Population genetics and mutational events at 6 Y-STRs in Korean population

Kim, Soon Hee; Kim, Nam Ye; Kim, Kyung Sook; Kim, Jong Jin; Park, Jong-Tae; Chung, Ki Wha; Han, Myun Soo; Kim, Won

doi:10.1016/j.fsigen.2008.06.004

Cited by 9 publications

(1 citation statement)

References 4 publications

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“…We used a population model of exponential growth from an initially constant-sized population with the settings and priors described previously (Xue, Zerjal, et al 2006), except for the mutation rate. Three sets of mutation rates were compared: 1) an “observed” mutation rate (OMR) for each Y-STR compiled from previously described mutation counts in father–son pairs (Dupuy et al 2004; Gusmao et al 2005; Lee et al 2007; Shi et al 2007; Decker et al 2008; Padilla-Gutierrez et al 2008; Toscanini et al 2008; Goedbloed et al 2009; Kim et al 2009) or in deep-rooted pedigrees (Vermeulen et al 2009) tabulated in supplementary table S2, Supplementary Material Online. 2) A widely used calibrated “evolutionary” mutation rate (EMR) based on well-dated historical events (Zhivotovsky et al 2004).…”

Section: Methodsmentioning

confidence: 99%

A Worldwide Survey of Human Male Demographic History Based on Y-SNP and Y-STR Data from the HGDP-CEPH Populations

Shi

Ayub

Vermeulen

et al. 2009

Molecular Biology and Evolution

101

122

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We have investigated human male demographic history using 590 males from 51 populations in the Human Genome Diversity Project - Centre d’Étude du Polymorphisme Humain worldwide panel, typed with 37 Y-chromosomal Single Nucleotide Polymorphisms and 65 Y-chromosomal Short Tandem Repeats and analyzed with the program Bayesian Analysis of Trees With Internal Node Generation. The general patterns we observe show a gradient from the oldest population time to the most recent common ancestors (TMRCAs) and expansion times together with the largest effective population sizes in Africa, to the youngest times and smallest effective population sizes in the Americas. These parameters are significantly negatively correlated with distance from East Africa, and the patterns are consistent with most other studies of human variation and history. In contrast, growth rate showed a weaker correlation in the opposite direction. Y-lineage diversity and TMRCA also decrease with distance from East Africa, supporting a model of expansion with serial founder events starting from this source. A number of individual populations diverge from these general patterns, including previously documented examples such as recent expansions of the Yoruba in Africa, Basques in Europe, and Yakut in Northern Asia. However, some unexpected demographic histories were also found, including low growth rates in the Hazara and Kalash from Pakistan and recent expansion of the Mozabites in North Africa.

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Section: Methodsmentioning

confidence: 99%

A Worldwide Survey of Human Male Demographic History Based on Y-SNP and Y-STR Data from the HGDP-CEPH Populations

Shi

Ayub

Vermeulen

et al. 2009

Molecular Biology and Evolution

101

122

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Substitution mutation induced migration anomaly of a D10S2325 allele on capillary electrophoresis

et al. 2012

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Microvariants of short tandem repeat (STR) have been reported for different commercially available multiplex STR systems. Sequence length variations caused by variant mechanisms were the central cause of these abnormal phenomena. Here, we reported a novel electrophoretic mobility of the variant allele 13 of D10S2325 in the Investigator HDplex(TM) Kit, which was induced by a special sequence structure containing a poly-G tract (ttg ggg ggg) as a result of only one single base substitution in the flanking regions of the core repeat structure. This migration anomaly can pose a potential risk of wrong designation of some off-ladder alleles in STR loci. Furthermore, population genetic data of the Investigator HDplex(TM) Kit in the Chinese Han population are also reported.

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