Ancient DNA Research

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Ancient DNA Research

Ancient DNA research, often called aDNA research or paleogenomics when genome-scale data are involved, uses genetic material preserved in archaeological, paleontological, historical, and environmental remains to investigate the biological past. Ancient DNA can be recovered from human and animal bones, teeth, dental calculus, preserved tissues, archaeological artifacts, sediments, and increasingly unconventional sources such as cave deposits and objects handled by people thousands of years ago. These materials provide direct genetic observations from past populations rather than requiring their histories to be inferred exclusively from people or species living today.

The field has developed from early experiments recovering short DNA sequences from extinct animals into a major interdisciplinary science capable of reconstructing whole ancient genomes. Improvements in DNA extraction, sequencing, contamination control, computational analysis, and authentication have greatly increased both the quantity and age of genetic material that can be studied. Large databases now combine thousands of ancient human genomes, making it possible to examine demographic change across entire regions and over thousands of years.

Ancient DNA has transformed understanding of human evolution, prehistoric migration, population replacement, admixture, natural selection, infectious disease, animal and plant domestication, ecosystem change, and social organization. At the same time, the rapid growth of paleogenomics has created important ethical questions concerning destructive sampling, archaeological stewardship, Indigenous data sovereignty, consultation with descendant communities, interpretation of genetic ancestry, and equitable international research partnerships.

Methods, Preservation, and Authentication

Ancient DNA is generally damaged, chemically modified, fragmented, and present in much smaller quantities than DNA from living organisms. Samples may also contain large amounts of DNA from microorganisms, soil organisms, excavators, museum workers, laboratory personnel, or other modern sources. Contamination control and authentication are therefore central to ancient-DNA research.

Specialized laboratories use clean-room procedures, protective equipment, surface decontamination, extraction methods designed for extremely short DNA fragments, and carefully controlled sequencing-library preparation. Dense skeletal tissues such as the inner portion of the petrous bone can preserve particularly high concentrations of endogenous human DNA, while tooth cementum, dentin, and dental calculus provide additional sources.

Single-stranded DNA-library methods have improved the recovery of exceptionally short and damaged molecules. Computational programs identify characteristic ancient-DNA damage patterns, including DNA fragmentation and nucleotide changes caused by cytosine deamination. Other tools estimate modern contamination and reconstruct ancient mitochondrial or nuclear sequences.

Authentication remains essential because apparent genetic findings can otherwise result from contamination or environmental movement of DNA. Sedimentary ancient DNA presents additional challenges because genetic molecules may move vertically or horizontally after deposition. Archaeological context, molecular damage, sequence length, contamination estimates, laboratory replication, and comparison with appropriate controls are therefore considered together when assessing authenticity.

Recent techniques have reduced the need for destructive sampling. Researchers have recovered human DNA from archaeological sediments, prehistoric artifacts, dental calculus, and even residues associated with objects. Sedimentary ancient DNA, or sedaDNA, can reveal organisms that occupied archaeological or environmental settings even when identifiable skeletal remains are absent.

The development of standardized databases and reproducible computational pipelines has become increasingly important as datasets grow. Resources containing thousands of published ancient genomes allow researchers to compare individuals and populations across large geographic areas and extended periods of time.

Human Evolution and Archaic Populations

Ancient DNA has fundamentally changed scientific understanding of human evolution. Genomic research demonstrated that Neanderthals and modern humans interbred and that many living populations outside Africa retain portions of Neanderthal ancestry. Ancient genomes have also shown that some early modern humans had Neanderthal ancestors only a few generations before they lived.

DNA recovered from Denisova Cave revealed another archaic population, now known as the Denisovans. Genomic comparisons established that Denisovans were genetically distinct from Neanderthals while also interbreeding with both Neanderthals and ancestors of some living human populations.

One remarkable genome came from an individual whose mother was Neanderthal and whose father was Denisovan, providing direct evidence that these archaic populations sometimes interbred. Other ancient genomes have allowed researchers to reconstruct changing distributions of Neanderthals, Denisovans, and modern humans across Eurasia.

Very old DNA recovered from Middle Pleistocene remains has pushed genetic investigations hundreds of thousands of years into the past. Ancient genomes from early modern humans in Europe and Asia have also helped refine estimates for the timing of Neanderthal admixture and the diversification of modern-human populations.

Rather than depicting human evolution as a simple sequence in which one population completely replaced another, paleogenomics reveals a complex history of population divergence, migration, isolation, interbreeding, and repeated contact.

Migration, Population Change, and the Spread of Farming

One of ancient DNA's most important contributions has been the direct identification of prehistoric migration. Genetic differences between populations separated in time can reveal population replacement, continuity, admixture, or movement in ways that archaeological objects alone sometimes cannot.

European prehistory provides particularly extensive examples. Ancient genomes have documented migrations associated with early farming populations from Anatolia and the Aegean, later interactions between farmers and hunter-gatherers, and major expansions of Steppe-related populations during the Late Neolithic and Bronze Age. These demographic movements substantially reshaped the ancestry of later European populations.

Ancient genomic research has similarly reconstructed population histories across Africa, Asia, the Americas, Oceania, and the Mediterranean. Studies have examined the Bantu expansions in Africa, population movements along the Swahili coast, prehistoric migrations across South and Central Asia, demographic change in Southeast Asia, settlement of the Pacific, population transformations in the Caribbean, and the diversification of Indigenous populations in the Americas.

The genetic history of the Americas has revealed early population branching followed by regional diversification and later movement. Ancient genomes from Siberia and Alaska have provided evidence concerning the ancestors of Native American populations, while genomes from Central and South America illuminate migrations occurring after the initial settlement of the continents.

Ancient DNA has also shown that migration cannot automatically be equated with cultural change. Material cultures may spread through movement of people, exchange of ideas, adoption of technologies, or mixtures of these processes. Consequently, genomic evidence is most informative when interpreted alongside archaeology, history, linguistics, geography, and other evidence.

Natural Selection, Adaptation, and Social Organization

Because ancient genomes can be arranged chronologically, they allow genetic change to be observed through time. Researchers can track changing frequencies of genetic variants rather than reconstructing all evolutionary history from modern populations.

Ancient genomic datasets have been used to investigate natural selection affecting immunity, metabolism, pigmentation, diet, adaptation to local environments, and disease susceptibility. Some genetic variants associated with present-day traits or disease risks have been traced to prehistoric populations and demographic expansions.

Paleogenomics has also begun moving beyond broad questions of ancestry to investigate individual communities. Genetic relationships among people buried in the same cemetery can reconstruct families and multigenerational pedigrees. When combined with burial practices and archaeological evidence, these relationships can reveal patterns of marriage, residence, inheritance, social inequality, patrilineality, female mobility, and community organization.

Studies of Neolithic, Bronze Age, and early medieval communities demonstrate that people sharing similar material cultures were not necessarily genetically homogeneous. In some societies, genetically differentiated communities coexisted while maintaining social or reproductive boundaries.

These findings demonstrate that ancient DNA can contribute to social archaeology while also requiring caution: genetic relatedness represents biological relationships and should not automatically be treated as equivalent to cultural identity, ethnicity, language, or social belonging.

Ancient Pathogens, Disease, and Microbiomes

Ancient DNA has created a direct record of infectious-disease evolution. Genetic material belonging to bacteria, viruses, and parasites can sometimes survive in human remains, dental calculus, or archaeological tissues and can be reconstructed into ancient pathogen genomes.

Research on Yersinia pestis, the bacterium responsible for plague, has revealed lineages circulating thousands of years before the historically documented Black Death. Ancient genomes have helped trace plague dispersal across Eurasia, reconstruct the origins of later pandemic strains, and identify geographic connections between prehistoric outbreaks.

Other studies have recovered ancient genomes of pathogens associated with tuberculosis, leprosy, hepatitis B, malaria, smallpox, Salmonella, and Helicobacter pylori. These discoveries demonstrate that pathogens can have complicated evolutionary histories involving extinction, replacement, geographic expansion, host adaptation, and long periods of coexistence with humans.

Dental calculus has emerged as a particularly valuable biological archive. Mineralized dental plaque can preserve microbial DNA, dietary residues, and host-associated molecules for thousands of years. Ancient oral microbiomes provide information about changing diets, agricultural transitions, health, disease, industrialization, and microbial ecology.

Ancient pathogen genomics therefore connects archaeology with epidemiology and evolutionary biology. By revealing genetic diversity that no longer exists, ancient genomes can change estimates of when diseases emerged and how they spread.

Animals, Plants, Domestication, and Environmental DNA

Ancient DNA has substantially revised theories of domestication. Instead of single, simple domestication events followed by uninterrupted descent, many domestic species show histories involving several wild populations, repeated admixture, population replacement, geographic expansion, and intentional or unintentional human selection.

Horse genomes have been especially informative. Ancient DNA has identified major changes in horse populations, revealed the expansion of lineages associated with widespread mounted mobility, documented the loss of ancient genetic diversity, and shown that some of the earliest managed horses were not the principal ancestors of most modern domestic horses.

Ancient dog genomes similarly reveal deep population structure and repeated movement alongside humans. Prehistoric dog populations accompanied people into new regions but were sometimes later replaced or absorbed by newly introduced canine populations.

Research involving cattle, aurochs, yak, bison, and other animals has illuminated domestication, adaptation, hybridization, and population decline. DNA from mammoths and exceptionally old horse remains has also pushed paleogenomics into increasingly remote periods of the Pleistocene.

