Ancient DNA reveals temporal population structure within the South‐Central Andes area

Abstract

Population structure in South America has been mostly studied on current native groups, mainly showing a west-to-east differentiation between the Andean and lowland regions. Here we demonstrated that genetic population differentiation preceded the European contact and might have been more complex than thought, being found within the South-central Andes Area. Moreover, divergence among temporally different populations might be reflecting socio-political changes occurred in the evermore complex pre-Hispanic Andean societies.

A Paleogenomic Reconstruction of the Deep Population History of the Andes

“…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 ).…”

Ancient DNA analysis reveals temporal and geographical patterns of mitochondrial diversity in pre‐Hispanic populations from Central Argentina

“…Another question we introduced was whether the horticultural groups described by the early colonizers' chronicles replaced the ancient hunter‐gatherer populations or if, instead, there was a biological continuity over time accompanied by a local cultural development. The high incidence of Hg B in Sierras in the post 1200 yBP subsample (44%, Table 2) was interpreted in a previous work (Nores et al, 2011) as a signal of gene flow into the Sierras region from populations with high incidence of Hg B, such as the South‐Central Andean region, including modern day Perú, Northern Chile and Northwestern Argentina (Russo, Mendisco, et al, 2018), or the Gran Chaco region (Demarchi et al, 2001). However, our analysis of mtDNA haplogroups and HVR‐I sequences does not support this hypothesis, since no genetic structure was observed between temporal subsets.…”

“…The HVR‐I sequences from the Plains and Sierras samples were compared with other ancient groups from Argentina to investigate their affinities (references in Supplementary Table 3). Sequences from different archeological sites and chronologies were grouped together based on their geographical proximity (Figure 1), except for the Los Amarillos site, located in Quebrada de Humahuaca, which was considered as a separate population given its relatively large sample size and its unusually high incidence of haplogroup (Hg) A2 (Mendisco et al, 2011; Russo, Mendisco, et al, 2018). The ancient data were also compared with those of contemporary individuals with Native American lineages from small, semi‐rural populations of Central Argentina (García et al, 2018; Pauro et al, 2013) to check for population continuity up to the present (Supplementary Table 3).…”

“…There is a growing body of research on the genetic profile of ancient American populations, which provides a temporal context for the study of the peopling of the continent (de la Fuente et al, 2015; Lindo et al, 2018; Llamas et al, 2016; Moraga et al, 2010; Moreno‐Mayar et al, 2018; Nakatsuka, Lazaridis, et al, 2020; Posth et al, 2018). Besides, several aDNA studies of pre‐Hispanic populations from Argentina have been published, covering most of the territory (Arencibia et al, 2019; Carnese et al, 2010; Crespo et al, 2016, 2018, 2020; García et al, 2021; Mendisco et al, 2014; Motti et al, 2015; Nakatsuka, Luisi, et al, 2020; Nores & Demarchi, 2011; Nores et al, 2011, 2017; Parolin et al, 2020; Postillone et al, 2017, 2020; Roca‐Rada et al, 2021; Russo, Dejean, et al, 2018; Russo et al, 2017; Russo, Mendisco, et al, 2018; Tavella et al, 2020).…”

New Evidence of Ancient Mitochondrial DNA of the Southern Andes (Calchaquí Valleys, Northwest Argentina, 3,600–1,900 Years before Present)

“…For the following Late or Regional Developments Period (RDP) (ca. AD 1000-1450), seven studies were carried out on samples from different regions of NWA: Quebrada de Humahuaca (Mendisco et al 2011(Mendisco et al , 2014(Mendisco et al , 2018Russo et al 2016Russo et al , 2018aRusso et al , 2018b, the Northern Calchaquí Valleys (Mendisco et al 2014), and the Puna highlands of Jujuy Province (Mendisco et al 2014;Postillone et al 2017). For the subsequent Inca Period (ca.…”