Where west meets east: the complex mtDNA landscape of the southwest and Central Asian corridor

Abstract

The southwestern and Central Asian corridor has played a pivotal role in the history of humankind, witnessing numerous waves of migration of different peoples at different times. To evaluate the effects of these population movements on the current genetic landscape of the Iranian plateau, the Indus Valley, and Central Asia, we have analyzed 910 mitochondrial DNAs (mtDNAs) from 23 populations of the region. This study has allowed a refinement of the phylogenetic relationships of some lineages and the identification of new haplogroups in the southwestern and Central Asian mtDNA tree. Both lineage geographical distribution and spatial analysis of molecular variance showed that populations located west of the Indus Valley mainly harbor mtDNAs of western Eurasian origin, whereas those inhabiting the Indo-Gangetic region and Central Asia present substantial proportions of lineages that can be allocated to three different genetic components of western Eurasian, eastern Eurasian, and south Asian origin. In addition to the overall composite picture of lineage clusters of different origin, we observed a number of deep-rooting lineages, whose relative clustering and coalescent ages suggest an autochthonous origin in the southwestern Asian corridor during the Pleistocene. The comparison with Y-chromosome data revealed a highly complex genetic and demographic history of the region, which includes sexually asymmetrical mating patterns, founder effects, and female-specific traces of the East African slave trade.

Figure 1

Map of the southwestern and Central Asian corridor, showing the samples analyzed in the present study. Population codes are as reported in table 1. Boxed populations are those used for the initial step of the study (see the “Materials And Methods” section). Pie charts show the distribution of the main mtDNA lineage groups in the populations studied. Colored sections reflect the frequency of different haplogroup clusters, which group the western Eurasian (HV, pre-HV, N1, J-T, U-K, I, W, and X), the South Asian (M*, U2a-c, U9, R*, R1-R2, R5-R6, N1d, and HV2), the eastern Eurasian (M-CDGZ, A, B, F, and N9a) and the sub-Saharan African (L1, L2, and L3A) lineages.

Figure 2

Schematic phylogenetic tree of mtDNA haplogroups observed in the populations analyzed. The diagnostic mutations used to classify the whole data set are reported on the branches. Restriction enzyme sites are numbered from the first nucleotide of the recognition sequence. A plus sign (+) indicates the presence of a restriction site; a minus sign (−) indicates the absence of such a site. The restriction enzymes are designated by the following single-letter codes: a, AluI; b, AvaII; c, DdeI; e, HaeIII; f, HhaI; g, HinfI; h, HpaI; i, MspI; j, MboI; k, RsaI; l, TaqI; m, BamHI; n, HaeII; o, HincII; p, BstOI; q, NlaIII; r, BfaI; s, AccI; t, MboII; u, MseI; v, HphI; z, MnlI. Mutations in the HVS-I region are transitions unless the base change is specified explicitly. Boxes indicate novel information.

Figure 3

Network of the U7 lineage. Circle areas are proportional to haplotype frequency. Population codes are as reported in table 1 and in the “Materials And Methods” section. Mutated sites (−16,000) are indicated along the branches. The number sign (#) indicates the assumed root.

Figure 4

Networks of (a) HV2 and (b) R2 lineages

Figure 5

Networks of (a) U2a, (b) U2b, (c) U2c, and (d) R5 lineages

Figure 6

PC plot based on haplogroup frequencies for the 23 population samples (population codes are as in table 1).