Plants can also preserve usable ancient DNA. Archaeological barley has provided direct evidence concerning early crop domestication, while ancient grapevine DNA documents thousands of years of cultivation, clonal propagation, and changing agricultural diversity.

Environmental and sedimentary ancient DNA broaden the field beyond identifiable fossils. DNA recovered directly from cave floors, lake deposits, soils, and other sediments can reconstruct past ecosystems and reveal organisms that left little or no visible skeletal record. Genome-scale DNA from humans and animals has even been recovered from Pleistocene sediments.

Ethics, Community Partnership, and Interpretation

The ability to extract genetic information from human remains raises questions that cannot be resolved through laboratory technique alone. Human remains can have cultural, spiritual, historical, and political importance to descendant communities, Indigenous peoples, local populations, museums, and nations.

Ethical ancient-DNA research increasingly emphasizes meaningful consultation and partnership with communities connected to the individuals being studied. Important issues include consent where possible, Indigenous data sovereignty, legal authority, respectful treatment of human remains, destructive sampling, repatriation, research priorities, access to data, and decisions about publication.

Equitable scientific collaboration is another major concern. Archaeological material has sometimes been transported from countries with limited research resources to laboratories in wealthier nations, leaving local researchers with restricted participation in analysis or publication. Calls for better practice emphasize long-term partnerships, recognition of local expertise, investment in regional research capacity, fair authorship, and shared decision-making.

Interpretation also requires caution. Genetic clusters produced by statistical analyses are analytical tools rather than self-evident ethnic groups. Archaeological cultures, languages, political identities, and genetic populations do not necessarily correspond directly to one another.

Ancient DNA is therefore most powerful when integrated with archaeology and historical context rather than treated as a replacement for them. Responsible paleogenomics requires both technical rigor and recognition that biological ancestry is only one dimension of human history.

The Expanding Scope of Paleogenomics

The field continues to expand as methods become more sensitive and datasets become larger. Genome imputation can increase the information obtained from low-coverage ancient samples, although its reliability depends on appropriate reference data and analytical validation. Large genomic time series now allow researchers to investigate natural selection across thousands of years.

Researchers are also exploring increasingly unusual sources of DNA, including archaeological artifacts, cave walls, pigments, sediments, and other surfaces that may retain biological traces left by ancient people. Such techniques could eventually connect individuals or populations more directly with objects and places while reducing damage to skeletal remains.

At the same time, increasingly detailed datasets are shifting paleogenomics from continental-scale population histories toward the reconstruction of individual communities, families, mobility patterns, disease environments, and social relationships.

Ancient DNA research consequently occupies an increasingly important position at the intersection of genetics, archaeology, anthropology, evolutionary biology, microbiology, history, ecology, and data science.

Conclusion

Ancient DNA has transformed the study of the past by making genomes themselves part of the historical and archaeological record. What began with the recovery of short genetic sequences from old or extinct specimens has developed into the analysis of thousands of ancient genomes and genetic material recovered from humans, animals, plants, pathogens, artifacts, and sediments.

The resulting evidence has revealed extensive movement and admixture among ancient human populations, direct contact between modern humans and archaic groups, repeated demographic transformations associated with farming and migration, evolutionary responses to changing environments, and previously unknown histories of infectious disease. Ancient genomes have also reshaped understanding of animal and plant domestication and opened new approaches to reconstructing vanished ecosystems.

The power of paleogenomics nevertheless depends on careful authentication, reproducible analysis, archaeological context, and responsible interpretation. Genetic ancestry should not be treated as synonymous with ethnicity, culture, nationality, or identity. Research involving human remains must also account for the interests and authority of descendant and Indigenous communities.

As techniques improve, ancient DNA will continue to extend genetic observation further into the past and into increasingly diverse materials. Its greatest contribution is not simply the discovery of isolated ancestral populations, but the recognition that biological history has been shaped by continual movement, interaction, adaptation, mixture, disease, environmental change, and complex relationships among people and the societies in which they lived.

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Ancient DNA Research

Methods, Authentication, Sediments, and Data Infrastructure (20)

[doi:10.1016/j.jgeb.2026.100778 | Abang Ulrich Akwo, Julius Luvanga & Ketonze Valademy Ketu | Journal of Genetic Engineering and Biotechnology | September 2026] Ancient DNA as a temporal lens: reconstructing evolution, migration, and disease dynamics

Reviews how ancient DNA illuminates migration, adaptation, pathogen evolution, ecosystem change, and the growing importance of ethical stewardship and interdisciplinary analysis.

[doi:10.1186/s41935-026-00576-z | Julius Luvanga, Abang Akwo, Ketonze Ketu et al. | Egyptian Journal of Forensic Sciences | 20 August 2026] Methodological advances and computational frameworks in ancient DNA research: a narrative review

Surveys preservation, clean-room procedures, extraction, library preparation, authentication, sequencing, contamination estimation, reference bias, and bioinformatic analysis of degraded DNA.

[doi:10.1016/j.jgeb.2026.100702 | Jay Silverstein & Amber Chapman | Journal of Genetic Engineering and Biotechnology | 7 May 2026] Recovery and analysis of ancient DNA: challenges, methods, and applications in forensic and archaeological science

Reviews ancient-DNA recovery, next-generation sequencing, hybridization capture, contamination control, forensic applications, archaeological interpretation, and ethical concerns.

[doi:10.1016/j.jas.2026.106537 | Rikai Sawafuji, Ryohei Sawaura, Masaki Yokoo et al. | Journal of Archaeological Science | 1 May 2026] From bones to sediments: Ancient human DNA from open-air archaeological sites

Demonstrates recovery of ancient human mitochondrial DNA from sediments around skeletal remains, offering a potentially less destructive source of genetic information.

[doi:10.1016/j.jas.2025.106424 | Xu Han, Nihanxue Jia, Shihua Hu et al. | Journal of Archaeological Science | December 2025] Translocation of sedimentary ancient DNA in archaeological cultural deposits: Mechanism and prospects

Examines how ancient DNA can move through archaeological sediments and discusses methods for assessing whether recovered sequences remain associated with their original contexts.

[doi:10.1016/j.ajhg.2025.10.011 | Yassine Souilmi, Adrien Oliva, Roberta Davidson et al. | American Journal of Human Genetics | 5 November 2025] Lessons learned: Recommendations for reproducible paleogenomic data analyses

Provides recommendations for improving transparency, reproducibility, documentation, data processing, and computational workflows in paleogenomic research.

[doi:10.1016/j.jas.2025.106317 | Roberta Davidson, Shyamsundar Ravishankar, Yassine Souilmi et al. | Journal of Archaeological Science | September 2025] The necessity for authentication of ancient DNA from archaeological artefacts

Emphasizes rigorous molecular authentication when DNA is recovered from archaeological objects, where contamination and uncertain biological associations can complicate interpretation.

[doi:10.1016/j.jas.2024.106132 | A.G. Brown, M. Lucas, I.G. Alsos, B. Fromm & S. Hudson | Journal of Archaeological Science | February 2025] The sedaDNA revolution and archaeology: Progress, challenges, and a research agenda

Reviews archaeological sedimentary ancient DNA, including metabarcoding, shotgun sequencing, target capture, sampling design, contamination issues, and future research priorities.

[doi:10.1038/s41597-024-03031-7 | Swapan Mallick, Adam Micco, Matthew Mah et al. | Scientific Data | 10 February 2024] The Allen Ancient DNA Resource (AADR) a curated compendium of ancient human genomes

Describes a standardized and version-controlled resource that brings together genome-wide data from thousands of published ancient human individuals.

[doi:10.1038/s41586-023-06035-2 | Elena Essel, Elena I. Zavala, Ellen Schulz-Kornas et al. | Nature | 3 May 2023] Ancient human DNA recovered from a Palaeolithic pendant

Demonstrates a non-destructive method for recovering human DNA left on a prehistoric bone pendant, potentially linking artifacts directly with people who handled them.

[doi:10.1038/s41598-021-86100-w | Andrew G. Farrer, Sterling L. Wright, Emily Skelly et al. | Scientific Reports | 2 April 2021] Effectiveness of decontamination protocols when analyzing ancient DNA preserved in dental calculus

Tests approaches for removing surface contamination from archaeological dental calculus while preserving authentic ancient microbial DNA.

[doi:10.1038/s43017-021-00158-8 | Sarah E. Crump | Nature Reviews Earth & Environment | 16 March 2021] Sedimentary ancient DNA as a tool in paleoecology

Reviews the use of DNA preserved in lake, terrestrial, and other sediments to reconstruct past organisms, ecosystems, and environmental change.

[doi:10.1038/s43586-020-00011-0 | Ludovic Orlando, Robin Allaby, Pontus Skoglund et al. | Nature Reviews Methods Primers | 11 February 2021] Ancient DNA analysis

Provides a comprehensive methodological primer covering sampling, DNA extraction, sequencing, authentication, computational analysis, applications, limitations, and future developments.

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Evaluates whether dental calculus and dentin can yield useful human genomic information after targeted whole-genome enrichment.

[doi:10.1038/nrg3935 | Ludovic Orlando, M. Thomas P. Gilbert & Eske Willerslev | Nature Reviews Genetics | 9 June 2015] Reconstructing ancient genomes and epigenomes

Reviews technological developments that made complete ancient genomes and aspects of ancient epigenetic regulation increasingly recoverable.

