Human Y chromosome sequences from Q Haplogroup reveal a South American settlement pre-18,000 years ago and a profound genomic impact during the Younger Dryas

Abstract

The settlement of the Americas has been the focus of incessant debate for more than 100 years, and open questions regarding the timing and spatial patterns of colonization still remain today. Phylogenetic studies with complete human Y chromosome sequences are used as a highly informative tool to investigate the history of human populations in a given time frame. To study the phylogenetic relationships of Native American lineages and infer the settlement history of the Americas, we analyzed Y chromosome Q Haplogroup, which is a Pan-American haplogroup and represents practically all Native American lineages in Mesoamerica and South America. We built a phylogenetic tree for Q Haplogroup based on 102 whole Y chromosome sequences, of which 13 new Argentine sequences were provided by our group. Moreover, 1,072 new single nucleotide polymorphisms (SNPs) that contribute to its resolution and diversity were identified. Q-M848 is known to be the most frequent autochthonous sub-haplogroup of the Americas. The present is the first genomic study of Q Haplogroup in which current knowledge on Q-M848 sub-lineages is contrasted with the historical, archaeological and linguistic data available. The divergence times, spatial structure and the SNPs found here as novel for Q-Z780, a less frequent sub-haplogroup autochthonous of the Americas, provide genetic support for a South American settlement before 18,000 years ago. We analyzed how environmental events that occurred during the Younger Dryas period may have affected Native American lineages, and found that this event may have caused a substantial loss of lineages. This could explain the current low frequency of Q-Z780 (also perhaps of Q-F4674, a third possible sub-haplogroup autochthonous of the Americas). These environmental events could have acted as a driving force for expansion and diversification of the Q-M848 sub-lineages, which show a spatial structure that developed during the Younger Dryas period.

New Y-SNPs in QM3 indigenous populations of Colombia

“…The CO12 sublineage was one of the oldest SNP type variants described by Rivera et al [21] and CO27 one of the oldest new variants of the present research, both from the sequencing of two Y chromosomes belonging to the Eastern Tucanos of the Colombian Amazon. These two sublineages correspond to two of the sites reported by Paz-Sepulveda et al [2] for the new sublineage MPB016. They are variants of great phylogenetic interest, since they are widely distributed throughout the Amazon region and in some samples from the Andean region typified in this study, a total of 153 samples out of 231.…”

“…The American continent was one of the last areas to be colonized by humans. Its settlement has been the subject of extensive debate at the level of evolutionary studies for more than 100 years [1][2][3][4]. A large number of genetic-population studies have been carried out on Amerindians, revealing some aspects of evolution and the various migrations that have taken place throughout history and prehistory [5][6][7][8][9][10][11][12][13][14][15][16][17][18][19][20][21].…”

“…However, questions related to the time of arrival, number of migrations, and migration patterns across the continent continue to be debated in the scientific community. The most widely accepted scenario to date proposes settlement beginning between about 18.000 to 15.000 years ago (kya) [1,2,[22][23][24][25], and entry into the southern cone shortly after [2,22,26].…”

SNPtotree—Resolving the Phylogeny of SNPs on Non-Recombining DNA

“…To date, there is no straightforward software available that sorts variants of nonrecombining DNA into their hierarchical order. When the phylogeny of linked SNPs is of interest, maximum likelihood calculations and manual sorting of SNPs are often performed [44,45]. However, high numbers of missing data can complicate the data analysis.…”

Tales from the end of the world: three decades of paleogenetic research in Patagonia

“…The only exception is a Late Holocene individual from Mitre Peninsula with Q-Z780 [76], which is a low frequency clade spread across South America and Mexico. This lineage has a coalescent time slightly older than Q-M3 (19.3ky BP versus 15.4ky BP) and has been proposed as genetic evidence of an older peopling of South America [77]. The potential of whole Y-chromosome analysis for a fine scale population dynamic has yet to be exploited.…”