Limits...
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.

Balanovsky O, Zhabagin M, Agdzhoyan A, Chukhryaeva M, Zaporozhchenko V, Utevska O, Highnam G, Sabitov Z, Greenspan E, Dibirova K, Skhalyakho R, Kuznetsova M, Koshel S, Yusupov Y, Nymadawa P, Zhumadilov Z, Pocheshkhova E, Haber M, A Zalloua P, Yepiskoposyan L, Dybo A, Tyler-Smith C, Balanovska E - PLoS ONE (2015)

Bottom Line: 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 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.

View Article: PubMed Central - PubMed

Affiliation: Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia; Research Centre for Medical Genetics, Russian Academy of Sciences, Moscow, Russia.

ABSTRACT
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.

Show MeSH

Related in: MedlinePlus

Y-chromosome haplogroup G1 phylogeny.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.
© Copyright Policy
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4388827&req=5

pone.0122968.g005: Y-chromosome haplogroup G1 phylogeny.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.

Mentions: The presence of additional clusters was confirmed when we included two GIH (Gujarat Indians from Houston) samples from the 1000 Genomes Project, which are the only publicly available data on haplogroup G1. Including the low coverage sequences halved the number of SNPs called in all samples (S4 Table), but tree revealed the same topology, and the Indian G1s formed their own cluster (Fig 5). One technical point is notable: the lengths of all the branches on the tree are similar, as they should be if the mutation rate is constant. The only exception is the very long branches of the samples from the 1000 Genomes Project, which is likely caused by the filtering criteria not being optimized for low coverage datasets. However, 26 SNPs were independently called in both samples, thus confirming the reality of the Indian-specific branch of haplogroup G1.


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.

Balanovsky O, Zhabagin M, Agdzhoyan A, Chukhryaeva M, Zaporozhchenko V, Utevska O, Highnam G, Sabitov Z, Greenspan E, Dibirova K, Skhalyakho R, Kuznetsova M, Koshel S, Yusupov Y, Nymadawa P, Zhumadilov Z, Pocheshkhova E, Haber M, A Zalloua P, Yepiskoposyan L, Dybo A, Tyler-Smith C, Balanovska E - PLoS ONE (2015)

Y-chromosome haplogroup G1 phylogeny.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.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4388827&req=5

pone.0122968.g005: Y-chromosome haplogroup G1 phylogeny.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.
Mentions: The presence of additional clusters was confirmed when we included two GIH (Gujarat Indians from Houston) samples from the 1000 Genomes Project, which are the only publicly available data on haplogroup G1. Including the low coverage sequences halved the number of SNPs called in all samples (S4 Table), but tree revealed the same topology, and the Indian G1s formed their own cluster (Fig 5). One technical point is notable: the lengths of all the branches on the tree are similar, as they should be if the mutation rate is constant. The only exception is the very long branches of the samples from the 1000 Genomes Project, which is likely caused by the filtering criteria not being optimized for low coverage datasets. However, 26 SNPs were independently called in both samples, thus confirming the reality of the Indian-specific branch of haplogroup G1.

Bottom Line: 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 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.

View Article: PubMed Central - PubMed

Affiliation: Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia; Research Centre for Medical Genetics, Russian Academy of Sciences, Moscow, Russia.

ABSTRACT
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.

Show MeSH
Related in: MedlinePlus