[doi:10.1016/j.jhevol.2014.06.018 | Laura S. Weyrich, Keith Dobney & Alan Cooper | Journal of Human Evolution | 1 December 2014] Ancient DNA analysis of dental calculus

Explains how mineralized dental plaque preserves microbial, dietary, and host biomolecules that can illuminate health and behavior in ancient populations.

[doi:10.1073/pnas.1318934111 | Pontus Skoglund et al. | Proceedings of the National Academy of Sciences | 27 January 2014] Separating endogenous ancient DNA from modern day contamination in a Siberian Neandertal

Develops methods for distinguishing genuinely ancient molecules from contaminating modern human DNA in archaic hominin sequence data.

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Reviews how ancient genomes can be integrated with present-day genetic variation to reconstruct migration, replacement, admixture, and population divergence.

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A foundational review discussing DNA survival, contamination, authenticity criteria, molecular methods, and the early evolutionary applications of ancient genetic material.

[doi:10.1038/312282a0 | Russell Higuchi, Barbara Bowman, Mary Freiberger, Oliver A. Ryder & Allan C. Wilson | Nature | 15 November 1984] DNA sequences from the quagga, an extinct member of the horse family

One of the foundational ancient-DNA studies, demonstrating that genetic sequences could be recovered from preserved remains of an extinct animal.

Archaic Humans and Human Evolution (16)

[doi:10.1038/s41588-026-02562-6 | Dina MemarMoshrefi, Olivia L. Johnson & Christian D. Huber | Nature Genetics | 28 April 2026] Insights into human adaptation from ancient DNA

Reviews how temporally sampled genomes make it possible to identify changing allele frequencies and investigate adaptation in past human populations.

[doi:10.1038/s41586-025-09811-4 | Mattias Jakobsson, Carolina Bernhardsson, James McKenna et al. | Nature | 3 December 2025] Homo sapiens-specific evolution unveiled by ancient southern African genomes

Uses ancient southern African genomes to investigate early modern-human population history and genetic changes specific to Homo sapiens.

[doi:10.1038/s41576-025-00855-w | Diyendo Massilani | Nature Reviews Genetics | 22 May 2025] A crossroads in the timeline of human evolution

Discusses ancient genomic evidence bearing on critical periods of divergence, contact, and demographic change in human evolutionary history.

[doi:10.1038/s41586-024-08420-x | Arev P. Sümer, Hélène Rougier, Vanessa Villalba-Mouco et al. | Nature | 12 December 2024] Earliest modern human genomes constrain timing of Neanderthal admixture

Early modern-human genomes refine estimates of when gene flow between Neanderthals and ancestors of non-African modern humans occurred.

[doi:10.1038/s41586-023-05726-0 | Cosimo Posth et al. | Nature | 1 March 2023] Palaeogenomics of Upper Palaeolithic to Neolithic European hunter-gatherers

Large-scale genomic analysis reveals population replacements, refugia, expansions, and long-term hunter-gatherer ancestry patterns across prehistoric Europe.

[doi:10.1038/s41586-021-03675-0 | Elena I. Zavala et al. | Nature | 23 June 2021] Pleistocene sediment DNA reveals hominin and faunal turnovers at Denisova Cave

Sedimentary DNA reconstructs changing occupations by Denisovans and Neanderthals alongside shifts in the animals inhabiting the Denisova Cave region.

[doi:10.1038/s41586-021-03335-3 | Mateja Hajdinjak et al. | Nature | 7 April 2021] Initial Upper Palaeolithic humans in Europe had recent Neanderthal ancestry

Genomes from early modern humans in Bulgaria show that some individuals had Neanderthal ancestors only several generations earlier.

[doi:10.1038/s41586-021-03336-2 | Chuan-Chao Wang et al. | Nature | 22 February 2021] Genomic insights into the formation of human populations in East Asia

Ancient genomes reveal repeated population movements and mixtures involved in forming the genetic structure of East Asian populations.

[doi:10.1038/nature21674 | Laura S. Weyrich et al. | Nature | 8 March 2017] Neanderthal behaviour, diet, and disease inferred from ancient DNA in dental calculus

Dental calculus DNA provides evidence concerning Neanderthal diet, oral microbial communities, health, and interactions with local environments.

[doi:10.1038/nature17405 | Matthias Meyer, Juan-Luis Arsuaga, Cesare de Filippo et al. | Nature | 14 March 2016] Nuclear DNA sequences from the Middle Pleistocene Sima de los Huesos hominins

Nuclear DNA from Spanish Middle Pleistocene remains clarifies evolutionary relationships between the Sima hominins, Neanderthals, and Denisovans.

[doi:10.1038/nature13810 | Qiaomei Fu, Heng Li, Priya Moorjani et al. | Nature | 22 October 2014] Genome sequence of a 45,000-year-old modern human from western Siberia

The Ust'-Ishim genome provides an early snapshot of modern humans in Eurasia and helps date ancient Neanderthal admixture.

[doi:10.1038/nature12736 | Maanasa Raghavan et al. | Nature | 20 November 2013] Upper Palaeolithic Siberian genome reveals dual ancestry of Native Americans

The Mal'ta genome provided evidence that Native American ancestry includes contributions related to both East Asian and ancient north Eurasian populations.

[doi:10.1126/science.1224344 | Matthias Meyer et al. | Science | 30 August 2012] A high-coverage genome sequence from an archaic Denisovan individual

A high-quality Denisovan genome enabled detailed comparisons among Denisovans, Neanderthals, and modern human populations.

[doi:10.1038/nature09710 | David Reich, Richard E. Green, Martin Kircher et al. | Nature | 22 December 2010] Genetic history of an archaic hominin group from Denisova Cave in Siberia

Genomic evidence established Denisovans as a distinct archaic population and revealed genetic contributions to some present-day populations.

[doi:10.1126/science.1188021 | Richard E. Green, Johannes Krause, Adrian W. Briggs et al. | Science | 7 May 2010] A Draft Sequence of the Neandertal Genome

The first draft Neanderthal genome demonstrated gene flow between Neanderthals and ancestors of many present-day people outside Africa.

[doi:10.1038/nature08835 | Morten Rasmussen, Yingrui Li, Stinus Lindgreen et al. | Nature | 11 February 2010] Ancient human genome sequence of an extinct Palaeo-Eskimo

A roughly 4,000-year-old Greenland genome demonstrated that ancient DNA could reconstruct individual ancestry and prehistoric population movements.

Population History, Migration, and Archaeogenomics (35)

[doi:10.1038/s41586-025-09437-6 | Joscha Gretzinger, Felix Biermann, Hellen Mager et al. | Nature | 3 September 2025] Ancient DNA connects large-scale migration with the spread of Slavs

Genome-wide ancient DNA provides evidence for substantial demographic movements associated with the early medieval spread of Slavic-speaking populations.

[doi:10.1186/s13059-025-03664-w | Matthew P. Williams & Christian D. Huber | Genome Biology | 16 July 2025] The genomic footprints of migration: how ancient DNA reveals our history of mobility

Reviews the methods and interpretations used to distinguish migration, population replacement, admixture, mobility, and continuity from ancient genomic datasets.

[doi:10.1038/s41586-025-09195-5 | Morez Jacobs et al. | Nature | 2 July 2025] Whole-genome ancestry of an Old Kingdom Egyptian

Genome-wide data from an ancient Egyptian individual provide direct evidence relevant to ancestry and population connections during the Old Kingdom.

[doi:10.1038/s41586-024-07509-7 | Rodrigo Barquera, Oana Del Castillo-Chávez, Kathrin Nägele et al. | Nature | 12 June 2024] Ancient genomes reveal insights into ritual life at Chichén Itzá

Genomic analysis of children buried at Chichén Itzá reveals biological relationships and adds evidence concerning Maya ritual practices and population continuity.

[doi:10.1038/s41586-023-06770-6 | Cesar Fortes-Lima et al. | Nature | 29 November 2023] The genetic legacy of the expansion of Bantu-speaking peoples in Africa

Ancient and modern genomes illuminate the routes, admixture patterns, and long-lasting demographic effects associated with Bantu-speaking expansions.

[doi:10.1038/d41586-023-03503-7 | Alan Izarraras-Gomez & Diego Ortega-Del Vecchyo | Nature | 22 November 2023] Ancient DNA uncovers past migrations in California

Discusses genomic evidence for population movements and continuity among Indigenous peoples of ancient and historic California.

[doi:10.1038/d41586-023-01768-6 | Louise Humphrey & Abdeljalil Bouzouggar | Nature | 7 June 2023] Ancient DNA reveals how farming spread into northwest Africa

Reviews evidence that Neolithic farming in northwestern Africa involved both local hunter-gatherer ancestry and migrations from neighboring regions.

[doi:10.1038/s41586-023-05754-w | Esther S. Brielle et al. | Nature | 29 March 2023] Entwined African and Asian genetic roots of medieval peoples of the Swahili coast

Ancient genomes reveal substantial African and Persian-associated ancestry in medieval Swahili communities and help reconstruct Indian Ocean population connections.

[doi:10.1073/pnas.2218375120 | Clemens Schmid & Stephan Schiffels | Proceedings of the National Academy of Sciences | 23 February 2023] Estimating human mobility in Holocene Western Eurasia with large-scale ancient genomic data

Uses thousands of ancient genomes to quantify how patterns of human mobility changed across Holocene western Eurasia.

[doi:10.1126/science.abq0762 | Iosif Lazaridis et al. | Science | 25 August 2022] Ancient DNA from Mesopotamia suggests distinct Pre-Pottery and Pottery Neolithic migrations into Anatolia

Genomic evidence indicates that different population movements contributed to the spread and development of Neolithic societies in Anatolia and Mesopotamia.

