The history of human inbreeding is controversial. The development of sedentary agricultural societies may have had opposite influences on inbreeding levels. On the one hand, agriculture and food surplus may have diminished inbreeding by increasing population sizes and lowering endogamy, i.e. inbreeding due to population isolation. On the other hand, increased sedentism, as well as the advent of private property may have promoted inbreeding through the emergence of consanguineous marriage customs or via ethnic and caste endogamy. The net impact is unknown, and to date, no systematic study on the temporal frequency of inbreeding in human societies has been conducted. Here we present a new approach for reliable estimation of runs of homozygosity (ROH) in genomes with ≥3x mean coverage across >1 million SNPs, and apply this to 440 ancient Eurasian genomes from the last 15,000 years. We show that the frequency of inbreeding, as measured by ROH, 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 endogamy, although singular cases of high consanguinity can also be found in the archaeogenomic record.
I think it is hard to think this is unrelated to decreased pairwise Fst between populations over the Holocene. Fst is a statistic that measures the proportion of genetic variation across two populations in relation to the total variance. In a Pleistocene world of small clans occupying a thinly populated landscape, one can envisage a scenario where gene flow is far more viscous than the more sedentary, but interconnected, world of agriculturalists.
Hunter-gatherers were probably not more xenophobic. Rather, increasing populations by an order of magnitude increases the number of potential geographically close mates a lot.
Another consequence of more gene flow and more partners is that inbreeding also declines, as people have more recent ancestors in their pedigree.
The main caveat I would put into this though is that this applies to dense Eurasian time transects. There is some reason to think that hominins on the northern Eurasian fringe were always on the knife’s edge of sustainability.