The haplomatch program for comparing Y-chromosome STR-haplotypes and its application to the analysis of the origin of Don Cossacks

@article{Chukhryaeva2016TheHP,
  title={The haplomatch program for comparing Y-chromosome STR-haplotypes and its application to the analysis of the origin of Don Cossacks},
  author={Marina Chukhryaeva and Ilya O. Ivanov and Svetlana Frolova and S. M. Koshel and O. M. Utevska and Roza A. Skhalyakho and Anastasia Agdzhoyan and Yu. V. Bogunov and Elena V. Balanovska and O. P. Balanovsky},
  journal={Russian Journal of Genetics},
  year={2016},
  volume={52},
  pages={521-529}
}
STR haplotypes of the Y chromosome are widely used as effective genetic markers in studies of human populations and in forensic DNA analysis. The task often arises to compare the spectrum of haplotypes in individuals or entire populations. Performing this task manually is too laborious and thus unrealistic. We propose an algorithm for counting similarity between STR haplotypes. This algorithm is suitable for massive analyses of samples. It is implemented in the computer program Haplomatch… 
Is there a Finno-Ugric component in the gene pool of Russians from Yaroslavl oblast? Evidence from Y-chromosome
TLDR
Preservation of the Finno-Ugric component in the gene pool of population of Mologa and a contribution of Slavic colonization in the formation of the gene Pool of the Yaroslavl Volga region populations make it possible to hypothesize the genetic contribution of the “downstream’ (Rostov- Suzdal) rather than “upstream” (Novgorod) Slavic migration wave.
Matrilineal and Patrilineal Genetic Continuity of Two Iron Age Individuals from a Pazyryk Culture Burial
TLDR
Despite the current focus on the two Pazyryk individuals, a rare glimpse into the ancient migrations was gained through the discovery of paternal and maternal haplotype matches across an immense geography that spans from Yakutia to Turkey.
The Connection of the Genetic, Cultural and Geographic Landscapes of Transoxiana
TLDR
Investigation of STR-based clusters of haplotypes and their ages revealed that cultural and demic expansions of Transoxiana were not closely connected with each other, and the main factor structuring the gene pool was the mode of subsistence: settled agriculture or nomadic pastoralism.
Uniparental Genetic Analyses Reveal the Major Origin of Fujian Tanka from Ancient Indigenous Daic Populations
TLDR
The interpopulation comparison revealed that the Fujian Tanka have a closer affinity with Daic populations than with Han Chinese in paternal lineages but are closely clustered with southern Han populations such as Hakka and Chaoshanese in maternal lineages.
Population biobanks: Organizational models and prospects of application in gene geography and personalized medicine
TLDR
The results obtained using the biobanks in transdisciplinary research and prospective applications for the purposes of genogeography, genomic medicine, and forensic science are presented.

References

SHOWING 1-10 OF 33 REFERENCES
Y chromosome haplotype reference database (YHRD): update.
Parallel evolution of genes and languages in the Caucasus region.
TLDR
Overall, in the Caucasus region, unmatched levels of gene-language coevolution occurred within geographically isolated populations, probably due to its mountainous terrain.
The new Y Chromosome Haplotype Reference Database.
Analysis of Y chromosome STR haplotypes in the European part of Russia reveals high diversities but non-significant genetic distances between populations
TLDR
Whereas gradual change in the Y chromosome pool exists between Russia and the Slavic-speaking populations to the West, remarkable discontinuities were observed with neighbouring populations in the East, North and South.
Expanding the forensic German mitochondrial DNA control region database: genetic diversity as a function of sample size and microgeography
TLDR
HV1 sequences of 700 male inhabitants of one village in Lower Saxony were generated and showed a nearly linear increase of the number of different haplotypes with increasing number of individuals, demonstrating that the commonly used haplotype diversity measure (Nei 1987) for population samples tends to underestimate mtDNA diversity in the actual population.
Genetic genealogy: History and methodology
The review surveys the development and the current state of genetic genealogy, a branch of science dealing with the history of individuals, families, and kins using molecular genetic methods. The
The effective mutation rate at Y chromosome short tandem repeats, with application to human population-divergence time.
TLDR
This value is used to estimate the times of the African Bantu expansion, the divergence of Polynesian populations (the Maoris, Cook Islanders, and Samoans), and the origin of Gypsy populations from Bulgaria.
Mitochondrial portraits of human populations using median networks.
TLDR
A novel network approach for portraying mtDNA relationships is proposed that reduces the complexity of the network by identifying parallelisms and is guided by a compatibility argument and an additional source of phylogenetic information: the frequencies of the mitochondrial haplotypes.
[Genetic genealogy: history and methodology].
The review surveys the development and the current state of genetic genealogy, a branch of science dealing with the history of individuals, families, and kins using molecular genetic methods. The
A measure of population subdivision based on microsatellite allele frequencies.
TLDR
It was found that, under the generalized stepwise mutation model, R( ST) provides relatively unbiased estimates of migration rates and times of population divergence while F(ST) tends to show too much population similarity, particularly when migration rates are low or divergence times are long.
...
...