[doi:10.1038/s41586-022-04430-9 | Mark Lipson et al. | Nature | 23 February 2022] Ancient DNA and deep population structure in sub-Saharan African foragers

Ancient genomes reveal long-standing regional population structure, interaction, and ancestry among African hunter-gatherer populations.

[doi:10.1038/s41586-021-03823-6 | Selina Carlhoff et al. | Nature | 25 August 2021] Genome of a middle Holocene hunter-gatherer from Wallacea

A genome from Sulawesi documents ancestry associated with an ancient population that differs from later regional population patterns.

[doi:10.1038/s41586-021-03499-y | Eske Willerslev & David J. Meltzer | Nature | 16 June 2021] Peopling of the Americas as inferred from ancient genomics

Synthesizes ancient genomic evidence concerning the timing, routes, diversification, and population history of the first peoples of the Americas.

[doi:10.1038/s41586-020-03053-2 | Daniel Fernandes et al. | Nature | 23 December 2020] A genetic history of the pre-contact Caribbean

Hundreds of ancient genomes reveal migrations, population sizes, kinship, and ancestry changes across the pre-contact Caribbean.

[doi:10.1038/s41586-020-2688-8 | Ashot Margaryan et al. | Nature | 16 September 2020] Population genomics of the Viking world

Genome-wide data from Viking Age individuals reveal extensive mobility, regional genetic structure, and ancestry extending beyond simplified ideas of Viking identity.

[doi:10.1038/s41576-020-0218-z | Fernando Racimo, Martin Sikora, Marc Vander Linden et al. | Nature Reviews Genetics | 3 March 2020] Beyond broad strokes: sociocultural insights from the study of ancient genomes

Explores how ancient genomes can address fine-scale questions about kinship, social organization, inequality, residence patterns, and cultural practices.

[doi:10.1126/science.aay6826 | Margaret L. Antonio et al. | Science | 8 November 2019] Ancient Rome: A genetic crossroads of Europe and the Mediterranean

Ancient genomes document repeated migration and ancestry shifts as Rome developed from a regional settlement into an imperial metropolis.

[doi:10.1016/j.cell.2019.08.048 | Vasant Shinde et al. | Cell | 17 October 2019] An Ancient Harappan Genome Lacks Ancestry from Steppe Pastoralists or Iranian Farmers

A genome associated with the Indus Civilization contributes evidence concerning South Asian population formation before later Steppe-related admixture.

[doi:10.1126/science.aat7487 | Vagheesh M. Narasimhan et al. | Science | 6 September 2019] The Formation of Human Populations in South and Central Asia

Hundreds of ancient genomes reveal multiple ancestry streams involved in the prehistoric formation of South and Central Asian populations.

[doi:10.1038/s41467-019-11357-9 | Éadaoin Harney et al. | Nature Communications | 20 August 2019] Ancient DNA from the skeletons of Roopkund Lake reveals Mediterranean migrants in India

Genetic analysis shows that individuals at Roopkund Lake came from multiple distinct populations and did not all die in a single event.

[doi:10.1038/s41586-019-1279-z | Martin Sikora et al. | Nature | 5 June 2019] The population history of northeastern Siberia since the Pleistocene

Ancient genomes identify major population transitions in northeastern Siberia and clarify relationships to Native American ancestry.

[doi:10.1126/science.aaw6275 | Mary E. Prendergast, Mark Lipson, Elizabeth A. Sawchuk et al. | Science | 30 May 2019] Ancient DNA reveals a multistep spread of the first herders into sub-Saharan Africa

Ancient genomes show that pastoralism spread through eastern Africa via multiple demographic processes rather than a single population expansion.

[doi:10.1038/s41559-019-0878-2 | Choongwon Jeong et al. | Nature Ecology & Evolution | 29 April 2019] The genetic history of admixture across inner Eurasia

Ancient and modern genomes reveal extensive admixture and population movement across the Eurasian steppe and neighboring regions.

[doi:10.1126/science.aav4040 | Iñigo Olalde et al. | Science | 15 March 2019] The genomic history of the Iberian Peninsula over the past 8000 years

Large-scale ancient genomic sampling documents migrations, sex-biased admixture, and population transformations across prehistoric and historic Iberia.

[doi:10.1038/s41467-018-08220-8 | Chuan-Chao Wang et al. | Nature Communications | 4 February 2019] Ancient human genome-wide data from a 3000-year interval in the Caucasus corresponds with eco-geographic regions

Ancient genomes reveal persistent genetic differentiation associated with geography in the Caucasus despite repeated contacts with surrounding populations.

[doi:10.1126/science.aat3188 | Mark Lipson et al. | Science | 17 May 2018] Ancient genomes document multiple waves of migration in Southeast Asian prehistory

Ancient DNA identifies several migrations that contributed to the ancestry of prehistoric Southeast Asian populations.

[doi:10.1038/s41586-018-0094-2 | Peter de Barros Damgaard et al. | Nature | 9 May 2018] 137 ancient human genomes from across the Eurasian steppes

A broad transect of ancient genomes reconstructs population movements, interactions, and ancestry changes across the Eurasian steppe.

[doi:10.1038/nature25738 | Iñigo Olalde et al. | Nature | 21 February 2018] The Beaker phenomenon and the genomic transformation of northwest Europe

Ancient DNA shows that Bell Beaker material culture spread through different mechanisms, including large-scale migration into Britain.

[doi:10.1038/nature25778 | Iain Mathieson et al. | Nature | 21 February 2018] The genomic history of southeastern Europe

Genome-wide data reveal repeated migrations and admixture accompanying the spread of farming and later demographic transformations in southeastern Europe.

[doi:10.1038/nature24476 | Mark Lipson et al. | Nature | 8 November 2017] Parallel palaeogenomic transects reveal complex genetic history of early European farmers

Ancient genomes from multiple regions show that European farming populations experienced differing histories of migration and hunter-gatherer admixture.

[doi:10.1038/nature19844 | Pontus Skoglund et al. | Nature | September 2016] Genomic insights into the peopling of the Southwest Pacific

Ancient genomes help distinguish population movements associated with the initial settlement and later demographic history of Oceania.

[doi:10.1038/nature14625 | Morten Rasmussen et al. | Nature | 18 June 2015] The ancestry and affiliations of Kennewick Man

Genome sequencing demonstrated close ancestry between Kennewick Man and contemporary Native American populations.

[doi:10.1038/nature14507 | Morten E. Allentoft, Martin Sikora, Karl-Göran Sjögren et al. | Nature | 10 June 2015] Population genomics of Bronze Age Eurasia

Bronze Age genomes reveal large-scale migrations and population restructuring across Eurasia during a period of major cultural change.

[doi:10.1038/nature14317 | Wolfgang Haak et al. | Nature | 2 March 2015] Massive migration from the steppe was a source for Indo-European languages in Europe

Ancient genomes provide evidence for substantial Steppe-related migration into Europe during the Late Neolithic and Bronze Age.

[doi:10.1038/nature13025 | Morten Rasmussen, Sarah L. Anzick, Michael R. Waters et al. | Nature | 12 February 2014] The genome of a Late Pleistocene human from a Clovis burial site in western Montana

The Anzick genome demonstrated close ancestry between a Clovis-associated child and Indigenous peoples of the Americas.

Ancient Pathogens, Disease, and Microbiomes (12)

[doi:10.1038/s41467-026-75911-y | Bing Sun, Yarong Wu, Daxuan Zhang et al. | Nature Communications | 24 July 2026] A prehistoric East-Asian Yersinia pestis genome and a ~5.3 ka trans-Eurasian expansion of plague

Ancient plague genomes extend prehistoric Yersinia pestis into East Asia and support a rapid trans-Eurasian expansion more than five millennia ago.

[doi:10.1016/j.dib.2025.111770 | Francesca J. Standeven, Gwyn Dahlquist-Axe, Jessica Hendy et al. | Data in Brief | 12 June 2025] An extensive archaeological dental calculus dataset spanning 5000 years for ancient human oral microbiome research

Presents a large metagenomic dental-calculus dataset designed for investigating long-term changes in diet, disease, oral ecology, and antimicrobial resistance.

[doi:10.1016/j.jasrep.2025.105038 | Sterling L. Wright | Journal of Archaeological Science: Reports | April 2025] Archaeological dental calculus: A rich bioarchive for exploring Classical Antiquity through ancient DNA methods

Reviews how dental calculus can reveal diet, health, microbiomes, and demographic information about populations of Classical Antiquity.

[doi:10.1016/j.tim.2024.10.008 | Emily Gaul & Maria A. Spyrou | Trends in Microbiology | 29 November 2024] Historical plague pandemics: perspectives from ancient DNA

Reviews how ancient Yersinia pestis genomes have transformed understanding of plague origins, persistence, transmission, and historical pandemic diversity.

[doi:10.1038/s41564-023-01527-3 | Abigail S. Gancz, Andrew G. Farrer, Michelle P. Nixon et al. | Nature Microbiology | 29 November 2023] Ancient dental calculus reveals oral microbiome shifts associated with lifestyle and disease in Great Britain

Dental calculus spanning thousands of years reveals changing oral microbial communities associated with diet, industrialization, oral hygiene, and disease.

[doi:10.1038/s41588-022-01265-y | Safia Danovi | Nature Genetics | 5 December 2022] Black Death and the evolution of immunity

Discusses ancient genomic evidence that severe plague mortality may have influenced frequencies of immune-related genetic variants in European populations.

