The peopling of South America and the trans-Andean gene flow of the first settlers

Abstract

Genetic and archaeological data indicate that the initial Paleoindian settlers of South America followed two entry routes separated by the Andes and the Amazon rainforest. The interactions between these paths and their impact on the peopling of South America remain unclear. Analysis of genetic variation in the Peruvian Andes and regions located south of the Amazon River might provide clues on this issue. We analyzed mitochondrial DNA variation at different Andean locations and >360,000 autosomal SNPs from 28 Native American ethnic groups to evaluate different trans-Andean demographic scenarios. Our data reveal that the Peruvian Altiplano was an important enclave for early Paleoindian expansions and point to a genetic continuity in the Andes until recent times, which was only marginally affected by gene flow from the Amazonian lowlands. Genomic variation shows a good fit with the archaeological evidence, indicating that the genetic interactions between the descendants of the settlers that followed the Pacific and Atlantic routes were extremely limited.

A Paleogenomic Reconstruction of the Deep Population History of the Andes

“…We detect significantly more allele sharing of SouthPeruHighlands , SouthPeruCoast , CentralPeruCoast , and Titicaca Basin groups to Argentina_LagunaChica_1600BP relative to Argentina_LagunaChica_6800BP . This likely reflects gene flow between the Pampas and the Central Andes, consistent with previous claims ( Gómez-Carballa et al., 2018 , Muzzio et al., 2018 ). Using qpAdm, we fit Argentina_LagunaChica_1600BP as a mixture of 80% ± 12% ancestry related to Argentina_LagunaChica_6800BP and 20% ± 12% ancestry related to a representative Andes group giving the lowest standard error ( CentralPeruCoast ).…”

“…This roughly corresponds to the onset of the Late Preceramic Period (∼5,000 BP), when increasing economic, political, and religious differentiation between Central Andean regions becomes evident archaeologically, and when levels of mobility decreased at the Coast and slightly later in the Highlands and Altiplano ( Aldenfelder, 2008 , Pozorski and Pozorski, 2008 , Quilter, 2013 ). This occurred in tandem with increasing reliance on plant cultivation ( Arriaza et al., 2008 , Dillehay et al., 2007 , Hastorf, 2008 , Quilter, 2013 , Rick, 1988 , Rivera, 1995 ), which has been hypothesized to have contributed to rapid population growth in some regions ( Gayo et al., 2015 , Goldberg et al., 2016 , Gómez-Carballa et al., 2018 ). A greater reliance on plant cultivation documented in the archaeological record from this period could plausibly contribute to increased sedentism and reduced gene flow, potentially contributing to the North-South substructure we observe beginning to develop by this period.…”

“…Archaeological research in the Central Andes is extraordinarily rich ( Silverman and Isbell, 2008 ), but ancient DNA (aDNA) studies to date have been limited, so there has been little information about demographic change over time. Studies of uniparental DNA indicated evidence for a degree of genetic homogeneity of the Central and Southern Highlands, especially for the Y chromosome ( Barbieri et al., 2014 , Gómez-Carballa et al., 2018 , Harris et al., 2018 , Sandoval et al., 2013 , Sandoval et al., 2016 ), while studies with aDNA suggested substantial continuity as well as gene flow between the Coast and the Highlands ( Baca et al., 2012 , Fehren-Schmitz et al., 2014 , Fehren-Schmitz et al., 2017 , Llamas et al., 2016 , Russo et al., 2018 , Valverde et al., 2016 ). High coverage genome-wide ancient DNA data from South America from the time before European contact began to be published in 2018, with most data from mid- to early-Holocene hunter-gatherers (in the Central and South-Central Andes, 23 individuals were reported) ( Lindo et al., 2018 , Moreno-Mayar et al., 2018b , Posth et al., 2018 ).…”

Fine-scale genomic analyses of admixed individuals reveal unrecognized genetic ancestry components in Argentina

“…This supports the hypothesis of many migrations back to Central America different from the Andeans ancestors [39]. It has also been described that the genetic interactions between the peopling routes on both sides of the Andes were limited [39, 40].…”

PIMA: A population informative multiplex for the Americas

“…The peopling of the Americas happened from north to south, beginning 15-18 KYA [4]. The initial source of migration was Beringia in the far northeast of Siberia, where ancestors of the first migrant groups into NW America were likely isolated from their own Siberian ancestral populations before entering the continent [5]. In the 15th Century, the arrival of European colonizers and the African slave trade led to the introduction and subsequent expansion of new population admixture contributors into the Americas.…”