Mitochondrial Population Genomics Supports a Single Pre-Clovis Origin with a Coastal Route for the Peopling of the Americas

Abstract

It is well accepted that the Americas were the last continents reached by modern humans, most likely through Beringia. However, the precise time and mode of the colonization of the New World remain hotly disputed issues. Native American populations exhibit almost exclusively five mitochondrial DNA (mtDNA) haplogroups (A-D and X). Haplogroups A-D are also frequent in Asia, suggesting a northeastern Asian origin of these lineages. However, the differential pattern of distribution and frequency of haplogroup X led some to suggest that it may represent an independent migration to the Americas. Here we show, by using 86 complete mitochondrial genomes, that all Native American haplogroups, including haplogroup X, were part of a single founding population, thereby refuting multiple-migration models. A detailed demographic history of the mtDNA sequences estimated with a Bayesian coalescent method indicates a complex model for the peopling of the Americas, in which the initial differentiation from Asian populations ended with a moderate bottleneck in Beringia during the last glacial maximum (LGM), around approximately 23,000 to approximately 19,000 years ago. Toward the end of the LGM, a strong population expansion started approximately 18,000 and finished approximately 15,000 years ago. These results support a pre-Clovis occupation of the New World, suggesting a rapid settlement of the continent along a Pacific coastal route.

Solutrean hypothesis: genetics, the mammoth in the room

“…One of these (Fagundes et al 2008), claims to refute the SH on the basis of theoretical modelling of a single entry because, on their estimates, American X has a similar age and diversity to the other American mtDNA founders. They argue it could have gone through a similar LGM bottleneck to the other lineages in Beringia and thus claim their… "…results strongly support the hypothesis that haplogroup X, together with the other four main mtDNA haplogroups, was part of the gene pool of a single Native American founding population; therefore they do not support models that propose haplogroup-independent migrations, such as the migration from Europe posed by the Solutrean hypothesis.…”

Different kinds of genetic markers permit inference of Paleolithic and Neolithic expansions in humans

“…For instance, although when and how early modern humans reached America for the first time was subject to debates (eg, Waters and Stafford 16 and Goebel et al 17 ), demographic inferences using mitochondrial DNA (mtDNA) sequences indicated an initial differentiation from Asian populations ended with a moderate bottleneck in Beringia during the last glacial maximum (LGM), around 23 000 to 19 000 years ago. 18 Then, toward the end of the LGM, a strong spatial and demographic population expansion started 18 000 and finished 15 000 years ago (thus well before the Neolithic transition).…”

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.…”