Mitochondrial genome diversity of Native Americans supports a single early entry of founder populations into America

Abstract

There is general agreement that the Native American founder populations migrated from Asia into America through Beringia sometime during the Pleistocene, but the hypotheses concerning the ages and the number of these migrations and the size of the ancestral populations are surrounded by controversy. DNA sequence variations of several regions of the genome of Native Americans, especially in the mitochondrial DNA (mtDNA) control region, have been studied as a tool to help answer these questions. However, the small number of nucleotides studied and the nonclocklike rate of mtDNA control-region evolution impose several limitations to these results. Here we provide the sequence analysis of a continuous region of 8.8 kb of the mtDNA outside the D-loop for 40 individuals, 30 of whom are Native Americans whose mtDNA belongs to the four founder haplogroups. Haplogroups A, B, and C form monophyletic clades, but the five haplogroup D sequences have unstable positions and usually do not group together. The high degree of similarity in the nucleotide diversity and time of differentiation (i.e., approximately 21,000 years before present) of these four haplogroups support a common origin for these sequences and suggest that the populations who harbor them may also have a common history. Additional evidence supports the idea that this age of differentiation coincides with the process of colonization of the New World and supports the hypothesis of a single and early entry of the ancestral Asian population into the Americas.

Figure 1

NJ tree based on the 8.8-kb mtDNA segment from 93 humans plus the sequence inferred by Anderson et al. (1981) through use of the proportional distance and rooted with the chimpanzee sequence. Bootstrap percent values (1,000 replicates) are shown on some nodes, and haplogroups A–D are indicated on the right. The population origin of the individuals are given in the twigs, and the 40 new sequences from the present study are capitalized. PNG = Papua New Guinea.

Figure 2

Data matrix showing the informative nucleotide positions for the 8.8-kb mtDNA segment. The trees on the left are cladograms with the same topology and numbering of individuals as the tree in figure 1. Gray blocks denote groups of nucleotide changes that are identical in several sequences of the four major Native American haplogroups and the two mutations common to many Asians.