File:Basal tree encompassing the roots of Native American mtDNA haplogroups.png

English: Basal tree encompassing the roots of Native American mtDNA haplogroups. The tree is rooted on the haplogroup L3 founder and the position of the revised Cambridge reference sequence (rCRS) [49] is indicated for reading off sequence motifs. Closely related Asian branches are indicated in green. Detailed phylogenies for the four pan-American haplogroups (A2, B2, C1, and D1, highlighted in red) are shown in the corresponding figures. The complete sequences that are currently available for the other four Native American haplogroups (X2a, C4c, D2a, and D4h3, highlighted in red) are also displayed. Haplogroup D3 is common among Inuit populations [16], but all complete sequences available are from Siberia [13], [18]. As for A2a, the HVS-I motif (16111 16192 16223 16233 16290 16319 16331) of the reported sequence (no. 1) is common in Na-Dené groups [5]. Sequence no. 2 has been revised taking into account that the originally reported transitions at 4732 and 5147 [8] were artifacts due to a sample mix-up, while sequence no. 6 represents the shared motif of six Aleutian mitochondrial genomes [13]. Mutations are transitions unless specified: suffixes indicate transversions (to A, G, C, or T) or indels (+, d). Mutations back to the rCRS nucleotide are prefixed with @. Recurrent mutational events are underlined. Mutations in italics are either disease-causing or heteroplasmic or likely erroneous (and do not enter age calculations). We have followed the recent guidelines for standardization of the alignment in long C stretches [50], but disregarded any length variation in the C stretches that would then be scored at 309 or 16193 (which is often subject to considerable heteroplasmy). A number flagging a circled haplotype indicates the number of individuals sharing the corresponding haplotype (if >1). Additional information is provided in Text S4, while Table S1 lists the source of the complete genomes.