Accurate detection of identity-by-descent segments in human ancient DNA
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Abstract
Long DNA segments shared between two individuals, known as identity-by-descent (IBD), reveal recent genealogical connections. Here we introduce ancIBD, a method for identifying IBD segments in ancient human DNA (aDNA) using a hidden Markov model and imputed genotype probabilities. We demonstrate that ancIBD accurately identifies IBD segments >8 cM for aDNA data with an average depth of >0.25× for whole-genome sequencing or >1× for 1240k single nucleotide polymorphism capture data. Applying ancIBD to 4,248 ancient Eurasian individuals, we identify relatives up to the sixth degree and genealogical connections between archaeological groups. Notably, we reveal long IBD sharing between Corded Ware and Yamnaya groups, indicating that the Yamnaya herders of the Pontic-Caspian Steppe and the Steppe-related ancestry in various European Corded Ware groups share substantial co-ancestry within only a few hundred years. These results show that detecting IBD segments can generate powerful insights into the growing aDNA record, both on a small scale relevant to life stories and on a large scale relevant to major cultural-historical events.
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L’ADN ancien parle de plus en plus
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Unveiling the complexity of post-Roman polity formation in Pannonia using ancient DNA
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Equal in death: Ancient genomic analysis of children’s early Christian burials
Krzewińska, M., Kjellström, A., Yaka, R., Varela, R., Pochon, Z., Lagerholm, V. K., Hedenstierna‐Jonson, C., Zachrisson, T., Kashuba, N., Sobrado, V., et al. (2026) · Science Advances · doi:10.1126/sciadv.aeb8588 · Cited by 1 · see citing works
Fraser, M., Sánchez‐Quinto, F., Kırdök, E., Ausmees, K., Kılınç, G. M., Larena, M., Correa-Mendoza, L., Meur, A. L., Blanchet, A., Bergfeldt, N., et al. (2026) · Communications Biology · doi:10.1038/s42003-026-10498-0 · Cited by 1 · see citing works
DNA insights into Neolithic society
Sirak, K. A. (2023) · Nature Human Behaviour · doi:10.1038/s41562-023-01668-9 · Cited by 1 · see citing works
Historic Genomes Uncover Demographic Shifts and Kinship Structures in Post-Roman Central EuropePreprint
Blöcher, J., Vallini, L., Velte, M., Eckel, R., Guyon, L., Winkelbach, L., Thomas, M., Gharehbaghi, N., Mitchell, C. T., Schümann, J., et al. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.03.01.640862 · Cited by 1 · see citing works
Olalde, Í., Altena, E., Bourgeois, Q. P. J., Fokkens, H., Amkreutz, L. W. S. W., Deguilloux, M., Fichera, A., Flas, D., Gandini, F., Kegler, J. F., et al. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.03.24.644985 · Cited by 1 · see citing works
Self-citationLong-distance kinship in megalithic EuropePreprint
Krause‐Kyora, B., da Silva, N. A., Nebel, A., Kolbe, D., Myburgh, D., Klimscha, F., Görner, I., Fuchs, K., Meyer, C., Schierhold, K., et al. (2025) · Research Square · doi:10.21203/rs.3.rs-6464608/v1 · Cited by 1 · see citing works
- Authors
- Ringbauer, H., Huang, Y., Akbari, A., Mallick, S., Olalde, I., Patterson, N., & Reich, D.
- Affiliations
- Harvard University (US)
- Max Planck Institute for Evolutionary Anthropology (DE)
- Broad Institute (US)
- Corresponding author
- Ringbauer, Harald
- Reich, David
- ORCID
- Venue
- Nature Genetics
- Published
- 2023-12-20
- Volume
- 56
- Issue
- 1
- Pages
- 143-151
- ISSN
- 1061-4036 (ISSN-L)
- 1546-1718
- PMC
- PMC10028887
- OpenAlex
- W4390070832
- Cited by
- 155
- References
- 65
- Citations by year
- 2026: 62 · 2025: 49 · 2024: 32 · 2023: 12
- FWCI
- 25.73
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Locations
- Nature Genetics (publishedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- PubMed Central (submittedVersion, cc-by-nc-nd)
- Funders
- Max-Planck-Gesellschaft
- U.S. Department of Health & Human Services | National Institutes of Health (HG012287)
- John Templeton Foundation (61220)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Forensic and Genetic Research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic diversity and population structure
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
- Keywords
- identity by descent, ancient DNA, hidden Markov models, genotype imputation, coancestry, Corded Ware, Yamnaya, Steppe ancestry
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