Reconstructing the Deep Population History of Central and South America

Abstract

SummaryWe report genome-wide ancient DNA from 49 individuals forming four parallel time transects in Belize, Brazil, the Central Andes, and the Southern Cone, each dating to at least ∼9,000 years ago. The common ancestral population radiated rapidly from just one of the two early branches that contributed to Native Americans today. We document two previously unappreciated streams of gene flow between North and South America. One affected the Central Andes by ∼4,200 years ago, while the other explains an affinity between the oldest North American genome associated with the Clovis culture and the oldest Central and South Americans from Chile, Brazil, and Belize. However, this was not the primary source for later South Americans, as the other ancient individuals derive from lineages without specific affinity to the Clovis-associated genome, suggesting a population replacement that began at least 9,000 years ago and was followed by substantial population continuity in multiple regions.

Removing reference bias and improving indel calling in ancient DNA data analysis by mapping to a sequence variation graph

“…To evaluate whether the improvements seen in the previous section mitigate reference bias in real ancient DNA data, we selected 34 previously published ancient DNA samples (Table 1), including Iron Age, Roman, and Anglo-Saxon period samples shotgun sequenced to low-medium coverage [20,21], high-coverage Yamnaya and Botai culture individuals [22], and target captured samples from South America [23]. These are representative of the different types of data produced in the field of aDNA, as they are of variable genomic coverage, they were generated as part of SNP array target capture or whole-genome shotgun sequencing experiments, and were subject to different enzymatic treatments.…”

“…Adapter trimming was done with AdapterRemoval [29] for [22] and [30] for [20]. Unaligned fastq data from the other two datasets [21,23] were already provided with trimmed adapters. We aligned trimmed reads to the human linear reference genome (hs37d5) using bwa aln [25] with parameters -l1024 -n 0.02 [31], keeping bases with quality above or equal to 15.…”

First analysis of mitochondrial lineages from the eastern Pampa–Patagonia transition during the final late Holocene

“…On the other hand, the D1 haplotypes network (Figure ) shows that D1 and D1g are the most shared, frequent, and well‐distributed haplogroups in southern South America, mainly among extant and pre‐Hispanic individuals in Central‐Northern Patagonia. Interestingly, a D1g lineage with nodal mutations was described at the Arroyo Seco 2 archaeological site (Posth et al, ), which suggests a certain continuity of this subhaplogroup in the region from about 7,700 YBP to the present. Particularly, the D1g4 lineage, characterized by transition 16290T and identified in one of the Paso Alsina 1 individuals, is shared with an extant individual from Central‐Southern Patagonia (de Saint Pierre, Bravi, et al, ; de Saint Pierre, Gandini, et al, ).…”

“…Genetic analysis of contemporary and past human groups has become increasingly important to improve understanding of the evolutionary history of human settlement in southern South America (Arencibia et al, ; Bobillo et al, ; Crespo, Favier Dubois, Russo, Lanata, & Dejean, ; de la Fuente et al, , ; de Saint Pierre et al, , ; García‐Bour et al, ; Llamas et al, ; Moraga et al, ; Motti et al, ; Parolin et al, ; Perez et al, ; Posth et al, ). The most widely used genetic marker is mitochondrial DNA (mtDNA), which indicates the maternal lineage of individuals.…”

“…YBP) (Borrero, 2016;Politis, 2014;Politis, Gutiérrez, Rafuse, & Blasi, 2016;Steele & Politis, 2009). Nevertheless, little is known about the molecular diversity and microevolutionary processes that took place in Pampa (e.g., Llamas et al, 2016;Posth et al, 2018) and Patagonia (e.g., Arencibia et al, 2019;Crespo, Favier Dubois, et al, 2017;Crespo, Russo, Hajduk, Lanata, & Dejean, 2017;Parolin et al, 2019).…”