Complete Mitochondrial DNA Diversity in Iranians

<div><p>Due to its pivotal geographical location and proximity to transcontinental migratory routes, Iran has played a key role in subsequent migrations, both prehistoric and historic, between Africa, Asia and Europe. To shed light on the genetic structure of the Iranian population as well as on the expansion patterns and population movements which affected this region, the complete mitochondrial genomes of 352 Iranians were obtained. All Iranian populations studied here exhibit similarly high diversity values comparable to the other groups from the Caucasus, Anatolia and Europe. The results of AMOVA and MDS analyses did not associate any regional and/or linguistic group of populations in the Anatolia/Caucasus and Iran region pointing to close genetic positions of Persians and Qashqais to each other and to Armenians, and Azeris from Iran to Georgians. By reconstructing the complete mtDNA phylogeny of haplogroups R2, N3, U1, U3, U5a1g, U7, H13, HV2, HV12, M5a and C5c we have found a previously unexplored genetic connection between the studied Iranian populations and the Arabian Peninsula, India, Near East and Europe, likely the result of both ancient and recent gene flow. Our results for Persians and Qashqais point to a continuous increase of the population sizes from ∼24 kya to the present, although the phase between 14-24 kya is thought to be hyperarid according to the Gulf Oasis model. Since this would have affected hunter-gatherer ranges and mobility patterns and forced them to increasingly rely on coastal resources, this transition can explain the human expansion across the Persian Gulf region.</p></div

Maximum-parsimony phylogenetic tree of complete mtDNA sequences belonging to haplogroup R2.

<p>Numbers along links refer to substitutions scored relative to rCRS <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0080673#pone.0080673-Andrews1" target="_blank">[42]</a>. Transversions are further specified; ins and del denote insertions and deletions of nucleotides, respectively; back mutations are underlined; symbol < denotes parallel mutation. Iranian samples labeled as in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0080673#pone.0080673.s005" target="_blank">Table S1</a>, for published data the accession number in indicated. The box containing the sample ID is color coded according to the geographic origin of the sample. Time estimates (in kya) shown along links next to clade labels are based on the complete mtDNA genome clock (marked in blue) and the synonymous clock (marked in green) <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0080673#pone.0080673-Soares2" target="_blank">[47]</a>. Established haplogroup labels are shown in black; blue are redefined and red are newly identified haplogroups in the present study.</p

Maximum-parsimony phylogenetic tree of complete mtDNA sequences belonging to haplogroup N3.

<p>Designations are as in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0080673#pone-0080673-g003" target="_blank">Figure 3</a>.</p

MDS plot based on Fst statistics calculated from complete mtDNA sequences for population samples from Iran, Anatolia, Caucasus, and Europe.

<p>The populations from <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0080673#pone.0080673-Schnberg1" target="_blank">[40]</a> labeled with “S” after underscore.</p

Mitochondrial haplogroup frequencies (%) in Iranian populations.

<p>Mitochondrial haplogroup frequencies (%) in Iranian populations.</p

BSP indicating the median of the hypothetical effective population size through time based on complete mtDNA genome data for Persians, Qashqais and Azeris.

<p>Maximum time (x axis) corresponds to the median posterior estimate of the genealogy root-height.</p

Maximum-parsimony phylogenetic tree of complete mtDNA sequences belonging to haplogroup HV2.

<p>Designations are as in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0080673#pone-0080673-g003" target="_blank">Figure 3</a>.</p

Diversity indices and neutrality test values for Iranian populations based on complete mtDNA sequences.

<p>Diversity indices and neutrality test values for Iranian populations based on complete mtDNA sequences.</p

Deep Phylogenetic Analysis of Haplogroup G1 Provides Estimates of SNP and STR Mutation Rates on the Human Y-Chromosome and Reveals Migrations of Iranic Speakers

<div><p>Y-chromosomal haplogroup G1 is a minor component of the overall gene pool of South-West and Central Asia but reaches up to 80% frequency in some populations scattered within this area. We have genotyped the G1-defining marker M285 in 27 Eurasian populations (n= 5,346), analyzed 367 M285-positive samples using 17 Y-STRs, and sequenced ~11 Mb of the Y-chromosome in 20 of these samples to an average coverage of 67X. This allowed detailed phylogenetic reconstruction. We identified five branches, all with high geographical specificity: G1-L1323 in Kazakhs, the closely related G1-GG1 in Mongols, G1-GG265 in Armenians and its distant brother clade G1-GG162 in Bashkirs, and G1-GG362 in West Indians. The haplotype diversity, which decreased from West Iran to Central Asia, allows us to hypothesize that this rare haplogroup could have been carried by the expansion of Iranic speakers northwards to the Eurasian steppe and via founder effects became a predominant genetic component of some populations, including the Argyn tribe of the Kazakhs. The remarkable agreement between genetic and genealogical trees of Argyns allowed us to calibrate the molecular clock using a historical date (1405 AD) of the most recent common genealogical ancestor. The mutation rate for Y-chromosomal sequence data obtained was 0.78×10^-9 per bp per year, falling within the range of published rates. The mutation rate for Y-chromosomal STRs was 0.0022 per locus per generation, very close to the so-called genealogical rate. The “clan-based” approach to estimating the mutation rate provides a third, middle way between direct farther-to-son comparisons and using archeologically known migrations, whose dates are subject to revision and of uncertain relationship to genetic events.</p></div

Haplotype diversity of haplogroup G1-M285 in South-Western and Central Asian populations.

<p>N—number of G1 samples genotyped by 17 Y-STRs;</p><p>N_HT—number of different Y-chromosomal STR haplotypes;</p><p>F_MAX—frequency of the most frequent haplotype;</p><p>HD—haplotype diversity; the populations were sorted according to the level of HD.</p><p>Haplotype diversity of haplogroup G1-M285 in South-Western and Central Asian populations.</p