Enclaves of genetic diversity resisted Inca impacts on population history

Abstract

The Inca Empire is claimed to have driven massive population movements in western South America, and to have spread Quechua, the most widely-spoken language family of the indigenous Americas. A test-case is the Chachapoyas region of northern Peru, reported as a focal point of Inca population displacements. Chachapoyas also spans the environmental, cultural and demographic divides between Amazonia and the Andes, and stands along the lowest-altitude corridor from the rainforest to the Pacific coast. Following a sampling strategy informed by linguistic data, we collected 119 samples, analysed for full mtDNA genomes and Y-chromosome STRs. We report a high indigenous component, which stands apart from the network of intense genetic exchange in the core central zone of Andean civilization, and is also distinct from neighbouring populations. This unique genetic profile challenges the routine assumption of large-scale population relocations by the Incas. Furthermore, speakers of Chachapoyas Quechua are found to share no particular genetic similarity or gene-flow with Quechua speakers elsewhere, suggesting that here the language spread primarily by cultural diffusion, not migration. Our results demonstrate how population genetics, when fully guided by the archaeological, historical and linguistic records, can inform multiple disciplines within anthropology.

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

“…Overall, this new genomic evidence points towards a demographic connection behind the diffusion of Quechua varieties not only in the southern highlands, as previously attested 31 , but also in the north, across ecogeographic domains. The genetic signature reconstructed can inform the historical reconstructions for the diffusion of this language family.…”

“…Previous results based on Y chromosome haplotype sharing did find a similar pattern of connections between lowland Quechua-speakers in Ecuador and north-eastern Peru, but did not find such long-distance connections with the Central and Southern Andes 31,32 . These different results can possibly be justified by sex-biased gene-flow (i.e.…”

“…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.…”

“…The diffusion of major language families is traditionally associated with demographic movements 25,26 : this association was validated with genetic data for some of the largest language families of the world 27-29 , but no strong candidates are found in South America, where genetic diversity overall does not correlated with linguistic diversity 30 . Previous genetic work 31,32 evaluated alternative models of cultural vs. demographic diffusion for Quechua, the most spoken language family of the Andes, present also in small pockets of the Amazonian lowlands 33 . These studies, based on uniparental markers, revealed intense contact routes in the southern highlands, but not in the northern regions nor in neighboring Amazonia.…”

Cultural Innovations Influence Patterns of Genetic Diversity in Northwestern Amazonia

“…The mtDNA comparative dataset contained the same number of sequences by country as the NRY dataset (Argentina=12, Mexico=15, and Peru=25, Colombia=25). Five dataset replicates were generated by randomly sampling mtDNA sequences from a big collection of sequences from the literature (Achilli et al 2013;Arias et al 2018;Barbieri et al 2017;Bodner et al 2012;Cardoso et al 2012;de Saint Pierre et al 2012;Fagundes et al 2008;Gomez-Carballa et al 2012;Kumar et al 2011;Lee and Merriwether 2015;Lippold et al 2014;Mizuno et al 2014;Perego et al 2009;Perego et al 2010;Tamm et al 2007). We estimated the nucleotide diversity and performed an AMOVA considering two hierarchical levels, namely differences among populations and within populations.…”