[doi:10.1038/s41586-022-04800-3 | Maria A. Spyrou, Lyazzat Musralina, Guido A. Gnecchi Ruscone et al. | Nature | 15 June 2022] The source of the Black Death in fourteenth-century central Eurasia

Ancient Yersinia pestis genomes from Central Asia provide evidence locating an ancestral source close to the emergence of the Black Death lineage.

[doi:10.1038/s41559-020-1106-9 | Felix M. Key, Cosimo Posth, Luis R. Esquivel-Gomez et al. | Nature Ecology & Evolution | 24 February 2020] Emergence of human-adapted Salmonella enterica is linked to the Neolithization process

Ancient bacterial genomes connect the evolution of some Salmonella lineages with changing human ecology during the transition to farming.

[doi:10.1038/s41576-019-0119-1 | Maria A. Spyrou, Kirsten I. Bos, Alexander Herbig & Johannes Krause | Nature Reviews Genetics | 5 April 2019] Ancient pathogen genomics as an emerging tool for infectious disease research

Reviews methods and discoveries showing how pathogen genomes recovered from human remains can reconstruct disease evolution and historical epidemics.

[doi:10.1038/s41586-018-0097-z | Barbara Mühlemann, Terry C. Jones, Peter de Barros Damgaard et al. | Nature | 9 May 2018] Ancient hepatitis B viruses from the Bronze Age to the Medieval period

Ancient viral genomes reveal that hepatitis B infected humans thousands of years ago and possessed greater historical diversity than modern samples alone suggest.

[doi:10.1016/j.cell.2015.10.009 | Simon Rasmussen et al. | Cell | October 2015] Early Divergent Strains of Yersinia pestis in Eurasia 5,000 Years Ago

Ancient genomes demonstrate that plague bacteria circulated widely in Eurasia during the Bronze Age before later historically documented pandemics.

[doi:10.1038/nature13591 | Kirsten I. Bos, Kelly Harkins, Alexander Herbig et al. | Nature | 20 August 2014] Pre-Columbian mycobacterial genomes reveal seals as a source of New World human tuberculosis

Ancient tuberculosis genomes support an unexpected transmission history connecting marine mammals with pre-Columbian human infections in the Americas.

Animal Domestication, Extinction, and Environmental Paleogenomics (9)

[doi:10.1038/s41586-024-07597-5 | Pablo Librado et al. | Nature | 6 June 2024] Widespread horse-based mobility arose around 2200 bce in Eurasia

Ancient horse genomes help date the rapid expansion of a domesticated horse lineage associated with increasing long-distance mobility across Eurasia.

[doi:10.1038/s41586-021-04018-9 | Pablo Librado et al. | Nature | 20 October 2021] The origins and spread of domestic horses from the Western Eurasian steppes

Ancient genomes identify the geographic origin and subsequent rapid expansion of the horse lineage ancestral to most modern domestic horses.

[doi:10.1038/s41586-021-03224-9 | Tom van der Valk, Patrícia Pečnerová, David Díez-del-Molino et al. | Nature | 17 February 2021] Million-year-old DNA sheds light on the genomic history of mammoths

DNA from Early and Middle Pleistocene mammoths dramatically extends the temporal range of paleogenomics and clarifies mammoth evolutionary history.

[doi:10.1126/science.aba9572 | Anders Bergström, Laurent Frantz, Ryan Schmidt et al. | Science | 30 October 2020] Origins and genetic legacy of prehistoric dogs

Ancient dog genomes reveal deep population structure, migration, admixture, and relationships between prehistoric dogs and human populations.

[doi:10.1016/j.jasrep.2020.102273 | Danijela Popović, Velia Mendoza España, Mariusz Ziółkowski et al. | Journal of Archaeological Science: Reports | June 2020] Molecular species assignment and dating of putative pre-Columbian dog remains excavated from Bolivia

Combines ancient DNA and dating to test the biological identity and antiquity of purported pre-Columbian dog remains.

[doi:10.1038/s41576-020-0225-0 | Laurent A. F. Frantz, Daniel G. Bradley, Greger Larson & Ludovic Orlando | Nature Reviews Genetics | 7 April 2020] Animal domestication in the era of ancient genomics

Reviews how ancient genomes have transformed models of domestication by revealing admixture, population turnover, selection, and complex relationships between wild and domestic animals.

[doi:10.1146/annurev-animal-022516-022747 | David E. MacHugh, Greger Larson & Ludovic Orlando | Annual Review of Animal Biosciences | 2017] Taming the Past: Ancient DNA and the Study of Animal Domestication

Synthesizes ancient-DNA research on livestock and companion animals and explains how paleogenomics can directly test competing domestication models.

[doi:10.1073/pnas.1416991111 | Mikkel Schubert, Hákon Jónsson, Dan Chang et al. | Proceedings of the National Academy of Sciences | 15 December 2014] Prehistoric genomes reveal the genetic foundation and cost of horse domestication

Ancient horse genomes identify genetic changes associated with domestication while also revealing loss of genetic diversity in domestic lineages.

[doi:10.1038/nature12323 | Ludovic Orlando, Aurélien Ginolhac, Guojie Zhang et al. | Nature | 26 June 2013] Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse

An exceptionally old horse genome pushed ancient-DNA research deeper into the Pleistocene and substantially revised the evolutionary timescale of Equus.

Ethics, Community Partnership, and Interpretation (8)

[doi:10.1016/j.xhgg.2022.100161 | Emma Kowal, Laura S. Weyrich, Juan Manuel Argüelles et al. | Human Genetics and Genomics Advances | 13 April 2023] Community partnerships are fundamental to ethical ancient DNA research

Argues that ancient-DNA projects should meaningfully involve descendant and stakeholder communities and take Indigenous data sovereignty and community authority seriously.

[doi:10.1038/d41586-021-03541-z | Mehmet Somel, N. Ezgi Altınışık, Füsun Özer et al. | Nature | 30 November 2021] Collaborate equitably in ancient DNA research and beyond

Calls for more equitable partnerships between well-funded paleogenomics laboratories and researchers and institutions in countries supplying archaeological material.

[doi:10.1038/d41586-021-03542-y | Krystal S. Tsosie, Alyssa C. Bader, Keolu Fox et al. | Nature | 30 November 2021] Ancient-DNA researchers write their own rules

Critiques universal ancient-DNA ethics frameworks that insufficiently incorporate Indigenous scholarship, community governance, and established principles for responsible research.

[doi:10.1038/s41586-021-04008-x | Songül Alpaslan-Roodenberg, David Anthony, Hiba Babiker et al. | Nature | 20 October 2021] Ethics of DNA research on human remains: five globally applicable guidelines

Proposes guidelines concerning legal compliance, research planning, minimizing destructive sampling, data availability, and engagement with stakeholders.

[Cambridge Core article B183556FE17AC85276281A1C7CF25E1C | Rachel J. Crellin & Oliver J.T. Harris | Archaeological Dialogues | 15 May 2020] Beyond binaries. Interrogating ancient DNA

Examines theoretical assumptions in archaeogenetics and argues against treating genetic populations, cultures, nature, and identity as simple bounded categories.

[doi:10.1038/s41598-018-31123-z | Stefanie Eisenmann, Eszter Bánffy, Peter van Dommelen et al. | Scientific Reports | 29 August 2018] Reconciling material cultures in archaeology with genetic data: The nomenclature of clusters emerging from archaeogenomic analysis

Warns against equating genetic clusters directly with archaeological cultures and recommends more careful terminology when integrating genetics and archaeology.

[doi:10.15184/aqy.2018.70 | Mary E. Prendergast & Elizabeth Sawchuk | Antiquity | 27 June 2018] Boots on the ground in Africa's ancient DNA ‘revolution’: archaeological perspectives on ethics and best practices

Examines destructive sampling, colonial legacies, local expertise, collections stewardship, and equitable research practice in African ancient-DNA projects.

[doi:10.1038/506142a | Ewen Callaway | Nature | 12 February 2014] Ancient genome stirs ethics debate

Uses an early high-profile Native American ancient-genome study to examine questions of consultation, ancestry, repatriation, and responsibilities to descendant communities.

Ancient DNA Research — Batch 2

Recent Human Paleogenomics, Selection, and Social Organization

[doi:10.1038/s41467-026-76204-0 | Marco Rosario Capodiferro et al. | Nature Communications | 6 August 2026] Archaic ancestry inference in imputed ancient human genomes

Uses imputed ancient genomes to improve detection of Neanderthal and Denisovan ancestry and investigate how archaic genomic segments changed through human prehistory.

[doi:10.1038/s41467-026-74234-2 | Bossoms Mesa et al. | Nature Communications | 23 June 2026] Investigating ancient human DNA preservation on cave walls and in rock art

Tests whether cave walls and prehistoric pigments can preserve ancient human DNA potentially associated with the people who created or interacted with rock art.

[doi:10.1038/s41586-026-10358-1 | Ali Akbari et al. | Nature | 15 April 2026] Ancient DNA reveals pervasive directional selection across West Eurasia

Analyzes thousands of ancient genomes to identify sustained allele-frequency changes and reconstruct natural selection across prehistoric West Eurasia.

[doi:10.1038/s41586-025-09856-5 | Éric Crubézy et al. | Nature | 7 January 2026] An ancient DNA perspective on the Russian conquest of Yakutia

Uses ancient genomes to investigate population continuity, demographic disruption, disease, and social change surrounding Russian expansion into Yakutia.

