforming views of human history.
If most evolutionary changes affect the regulation rather than the structure of proteins, then studying the evolution of gene expression levels will help us to understand phenotypic changes. How can this approach identify the defining differences between humans and chimpanzees?
Researchers rushing to apply powerful sequencing techniques to ancient-human remains must think harder about safeguarding, urge Keolu Fox and John Hawks.
Use of origins research for political point-scoring is depressingly frequent, but scientists must take what care they can to ensure that their work is not abused.
In Africa, there is a disparity in ethics and permission requirements for molecular research on samples from living people versus ancient DNA. At the precipice of the archaeogenomics revolution, heritage agencies require updated policies and procedures for genetic and genomic research on African ancient DNA.
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.
Inferred gene expression differences between modern humans and our extinct archaic relatives suggest potential mechanistic bases for the evolution of hominin phenotypes.
Four new Late Pleistocene European modern human genomes had Neanderthal ancestors in their immediate family history, suggesting that interbreeding with the last Neanderthals was common.
The presence of Neanderthal DNA fragments in the genomes of modern humans from Europe and East Asia indicates multiple episodes of interbreeding between Neanderthals and the ancestors of both populations.
To celebrate the first 20 years of Nature Reviews Genetics, we asked 12 leading scientists to reflect on the key challenges and opportunities faced by the field of genetics and genomics.