Convergence of Y Chromosome STR Haplotypes from Different SNP Haplogroups Compromises Accuracy of Haplogroup Prediction

a.
State Key Laboratory of Genetic Engineering and MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences and Institutes of Biomedical Sciences, Fudan University, Shanghai 200433, China
b.
CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences of Chinese Academy of Sciences, Shanghai 200031, China

More Information

Corresponding author: E-mail address: lihui.fudan@gmail.com (Hui Li)

摘要

HTML全文

参考文献(25)

[1]	Athey, W.T. Haplogroup prediction from Y-STR values using an allele-frequency approach J. Genet. Geneal., 1 (2005),pp. 1-7
[2]	Athey, W.T. Haplogroup prediction from Y-STR values using a Bayesian-allele-frequency approach J. Genet. Geneal., 2 (2006),pp. 34-39
[3]	Athey, W. Comments on the article, “Software for Y haplogroup predictions, a word of caution” Int. J. Legal. Med., 125 (2011),pp. 901-903
[4]	Ballantyne, K.N., Goedbloed, M., Fang, R. et al. Mutability of Y-chromosomal microsatellites: rates, characteristics, molecular bases, and forensic implications Am. J. Hum. Genet., 87 (2010),pp. 341-353
[5]	Behar, D.M., Garrigan, D., Kaplan, M. et al. Contrasting patterns of the Y chromosome variation in Ashkenazi Jewish and host non-Jewish European populations Hum. Genet., 114 (2004),pp. 354-365
[6]	Bembea, M., Patocs, A., Kozma, K. et al. Y-chromosome STR haplotype diversity in three ethnically isolated population from North-Western Romania Forensic. Sci. Int. Genet., 5 (2011),pp. e99-e100
[7]	Bosch, E., Calafell, F., Santos, F. et al. Variation in short tandem repeats is deeply structured by genetic background on the human Y chromosome Am. J. Hum. Genet., 65 (1999),pp. 1623-1638
[8]	Excoffier, L., Lischer, H.E. Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows Mol. Ecol. Resour., 10 (2010),pp. 564-567
[9]	Gusmão, L., Sanchez-Diz, P., Calafell, F. et al. Mutation rates at Y chromosome specific microsatellites Hum. Mutat., 26 (2005),pp. 520-528
[10]	International Society of Genetic Genealogy
[11]	Karafet, T.M., Mendez, F.L., Meilerman, M.B. et al. New binary polymorphisms reshape and increase resolution of the human Y chromosomal haplogroup tree Genome Res., 18 (2008),pp. 830-838
[12]	Larmuseau, M.H., Ottoni, C., Raeymaekers, J.A. et al. Temporal differentiation across a West-European Y-chromosomal cline: genealogy as a tool in human population genetics Eur. J. Hum. Genet., 20 (2012),pp. 434-440
[13]	Larmuseau, M.H., Vanderheyden, N., Jacobs, M. et al. Micro-geographic distribution of Y-chromosomal variation in the central-western European region Brabant Forensic. Sci. Int. Genet., 5 (2010),pp. 95-99
[14]	Larmuseau, M.H., Vanderheyden, N., Van Geystelen, A. et al. Recent radiation within Y-chromosomal haplogroup R-M269 resulted in high Y-STR haplotype resemblance Ann. Hum. Genet., 78 (2014),pp. 92-103
[15]	Muzzio, M., Ramallo, V., Motti, J.M. et al. Software for Y-haplogroup predictions: a word of caution Int. J. Legal. Med., 125 (2011),pp. 143-147
[16]	Pritchard, J.K., Stephens, M., Donnelly, P. Inference of population structure using multilocus genotype data Genetics, 155 (2000),pp. 945-959
[17]	Schlecht, J., Kaplan, M.E., Barnard, K. et al. Machine-Learning approaches for classifying Haplogroup from Y Chromosome STR data PLoS Comput. Biol., 4 (2008),p. e1000093
[18]	Slatkin, M. A measure of population subdivision based on microsatellite allele frequencies Genetics, 139 (1995),pp. 457-462
[19]	Tamura, K., Peterson, D., Peterson, N. et al. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods Mol. Biol. Evol., 28 (2011),pp. 2731-2739
[20]	Tarlykov, P.V., Zholdybayeva, E.V., Akilzhanova, A.R. et al. Mitochondrial and Y-chromosomal profile of the Kazakh population from East Kazakhstan Croat. Med. J., 54 (2013),pp. 17-24
[21]	Wang, C.C., Li, H. Inferring human history in East Asia from Y chromosomes Investig. Genet., 4 (2013),pp. 1-10
[22]	Wang, C.C., Jin, L., Li, H. Natural selection on human Y chromosomes J. Genet. Genomics, 41 (2014),pp. 47-52
[23]	Wang, C.C., Yan, S., Li, H. Surnames and the Y chromosomes Commun. Contemp. Anthropol., 4 (2010),pp. 26-33
[24]	Xue, Y., Wang, Q., Long, Q. et al. Human Y chromosome base-substitution mutation rate measured by direct sequencing in a deep-rooting pedigree Curr. Biol., 19 (2009),pp. 1453-1457
[25]	Yan, S., Wang, C.C., Li, H. et al. An updated tree of Y-chromosome haplogroup O and revised phylogenetic positions of mutations P164 and PK4 Eur. J. Hum. Genet., 19 (2011),pp. 1013-1015