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.
Highlights
An individual’s genome is a mosaic of different segments inherited from our various direct ancestors
The data is assumed to be pseudo-haploid as the low coverage in ancient DNA (aDNA) studies normally does not allow to call heterozygous genotypes. This procedure of randomly sampling one sequencing read per Single Nucleotide Polymorphism (SNP) site is widely used in aDNA studies of low coverage data, see e.g. [23, 28,29,30,31, 33,34,35,36, 39, 42, 45]
We can show that obtaining as little as 2,500 overlapping common SNPs is enough to classify up to second degree relationships from effectively haploid data
Summary
An individual’s genome is a mosaic of different segments inherited from our various direct ancestors. These segments, shared between individuals, can be referred to as identical by descent (IBD). Knowledge about IBD segments has been used for haplotype phasing [1, 2], heritability estimation [3, 4], population history [5], inference of natural selection [6] and to estimate the degree of biological relationship among individuals [7]. A number of methods have been developed to estimate the degree of biological relationship by inferring IBD from. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript
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