New binary polymorphisms reshape and increase resolution of the human Y chromosomal haplogroup tree

Abstract

Markers on the non-recombining portion of the human Y chromosome continue to have applications in many fields including evolutionary biology, forensics, medical genetics, and genealogical reconstruction. In 2002, the Y Chromosome Consortium published a single parsimony tree showing the relationships among 153 haplogroups based on 243 binary markers and devised a standardized nomenclature system to name lineages nested within this tree. Here we present an extensively revised Y chromosome tree containing 311 distinct haplogroups, including two new major haplogroups (S and T), and incorporating approximately 600 binary markers. We describe major changes in the topology of the parsimony tree and provide names for new and rearranged lineages within the tree following the rules presented by the Y Chromosome Consortium in 2002. Several changes in the tree topology have important implications for studies of human ancestry. We also present demography-independent age estimates for 11 of the major clades in the new Y chromosome tree.

Temporal differentiation across a West-European Y-chromosomal cline: genealogy as a tool in human population genetics

“…DYS635 was additionally genotyped for all individuals who were already genotyped for 37 Y-STRs in Larmuseau et al 12 All haplotypes were submitted to Whit Atheys' Haplogroup Predictor 16 to obtain probabilities for the inferred haplogroups. On the basis of these results, the samples were assigned to specific SNP assays to confirm the haplogroup and to assign the sub-haplogroup to the lowest possible level of the latest Y-chr tree reported by Karafet et al 17 and according to the update on the Y Chromosome Consortium web page (http://ycc.biosci.arizona.edu/nomenclature_system/index.html), with the exception of the substructuring within haplogroup A, R1b1b2a1 (R-U106) and R1b1b2a2g (R-U152). Also a set of recently characterized Y-SNPs, which improved resolution of the haplogroup G phylogeny was included.…”

The history of the Y chromosome in man

“…The structure of this new tree mirrors previous trees, which were based on 100-fold fewer SNVs 3,4,6 . However, the wealth of information provided by both the large number of Y chromosomes and variants included in the current study further refine the tree and provide new insight into human population dynamics.…”

Retrieving Y chromosomal haplogroup trees using GWAS data

“…To reconcile our results with the widely accepted Y chromosomal phylogeny and haplogroup definitions, 4 we consulted Y-DNA Haplogroup Tree 2013 of ISOGG (http://www.isogg.org/tree/), 19 which was based on Karafet et al 4 but constantly updated. We followed the previously used nomenclature (ie, lineage-marker) for each haplogroup proposed by Karafet et al 4 To automatically address the data conversion, filtering, and annotation, we also developed C þ þ stand-alone software with GUI: YTool (http://mitotool.org/ ytool/; Supplementary Methods). YTool was also designed to export Y-SNP data in the FASTA format for use in alternative software.…”

“…The PCR amplification and sequencing primers were previously reported. 4 In terms of the diagnostic Y-SNPs, we classified each of the 117 males into their known haplogroup, and then compared the results with those based on DNA chips. Second, we consulted the 6662 Y-SNPs reported in a recent study of Y chromosome using next-generation sequencing (ie, NGS data).…”

“…2 Subsequently, the Y chromosome tree was modified 1,3 and updated. 4 The updated tree provides an important foundation for studies of evolutionary anthropology, 5 genealogical reconstruction, 6 molecular forensics, 7 and medical genetics. 8 Current commercial DNA chips (microarrays) for massive genomewide association studies (GWAS) 9 are designed to contain many Y-SNPs.…”