[doi:10.1038/s41586-025-08793-7 | Nada Salem et al. | Nature | 2 April 2025] Ancient DNA from the Green Sahara reveals ancestral North African lineage

Genomes from approximately 7,000-year-old individuals in Libya reveal a deeply divergent North African lineage during the African Humid Period.

[doi:10.1038/s41586-024-08531-5 | Iosif Lazaridis et al. | Nature | 5 February 2025] The genetic origin of the Indo-Europeans

Large-scale ancient genomic analysis investigates the formation of Yamnaya ancestry and its relationship to populations associated with Indo-European dispersals.

[doi:10.1038/s41586-024-08372-2 | Alexey G. Nikitin et al. | Nature | 5 February 2025] A genomic history of the North Pontic Region from the Neolithic to the Bronze Age

Reconstructs prehistoric population interactions north of the Black Sea where European farmers, hunter-gatherers, and steppe populations repeatedly met.

[doi:10.1038/s41586-024-08418-5 | Ke Wang et al. | Nature | 15 January 2025] Ancient DNA reveals reproductive barrier despite shared Avar-period culture

Finds genetically differentiated communities living within a broadly shared Avar cultural environment and investigates patterns of marriage and social interaction.

[doi:10.1038/s41586-024-08275-2 | Leo Speidel et al. | Nature | 1 January 2025] High-resolution genomic history of early medieval Europe

Uses fine-scale genomic methods to reconstruct movements and ancestry connections across Europe during the first millennium CE.

[doi:10.1038/s41586-024-08113-5 | Ayshin Ghalichi et al. | Nature | 30 October 2024] The rise and transformation of Bronze Age pastoralists in the Caucasus

Ancient genomes reveal demographic changes associated with pastoral societies and cultural transformations in the prehistoric Caucasus.

[doi:10.1038/s41559-024-02532-3 | Joscha Gretzinger et al. | Nature Ecology & Evolution | 19 September 2024] 9,000 years of genetic continuity in southernmost Africa demonstrated at Oakhurst rockshelter

A Holocene genomic transect from South Africa reveals unusually long-term genetic continuity among ancestors of southern African San populations.

[doi:10.1038/s41559-024-02539-w | Xiaoyan Yang et al. | Nature Ecology & Evolution | 16 September 2024] Lake-centred sedentary lifestyle of early Tibetan Plateau Indigenous populations at high elevation 4,400 years ago

Combines ancient DNA and archaeology to identify Indigenous high-altitude populations living a largely sedentary fishing-based lifestyle on the Tibetan Plateau.

[doi:10.1038/s41586-024-07312-4 | Guido Alberto Gnecchi-Ruscone et al. | Nature | 24 April 2024] Network of large pedigrees reveals social practices of Avar communities

Reconstructs pedigrees spanning multiple generations and identifies patrilineality, female exogamy, and other kinship practices in Avar-period communities.

[doi:10.1038/s41559-024-02322-x | Kendra Sirak et al. | Nature Ecology & Evolution | 8 February 2024] Medieval DNA from Soqotra points to Eurasian origins of an isolated population at the crossroads of Africa and Arabia

Ancient genomes from Soqotra reveal strong connections with southern Arabia and additional ancestry associated with long-distance Indian Ocean contacts.

[doi:10.1038/s41586-023-06862-3 | Morten E. Allentoft et al. | Nature | 10 January 2024] 100 ancient genomes show repeated population turnovers in Neolithic Denmark

A dense genomic time series reveals major population replacements associated with farming and later Steppe-related ancestry in prehistoric Denmark.

[doi:10.1038/s41586-023-06865-0 | Morten E. Allentoft et al. | Nature | 10 January 2024] Population genomics of post-glacial western Eurasia

Hundreds of ancient genomes reveal contrasting population histories east and west of a major post-glacial genetic boundary across Eurasia.

[doi:10.1038/s41586-023-06705-1 | Evan K. Irving-Pease et al. | Nature | 10 January 2024] The selection landscape and genetic legacy of ancient Eurasians

Examines how prehistoric migrations and natural selection contributed to present-day European genetic variation and disease-associated alleles.

[doi:10.1038/s41586-023-06618-z | William Barrie et al. | Nature | 10 January 2024] Elevated genetic risk for multiple sclerosis emerged in steppe pastoralist populations

Traces part of the modern genetic risk for multiple sclerosis to immune variants enriched among prehistoric Steppe pastoralists.

[doi:10.1038/s41586-023-06350-8 | Maïté Rivollat et al. | Nature | 26 July 2023] Extensive pedigrees reveal the social organization of a Neolithic community

Genome-wide relatedness reconstructs multigenerational pedigrees and provides unusually detailed evidence about household and marriage organization in Neolithic France.

[doi:10.1038/s41467-023-39202-0 | Bárbara Sousa da Mota et al. | Nature Communications | 20 June 2023] Imputation of ancient human genomes

Evaluates genotype imputation in low-coverage ancient genomes and shows when reconstructed diploid genotypes can reliably support population-genetic analyses.

Early Human Genomes, Archaic Humans, and Foundational Paleogenomics

[doi:10.1038/s41559-021-01443-x | Kay Prüfer et al. | Nature Ecology & Evolution | 7 April 2021] A genome sequence from a modern human skull over 45,000 years old from Zlatý kůň in Czechia

Sequences one of the oldest modern-human genomes known from Europe and investigates early Eurasian ancestry and Neanderthal admixture.

[doi:10.1038/s41586-018-0870-z | Katerina Douka et al. | Nature | 30 January 2019] Age estimates for hominin fossils and the onset of the Upper Palaeolithic at Denisova Cave

Integrates genetic, archaeological, and chronological evidence to establish the sequence of Denisovan and Neanderthal occupations at Denisova Cave.

[doi:10.1038/s41586-018-0455-x | Viviane Slon et al. | Nature | 22 August 2018] The genome of the offspring of a Neanderthal mother and a Denisovan father

DNA from a bone fragment identifies a first-generation individual whose mother was Neanderthal and whose father was Denisovan.

[doi:10.1126/science.aao1887 | Kay Prüfer et al. | Science | 5 October 2017] A high-coverage Neandertal genome from Vindija Cave in Croatia

A high-quality Croatian Neanderthal genome refines estimates of Neanderthal population history and genetic contributions to living humans.

[doi:10.1038/nature17993 | Qiaomei Fu et al. | Nature | 2 May 2016] The genetic history of Ice Age Europe

Genomes spanning tens of thousands of years reveal repeated population replacement, refugia, and admixture during the European Upper Palaeolithic.

[doi:10.1038/nature16152 | Iain Mathieson et al. | Nature | 23 November 2015] Genome-wide patterns of selection in 230 ancient Eurasians

Uses ancient genomes to track changes in traits associated with pigmentation, diet, immunity, and adaptation after the development of agriculture.

[doi:10.1038/ncomms9912 | Eppie R. Jones et al. | Nature Communications | 16 November 2015] Upper Palaeolithic genomes reveal deep roots of modern Eurasians

Genomes from the Caucasus reveal a deeply divergent hunter-gatherer ancestry that later contributed substantially to Steppe populations.

[doi:10.1073/pnas.1509851112 | Torsten Günther et al. | Proceedings of the National Academy of Sciences | September 2015] Ancient genomes link early farmers from Atapuerca in Spain to modern-day Basques

Early Iberian farmer genomes clarify relationships among Neolithic migrants, later Europeans, and the ancestry of present-day Basque populations.

[doi:10.1038/nature14558 | Qiaomei Fu et al. | Nature | 22 June 2015] An early modern human from Romania with a recent Neanderthal ancestor

The Oase genome demonstrates that some early European modern humans had Neanderthal ancestors only a few generations previously.

[doi:10.1126/science.aaa0114 | Andaine Seguin-Orlando et al. | Science | November 2014] Genomic structure in Europeans dating back at least 36,200 years

The Kostenki genome shows that important components of European ancestry were already present during the Upper Palaeolithic.

[doi:10.1038/nature13673 | Iosif Lazaridis et al. | Nature | 17 September 2014] Ancient human genomes suggest three ancestral populations for present-day Europeans

Identifies hunter-gatherer, early farmer, and Ancient North Eurasian ancestry as major components in the formation of later European populations.

[doi:10.1038/nature12960 | Iñigo Olalde et al. | Nature | 26 January 2014] Derived immune and ancestral pigmentation alleles in a 7,000-year-old Mesolithic European

The La Braña genome provides evidence about Mesolithic European ancestry, immune variation, eye color, and pigmentation.

[doi:10.1126/science.1236573 | Beth Shapiro & Michael Hofreiter | Science | 24 January 2014] A paleogenomic perspective on evolution and gene function: new insights from ancient DNA

Reviews how paleogenomic datasets permit direct study of evolutionary change, extinction, adaptation, and past genomic diversity.

[doi:10.1038/nature12886 | Kay Prüfer et al. | Nature | 18 December 2013] The complete genome sequence of a Neanderthal from the Altai Mountains

A high-coverage Altai Neanderthal genome reveals inbreeding, archaic population relationships, and gene flow among ancient hominin groups.

[doi:10.1038/nature12788 | Matthias Meyer et al. | Nature | December 2013] A mitochondrial genome sequence of a hominin from Sima de los Huesos

DNA from a roughly 400,000-year-old hominin demonstrated that genetic material could survive far deeper into the Middle Pleistocene than previously established.

