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(2014) with minor modifications that are aimed to make the haplogroup nomenclature more amenable to the incorporation of novel haplotypes than it is now (Supplemental Information 6).
Using standard and custom filters (Supplemental Information 2; Supplemental Table S2), we first identified reliable regions on the Chr Y and retained 8.8 Mb of sequence per individual.
S20) and another clade containing all the other C lineages including two new highly divergent subclades detected in our Island Southeast Asian samples that we call C7 and C9 (Supplemental Fig. Regional representations of pairwise divergence times of Y chromosomes also revealed clustering of coalescence events consistent with the peopling of the Americas at around 15 kya (Supplemental Fig. We used Bayesian skyline plots (BSP) to infer temporal changes of regional male and female effective population sizes () (Supplemental Fig. The cumulative global BSP of 320 Y chromosomes with known geographic affiliation and the plot inferred from mt DNA sequences from the same individuals both showed increases in the estimates based on mt DNA are consistently more than twice as high as those based on the Y chromosome (Supplemental Fig. Secondly, both mt DNA and Y plots (Supplemental Fig. was performed according to the Russian Government Program of Competitive Growth of Kazan Federal University and funded by the subsidy allocated to Kazan Federal University for the state assignment in the sphere of scientific activities.The proposed structure of Y chromosome haplogroup naming (Supplemental Table S5) is given in Roman numbers on the In labeling Y chromosome haplogroups, we follow the principles and rules set out by the Y Chromosome Consortium (YCC) (The Y Chromosome Consortium 2002).As we introduce a large number of new whole Chr Y sequences that substantially increase the resolution of the internal branches of the Chr Y tree, we try to both incorporate the new information and to maintain the integrity and historical coherence of the initial YCC haplogroup nomenclature as introduced in 2002 and its updates (Jobling and Tyler-Smith 2003; Karafet et al. We use an approach similar to the concise reference phylogeny proposed by van Oven et al.Previous studies have established a standard Y chromosome haplogroup nomenclature based on resequencing of limited tracts of the locus in small numbers of geographically diverse samples (The Y Chromosome Consortium 2002; Karafet et al. Asterisk (*) marks the inclusion of samples from Caucasus area. 2014), the factors affecting its dynamics are still poorly understood.
S9) fits well with archaeological evidence for the dates of colonization of Eurasia and Australia by anatomically modern humans as a single wave ∼50 kya (Bowler et al. A change in social structures that increased male variance in offspring number may explain the results, especially if male reproductive success was at least partially culturally inherited (Heyer et al. Changes in population structure can also drastically affect the .