Cultural Innovations Influence Patterns of Genetic Diversity in Northwestern Amazonia

Abstract

Human populations often exhibit contrasting patterns of genetic diversity in the mtDNA and the nonrecombining portion of the Y-chromosome (NRY), which reflect sex-specific cultural behaviors and population histories. Here, we sequenced 2.3 Mb of the NRY from 284 individuals representing more than 30 Native American groups from Northwestern Amazonia (NWA) and compared these data to previously generated mtDNA genomes from the same groups, to investigate the impact of cultural practices on genetic diversity and gain new insights about NWA population history. Relevant cultural practices in NWA include postmarital residential rules and linguistic exogamy, a marital practice in which men are required to marry women speaking a different language. We identified 2,969 SNPs in the NRY sequences, only 925 of which were previously described. The NRY and mtDNA data showed different sex-specific demographic histories: female effective population size has been larger than that of males through time, which might reflect larger variance in male reproductive success. Both markers show an increase in lineage diversification beginning ∼5,000 years ago, which may reflect the intensification of agriculture, technological innovations, and the expansion of regional trade networks documented in the archaeological evidence. Furthermore, we find similar excesses of NRY versus mtDNA between-population divergence at both the local and continental scale, suggesting long-term stability of female versus male migration. We also find evidence of the impact of sociocultural practices on diversity patterns. Finally, our study highlights the importance of analyzing high-resolution mtDNA and NRY sequences to reconstruct demographic history, since this can differ considerably between sexes.

The paternal and maternal genetic history of Vietnamese populations

“…Second, there has been limited contact between some groups, leading to some haplotype sharing. The levels of genetic differentiation among groups of 10% based on mtDNA and 23% based on the MSY (Table 1) are similar to what was found previously for isolated populations from Northwestern Amazonia (13% mtDNA and 27% MSY; (28)) and higher than those found for Thai populations (8.5% mtDNA and 11% MSY; (42)). We also found particularly low levels of diversity in some specific groups, like the Mang and Sila (Figure 2, Supplemental Material Table S5).…”

“…We enriched for ~2.3 million bases of the male-specific Y-chromosome (MSY) from the same libraries used for mtDNA capture-enrichment (27). The MSY sequence processing pipeline is described elsewhere (28). To increase the quality of the data set, we removed 41 positions with more than 16.6% missing information across the Vietnam MSY sequences and then imputed the remaining missing genotypes with BEAGLE 4.0 (ref.…”

Contrasting paternal and maternal genetic histories of Thai and Lao populations

“…Moreover, while the expected difference between patrilocal and matrilocal groups holds in some regions (Oota et al 2001;Besaggio et al 2007), in other regions patterns of mtDNA and MSY variation do not conform to expectations (Kumar et al 2006;Arias et al 2018), which is to be expected if other factors are also influencing patterns of genetic variation (Wilkins and Marlowe 2006).…”

The genomic landscape of western South America: Andes, Amazonia and Pacific Coast

“…Y chromosome haplogroup assignment was performed with the yHaplo software 76 . Data was cross-checked with available published mtDNA and Y chromosome data for the same individuals, assigned via direct genotyping/sequencing in previous studies 12,31,53 : the SNPs available allowed the correct macro haplogroup to be detected in 97% of cases.…”