The role of selection in the evolution of human mitochondrial genomes - PubMed (original) (raw)
Maximum parsimony tree of 277 human mtDNA coding region sequences. Locations of branch-defining mutations are listed relative to the revised reference sequence (A
ndrews
et al. 1999). Transversions are specified in capital letters, del indicates deletion, and + indicates insertion. Amino acid replacements are specified in parentheses with threonine- and valine-affecting changes highlighted in red and blue, respectively. ∼t, change in tRNA; ∼r, change in rRNA gene. Haplogroup labels follow existing classifications (C
hen
et al. 1995; T
orroni
et al. 1993, 1996, 2001; W
atson
et al. 1997; M
acaulay
et al. 1999; B
andelt
et al. 2001; F
orster
et al. 2001; K
ivisild
et al. 2002, 2004; K
ong
et al. 2003; A
chilli
et al. 2004; P
alanichamy
et al. 2004; S
hen
et al. 2004; T
anaka
et al. 2004; F
riedlaender
et al. 2005). Substitutions at np 709, 3693, and 4715 in haplogroups B4, L2, and Z, respectively, are reconstructed less parsimoniously, yet in accordance with the phylogenetic relations suggested by additional data (F
innilä
et al. 2001; T
orroni
et al. 2001; K
ivisild
et al. 2002; K
ong
et al. 2003). Coalescent estimates of haplogroups, shown in thousands of years in italics next to clade labels, are based on the average number of synonymous transitions to the root of the clade. The tree was rooted using as outgroup the nuclear inserts of mtDNA and the majority consensus of complete sequences of two P. troglodytes and one P. paniscus (for details see
materials and methods
). The numbers in triangles indicate the additional mutational steps required in comparison to the optimally rooted tree using only the chimpanzee outgroup with red type indicating the root that was rejected (P < 0.01) under the assumption of equal evolutionary rate over branches. The positions at which the derived character states in humans and the chimpanzee consensus match are shown above the triangles. Disease-implicated substitutions confirmed by two independent studies (
) are indicated by “#.” Ad, Af, Am, As, Eu, and Oc correspond to African descent, African, Amerindian, Asian, European, and Oceanian, respectively. The continent of origin is distinguished for each individual sample by box color and subcontinental affiliation is indicated with letters below the boxes where N, E, W, S, C, and SW refer to north, east, west, south, central, and southwest parts of the continents, respectively. BP, Biaka Pygmies; MP, Mbuti Pygmies; A, Australian; P, Papuan; M, Melanesian; H, Hungarian LHON patients; G, Georgian. The two African mtDNAs (L0a2 and L1b1) found in West Asia (Pakistan) are likely due to recent admixture as indicated by their low genetic distance from related African samples presented in the tree and by the fact that they were detected in a Makrani and a Sindhi. According to Q
uintana
-M
urci
et al. (2004), the Makrani harbor an extremely high frequency (39%) of the African haplogroups L3d, L3b, L2a, and L1a, most likely as a result of the forced migration of slave women from Africa that began in the seventh century and increased considerably during the Omani Empire. European gene flow, on the other hand, may account for the presence of European K and X sequences in one Aboriginal Australian and in one Native American (Muskogee), respectively.