Estimating genetic kin relationships in prehistoric populations
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Abstract
Archaeogenomic research has proven to be a valuable tool to trace migrations of historic and prehistoric individuals and groups, whereas relationships within a group or burial site have not been investigated to a large extent. Knowing the genetic kinship of historic and prehistoric individuals would give important insights into social structures of ancient and historic cultures. Most archaeogenetic research concerning kinship has been restricted to uniparental markers, while studies using genome-wide information were mainly focused on comparisons between populations. Applications which infer the degree of relationship based on modern-day DNA information typically require diploid genotype data. Low concentration of endogenous DNA, fragmentation and other post-mortem damage to ancient DNA (aDNA) makes the application of such tools unfeasible for most archaeological samples. To infer family relationships for degraded samples, we developed the software READ (Relationship Estimation from Ancient DNA). We show that our heuristic approach can successfully infer up to second degree relationships with as little as 0.1x shotgun coverage per genome for pairs of individuals. We uncover previously unknown relationships among prehistoric individuals by applying READ to published aDNA data from several human remains excavated from different cultural contexts. In particular, we find a group of five closely related males from the same Corded Ware culture site in modern-day Germany, suggesting patrilocality, which highlights the possibility to uncover social structures of ancient populations by applying READ to genome-wide aDNA data. READ is publicly available from https://bitbucket.org/tguenther/read.
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We excluded two individuals from further analysis because genetic patterns showed they were first-degree relatives of higher coverage samples in the dataset.
“We excluded two individuals from further analysis, as the genetic patterns observed using the method described in Kuhn et al.73. Showed that they were first-degree relatives of higher coverage samples in the dataset.”
From Ancient DNA from Chalcolithic Israel reveals the role of population mixture in cultural transformation (2018) · cites this paper as [73]
No first- or second-degree relatives were found among the Ancient Rapanui, and a single pair of third- to fourth-degree relatives was detected.
“Using READ42 and NGSrelate243, we did not find any first- or second-degree relatives among the Ancient Rapanui (Supplementary Figs. 23 and 24 and Supplementary Information section 9) and detected a single pair of third- to fourth-degree relatives on the basis of IBD sharing (highest estimated IBD sharing >15 cM between any two individuals is <1,000 cM; Supplementary Information section 8 and”
From Ancient Rapanui genomes reveal resilience and pre-European contact with the Americas (2024) · cites this paper as [42]
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- Authors
- Monroy Kuhn, J. M., Jakobsson, M., & Günther, T.
- Affiliations
- Uppsala University (SE)
- Corresponding author
- Jakobsson, Mattias
- Günther, Torsten
- Venue
- PLOS ONE
- Publisher
- Public Library of Science (PLoS)
- Published
- 2018-04-23
- Volume
- 13
- Issue
- 4
- Pages
- e0195491
- ISSN
- 1932-6203 (ISSN-L)
- PMC
- PMC5912749
- OpenAlex
- W2950454348
- Cited by
- 330
- References
- 79
- Citations by year
- 2026: 31 · 2025: 47 · 2024: 53 · 2023: 62 · 2022: 40 · 2021: 42 · 2020: 23 · 2019: 19 · 2018: 11 · 2017: 2
- FWCI
- 14.33
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- PLoS ONE (publishedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc)
- Europe PMC (PubMed Central) (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Uppsala University Publications (Uppsala University) (submittedVersion, other-oa)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion)
- Figshare (submittedVersion, cc-by)
- FreiDok plus (Universitätsbibliothek Freiburg) (submittedVersion)
- Funders
- Erasmus Mundus Master Programme in Evolutionary Biology
- Consejo Nacional de Ciencia y Tecnología
- European Research Council (311413)
- Vetenskapsrådet
- Wenner-Gren-Foundations
- Riksbankens Jubileumsfond
- Knut och Alice Wallenbergs Stiftelse
- 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
- Social Sciences › Arts and Humanities › Archeology › Forensic Anthropology and Bioarchaeology Studies
- Keywords
- genetic relatedness, ancient DNA, prehistoric humans, Corded Ware culture, patrilocality, social structure, degraded DNA, shotgun sequencing, human remains
- MeSH terms
- DNA, Ancient, Computer Simulation, DNA, Mitochondrial, Family, Germany, Haplotypes, Humans, Male, Models, Genetic, Software, Sequence Analysis, DNA, Polymorphism, Single Nucleotide, Chromosomes, Human, Y, DNA Fragmentation
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