Human inbreeding has decreased in time through the Holocene

• Published in: Current biology 2021-09, Vol.31 (17), p.3925-3934.e8
• Main Authors: Ceballos, Francisco C., Gürün, Kanat, Altınışık, N. Ezgi, Gemici, Hasan Can, Karamurat, Cansu, Koptekin, Dilek, Vural, Kıvılcım Başak, Mapelli, Igor, Sağlıcan, Ekin, Sürer, Elif, Erdal, Yılmaz Selim, Götherström, Anders, Özer, Füsun, Atakuman, Çiğdem, Somel, Mehmet
• Format: Article
• Language: English
• Subjects: agriculture; archaeogenomics; autozygosity; consanguinity; human population genetics; hunter-gatherers; inbreeding; Neolithic transition; runs of homozygosity
• ISSN: 0960-9822; 1879-0445; 1879-0445
• DOI: 10.1016/j.cub.2021.06.027

The history of human inbreeding is controversial.1 In particular, how the development of sedentary and/or agricultural societies may have influenced overall inbreeding levels, relative to those of hunter-gatherer communities, is unclear.2–5 Here, we present an approach for reliable estimation of runs of homozygosity (ROHs) in genomes with ≥3× mean sequence coverage across >1 million SNPs and apply this to 411 ancient Eurasian genomes from the last 15,000 years.5–34 We show that the frequency of inbreeding, as measured by ROHs, has decreased over time. The strongest effect is associated with the Neolithic transition, but the trend has since continued, indicating a population size effect on inbreeding prevalence. We further show that most inbreeding in our historical sample can be attributed to small population size instead of consanguinity. Cases of high consanguinity were rare and only observed among members of farming societies in our sample. Despite the lack of evidence for common consanguinity in our ancient sample, consanguineous traditions are today prevalent in various modern-day Eurasian societies,1,35–37 suggesting that such practices may have become widespread within the last few millennia. •A study of 411 ancient genomes shows inbreeding decreased over time•The decrease appears linked with population size increase enabled by agriculture•Extreme consanguineous matings did occur among agriculturalists but were rare Ceballos et al. study 411 ancient genomes from west and central Eurasia to show that overall inbreeding levels have decreased over time, most likely owing to population size increases with agriculture. The sample contains highly consanguineous ancient individuals, but these are rare, and all come from agriculturalist backgrounds.