Computational protocol: Deep Roots for Aboriginal Australian Y Chromosomes

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Protocol publication

[…] This study received ethical approval from the La Trobe University Human Ethics Committee, Melbourne, Australia (HEC 05/94, April 11, 2006; amended April 18, 2012, June 26, 2012) and The Wellcome Trust Sanger Institute Human Materials and Data Management Committee, Hinxton, UK (12/055). Conclusions from the study have been returned to the participants. We sequenced the whole genomes of 13 Aboriginal Australian males to high coverage on the Illumina HiSeq platform and then analyzed only the reads mapping to the Y chromosome. We used FreeBayes to determine the genotypes of these individuals, along with those of 1,244 males sequenced to low coverage in the 1000 Genomes Project [] and 12 males from Papua New Guinea sequenced to high coverage [], at ∼10 million Y chromosome sites accessible by short read sequencing. We then used RAxML [] to infer a maximum-likelihood phylogeny of all the 1,269 Y chromosomes. We estimated the divergence times between clades in the tree by applying the ρ statistic [], aggregating data across low-coverage samples where relevant, and converted divergence times to units of years by applying a mutation rate of 0.76 × 10−9 per site per year []. For more detailed descriptions of the sequence data processing, genotyping and filtering, phylogenetic inference, and dating, see the . provides information on the SNPs called that are phylogenetically informative for the branches of the Y chromosome phylogeny specific to Aboriginal Australians and Papuans (see the for a description of this table). […]

Pipeline specifications

Software tools FreeBayes, RAxML
Application Phylogenetics
Organisms Homo sapiens