Increasing phylogenetic resolution still informative for y chromosomal studies on West-European populations

Forensic Science International: Genetics

Volumn 9, Issue 1, 2014, Pages 179-185

  Larmuseau, M H D ^a,b,c   Vanderheyden, N ^a   Van Geystelen, A ^a,c   Van Oven, M ^d   Kayser, M ^d   Decorte, R ^a,b  

^a UNIVERSITY HOSPITALS LEUVEN   (Belgium)

^b DEPARTMENT OF IMAGING AND PATHOLOGY   (Belgium)

^c UNIVERSITY OF LEUVEN   (Belgium)

^d ERASMUS MEDICAL CENTER   (Netherlands)

Author keywords

Discrimination power; Flanders; Genetic genealogy; Population structure; Y chromosomal phylogeny; Y SNPs

Indexed keywords

EUROPE; GENETICS; GENOTYPE; HAPLOTYPE; HUMAN; MALE; PHYLOGENY; PHYLOGEOGRAPHY; POPULATION GENETICS; SINGLE NUCLEOTIDE POLYMORPHISM; Y CHROMOSOME;

CHROMOSOMES, HUMAN, Y; EUROPE; GENETICS, POPULATION; GENOTYPE; HAPLOTYPES; HUMANS; MALE; PHYLOGENY; PHYLOGEOGRAPHY; POLYMORPHISM, SINGLE NUCLEOTIDE;

EID: 84894083672     PISSN: 18724973     EISSN: 18780326     Source Type: Journal    
DOI: 10.1016/j.fsigen.2013.04.002     Document Type: Article

References (34)