[doi:10.1073/pnas.1221359110 | Qiaomei Fu et al. | Proceedings of the National Academy of Sciences | 22 January 2013] DNA analysis of an early modern human from Tianyuan Cave, China

A roughly 40,000-year-old genome from China illuminates early East Eurasian population relationships and links to later Asian populations.

[doi:10.1038/nature08976 | Johannes Krause et al. | Nature | March 2010] The complete mitochondrial DNA genome of an unknown hominin from southern Siberia

Mitochondrial DNA from Denisova Cave provided the first genetic indication of a previously unknown archaic human lineage.

[doi:10.1016/S0092-8674(00)80310-4 | Matthias Krings et al. | Cell | 1997] Neanderthal DNA sequences and the origin of modern humans

Landmark mitochondrial DNA analysis of a Neanderthal established ancient hominin genetics as a practical approach to studying human evolution.

Migration, Farming, and Population History

[doi:10.1038/s41586-022-05247-2 | Joscha Gretzinger et al. | Nature | 21 September 2022] The genomic signal of migration to Britain in the Anglo-Saxon period

Hundreds of ancient genomes reveal substantial continental European migration into Britain during the early medieval period.

[doi:10.1126/science.abm4247 | Iosif Lazaridis et al. | Science | 26 August 2022] The genetic history of the Southern Arc: A bridge between West Asia and Europe

Ancient genomes reconstruct population movements across Anatolia, the Caucasus, southeastern Europe, and neighboring regions over several millennia.

[doi:10.1126/science.abq0755 | Iosif Lazaridis et al. | Science | 26 August 2022] A genetic probe into the ancient and medieval history of Southern Europe and West Asia

Examines ancestry transformations from the Bronze Age through medieval times across the Mediterranean, Anatolia, Armenia, and surrounding regions.

[doi:10.1038/s41586-021-04287-4 | Nick Patterson et al. | Nature | 22 December 2021] Large-scale migration into Britain during the Middle to Late Bronze Age

Ancient genomes show substantial migration from continental Europe into Britain during the later Bronze Age.

[doi:10.1038/s41467-020-17656-w | Nathan Nakatsuka et al. | Nature Communications | 3 August 2020] Ancient genomes in South Patagonia reveal population movements associated with technological shifts and geography

Ancient South American genomes document migration and population restructuring associated with geography and changing technologies.

[doi:10.1038/s41467-020-16557-2 | Chao Ning et al. | Nature Communications | 1 June 2020] Ancient genomes from northern China suggest links between subsistence changes and human migration

Genomes spanning changing economies in northern China connect population movements with transitions involving farming and pastoralism.

[doi:10.1016/j.cell.2020.04.015 | Nathan Nakatsuka et al. | Cell | May 2020] A Paleogenomic Reconstruction of the Deep Population History of the Andes

Large-scale ancient genomic data reconstruct population structure, migration, and continuity across thousands of years of Andean prehistory.

[doi:10.1038/s41467-020-15560-x | Anja Furtwängler et al. | Nature Communications | 20 April 2020] Ancient genomes reveal social and genetic structure of Late Neolithic Switzerland

Ancient DNA reveals changing ancestry, kinship, and social organization during the transition toward Steppe-related ancestry in central Europe.

[doi:10.1038/s41467-020-14523-6 | Joseph H. Marcus et al. | Nature Communications | 24 February 2020] Genetic history from the Middle Neolithic to present on the Mediterranean island of Sardinia

Ancient Sardinian genomes document long periods of continuity followed by increasing ancestry from wider Mediterranean and European populations.

[doi:10.1126/sciadv.aaz5344 | Alissa Mittnik et al. | Science Advances | 2020] Genomic transformation and social organization during the Copper Age–Bronze Age transition in southern Germany

Combines ancient DNA, archaeology, and kinship to study immigration and household organization during a major prehistoric transition.

[doi:10.1126/science.aax6219 | Alissa Mittnik et al. | Science | 10 October 2019] Kinship-based social inequality in Bronze Age Europe

Genomic and archaeological evidence reveals household structures and inherited social differences within Bronze Age communities.

[doi:10.1038/s41559-019-0871-9 | Selina Brace et al. | Nature Ecology & Evolution | 15 April 2019] Ancient genomes indicate population replacement in Early Neolithic Britain

Genomes show that farming reached Britain largely through immigration by populations related to continental European Neolithic farmers.

[doi:10.1126/sciadv.aau4921 | John Lindo et al. | Science Advances | 8 November 2018] The genetic prehistory of the Andean highlands 7000 years BP through European contact

Ancient genomes track adaptation, population continuity, and demographic changes in high-altitude Andean populations.

[doi:10.1016/j.cell.2018.10.027 | Cosimo Posth et al. | Cell | November 2018] Reconstructing the Deep Population History of Central and South America

Ancient genomes reveal rapid early diversification followed by later migrations and regional population connections throughout the Americas.

[doi:10.1126/science.aav2621 | J. Víctor Moreno-Mayar et al. | Science | November 2018] Early human dispersals within the Americas

Ancient genomic data clarify early population branching, migration, and later gene flow among Indigenous American populations.

[doi:10.1126/science.aat3628 | Hugh McColl et al. | Science | July 2018] The prehistoric peopling of Southeast Asia

Ancient genomes demonstrate multiple migrations involving hunter-gatherers, early farmers, and later East Asian-related populations.

[doi:10.1038/s41467-018-05649-9 | Éadaoin Harney et al. | Nature Communications | 20 August 2018] Ancient DNA from Chalcolithic Israel reveals the role of population mixture in cultural transformation

Genomes from Peqi'in Cave indicate that migration and admixture contributed to cultural changes in Chalcolithic southern Levant populations.

[doi:10.1038/nature25173 | J. Víctor Moreno-Mayar et al. | Nature | 3 January 2018] Terminal Pleistocene Alaskan genome reveals first founding population of Native Americans

The Upward Sun River genome identifies an ancient population related to the founding ancestry of Indigenous peoples of the Americas.

[doi:10.1038/ncomms15694 | Verena J. Schuenemann et al. | Nature Communications | 30 May 2017] Ancient Egyptian mummy genomes suggest an increase of Sub-Saharan African ancestry in post-Roman periods

Ancient Egyptian mitochondrial and genome-wide data reveal affinities with Near Eastern populations and changing ancestry through time.

[doi:10.1038/nature19310 | Iosif Lazaridis et al. | Nature | 25 August 2016] Genomic insights into the origin of farming in the ancient Near East

Ancient genomes show that early farming communities of the Near East were genetically differentiated and contributed differently to later populations.

[doi:10.1016/j.cub.2016.05.037 | Zuzana Hofmanová et al. | Current Biology | 2016] Early farmers from across Europe directly descended from Neolithic Aegeans

Ancient genomes strengthen evidence that European farming populations descended substantially from migrations beginning in the Aegean and Anatolian region.

[doi:10.1126/science.1253448 | Pontus Skoglund et al. | Science | 2014] Genomic diversity and admixture differs for Stone-Age Scandinavian foragers and farmers

Ancient Scandinavian genomes reveal genetically distinct hunter-gatherer and farmer populations and evidence of admixture between them.

[doi:10.1126/science.1241844 | Guido Brandt et al. | Science | 11 October 2013] Ancient DNA reveals key stages in the formation of Central European mitochondrial genetic diversity

Mitochondrial genomes across prehistoric Central Europe identify major demographic transitions associated with farming and later population movements.

[doi:10.1126/science.1245049 | Joachim Burger, Ruth Bollongino et al. | Science | 2013] 2000 years of parallel societies in Stone Age Central Europe

Ancient DNA indicates that hunter-gatherers and farmers remained genetically differentiated for many generations while living in neighboring regions.

[doi:10.1016/j.cub.2012.06.005 | Federico Sánchez-Quinto et al. | Current Biology | 2012] Genomic affinities of two 7,000-year-old Iberian hunter-gatherers

Mesolithic Iberian genomes reveal genetic relationships among European hunter-gatherers before widespread agricultural migration.

[doi:10.1073/pnas.1113061108 | Marie Lacan et al. | Proceedings of the National Academy of Sciences | 31 October 2011] Ancient DNA suggests the leading role played by men in the Neolithic dissemination

Genetic data from early Iberian farmers investigate paternal and maternal lineages associated with the spread of Neolithic populations.

[doi:10.1371/journal.pbio.1000536 | Wolfgang Haak et al. | PLOS Biology | 9 November 2010] Ancient DNA from European Early Neolithic Farmers Reveals Their Near Eastern Affinities

DNA from Linear Pottery Culture farmers supports substantial demographic input from Anatolia and the Near East during Europe's Neolithic transition.

Animals, Plants, Domestication, and Environmental Ancient DNA

[doi:10.1038/s41586-026-10112-7 | Bergström et al. | Nature | 25 March 2026] Genomic history of early dogs in Europe

Ancient dog genomes reconstruct changing canine populations in prehistoric Europe and their relationships with later domestic dogs.

[doi:10.1038/s41586-026-10170-x | Bergström et al. | Nature | 25 March 2026] Dogs were widely distributed across western Eurasia during the Palaeolithic

Ancient genetic evidence indicates that dog-like populations were geographically widespread across western Eurasia well before the Holocene.

[doi:10.1038/s41467-026-70166-z | Ramos-Madrigal et al. | Nature Communications | 24 March 2026] Ancient DNA reveals 4000 years of grapevine diversity, viticulture and clonal propagation in France

Ancient grape DNA documents long-term cultivation, clonal propagation, and changing grapevine diversity through European agricultural history.

