The initial peopling of the Americas: a growing number of founding mitochondrial genomes from Beringia

Abstract

Pan-American mitochondrial DNA (mtDNA) haplogroup C1 has been recently subdivided into three branches, two of which (C1b and C1c) are characterized by ages and geographical distributions that are indicative of an early arrival from Beringia with Paleo-Indians. In contrast, the estimated ages of C1d--the third subset of C1--looked too young to fit the above scenario. To define the origin of this enigmatic C1 branch, we completely sequenced 63 C1d mitochondrial genomes from a wide range of geographically diverse, mixed, and indigenous American populations. The revised phylogeny not only brings the age of C1d within the range of that of its two sister clades, but reveals that there were two C1d founder genomes for Paleo-Indians. Thus, the recognized maternal founding lineages of Native Americans are at least 15, indicating that the overall number of Beringian or Asian founder mitochondrial genomes will probably increase extensively when all Native American haplogroups reach the same level of phylogenetic and genomic resolution as obtained here for C1d.

Figure 1.

Detailed tree of C1d in the context of haplogroup C1. All 73 C1d mtDNA sequences (63 novel and 10 published) are complete except for samples 36 and 65, for which only coding-region data are available. The basal motifs for Native American haplogroups C1b and C1c are also included together with the motif of the Asian-specific branch C1a. The position of the revised Cambridge reference sequence (rCRS) (Andrews et al. 1999) is indicated for reading off-sequence motifs. Mutations are shown on the branches; they are transitions unless a base is explicitly indicated. The prefix @ designates reversions, while suffixes indicate transversions (to A, G, C, or T), indels (+, d), gene locus (∼t, tRNA; ∼r, rRNA; ∼nc, noncoding region outside of the control-region), synonymous or nonsynonymous changes (s or ns), and T/C heteroplasmy (Y). Recurrent mutations within the phylogeny are underlined. We have followed the guidelines for standardization of the alignment in long C stretches (Bandelt and Parson 2008), but disregarded any length variation in the C-stretch between nucleotides 303 and 315, with the exception of the well-known 315+C insertion. Additional information regarding each mtDNA is available in Supplemental Table S1. Coalescence times shown for C1d, C1d*, and C1d1 are maximum-likelihood (ML) estimates, while the corresponding averaged distance (ρ) accompanied by a heuristic estimate of SE (σ) are shown in Table 1. As for the geographic affiliation (top left corner), North America refers to USA and Canada; northern South America refers to Colombia, Venezuela, Ecuador, Peru, and Brazil; southern South America corresponds to Chile, Argentina, Uruguay, and Paraguay.

Figure 2.

MtDNA tree encompassing the roots of all known Native American haplogroups. The distinguishing mutational motifs for the 15 known Native American haplogroups are reported on the branches. The position of the revised Cambridge reference sequence (rCRS) (Andrews et al. 1999) is indicated for reading off-sequence motifs. Mutations in the control region are in red, while mutations in the coding region are listed in black; they are transitions unless a base is explicitly indicated. The prefix @ designates reversions, while suffixes indicate transversions (to A, G, C, or T), indels (+, d). Recurrent mutations within the tree are underlined. The percent frequency of each Native American haplogroup in the entire double continent is reported in parentheses and has been obtained from the Sorenson Molecular Genealogy Foundation Mitochondrial (SMGF) mtDNA database (http://www.smgf.org) (entire control region) excluding all non-Native American mtDNAs. For each haplogroup, the relative frequencies in northern America (Canada and USA), Mexico, Central America, and South America are reported in different colors in the corresponding pie chart. Some haplogroups are completely absent in the SMGF mtDNA database because either they are extremely rare (X2g) or harbor a restricted distribution range (D3 in the Eskimos and Aleuts). For C4c, C1d*, and C1d1 frequency values are not available (n.a.) due to the lack of distinguishing control region mutations, but the overall C1d incidence (C1d* plus C1d1) is reported.

Figure 3.

Spatial frequency distribution of haplogroup C1d. The top map shows the frequency distribution of haplogroup C1d in general mixed populations of national states, while the bottom map illustrates the distribution in Native American tribes or communities. Note that the frequency scales (%) used in the two maps are different. The dots indicate the geographic location of the population samples included in each survey (Supplemental Tables S2, S3). Frequency maps were obtained as in Pala et al. (2009).