1. M.A. Jobling, M.E. Hurles, and C. Tyler-Smith Human Evolutionary Genetics: Origins, Peoples and Disease 2004 Garland Science Publishing London/New York 523
2. P.A. Underhill, and T. Kivisild Use of Y chromosome and mitochondrial DNA population structure in tracing human migrations Annu. Rev. Genet. 41 2007 539 564
3. M.A. Jobling, and C. Tyler-Smith The human Y chromosome: an evolutionary marker comes of age Nat. Rev. Genet. 4 2003 598 612 (Pubitemid 36917502)
4. J.M. Butler Y-chromosomal DNA testing J.M. Butler, Advanced Topics in Forensic DNA Typing: Methodology 2011 Academic Press London 371 403 (Chapter 13)
5. J. Chiaroni, P.A. Underhill, and L.L. Cavalli-Sforza Y chromosome diversity, human expansion, drift, and cultural evolution Proc. Natl. Acad. Sci. U.S.A. 106 2009 20174 20179
6. T.M. Karafet, F.L. Mendez, M.B. Meilerman, P.A. Underhill, S.L. Zegura, and M.F. Hammer New binary polymorphisms reshape and increase resolution of the human Y chromosomal haplogroup tree Genome Res. 18 2008 830 838 (Pubitemid 351645073)
7. D.L. Altshuler, R.M. Durbin, G.R. Abecasis, D.R. Bentley, A. Chakravarti, A.G. Clark, F.S. Collins, F.M. De la Vega, P. Donnelly, and M. Egholm et al. A map of human genome variation from population-scale sequencing Nature 467 2010 1061 1073
8. N.M. Myres, S. Rootsi, A.A. Lin, M. Jarve, R.J. King, I. Kutuev, V.M. Cabrera, E.K. Khusnutdinova, A. Pshenichnov, and B. Yunusbayev et al. A major Y-chromosome haplogroup R1b Holocene era founder effect in Central and Western Europe Eur. J. Hum. Genet. 19 2011 95 101
9. R.A. Rocca, G. Magoon, D.F. Reynolds, T. Krahn, V.O. Tilroe, P.M.O. Boots, and A.J. Grierson Discovery of Western European R1b1a2 Y chromosome variants in 1000 Genomes project data: an online community approach PLoS ONE 7 2012 e41634
10. M.H.D. Larmuseau, N. Vanderheyden, M. Jacobs, M. Coomans, L. Larno, and R. Decorte Micro-geographic distribution of Y-chromosomal variation in the central-western European region Brabant Forensic Sci Int Genet 5 2011 95 99
11. M.H.D. Larmuseau, J. Vanoverbeke, G. Gielis, N. Vanderheyden, H.F.M. Larmuseau, and R. Decorte In the name of the migrant father - analysis of surname origin identifies historic admixture events undetectable from genealogical records Heredity 109 2012 90 95
12. M.H.D. Larmuseau, C. Ottoni, J.A.M. Raeymaekers, N. Vanderheyden, H.F.M. Larmuseau, and R. Decorte Temporal differentiation across a West-European Y-chromosomal cline - genealogy as a tool in human population genetics Eur. J. Hum. Genet. 20 2012 434 440
13. M. Van den Cloot DNA Brabant - DNA-project 2009 oud-hertogdom Brabant 2010 Familiekunde Vlaanderen Antwerpen 352
14. M. Van den Cloot DNA België - DNA-project 2010 België, exclusief oud-hertogdom Brabant 2011 Familiekunde Vlaanderen Antwerpen 328
15. M.H.D. Larmuseau, A. Van Geystelen, M. van Oven, and R. Decorte Genetic genealogy comes of age - perspectives on the use of deep-rooted pedigrees in human population genetics Am. J. Phys. Anthropol. 150 2013 505 511
16. F. Debrabandere Woordenboek van de familienamen in België en Noord-Frankrijk 2003 L.J. Veen/Het Taalfonds Amsterdam/Antwerpen
17. W.T. Athey Haplogroup prediction from Y-STR values using a Bayesian-allele-frequency approach J. Genet. Geneal. 2 2006 34 39
18. L.M. Sims, D. Garvey, and J. Ballantyne Improved resolution haplogroup G phylogeny in the Y-chromosome, revealed by a set of newly characterized SNPs PLoS ONE 4 2009 e5792
19. F.L. Mendez, T.M. Karafet, T. Krahn, H. Ostrer, H. Soodyall, and M.F. Hammer Increased resolution of Y chromosome haplogroup T defines relationships among populations of the Near East, Europe, and Africa Hum. Biol. 83 2011 39 53
20. A. Van Geystelen, R. Decorte, and M.H.D. Larmuseau AMY-tree: an algorithm to use whole genome SNP calling for Y chromosomal phylogenetic applications BMC Genom. 14 2013 101
21. S. Caratti, S. Gino, C. Torre, and C. Robino Subtyping of Y-chromosomal haplogroup E-M78 (E1b1b1a) by SNP assay and its forensic application Int. J. Legal Med. 123 2009 357 360
22. M. van Oven, A. Ralf, and M. Kayser An efficient multiplex genotyping approach for detecting the major worldwide human Y-chromosome haplogroups Int. J. Legal Med. 125 2011 879 885
23. L. Excoffier, G. Laval, and S. Schneider ARLEQUIN ver.3.0: an integrated software package for population genetics data analysis Evol. Bioinform. Online 1 2005 47 50
24. W.R. Rice Analyzing tables of statistical tests Evolution 43 1989 223 225
25. T. Hothorn, K. Hornik, M.A.V. van de Wiel, and A. Zeileis Implementing a class of permutation tests: the coin Package J. Stat. Softw. 28 2008 1 23
26. R. Scozzari, A. Massaia, E. D'Atanasio, N.M. Myres, U.A. Perego, B. Trombetta, and F. Cruciani Molecular dissection of the basal clades in the human Y chromosome phylogenetic tree PLoS ONE 7 2012 e49170
27. H. Skaletsky, T. Kuroda-Kawaguchi, P.J. Minx, H.S. Cordum, L. Hillier, L.G. Brown, S. Repping, T. Pyntikova, J. Ali, and T. Bieri et al. The male-specific region of the human Y chromosome is a mosaic of discrete sequence classes Nature 423 2003 825 837 (Pubitemid 36781267)
28. W. Wei, Q. Ayub, Y. Chen, S. McCarthy, Y. Hou, I. Carbone, Y. Xue, and C. Tyler-Smith A calibrated human Y-chromosomal phylogeny based on resequencing Genome Res. 23 2013 388 395
29. D.L. Hartl, and A.G. Clark Principles of Population Genetics 4th ed. 2006 Sinauer Associates Inc. Sunderland, USA 545
30. G.B.J. Busby, F. Brisighelli, P. Sánchez-Diz, E. Ramos-Luis, C. Martinez-Cadenas, M.G. Thomas, D.G. Bradley, L. Gusmao, B. Winney, and W. Bodmer et al. The peopling of Europe and the cautionary tale of Y chromosome lineage R-M269 Proc. Roy. Soc. B 279 2012 884 892
31. M. Cloet, and C. Vandenbroeke Tien bijdragen tot de lokale en regionale demografie in Vlaanderen 1989 Gemeentekrediet Brussel 291
32. T.E. King, and M.A. Jobling What's in a name? Y chromosomes, surnames and the genetic genealogy revolution Trends Genet. 25 2009 351 360
33. F. Cruciani, B. Trombetta, C. Antonelli, R. Pascone, G. Valesini, V. Scalzi, G. Vona, B. Melegh, B. Zagradisnik, and G. Assum et al. Strong intra- and inter-continental differentiation revealed by Y chromosome SNPs M269, U106 and U152 Forensic Sci. Int. Genet. 5 2011 E49 E52
34. M. Brion, B. Quintans, M. Zarrabeitia, A. Gonzalez-Neira, A. Salas, V. Lareu, C. Tyler-Smith, and A. Carracedo Micro-geographical differentiation in Northern Iberia revealed by Y-chromosomal DNA analysis Gene 329 2004 17 25 (Pubitemid 38366491)