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

Genetic and genealogical reconstructions of the relationship between members of the Argyn tribe of the Kazakh:

<p>A) Genetic tree reconstructed from Y-chromosome sequences of the Kazakh samples. B) Genealogical tree of the Argyn tribe of the Kazakh. Each sequenced Kazakh sample is attributed to the clan it originates from. The genealogical ancestor with the known historical date is marked in grey.</p

Network of Y-STR haplotypes within haplogroup G1.

<p>Arrows mark samples chosen for Y-chromosomal sequencing.</p

Y-chromosome haplogroup G1 phylogeny.

<p>The tree combines the high-coverage dataset reported in this study with data from 1000 Genomes Project. Dotted lines indicate the approximate phylogenetic position of two previously reported G1 branches which were absent among our samples.</p

Ancient migrations of Iranic-speaking populations.

<p>A) Area populated by Iranic speakers in the middle of the first millennium BC. States whose languages belonged to the Iranic and Armenian linguistic groups are shown in red (modified from [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0122968#pone.0122968.ref039" target="_blank">39</a>]). B) Homeland and migration of Iranic speakers according to the major competing theories (modified from [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0122968#pone.0122968.ref034" target="_blank">34</a>]).</p

Map of haplotype diversity of haplogroup G1.

<p>The black points represent the populations for which diversity values were calculated. Abbreviations in the statistical legend indicate the following: MIN and MAX, the minimal and maximum values on the map.</p

Frequencies of the haplogroup G1-M285 in Eurasian populations.

<p>Frequencies of the haplogroup G1-M285 in Eurasian populations.</p