Evaluating the Y chromosomal STR dating in deep-rooting pedigrees

Investigative Genetics

Volumn 6, Issue 1, 2015, Pages

  Wang, Chuan Chao ^a   Li, Hui ^a  

^a FUDAN UNIVERSITY   (China)

Author keywords

Mutation rate; STR; Time estimation; Y chromosome

Indexed keywords

ANTHROPOLOGY; ARTICLE; GENE MUTATION; GENEALOGY; HAPLOGROUP; HUMAN; MONTE CARLO METHOD; MUTATION RATE; PEDIGREE ANALYSIS; PRIORITY JOURNAL; PROBABILITY; SHORT TANDEM REPEAT; SINGLE NUCLEOTIDE POLYMORPHISM; TIME PERCEPTION; Y CHROMOSOME;

EID: 84931093522     PISSN: None     EISSN: 20412223     Source Type: Journal    
DOI: 10.1186/s13323-015-0025-z     Document Type: Article

References (24)

1. Wang CC, Li H. Inferring human history in East Asia from Y chromosomes. Investig Genet. 2013;4:11.
2. Xue Y, Wang Q, Long Q, Ng BL, Swerdlow H, Burton J, et al. Human Y chromosome base-substitution mutation rate measured by direct sequencing in a deep-rooting pedigree. Curr Biol. 2009;19:1453-7.
3. Y Chromosome Consortium. A nomenclature system for the tree of human Y-chromosomal binary haplogroups. Genome Res. 2002;12:339-48.
4. Karafet TM, Mendez FL, Meilerman MB, Underhill PA, Zegura SL, Hammer MF. New binary polymorphisms reshape and increase resolution of the human Y chromosomal haplogroup tree. Genome Res. 2008;18:830-8.
5. Wang CC, Yan S, Li H. Surnames and the Y chromosomes. Commun Contemp Anthropol. 2010;4:26-33.
6. Zerjal T, Xue Y, Bertorelle G, Wells RS, Bao W, Zhu S, et al. The genetic legacy of the Mongols. Am J Hum Genet. 2003;72:717-21.
7. Wei W, Ayub Q, Xue Y, Tyler-Smith C. A comparison of Y-chromosomal lineage dating using either resequencing or Y-SNP plus Y-STR genotyping. Forensic Sci Int Genet. 2013;7:568-72.
8. Zhivotovsky LA, Underhill PA, Cinnioglu C, Kayser M, Morar B, Kivisild T, et al. The effective mutation rate at Y chromosome short tandem repeats, with application to human population-divergence time. Am J Hum Genet. 2004;74:50-61.
9. Zhivotovsky LA. Estimating divergence time with the use of microsatellite genetic distances: impacts of population growth and gene flow. Mol Biol Evol. 2001;18:700-9.
10. Ramakrishnan U, Mountain JL. Precision and accuracy of divergence time estimates from STR and SNP-STR variation. Mol Biol Evol. 2004;21:1960-71.
11. Sengupta S, Zhivotovsky LA, King R, Mehdi SQ, Edmonds CA, Chow CE, et al. Polarity and temporality of high-resolution y-chromosome distributions in India identify both indigenous and exogenous expansions and reveal minor genetic influence of Central Asian pastoralists. Am J Hum Genet. 2006;78:202-21.
12. Thomas MG, Skorecki K, Ben-Ami H, Parfitt T, Bradman N, Goldstein DB. Origins of old testament priests. Nature. 1998;394:138-40.
13. Thomas MG, Parfitt T, Weiss DA, Skorecki K, Wilson JF, le Roux M, et al. Y chromosomes traveling south: the Cohen modal haplotype and the origins of the Lemba-the "Black Jews of Southern Africa". Am J Hum Genet. 2000;66:674-86.
14. Wilson JF, Weiss DA, Richards M, Thomas MG, Bradman N, Goldstein DB. Genetic evidence for different male and female roles during cultural transitions in the British Isles. Proc Natl Acad Sci U S A. 2001;98:5078-83.
15. Behar DM, Thomas MG, Skorecki K, Hammer MF, Bulygina E, Rosengarten D, et al. Multiple origins of Ashkenazi Levites: Y chromosome evidence for both near Eastern and European ancestries. Am J Hum Genet. 2003;73:768-79.
16. Wilson IJ, Weale ME, Balding DJ. Inferences from DNA data: population histories, evolutionary processes and forensic match probabilities. J R Stat Soc. 2003;116:155-88.
17. Shi D, Yan C. Kinship and heritage of Ningbo Siming SHI clan. Commun Contemp Anthropol. 2013;7:100-4.
18. Wang CC, Yan S, Han S, Jin L, Li H. Poyang CàO clan has no genetic origin in the CáO Cào clan. Commun Contemp Anthropol. 2012;6:14-6.
19. Yan S, Wang CC, Li H, Li SL, Jin L. An updated tree of Y chromosome Haplogroup O and revised phylogenetic positions of mutations P164 and PK4. Eur J Hum Genet. 2011;19:1013-5.
20. Wang C, Yan S, Hou Z, Fu W, Xiong M, Han S, et al. Present Y chromosomes reveal the ancestry of Emperor CAO Cao of 1800 years ago. J Hum Genet. 2012;57:216-8.
21. Burgarella C. Navascue's M. Mutation rate estimates for 110 Y chromosome STRs combining population and father-son pair data. Eur J Hum Genet. 2011;19:70-5.
22. Shi W, Ayub Q, Vermeulen M, Shao RG, Zuniga S, van der Gaag K, et al. A world wide survey of human male demographic history based on Y-SNP and Y-STR datafrom the HGDP-CEPH populations. Mol Biol Evol. 2010;27:385-93.
23. Fenner JN. Cross-cultural estimation of the human generation interval for use in genetics-based population divergence studies. Am J Phys Anthropol. 2005;128:415-23.
24. Xue Y, Zerjal T, Bao W, Zhu S, Shu Q, Xu J, et al. Male demography in East Asia: a north-south contrast in human population expansion times. Genetic. 2006;172:2431-9.