Highlights
- •An overview of four defined categories of currently used Y-chromosomal phylogenies.
- •A reduced consensus tree is the most appropriate reference resource for forensics.
- •Initiatives to reach an international consensus phylogeny are highly recommended.
Abstract
Currently, several different Y-chromosomal phylogenies and haplogroup nomenclatures
are presented in scientific literature and at conferences demonstrating the present
diversity in Y-chromosomal phylogenetic trees and Y-SNP sets used within forensic
and anthropological research. This situation can be ascribed to the exponential growth
of the number of Y-SNPs discovered due to mostly next-generation sequencing (NGS)
studies. As Y-SNPs and their respective phylogenetic positions are important in forensics,
such as for male lineage characterization and paternal bio-geographic ancestry inference,
there is a need for forensic geneticists to know how to deal with these newly identified
Y-SNPs and phylogenies, especially since these phylogenies are often created with
other aims than to carry out forensic genetic research. Therefore, we give here an
overview of four categories of currently used Y-chromosomal phylogenies and the associated
Y-SNP sets in scientific research in the current NGS era. We compare these categories
based on the construction method, their advantages and disadvantages, the disciplines
wherein the phylogenetic tree can be used, and their specific relevance for forensic
geneticists. Based on this overview, it is clear that an up-to-date reduced tree with
a consensus Y-SNP set and a stable nomenclature will be the most appropriate reference
resource for forensic research. Initiatives to reach such an international consensus
are therefore highly recommended.
Keywords
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References
- AMY-tree: an algorithm to use whole genome SNP calling for Y chromosomal phylogenetic applications.BMC Genomics. 2013; : 14
- Chapter 13 Y-chromosomal DNA testing.in: Butler J.M. Advanced Topics in Forensic DNA Typing: Methodology. Academic Press, London2011: 371-403
- Y chromosome in forensic science.in: Primorac D. Shanfield M. Forensic DNA Applications: An Interdisciplinary Perspective. CRC Press Taylor & Francis Group, 2014
- A nomenclature system for the tree of human Y-chromosomal binary haplogroups.Genome Research. 2002; 12: 339-348
- The human Y chromosome: an evolutionary marker comes of age.Nature Reviews Genetics. 2003; 4: 598-612
- New binary polymorphisms reshape and increase resolution of the human Y chromosomal haplogroup tree.Genome Research. 2008; 18: 830-838
- Discovery of Western European R1b1a2 Y chromosome variants in 1000 Genomes project data: an online community approach.PLOS One. 2012; 7: e41634
- Updating the Y-chromosomal phylogenetic tree for forensic applications based on whole genome SNPs.Forensic Science International: Genetics. 2013; 7: 573-580
- Low-pass DNA sequencing of 1200 Sardinians reconstructs European Y-chromosome phylogeny.Science. 2013; 341: 565-569
- Y chromosomes of 40% Chinese descend from three Neolithic Super-Grandfathers.PLOS One. 2014; 9: e105691
- Molecular dissection of the basal clades in the human Y chromosome phylogenetic tree.PLOS One. 2012; 7: e49170
- An unbiased resource of novel SNP markers provides a new chronology for the human Y chromosome and reveals a deep phylogenetic structure in Africa.Genome Research. 2014; 24: 535-544
G.R. Magoon, R.H. Banks, C. Rottensteiner, B.E. Schrack, V.O. Tilroe, T. Robb, A.J. Grierson. Generation of high-resolution a priori Y-chromosome phylogenies using next-generation sequencing data. ArXiv, 2013. http://dx.doi.org/10.1101/000802.
- Sequencing Y chromosomes resolves discrepancy in time to common ancestor of males versus females.Science. 2013; 341: 562-565
C.-C. Wang, H. Li H. Discovery of phylogenetic relevant Y-chromosome variants in 1000 Genomes Project data. ArX*iv:arX*iv:1310.6590, 2013.
- A calibrated human Y-chromosomal phylogeny based on resequencing.Genome Research. 2013; 23: 388-395
- Retrieving Y chromosomal haplogroup trees using GWAS data.European Journal of Human Genetics. 2014; 22: 1046-1050
P. Hallast, C. Batini, D. Zadik, P. Maisano Delser, J. Wetton, E. Arroyo-Pardo, W. Bodmer, G.L. Cavalleri, P. de Knijff, G. Destro-Bisol et al. The Y-chromosome tree bursts into leaf: 13,000 high-confidence SNPs covering the majority of known clades. Molecular Biology & Evolution, in press.
- The human Y chromosome haplogroup tree: nomenclature and phylogeography of its major divisions.Annual Review of Anthropology. 2002; 31: 303-321
A. Van Geystelen, T. Wenseleers, R. Decorte, M. Caspers, M.H.D. Larmuseau. In silico detection of phylogenetic informative Y-chromosomal SNPs from WGS data. Electrophoresis. In press.
- Seeing the wood for the trees: a minimal reference phylogeny for the human Y chromosome.Human Mutation. 2014; 35: 187-191
- Inferring population structure and relationship using minimal independent evolutionary markers in Y-chromosome: a hybrid approach of recursive feature selection for hierarchical clustering.Nucleic Acids Research. 2014; 42: e122
- High resolution mapping of Y haplogroup G in Tyrol (Austria).Forensic Science International: Genetics. 2013; 7: 529-536
- Multiplex genotyping assays for fine-resolution subtyping of the major human Y-chromosome haplogroups E, G, I, J and R in anthropological, genealogical, and forensic investigations.Electrophoresis. 2013; 34: 3029-3038
- Increasing phylogenetic resolution still informative for Y chromosomal studies on West-European populations.Forensic Science International: Genetics. 2014; 9: 179-185
Article info
Publication history
Published online: November 14, 2014
Accepted:
November 9,
2014
Received in revised form:
November 7,
2014
Received:
July 30,
2014
Identification
Copyright
© 2014 Elsevier Ireland Ltd. Published by Elsevier Inc. All rights reserved.
