Estimating genetic kin relationships in prehistoric populations

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.考古基因组学（Archaeogenomic）研究已被证实是追踪历史及史前人类个体与群体迁徙的重要工具，但针对群体内部或墓葬遗址内的亲缘关系的大规模探究仍相对不足。明确历史与史前人类个体的遗传亲缘关系，可深入揭示古代及历史时期文明的社会结构。目前绝大多数涉及亲缘关系的考古遗传学研究均局限于单亲遗传标记（uniparental markers），而采用全基因组（genome-wide）信息的研究则主要聚焦于群体间的比较分析。基于现代DNA信息推断亲缘等级的现有应用，通常均要求获取二倍体基因型（diploid genotype）数据。古代DNA（ancient DNA, aDNA）存在内源性DNA浓度低、片段化严重及其他死后损伤等问题，导致这类工具无法适用于多数考古样本。为实现对降解样本的家族亲缘关系推断，我们开发了READ软件（Relationship Estimation from Ancient DNA，即古代DNA亲缘关系推断工具）。本研究证实，该启发式方法可在个体基因组鸟枪法测序覆盖度（shotgun coverage）仅为0.1×的情况下，成功推断至多二级亲缘关系。我们将READ应用于不同文化背景下出土的人类遗骸的已公开aDNA数据集，揭示了史前人类间此前未被发现的亲缘关系。尤为重要的是，我们在现代德国境内同一绳纹器文化（Corded Ware culture）遗址中发现了5名亲缘关系密切的男性个体，这一结果提示存在从夫居（patrilocality）社会结构，也凸显了通过将READ应用于全基因组aDNA数据，以揭示古代人群社会结构的可行性。READ软件可从https://bitbucket.org/tguenther/read公开获取。