Overview of the Americas’ First Peopling from a Patrilineal Perspective: New Evidence from the Southern Continent

Abstract

Uniparental genetic systems are unique sex indicators and complement the study of autosomal diversity by providing landmarks of human migrations that repeatedly shaped the structure of extant populations. Our knowledge of the variation of the male-specific region of the Y chromosome in Native Americans is still rather scarce and scattered, but by merging sequence information from modern and ancient individuals, we here provide a comprehensive and updated phylogeny of the distinctive Native American branches of haplogroups C and Q. Our analyses confirm C-MPB373, C-P39, Q-Z780, Q-M848, and Q-Y4276 as the main founding haplogroups and identify traces of unsuccessful (pre-Q-F1096) or extinct (C-L1373*, Q-YP4010*) Y-chromosome lineages, indicating that haplogroup diversity of the founder populations that first entered the Americas was greater than that observed in the Indigenous component of modern populations. In addition, through a diachronic and phylogeographic dissection of newly identified Q-M848 branches, we provide the first Y-chromosome insights into the early peopling of the South American hinterland (Q-BY104773 and Q-BY15730) and on overlying inland migrations (Q-BY139813).

Indigenous peoples in eastern Brazil: insights from 19th century genomes and metagenomes

“…The Y-chromosome and mitochondrial haplogroups of the individuals studied here (Table 1) are characteristic of Indigenous American populations (Kivisild 2017; Alves-Silva et al 2000; Ramallo et al 2013; Colombo et al 2022). The Y-chromosome haplogroups of six out of eleven “Botocudo” males could be typed and were determined to be Q1a2a1-L54 and Q1a2a1a1-M3 (Table 1).…”

New Y-SNPs in QM3 indigenous populations of Colombia

“…The tree version proposed by [21,41] was considered as a base, to which the new variants observed in the present study were added. SNPs and subhaplogroups were considered valid if they fulfilled the ISOGG inclusion criteria [46].…”

“…However, the phylogenetic position of both mutations in the tree of the Y-chromosome haplogroup Q is controversial because the M3 mutation may have originated before the first human settlement in the Americas [37]. Other Q lineages have also been described in the Americas at lower frequencies, such as Q-Z780, which is found throughout the continent but at lower frequencies than Q-M3 [41].…”

“…However, the genomic era and advances in DNA sequencing technologies have made it possible to carry out large-scale analyses, obtaining almost complete sequences of the Y chromosome, which has allowed us to identify some Y SNPs defining Q-M3 sublineages. One of great importance has been described, present at high frequencies and widely distributed throughout the American continent, Q-M848 [41]. Despite the existence of other Y-SNP reports related to new Q-M3 sublineages, their resolution is still weak to explore the history and demography of these groups, mainly due to the low frequency in the number of samples, therefore, it is still premature to make population genetic inferences from these new sublineages [32,42].…”

A critical assessment of claims that human footprints in the Lake Otero basin, New Mexico date to the Last Glacial Maximum

“…Many of these data are derived from age estimates provided by paleogenetics, with molecular clocks indicating that initial occupation of the Americas south of the ice sheets occurred sometime after ca. 20,000 yr BP (e.g., Raghavan et al, 2015; Llamas et al, 2016; Moreno-Mayar et al, 2018; Pinotti et al, 2019; Roca-Rada et al, 2021; Willerslev and Meltzer, 2021; Colombo et al, 2022). If the Lake Otero footprint ages are valid, then as Pigati et al (2022a, p. 2) suggested, “researchers in archaeology and allied fields may need to reexamine existing hypotheses and the underlying data related to the peopling of the Americas in light of these discoveries.” It is certainly possible the Ruppia ages from a single site in a New Mexico lake basin are valid and that age estimates from a variety of other fields are invalid, but we think the Ruppia 14 C ages should be confirmed with results from other dating methods.…”