The Paleo-Indian Entry into South America According to Mitogenomes

Abstract

Recent and compelling archaeological evidence attests to human presence ∼14.5 ka at multiple sites in South America and a very early exploitation of extreme high-altitude Andean environments. Considering that, according to genetic evidence, human entry into North America from Beringia most likely occurred ∼16 ka, these archeological findings would imply an extremely rapid spread along the double continent. To shed light on this issue from a genetic perspective, we first completely sequenced 217 novel modern mitogenomes of Native American ancestry from the northwestern area of South America (Ecuador and Peru); we then evaluated them phylogenetically together with other available mitogenomes (430 samples, both modern and ancient) from the same geographic area and, finally, with all closely related mitogenomes from the entire double continent. We detected a large number (N = 48) of novel subhaplogroups, often branching into further subclades, belonging to two classes: those that arose in South America early after its peopling and those that instead originated in North or Central America and reached South America with the first settlers. Coalescence age estimates for these subhaplogroups provide time boundaries indicating that early Paleo-Indians probably moved from North America to the area corresponding to modern Ecuador and Peru over the short time frame of ∼1.5 ka comprised between 16.0 and 14.6 ka.

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

“…Here, Paleoindians split-one subset followed the Pacific and colonized the Andean region, and another one expanded along the Atlantic . The rapid coastal migration movements played a major role in the colonization of the whole South American subcontinent, and genetic age estimates fit well with the archaeological evidence of human presence in the Southern Cone at the Monte Verde site (Chile) at least ∼14.5 kya (Dillehay 1989;Dillehay et al 2015;Brandini et al 2018).…”

“…B2b is defined by the transition G6755A and probably arose ∼16.6 kya (15.6-17.5 kya), a little earlier than B2y. Phylogeographic patterns of B2b mtDNAs suggest that this clade most likely arose in the north of Mesoamerica (Brandini et al 2018). The greatest proportion of mitogenomes are from South America (93.3%), mostly from the Andean region, especially from Peru (46.6%) ( Fig.…”

“…4B), representing 100% of the B2 haplotypes found on this island (The 1000 Genomes Project Consortium 2012; Vilar et al 2014). Outside Puerto Rico, there are only members of B2b3a1a on the northern coast of Venezuela (probably a crossing point to the Caribbean from Brazil) (Castro de Guerra et al 2012;Brandini et al 2018), in Cuba (Mendizabal et al 2008), and the Dominican Republic (Tajima et al 2004). The two mitogenomes and one CR sequence sampled in the US (Fig.…”

“…The analysis of geographically restricted sub-haplogroups added further support to the scenario of an initial split of the first Paleoindian settlers of South America into two main groups whose expansion routes followed different paths-along the Pacific and the Atlantic coastlines-and highlighted the possibility of trans-Andean events of gene flow at different latitudes (Bodner et al 2012). Finally, there is recent mtDNA evidence that present-day Peru and Ecuador were first populated by Paleoindian settlers of North American ancestry in the short time frame of 16.0-14.6 kya (Brandini et al 2018). Despite this recent insight, the colonization process and subsequent population movements that led to the peopling of South America remain poorly known.…”

Measuring the impact of European colonization on Native American populations in Southern Brazil and Uruguay: Evidence from mtDNA

“…The θ value can be used to estimate N ef , the effective female population size, by solving the equation θ = 2× N ef × μ , where μ is the mutation rate per site per generation. In this case, we used a generation time of 25 years (Brandini et al, ; Fagundes, Kanitz, & Bonatto, ) and the sex ratio adopted was 1.0 (ie, the same number of males and females). Thus, doubling N ef resulted in the estimates of N e used as prior information in the ABC analysis (see below).…”