Large scale mitochondrial sequencing in Mexican Americans suggests a reappraisal of Native American origins

Abstract

BackgroundThe Asian origin of Native Americans is largely accepted. However uncertainties persist regarding the source population(s) within Asia, the divergence and arrival time(s) of the founder groups, the number of expansion events, and migration routes into the New World. mtDNA data, presented over the past two decades, have been used to suggest a single-migration model for which the Beringian land mass plays an important role.ResultsIn our analysis of 568 mitochondrial genomes, the coalescent age estimates of shared roots between Native American and Siberian-Asian lineages, calculated using two different mutation rates, are A4 (27.5 ± 6.8 kya/22.7 ± 7.4 kya), C1 (21.4 ± 2.7 kya/16.4 ± 1.5 kya), C4 (21.0 ± 4.6 kya/20.0 ± 6.4 kya), and D4e1 (24.1 ± 9.0 kya/17.9 ± 10.0 kya). The coalescent age estimates of pan-American haplogroups calculated using the same two mutation rates (A2:19.5 ± 1.3 kya/16.1 ± 1.5 kya, B2:20.8 ± 2.0 kya/18.1 ± 2.4 kya, C1:21.4 ± 2.7 kya/16.4 ± 1.5 kya and D1:17.2 ± 2.0 kya/14.9 ± 2.2 kya) and estimates of population expansions within America (~21-16 kya), support the pre-Clovis occupation of the New World. The phylogeography of sublineages within American haplogroups A2, B2, D1 and the C1b, C1c andC1d subhaplogroups of C1 are complex and largely specific to geographical North, Central and South America. However some sub-branches (B2b, C1b, C1c, C1d and D1f) already existed in American founder haplogroups before expansion into the America.ConclusionsOur results suggest that Native American founders diverged from their Siberian-Asian progenitors sometime during the last glacial maximum (LGM) and expanded into America soon after the LGM peak (~20-16 kya). The phylogeography of haplogroup C1 suggest that this American founder haplogroup differentiated in Siberia-Asia. The situation is less clear for haplogroup B2, however haplogroups A2 and D1 may have differentiated soon after the Native American founders divergence. A moderate population bottle neck in American founder populations just before the expansion most plausibly resulted in few founder types in America. The similar estimates of the diversity indices and Bayesian skyline analysis in North America, Central America and South America suggest almost simultaneous (~ 2.0 ky from South to North America) colonization of these geographical regions with rapid population expansion differentiating into more or less regional branches across the pan-American haplogroups.

Genetic Affiliation of Pre-Hispanic and Contemporary Mayas through Maternal Linage

“…All mtDNA haplotypes were in lineages A (2.6%), A2 (44.73%), A2v (13.16%), C (2.6%), C1 (15.8%), C1b14 (15.8%), and D (5.3%; Table 2). One sequence was classified in haplogroup A based on the presence of a C>T transition at position 16223 and a G>A transition at position 16319 (G16319A) (Torroni et al 1993); 17 sequences were classified as haplogroup A2 base on the presence of C>T transitions at positions 16111 (C16111T), 16223 (C16223T), and 16290 (C16290T), a G>A transition at position 16319 (G16319A), and a T>C transition at position 16362 (T16362C) (Torroni et al 1993;Starikovskaya et al 1998); and five sequences were classified as haplogroup A2v based on the presence of the transitions observed in haplogroup A2 and a T>C transition at position 16239 (C16223T) (Kumar et al 2011). No haplogroup B sequences were found in this pre-Hispanic group.…”

“…Finally, to classify the mtDNA haplotypes into haplogroups, we adopted the nomenclature system of Starikovskaya et al (2005), Achilli et al (2008), Derenko et al (2010), Gómez-Carballa et al (2015), Kumar et al (2011), andRieux et al (2014). All detected polymorphic positions were confirmed with Mitomaster (http://www.mitomap.org/bin/ view.pl/MITOMASTER/WebHome).…”

“…com/sharenet_rn.htm), accounting for different rates of transitions and transversions for all mutations and setting the parameter to zero to restrict the choices of feasible links in the final network. Neighbor joining tree clustering was constructed according to Kumar et al (2011) using MEGA, version 6 (Tamura et al 2013). …”

Primer genoma mitocondrial en restos humanos de la Costa de Santa Cruz, Argentina

“…El avance en las técnicas de análisis molecular que ha tenido lugar en los últimos años ha permitido superar la clásica distinción de cinco haplogrupos (hgs) nativos de América (A, B, C, D y X), identificándose actualmente por lo menos 13 subhaplogrupos que ya estaban diferenciados al momento de ingreso al continente americano (Tamm et al 2007;Malhi et al 2010;Perego et al 2010;Kumar et al 2011), algunos de los cuales presentan patrones de distribución que darían cuenta de distintas rutas de poblamiento, como el caso de D4h3a que se distribuye casi exclusivamente en el oeste del continente, desde Alaska hasta Tierra del Fuego y se asocia con un poblamiento por costa pacífica (Perego et al 2009). Asimismo, al interior de cada subhaplogrupo se está avanzando en la definición de clados con distribuciones geográficas acotadas, que se habrían diferenciado localmente (Gayà-Vidal et al 2011;Bodner et al 2012;de Saint Pierre et al 2012a,b;García et al 2012;Motti, 2012;Taboada-Echalar et al 2013).…”

Mitochondrial genome diversity at the Bering Strait area highlights prehistoric human migrations from Siberia to northern North America

“…7 The last inhabitants of former Beringia, reflected genetically in the Yukaghir, Chukchi, Eskimo-Aleuts, Na-Dene, and Northwestern North American Indians, have been a focus of extensive comparisons between complete mtDNA sequences from Siberia and from North America. As a result, the Siberian affinities of major Native American mtDNA haploclusters (A-D), initially detected by comparing a few single-nucleotide polymorphisms of similar haplotypes from Eurasia and the Americas, [7][8][9][10][11][12][13][14] have been revised and extended. It has become evident that the range of distinct lineages confined to the entire Eskimo Arctic is a subset of haplogroups A2a, A2b, D2a, and D4b1a2a1, though each of their evolutionary histories is far from being explicitly clear.…”