Abstract
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.
Highlights
We found that runs of homozygosity (ROHs) < 1Mb cannot be identified reliably at low coverage, and we did not include such short ROHs in downstream analyses (STAR Methods)
Simulations using in silico-generated ancient DNA reads with spiked-in ROH showed that PLINK calls ROHs accurately down to 53 coverage
We could empirically account for this bias by varying the parameters of PLINK with respect to the number of heterozygous SNP allowed per window conditional on coverage, and we could estimate number of ROH > 1Mb (NROH) and sum of ROH > 1Mb (SROH) > 1Mb reliably for R33 coverage genomes in downsampling simulations (Figures S2A and S2B; STAR Methods)
Summary
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.[2,3,4,5] Here, we present an approach for reliable estimation of runs of homozygosity (ROHs) in genomes with R33 mean sequence coverage across >1 million SNPs and apply this to 411 ancient Eurasian genomes from the last 15,000 years.[5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34] 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,[1,35,36,37] suggesting that such practices may have become widespread within the last few millennia
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