Additional file 4: Figure S1. of A SNP panel for identification of DNA and RNA specimens

Plot of the expected heterozygosity (x-axis) and observed heterozygosity (y-axis) for the 50 SNPs in the panel. Pearson correlation is 0.98. (DOC 54 kb

Additional file 7: Figure S5. of A SNP panel for identification of DNA and RNA specimens

The average of population genetic parameters for 50 selected SNPs. (DOC 46 kb

Additional file 3: Figure S1. of A SNP panel for identification of DNA and RNA specimens

Distribution of MAF calculated from DNA and RNA data. (DOC 58 kb

Additional file 5: Figure S3. of A SNP panel for identification of DNA and RNA specimens

Individual heterozygosity across loci for each sample determined by GenAlEx software. (DOC 46 kb

Additional file 2: Table S2. of A SNP panel for identification of DNA and RNA specimens

Characteristics of 50 selected SNPs. (CSV 15 kb

Structural variation on the short arm of the human Y chromosome: recurrent multigene deletions encompassing Amelogenin Y

Structural polymorphism is increasingly recognised as a major form of human genome variation, and is particularly prevalent on the Y chromosome. Assay of the Amelogenin Y gene (AMELY) on Yp is widely used in DNA-based sex testing, and sometimes reveals males who have interstitial deletions. In a collection of 45 deletion males from 12 populations, we used a combination of STS (sequence-tagged site) mapping, and binary-marker and Y-STR (short tandem repeat) haplotyping to understand the structural basis of this variation. 41/45 males carry indistinguishable deletions, 3.0-3.8Mb in size. Breakpoint mapping strongly implicates a mechanism of non-allelic homologous recombination between the proximal major array of TSPY-genecontaining repeats, and a single distal copy of TSPY; this is supported by estimation of TSPY copy number in deleted and non-deleted males. The remaining four males carry three distinct non-recurrent deletions (2.5-4.0Mb) which may be due to non-homologous mechanisms. Haplotyping shows that TSPY-mediated deletions have arisen seven times independently in the sample. One instance, represented by 30 chromosomes mostly of Indian origin within haplogroup J2e1*/M241, has a time-to-most-recent-commonancestor of ~7700 ± 1300 years. In addition to AMELY, deletion males all lack the genes PRKY and TBL1Y, and the rarer deletion classes also lack PCDH11Y. The persistence and expansion of deletion lineages, together with direct phenotypic evidence, suggests that absence of these genes has no major deleterious effects

Summary of Mantel tests in zt.

<p>The results of the simple Mantel tests are shown above the diagonal; the results of the partial Mantel tests are shown below the diagonal. r_p: correlation coefficient for Mantel test on population level with 100 thousand randomisations, r_i: correlation coefficient for Mantel test on individual level with 10 thousand randomisations. Corresponding p-values are shown between brackets.</p

Summary of Admixture analysis.

<p>IE: Indo-European, TB: Tibeto-Burman, DR: Dravidian, AL: Altaic.</p

MDS plot.

<p>Populations have been colour coded according to linguistic phylum and geographical origin, as is explained within the figure. The population-codes used in this plot are explained in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0091534#pone-0091534-t001" target="_blank">table 1</a> and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0091534#pone.0091534.s005" target="_blank">table S1</a>. The stress values for the dimensions used to construct this plot were 0.333475 and 0.216317 respectively.</p

Summary of Mantel tests in zt.

<p>The results of the simple Mantel tests are shown above the diagonal; the results of the partial Mantel tests are shown below the diagonal. r_p: correlation coefficient for Mantel test on population level with 100 thousand randomisations, r_i: correlation coefficient for Mantel test on individual level with 10 thousand randomisations. Corresponding p-values are shown between brackets.</p