Origin and diffusion of mtDNA haplogroup X

Abstract

A maximum parsimony tree of 21 complete mitochondrial DNA (mtDNA) sequences belonging to haplogroup X and the survey of the haplogroup-associated polymorphisms in 13,589 mtDNAs from Eurasia and Africa revealed that haplogroup X is subdivided into two major branches, here defined as "X1" and "X2." The first is restricted to the populations of North and East Africa and the Near East, whereas X2 encompasses all X mtDNAs from Europe, western and Central Asia, Siberia, and the great majority of the Near East, as well as some North African samples. Subhaplogroup X1 diversity indicates an early coalescence time, whereas X2 has apparently undergone a more recent population expansion in Eurasia, most likely around or after the last glacial maximum. It is notable that X2 includes the two complete Native American X sequences that constitute the distinctive X2a clade, a clade that lacks close relatives in the entire Old World, including Siberia. The position of X2a in the phylogenetic tree suggests an early split from the other X2 clades, likely at the very beginning of their expansion and spread from the Near East.

Figure 1

Maximum parsimony phylogenetic tree of complete mtDNA sequences belonging to haplogroup X. Five mtDNAs were selected for complete sequence analysis in the course of the present study (Dr09, Es39, Gm66, Go41, and Om1538), 11 coding region sequences were from the work of Herrnstadt et al. (2002), but their control region sequences have now been added, and 5 complete sequences (Lev2, MM, E18, Nav125, and Oj2) were taken from the literature (Levin et al.; Maca-Meyer et al.; Mishmar et al. ; Bandelt et al., in press). The diagnostic mutations relative to the revised reference sequence (Andrews et al. 1999) are indicated on the branches. Transversions are specified by suffixes, and underlined mutations appear more than once in the tree. For protein-coding genes, “ns” indicates nonsynonymous and “s” synonymous mutations. For coalescence-time estimates, a mutation rate of 1 mutation per 5,139 years in the coding region (nps 577–16023) was used (Mishmar et al. 2003). mtDNA sequence data are available at the Estonian Biocentre Web page.

Figure 2

Median-joining (MJ) network of 175 haplogroup X partial sequences. The MJ (Bandelt et al. 1999) algorithm was implemented within the Network 3111 program (A. Röhl; Shareware Phylogenetic Software Web site). Default settings were used for HVS-I (nps 16024–16383), HVS-II (nps 16518–310), and coding-region sequence variation as given in table 2. Highly variable (Hasegawa et al. 1993) positions of HVS-I (16093, 16126, 16129, 16187, 16189, 16223, 16234, 16278, 16292, 16293, 16311, 16325, 16355, and 16362) were assigned a weight of 1, other HVS-I and HVS-II sites were assigned a weight of 2, and coding-region sites were assigned a weight of 10. Areas of the circles are proportional to haplotype frequencies. Populations are indicated by the following abbreviations: ab = Abazin, ad = Adygei, alb = Albanian, alg = Algerian, alt = Altaian, ar = Armenian, arb = Arab from Uzbekistan, be = Bengali, cz = Czech, dr = Druze, eg = Egyptian, es = Estonian, et = Ethiopian, ev = Evenk, fr = French, go = Georgian, gr = Greek, ho = Croat, hu = Hungarian, ir = Iranian, it = Italian, jo = Jordanian, kir = Kyrgyz, kr = Karachay, ku = Kumyk, kw = Kuwaiti, le = Lebanese, mo = Moroccan, ng = Nogay, os = Ossetian, sa = Saudi Arabian, sw = Swede, sy = Syrian, td = Tadjik, tu = Turk, and ukr = Ukrainian. Variant bases are numbered (Anderson et al. 1981) and are shown along links between haplotypes. Nucleotide changes are specified by suffixes only for transversions, and a “d” indicates a deletion. The node marked with a large asterisk (★) matches the root type of haplogroup X. The coalescence times of the clades are shown near the clades. Coalescence times of HVS-I clusters were calculated by means of ρ, the average mutational distance to the founder haplotype of the cluster, by using a mutation rate of 1 transition per 20,180 years in the segment between nps 16090 and 16365 (Forster et al. 1996). Standard deviations for ρ were calculated as in the work of Saillard et al. (2000), a procedure which ignores the variance due to molecular clock calibration. mtDNA sequence data are available at the Estonian Biocentre Web page.