Reduced-median-network analysis of complete mitochondrial DNA coding-region sequences for the major African, Asian, and European haplogroups

Abstract

The evolution of the human mitochondrial genome is characterized by the emergence of ethnically distinct lineages or haplogroups. Nine European, seven Asian (including Native American), and three African mitochondrial DNA (mtDNA) haplogroups have been identified previously on the basis of the presence or absence of a relatively small number of restriction-enzyme recognition sites or on the basis of nucleotide sequences of the D-loop region. We have used reduced-median-network approaches to analyze 560 complete European, Asian, and African mtDNA coding-region sequences from unrelated individuals to develop a more complete understanding of sequence diversity both within and between haplogroups. A total of 497 haplogroup-associated polymorphisms were identified, 323 (65%) of which were associated with one haplogroup and 174 (35%) of which were associated with two or more haplogroups. Approximately one-half of these polymorphisms are reported for the first time here. Our results confirm and substantially extend the phylogenetic relationships among mitochondrial genomes described elsewhere from the major human ethnic groups. Another important result is that there were numerous instances both of parallel mutations at the same site and of reversion (i.e., homoplasy). It is likely that homoplasy in the coding region will confound evolutionary analysis of small sequence sets. By a linkage-disequilibrium approach, additional evidence for the absence of human mtDNA recombination is presented here.

Figure 1

Phylogenetic network of 56 African mtDNA sequences based on coding-region variations relative to the rCRS. Weights of all nucleotide positions, including site 10398, were equal. Numbers in nodes indicate mtDNA sequences. Nucleotide positions in red are haplogroup specific and appear only on one branch of one haplogroup; nucleotide positions in black are haplogroup associated and occur at least twice within and/or outside this network (see table 2). Underlined nucleotide positions are novel and are reported here for the first time. The black square was chosen deliberately as the center point of the network. In this network, as well as in all other networks (figs. 2–4), nucleotide substitutions are transitions unless indicated otherwise by suffixes, which denote transversions. Some branch lengths have been distorted to increase legibility.

Figure 2

Phylogenetic network of 69 Asian mtDNA sequences based on coding-region variations relative to the rCRS. True Asian sequences are indicated by blue nodes or blue numbers inside white nodes. Weights of all nucleotide positions, including site 10398, were equal, except that a T→C substitution at nucleotide position 961 creates an unstable poly C tract. Numbers in nodes indicate mtDNA sequences. Red, black, and underlined nucleotides are as defined in the legend for figure 1. Broken lines indicate the presence of reticulations, and unbroken lines show the most likely route of evolution. The outgroup is an mtDNA sequence of African ancestry that belongs to haplogroup L3e (sample 216 from the African network).

Figure 3

Skeleton network of H/V mtDNA sequences. A set of 226 mtDNA sequences that belong to haplogroup H and 8 sequences of haplogroup V were used to build a skeleton phylogenetic network. Sequences that are included in the skeleton network were limited to haplotypes that appeared at least twice within the data set, with the provision that the use of the term “haplotypes” in the present article is limited to haplogroup-associated polymorphisms in the coding region. A total of 40 different haplotypes (nodes) were obtained. Weights of all nucleotide positions were equal. Red, black, and underlined nucleotides are as defined in the legend for figure 1. The outgroup is an mtDNA sequence of African ancestry that belongs to haplogroup L3e (sample 216 from the African network).

Figure 4

Phylogenetic network of 259 European mtDNA sequences based on coding-region variations relative to the rCRS. All members of haplogroups I–K and T–X are displayed plus 50 randomly selected sequences of haplogroup H. Weights of all nucleotide positions, including site 10398, were equal. Numbers in nodes indicate samples. Red, black, and underlined nucleotides are as defined in the legend for figure 1. The outgroup is an mtDNA sequence of African ancestry that belongs to haplogroup L3e (sample 216 from the African network).