An African American Paternal Lineage Adds an Extremely Ancient Root to the Human Y Chromosome Phylogenetic Tree

Division of Biotechnology, Arizona Research Laboratories, University of Arizona, Tucson, AZ 85721, USA.
The American Journal of Human Genetics (Impact Factor: 10.93). 02/2013; 92(3). DOI: 10.1016/j.ajhg.2013.02.002
Source: PubMed


We report the discovery of an African American Y chromosome that carries the ancestral state of all SNPs that defined the basal portion of the Y chromosome phylogenetic tree. We sequenced ∼240 kb of this chromosome to identify private, derived mutations on this lineage, which we named A00. We then estimated the time to the most recent common ancestor (TMRCA) for the Y tree as 338 thousand years ago (kya) (95% confidence interval = 237-581 kya). Remarkably, this exceeds current estimates of the mtDNA TMRCA, as well as those of the age of the oldest anatomically modern human fossils. The extremely ancient age combined with the rarity of the A00 lineage, which we also find at very low frequency in central Africa, point to the importance of considering more complex models for the origin of Y chromosome diversity. These models include ancient population structure and the possibility of archaic introgression of Y chromosomes into anatomically modern humans. The A00 lineage was discovered in a large database of consumer samples of African Americans and has not been identified in traditional hunter-gatherer populations from sub-Saharan Africa. This underscores how the stochastic nature of the genealogical process can affect inference from a single locus and warrants caution during the interpretation of the geographic location of divergent branches of the Y chromosome phylogenetic tree for the elucidation of human origins.

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    • "The depth of population substructure is demonstrated by the discovery that the most basal Y-chromosome lineage has a time to most recent common ancestor (TMRCA) of ~338 ka (Mendez et al., 2013). Like the evidence from the Iwo Eleru rockshelter supporting a late persistence of population substructure, this very early evidence is also linked to West Africa, specifically to West African Mbo populations (Mendez et al., 2013). Of note in this context, is the fact that after the Khoe-San of southern Africa, the Pygmy populations of central and the fringes of western Africa are the most genetically divergent contemporary human populations in the world (Veeramah and Hammer, 2014). "
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    ABSTRACT: The importance of Africa in human origins is widely recognised, yet knowledge remains strongly biased towards certain regions of the continent at the expense of others. West Africa in particular is a vast area with extremely limited archaeological, environmental and fossil records. In this paper, we contribute towards redressing this imbalance though a summary of the state of knowledge of the West African Middle Stone Age (MSA), and the presentation of preliminary analyses of ten newly discovered MSA archaeological sites situated along the Senegal River. Archaeological, fossil and genetic data relevant to the West African MSA, a period currently thought to span from at least ~150 ka until the Terminal Pleistocene, are first discussed. Technological analyses of newly discovered MSA assemblages in Senegal are then presented and contextualised with the ecology and environmental evolution of West Africa. Our preliminary findings suggest an overall high level of technological diversity along the Senegal River, but identify common technological features between assemblages in northern Senegal. These include an emphasis on centripetal methods of Levallois reduction (both preferential and recurrent). The discovery of tools in northern Senegal with basal modifications consistent with tanging may also suggest some form of connection with North African assemblages and is commensurate with the role of Senegal as a transitional zone between sub-Saharan and Saharan Africa. Although preliminary, the emerging results demonstrate the potential of the region to contribute to debates on intra-African dispersals, including population persistence and turnovers.
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    • "In haplogroup A we keep the A00, A0, and A1 definitions according to (Cruciani et al. 2011; Mendez et al. 2013). Following Table S5 scheme we define four subclades (A2-A5) in the A2'5 clade defined by L419 (Figure S14). "

    Full-text · Dataset · Mar 2015
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    • "Applying the widely-employed 'evolutionary' STR mutation rate (Zhivotovsky et al. 2004) leads to systematic overestimation of TMRCAs compared to SNP data (though this is no longer true for all nodes if we apply a slower SNP mutation rate (Mendez et al. 2013); Table S6); the much faster 'pedigree' STR rate leads to underestimation generally, but performs better for younger clades. This probably reflects the increasing importance of back-mutation in older clades. "
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    ABSTRACT: Many studies of human populations have used the male-specific region of the Y chromosome (MSY) as a marker, but MSY sequence variants have traditionally been subject to ascertainment bias. Also, dating of haplogroups has relied on Y-specific short tandem repeats (STRs), involving problems of mutation rate choice, and possible long-term mutation saturation. Next-generation sequencing can ascertain single nucleotide polymorphisms (SNPs) in an unbiased way, leading to phylogenies in which branch-lengths are proportional to time, and allowing the times-to-most-recent-common-ancestor (TMRCAs) of nodes to be estimated directly. Here we describe the sequencing of 3.7 Mb of MSY in each of 448 human males at a mean coverage of 51 ×, yielding 13,261 high-confidence SNPs, 65.9% of which are previously unreported. The resulting phylogeny covers the majority of the known clades, provides date estimates of nodes, and constitutes a robust evolutionary framework for analysing the history of other classes of mutation. Different clades within the tree show subtle but significant differences in branch lengths to the root. We also apply a set of 23 Y-STRs to the same samples, allowing SNP- and STR-based diversity and TMRCA estimates to be systematically compared. Ongoing purifying selection is suggested by our analysis of the phylogenetic distribution of non-synonymous variants in 15 MSY single-copy genes.
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