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. 2013 Aug 21;8(8):e71390.
doi: 10.1371/journal.pone.0071390. eCollection 2013.

The First Peopling of South America: New Evidence From Y-chromosome Haplogroup Q

Free PMC article

The First Peopling of South America: New Evidence From Y-chromosome Haplogroup Q

Vincenza Battaglia et al. PLoS One. .
Free PMC article


Recent progress in the phylogenetic resolution of the Y-chromosome phylogeny permits the male demographic dynamics and migratory events that occurred in Central and Southern America after the initial human spread into the Americas to be investigated at the regional level. To delve further into this issue, we examined more than 400 Native American Y chromosomes (collected in the region ranging from Mexico to South America) belonging to haplogroup Q - virtually the only branch of the Y phylogeny observed in modern-day Amerindians of Central and South America - together with 27 from Mongolia and Kamchatka. Two main founding lineages, Q1a3a1a-M3 and Q1a3a1-L54(xM3), were detected along with novel sub-clades of younger age and more restricted geographic distributions. The first was also observed in Far East Asia while no Q1a3a1-L54(xM3) Y chromosome was found in Asia except the southern Siberian-specific sub-clade Q1a3a1c-L330. Our data not only confirm a southern Siberian origin of ancestral populations that gave rise to Paleo-Indians and the differentiation of both Native American Q founding lineages in Beringia, but support their concomitant arrival in Mesoamerica, where Mexico acted as recipient for the first wave of migration, followed by a rapid southward migration, along the Pacific coast, into the Andean region. Although Q1a3a1a-M3 and Q1a3a1-L54(xM3) display overlapping general distributions, they show different patterns of evolution in the Mexican plateau and the Andean area, which can be explained by local differentiations due to demographic events triggered by the introduction of agriculture and associated with the flourishing of the Great Empires.

Conflict of interest statement

Competing Interests: SRW and NM are employed by a commercial company: This does not alter the authors' adherence to all the PLoS ONE policies on sharing data and materials.


Figure 1
Figure 1. Phylogenetic tree of Y-chromosome haplogroup Q.
Haplogroup nomenclature and frequencies (%) of haplogroup branches in the analyzed populations (new markers are in bold). The haplogroup labeling is in agreement with the YCC conventions and recent updates , . *Paragroups: Y chromosomes not defined by any phylogenetic downstream-reported and -examined mutation.
Figure 2
Figure 2. PCoA plots.
Analyses were performed on 433 Native American haplogroup Q Y chromosomes and based on pairwise, individual-by-individual genetic distances generated from 33 loci Y-STR haplotypes (Table S2) represented in their (A) geographic (Andes: Bolivia, Chile, Colombia, Ecuador, Peru; Central America: Costa Rica, El Salvador, Guatemala, Nicaragua, Panama; South East America: Argentina, Brazil, Paraguay, Uruguay) and (B) sub-haplogroup Q contexts. Ancient DNA (aDNA) matching haplotypes are indicated by arrows. Three separated (Central American, Mexican and Andean) clusters are indicated by ovals.
Figure 3
Figure 3. Network of 7 loci Y-STR haplotypes belonging to Q sub-haplogroups.
Network analysis were performed on Native American [Alaskan, Canadian, North American, Caribbean , Central American (from Costa Rica, El Salvador, Guatemala, Nicaragua, Panama), Mexican, Andean (from Bolivia, Chile, Colombia, Ecuador, Peru), South Eastern American (from Argentina, Brazil, Paraguay, Uruguay) (present study)] and Asian [Northern and Southern Altaians , Mongolian and Far Eastern Asian (from Kamchatka, Chukotka and Sea of Okhotsk coast) , ; present study)] samples (Table S4). Light blue loop is referred to the unusual DYS391-6 repeat allele. Arrows indicate the 7 loci haplotypes matching aDNA . Within the single network, circles and colored sectors are proportional to the number of subjects, with the smallest circle equal to one Y chromosome; connecting lines are proportional to the number of mutations.

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Grant support

This research received support from the Sorenson Molecular Genealogy Foundation (to UAP, NM, JEG-P and SRW), the Italian Ministry of the University: Progetti di Ricerca Interesse Nazionale 2009 and 2012 (to AA, AT and OS) and FIRB-Futuro in Ricerca (to AA). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.