Inbreeding avoidance in the Raute hunter-gatherers from Nepal

Inbreeding can reduce fitness and genetic diversity, posing significant challenges for small human populations. While mobility and exogamy are known mechanisms of inbreeding avoidance among hunter-gatherers, the effects of cultural systems in mitigating these risks have not been studied in detail. Here, we investigate inbreeding patterns and avoidance strategies in the Raute of Nepal in comparison with two other contemporary hunter-gatherer populations, the Agta of the Philippines and the Mbendjele BaYaka of the Republic of Congo, using genome-wide single nucleotide polymorphism data and kinship analysis. We find evidence for heightened levels of homozygosity and a general preference towards genetically dissimilar mates among these populations, despite wide variation in population structure and connectivity. In addition, our simulations also show that the Raute's patrilineal clan-based exogamic marriage system reduces expected offspring inbreeding more effectively than random mating or close-kin avoidance. These results suggest that the Raute's cultural rules may be a compensatory strategy for their demographic isolation. Our findings highlight the importance of social structure in shaping genetic outcomes and demonstrate how cultural practices can evolve as adaptive responses to the constraints of small population size.