[doi:10.1038/s41467-025-62266-z | Pablo Librado et al. | Nature Communications | 2 August 2025] The genomic history of Iberian horses since the last Ice Age

Ancient horse genomes reconstruct population changes in Iberia from wild Pleistocene horses through domestication and historic breeding.

[doi:10.1038/s41586-025-09533-7 | Liu et al. | Nature | 2025] A haplotype-based evolutionary history of barley domestication

Ancient and modern barley genomes help reconstruct domestication, dispersal, and selection in one of the world's earliest cultivated cereals.

[doi:10.1038/s41586-024-08112-6 | Conor Rossi et al. | Nature | 30 October 2024] The genomic natural history of the aurochs

Genome-wide ancient DNA from wild cattle reconstructs aurochs population structure and contributions to domestic cattle ancestry.

[doi:10.1016/j.jas.2022.105703 | Lisa M. Atmore et al. | Journal of Archaeological Science | January 2023] Ancient DNA sequence quality is independent of fish bone weight

Tests assumptions about archaeological fish-bone sampling and shows that bone size alone is not a reliable predictor of ancient DNA quality.

[doi:10.1016/j.cub.2021.06.023 | Pere Gelabert et al. | Current Biology | 2021] Genome-scale sequencing and analysis of human, wolf, and bison DNA from 25,000-year-old sediment

Demonstrates genome-scale recovery of mammalian DNA directly from Pleistocene cave sediment without requiring identifiable skeletal remains.

[doi:10.1038/s41598-018-27363-8 | Nicolas J. Rawlence et al. | Scientific Reports | 2018] Complex history of dog origins and translocations in the Pacific revealed by ancient mitogenomes

Ancient dog mitochondrial genomes reconstruct introductions, replacements, and human-mediated canine movement across Pacific islands.

[doi:10.1126/science.aao4776 | Máire Ní Leathlobhair et al. | Science | 2018] The evolutionary history of dogs in the Americas

Ancient American dog genomes document a distinct lineage that accompanied prehistoric people and was later largely replaced by introduced dogs.

[doi:10.1126/science.aao3297 | Charleen Gaunitz et al. | Science | 2018] Ancient genomes revisit the ancestry of domestic and Przewalski's horses

Ancient Botai horse genomes show that the earliest known managed horses were not the primary ancestors of modern domestic horses.

[doi:10.1038/s41467-018-04737-0 | Chen et al. | Nature Communications | 2018] Whole-genome resequencing reveals world-wide ancestry and adaptive introgression events of domesticated cattle in East Asia

Genomic data illuminate cattle dispersal, admixture, and adaptation, including genetic contributions from distinct bovine populations.

[doi:10.1038/ncomms16082 | Morgane Ollivier, Laurent Frantz, Greger Larson et al. | Nature Communications | 2017] Ancient European dog genomes reveal continuity since the Early Neolithic

Ancient dog genomes indicate long-term continuity while also documenting gene flow among prehistoric European canine populations.

[doi:10.1038/ng.3611 | Mascher et al. | Nature Genetics | 2016] Genomic analysis of 6,000-year-old cultivated grain illuminates the domestication history of barley

Sequencing archaeological barley provides a direct genomic view of early crop domestication and agricultural dispersal.

[doi:10.1038/ncomms13158 | Julien Soubrier et al. | Nature Communications | 2016] Early cave art and ancient DNA record the origin of European bison

Genetic and archaeological evidence reveals the hybrid origins and deep history of the European bison lineage.

[doi:10.1038/ncomms10283 | Qiu et al. | Nature Communications | 2015] Yak whole-genome resequencing reveals domestication signatures and prehistoric population expansions

Genomic analysis identifies selection and demographic changes accompanying yak domestication and adaptation to high-altitude environments.

[doi:10.1038/ncomms3755 | Jing Yuan et al. | Nature Communications | 2013] Morphological and genetic evidence for early Holocene cattle management in northeastern China

Ancient DNA combined with skeletal evidence investigates early cattle management and domestication-related practices in prehistoric China.

[doi:10.1038/ncomms1447 | Barbara Wallner et al. | Nature Communications | 2011] Discovery of lost diversity of paternal horse lineages using ancient DNA

Ancient Y-chromosomal DNA reveals that prehistoric horses possessed substantially greater paternal diversity than modern domestic horse populations.

Ancient Pathogens, Preservation, and Laboratory Methods

[doi:10.1038/s41586-024-07546-2 | Megan Michel et al. | Nature | 12 June 2024] Ancient Plasmodium genomes shed light on the history of human malaria

Ancient parasite genomes reveal the historical distribution and evolutionary relationships of malaria-causing Plasmodium species.

[doi:10.1038/s41467-022-34416-0 | James A. Fellows Yates et al. | Nature Communications | 2022] Ancient oral microbiomes support gradual Neolithic dietary shifts towards agriculture

Dental-calculus metagenomes reveal how oral microbial communities changed as prehistoric populations progressively adopted agricultural diets.

[doi:10.1038/s41596-020-0338-0 | Matthias T. Gansauge et al. | Nature Protocols | 1 July 2020] Manual and automated preparation of single-stranded DNA libraries for the sequencing of DNA from ancient biological remains and other sources of highly degraded DNA

Provides detailed laboratory procedures for constructing sequencing libraries optimized for highly fragmented ancient DNA molecules.

[doi:10.1016/j.cell.2018.11.005 | Nicolás Rascovan et al. | Cell | 2019] Emergence and Spread of Basal Lineages of Yersinia pestis during the Neolithic Decline

Ancient plague genomes illuminate early diversification of Yersinia pestis and its spread across prehistoric Eurasia.

[doi:10.1371/journal.pone.0170940 | Henrik B. Hansen et al. | PLOS ONE | 2017] Comparing Ancient DNA Preservation in Petrous Bone and Tooth Cementum

Compares skeletal tissues to determine which anatomical sources provide higher endogenous DNA yields for ancient genomic studies.

[doi:10.1016/j.cub.2016.10.061 | Ana T. Duggan et al. | Current Biology | 2016] 17th Century Variola Virus Reveals the Recent History of Smallpox

A historical variola genome suggests that major smallpox viral lineages may have diversified much more recently than previously assumed.

[doi:10.1126/science.aad2545 | Frank Maixner et al. | Science | 2016] The 5300-year-old Helicobacter pylori genome of the Iceman

Reconstructs Helicobacter pylori from Ötzi and provides evidence about the prehistoric history and admixture of human-associated stomach bacteria.

[doi:10.1186/s13059-015-0776-0 | Gabriel Renaud et al. | Genome Biology | 12 October 2015] Schmutzi: estimation of contamination and endogenous mitochondrial consensus calling for ancient DNA

Introduces software for estimating modern human contamination and reconstructing authentic mitochondrial genomes from ancient sequencing data.

[doi:10.1371/journal.pone.0129102 | Ron Pinhasi et al. | PLOS ONE | 18 June 2015] Optimal Ancient DNA Yields from the Inner Ear Part of the Human Petrous Bone

Demonstrates exceptionally high endogenous DNA preservation in the dense inner-ear region of the human petrous bone.

[doi:10.1126/science.1238286 | Verena J. Schuenemann et al. | Science | 2013] Ancient leprosy genomes from a medieval European population reveal a recent origin of the pathogen

Medieval Mycobacterium leprae genomes reveal remarkable genomic conservation and clarify the historical evolution of leprosy.

[doi:10.1038/nprot.2013.038 | Matthias T. Gansauge & Matthias Meyer | Nature Protocols | 14 March 2013] Single-stranded DNA library preparation for the sequencing of ancient or damaged DNA

Describes a single-stranded library method that substantially improves recovery of extremely short and damaged ancient DNA fragments.

[doi:10.1073/pnas.1314445110 | Jesse Dabney et al. | Proceedings of the National Academy of Sciences | September 2013] Complete mitochondrial genome sequence of a Middle Pleistocene cave bear reconstructed from ultrashort DNA fragments

Demonstrates recovery of highly fragmented DNA from Middle Pleistocene material using extraction methods optimized for ultrashort molecules.

[doi:10.1093/bioinformatics/btt193 | Hákon Jónsson et al. | Bioinformatics | 2013] mapDamage2.0: fast approximate Bayesian estimates of ancient DNA damage parameters

Provides computational tools for measuring and modeling characteristic nucleotide damage patterns used to authenticate ancient DNA.

[doi:10.1093/bioinformatics/btr347 | Aurélien Ginolhac et al. | Bioinformatics | 2011] mapDamage: testing for damage patterns in ancient DNA sequences

Introduces software for identifying fragmentation and nucleotide misincorporation patterns characteristic of genuinely ancient DNA.

[doi:10.1038/nature10549 | Kirsten I. Bos et al. | Nature | 2011] A draft genome of Yersinia pestis from victims of the Black Death

Reconstructs plague bacterial DNA from fourteenth-century victims and provides direct genomic evidence about the organism responsible for the Black Death.

[doi:10.1073/pnas.0704665104 | Adrian W. Briggs et al. | Proceedings of the National Academy of Sciences | 2007] Patterns of damage in genomic DNA sequences from a Neandertal

Characterizes fragmentation and cytosine deamination in Neanderthal DNA and establishes principles still used to recognize authentic ancient sequence data.

[doi:10.1038/nprot.2007.247 | Nadin Rohland & Michael Hofreiter | Nature Protocols | 2007] Ancient DNA extraction from bones and teeth

Presents laboratory procedures for extracting degraded DNA from archaeological skeletal material while addressing contamination and low DNA concentration.