Sequencing Y Chromosomes Resolves Discrepancy in Time to Common Ancestor of Males Versus Females

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Science  02 Aug 2013:
Vol. 341, Issue 6145, pp. 562-565
DOI: 10.1126/science.1237619

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  1. Fig. 1 Callability mask for the Y chromosome.

    Exponentially weighted moving averages of read depth (blue line) and the proportion of reads mapping ambiguously (MQ0 ratio; violet line) versus physical position. Regions with values outside the envelopes defined by the dashed lines (depth) or dotted lines (MQ0) were flagged (blue and violet boxes) and merged for exclusion (gray boxes). The complement (black boxes) defines the regions within which reliable genotype calls can be made. Below, a scatter plot indicates the positions of all observed SNVs. Those incompatible with the inferred phylogenetic tree (red) are uniformly distributed. The X-degenerate regions yield quality sequence data, ampliconic sequences tend to fail both filters, and mapping quality is poor in the X-transposed region.

  2. Fig. 2 Y-chromosome phylogeny inferred from genomic sequencing.

    This tree recapitulates the previously known topology of the Y-chromosome phylogeny; however, branch lengths are now free of ascertainment bias. Branches are drawn proportional to the number of derived SNVs. Internal branches are labeled with defining ISOGG variants inferred to have arisen on the branch. Leaves are colored by major haplogroup cluster and labeled with the most derived mutation observed and the population from which the individual was drawn. Previously uncharacterized structure within African hgB2 is indicated in orange. (Inset) Resolution of a polytomy was possible through the identification of a variant for which hgG retains the ancestral allele, whereas hgH and hgIJK share the derived allele.

  3. Fig. 3 Similarity of TMRCA does not imply equivalent Ne of males and females.

    The TMRCA for a given locus is drawn from a predata (i.e., prior) distribution that is a function of Ne, generation time, sample size, and demographic history. Consider the distribution of possible TMRCAs for a set of 100 uniparental chromosomes. Although the Mbuti mtDNA Ne is twice as large as that of the Baka Y chromosome, the corresponding predata TMRCA distributions overlap considerably.