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.2014 Mar;24(3):535-44.
doi: 10.1101/gr.160788.113. Epub 2014 Jan 6.

An unbiased resource of novel SNP markers provides a new chronology for the human Y chromosome and reveals a deep phylogenetic structure in Africa

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An unbiased resource of novel SNP markers provides a new chronology for the human Y chromosome and reveals a deep phylogenetic structure in Africa

Rosaria Scozzari et al. Genome Res.2014 Mar.

Abstract

Sequence diversity and the ages of the deepest nodes of the MSY phylogeny remain largely unexplored due to the severely biased collection of SNPs available for study. We characterized 68 worldwide Y chromosomes by high-coverage next-generation sequencing, including 18 deep-rooting ones, and identified 2386 SNPs, 80% of which were novel. Many aspects of this pool of variants resembled the pattern observed among genome-wide de novo events, suggesting that in the MSY, a large proportion of newly arisen alleles has survived in the phylogeny. Some degree of purifying selection emerged in the form of an excess of private missense variants. Our tree recapitulated the previously known topology, but the relative lengths of major branches were drastically modified and the associated node ages were remarkably older. We found significantly different branch lengths when comparing the rare deep-rooted A1b African lineage with the rest of the tree. Our dating results and phylogeography led to the following main conclusions: (1) Patrilineal lineages with ages approaching those of early AMH fossils survive today only in central-western Africa; (2) only a few evolutionarily successful MSY lineages survived between 160 and 115 kya; and (3) an early exit out of Africa (before 70 kya), which fits recent western Asian archaeological evidence, should be considered. Our experimental design produced an unbiased resource of new MSY markers informative for the initial formation of the anatomically modern human gene pool, i.e., a period of our evolution that had been previously considered to be poorly accessible with paternally inherited markers.

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Figures

Figure 1.
Figure 1.
Regions of the Y chromosome analyzed and distribution of variants discovered. The different tracks fromtop tobottom report the following features: Y chromosome ideogram, Y chromosome position according to the human Y chromosome reference GRCh37/hg19, the five regions targeted for capture (black bars), variant positions (thin marks), and UCSC genes.
Figure 2.
Figure 2.
Maximum parsimony tree obtained with 2386 variable positions. The number of mutational events defining each branch is shownabove it. For the collapsed haplogroups E, I, and P, the average number of mutations is shown. Dating estimates are reported in boxes near each node (upper and lower values obtained with BEAST and the rho method, respectively). Colored belts indicate major haplogroups according to current nomenclature (Karafet et al. 2008; Scozzari et al. 2012).
Figure 3.
Figure 3.
Geographic distribution of deep-rooting haplogroups in the African continent. Map of Africa showing schematically the present-day home ranges of the MSY haplogroups discussed in the text (redrawn from Chiaroni et al. [2009], with modifications and updates based on haplogroup frequencies reported in Supplemental Table S7). Colors are as in Figure 2, and their intensity does not reflect haplogroup frequencies in the corresponding populations. Haplogroup B2, ubiquitous in sub-Saharan Africa, was omitted.
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