Do the four clades of the mtDNA haplogroup L2 evolve at different rates?

Abstract

Forty-seven mtDNAs collected in the Dominican Republic and belonging to the African-specific haplogroup L2 were studied by high-resolution RFLP and control-region sequence analyses. Four sets of diagnostic markers that subdivide L2 into four clades (L2a-L2d) were identified, and a survey of published African data sets appears to indicate that these clades encompass all L2 mtDNAs and harbor very different geographic/ethnic distributions. One mtDNA from each of the four clades was completely sequenced by means of a new sequencing protocol that minimizes time and expense. The phylogeny of the L2 complete sequences showed that the two mtDNAs from L2b and L2d seem disproportionately derived, compared with those from L2a and L2c. This result is not consistent with a simple model of neutral evolution with a uniform molecular clock. The pattern of nonsynonymous versus synonymous substitutions hints at a role for selection in the evolution of human mtDNA. Regardless of whether selection is shaping the evolution of modern human mtDNAs, the population screening of L2 mtDNAs for the mutations identified by our complete sequence study should allow the identification of marker motifs of younger age with more restricted geographic distributions, thus providing new clues about African prehistory and the origin and relationships of African ethnic groups.

Figure 1

Unweighted reduced median network (Bandelt et al. 1995) of the 47 L2 samples from the Dominican Republic, showing the four clades L2a–L2d. The circles represent combined high-resolution RFLP and HVS-I haplotypes, with their areas proportional to the frequency. The smallest circles are singletons, whereas the largest have frequency 5. The black circles denote the four mtDNAs (one for each clade) that have been completely sequenced. RFLP mutations are indicated next to the branches, with the arrow pointing in the direction of a site gain. The label is the nucleotide at the beginning of the recognition sequence (in the numbering of the reference sequence of Anderson et al. [1981]); the letter suffix indicates the enzyme (see table 1). HVS-I mutations (between 16003 and 16474) are shown on the branches; they are transitions unless the base change is explicitly indicated. Underlining indicates resolved recurrent mutations, and unresolved events are shown by reticulation. Implausible links are shown with a dotted line. The node marked with an asterisk (*) has the RFLP motif +3592h, +10394c, −10871z, +16390g/−16390b and the HVS-I motif 223-278-390. The lengths of branches in L2a and L2d are shown distorted, for convenience of display. The hypervariable RFLP 16517e was not considered, nor were indel events.

Figure 2

Most-parsimonious reconstruction of the character evolution on a most-parsimonious tree of complete L2 sequences, rooted by use of a complete haplogroup L1a sequence. This tree includes the four L2 mtDNAs sequenced in the course of the present study (blackened circles) and the three L2 complete sequences (blackened squares) previously reported by Ingman et al. (2000). The L1a sequence used as an outgroup, as suggested by the phylogenies of Watson et al. (1997) and Ingman et al. (2000), was also obtained in the course of the present study and is from a Dominican subject. Mutations are shown on the branches; they are transitions, unless the base change is explicitly indicated. Deletions are indicated by a “d” preceding the deleted nucleotides. Insertions are indicated by a plus sign (+) preceding the number and type of inserted nucleotides. Underlining indicates recurrent mutations. “s” indicates synonymous mutations, whereas “ns” indicates nonsynonymous mutations. The asterisk (*) indicates the most recent common ancestor of the L2 mtDNAs in our sample. This differs from the revised CRS (Andrews et al. 1999) by mutations (transitions unless otherwise indicated) at the following positions: 73, 146, 150, 152, 182, 263, 315+C, 750, 769, 1018, 1438, 2416, 2706, 3594, 4104, 4769, 7028, 7256, 7521, 8206, 8701, 8860, 9221, 9540, 10115, 10398, 10873, 11719, 12705, 13590, 13650, 14766, 15301, 15326, 16223, 16278, 16311, 16390, and 16519.