Cited by 155Forensic and Genetic ResearchGenetic diversity and population structureGenetic Associations and Epidemiology

Accurate detection of identity-by-descent segments in human ancient DNA

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Ringbauer, Harald, Huang, Yilei, Akbari, Ali, Mallick, Swapan, Olalde, Iñigo, Patterson, Nick, Reich, David·2024·Nature Genetics

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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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  1. Allentoft Morten E, Sikora Martin, Refoyo-Martínez Alba, Irving-Pease Evan K, Fischer Anders, Barrie William, Ingason Andres, Stenderup Jesper, Sjögren Karl-Göran, Pearson Alice, Population genomics of stone age eurasia. bioRxiv, 2022.
  2. Bishop Christopher M.. Pattern Recognition and Machine Learning (Information Science and Statistics), pages 627– 628. Springer, 2006.

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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
Venue
Nature Genetics
Published
2023-12-20
Volume
56
Issue
1
Pages
143-151
ISSN
  • 1061-4036 (ISSN-L)
  • 1546-1718
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
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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