Maximum parsimony tree showing the phyletic relationships of 104 chromosomes.

<p>The individual Id's (as in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0134646#pone.0134646.s005" target="_blank">S1 Table</a>) are reported on the right, aligned with the corresponding branch. Clades corresponding to major haplogroups are bracketed or indicated individually at the far right, following the nomenclature of van Oven et al. [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0134646#pone.0134646.ref064" target="_blank">64</a>](note the difference with ref. [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0134646#pone.0134646.ref004" target="_blank">4</a>]). Branches are numbered (in italics) and mutations assigned to them are listed in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0134646#pone.0134646.s006" target="_blank">S2 Table</a>. Note that the tree is unrooted and variants defining branch 0 are identified solely as different from the reference sequence. The clade corresponding to Hg E1b1b-M35 has been collapsed since it is discussed in detail in a dedicated paper [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0134646#pone.0134646.ref065" target="_blank">65</a>].</p

Dated tree including 104 subjects plus the Ust'-Ishim [27] and Loschbour [28] specimens (arrowed).

<p>These latter were used as calibration points, by means of normally distributed priors with means 45,000 and 7,205 years ago, respectively. The 95% C.I.'s for the age of each node are represented as grey bars. The clade corresponding to Hg E1b1b-M35 has been collapsed since it is discussed in detail in a dedicated paper [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0134646#pone.0134646.ref065" target="_blank">65</a>]. Groups of branches discussed in the text and in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0134646#pone.0134646.t004" target="_blank">Table 4</a> are shadowed: a) deep branches; b) terminal branches with rho < = 20; c) terminal branches with length < = 10 mutations. Note that the positioning of the root is the result of the Bayesian process and not of the assessment of ancestral/derived states in branch 0 based on an outgroup (e.g. the chimpanzee).</p

Distribution of mutational events in 19 bins in total.

<p>1. Mutations at CpG dinucleotides every 100 kb of positions in CpG dinucleotides.</p><p>Distribution of mutational events in 19 bins in total.</p

Distribution of mutational events in 19 bins, by time windows.

<p>Distribution of mutational events in 19 bins, by time windows.</p

Distribution of mutational events in 19 bins, by haplogroup.

<p>1. Nomenclature as in ref. [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0134646#pone.0134646.ref064" target="_blank">64</a>]</p><p>2. Includes R1</p><p>3. The sum across haplogroups is not 3390 as some Hg's are not shown and R1 is also considered in CF</p><p>Distribution of mutational events in 19 bins, by haplogroup.</p

Information on the mutations here reported and analyzed for the first time.

a<p>Position according to the February 2009 human Y-chromosome reference sequence (GRCh37).</p>b<p>PCR primers amplify three paralogous MSY regions.</p