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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.

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Network of Y-STR haplotypes within haplogroup G1.Arrows mark samples chosen for Y-chromosomal sequencing.
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pone.0122968.g003: Network of Y-STR haplotypes within haplogroup G1.Arrows mark samples chosen for Y-chromosomal sequencing.

Mentions: On the network (Fig 3) four clusters are visible: two include only Armenian samples, while other two are specific to Kazakhs and Bashkirs, respectively. Samples from other populations are spread all around the network and do not form clusters. The Kazakh cluster is highly specific to the Argyn tribe within the Kazakhs; the Armenian cluster includes more Hemsheni Armenians than other Armenian populations; all but one members of the Bashkir cluster belong to the Kangly tribe of Bashkirs. The Y-STR pattern thus shows that haplogroup G1 is genetically diverse and widespread, with some sub-branches at high frequencies due to founder effects, while others remain at very low frequencies in occasional locations within the area of the haplogroup.


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)

Network of Y-STR haplotypes within haplogroup G1.Arrows mark samples chosen for Y-chromosomal sequencing.
© Copyright Policy
Related In: Results  -  Collection

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

pone.0122968.g003: Network of Y-STR haplotypes within haplogroup G1.Arrows mark samples chosen for Y-chromosomal sequencing.
Mentions: On the network (Fig 3) four clusters are visible: two include only Armenian samples, while other two are specific to Kazakhs and Bashkirs, respectively. Samples from other populations are spread all around the network and do not form clusters. The Kazakh cluster is highly specific to the Argyn tribe within the Kazakhs; the Armenian cluster includes more Hemsheni Armenians than other Armenian populations; all but one members of the Bashkir cluster belong to the Kangly tribe of Bashkirs. The Y-STR pattern thus shows that haplogroup G1 is genetically diverse and widespread, with some sub-branches at high frequencies due to founder effects, while others remain at very low frequencies in occasional locations within the area of the haplogroup.

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