Article

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: 11.2). 02/2013; 92(3). DOI: 10.1016/j.ajhg.2013.02.002
Source: PubMed

ABSTRACT 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.

2 Bookmarks
 · 
234 Views
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Comparisons of maternally-inherited mitochondrial DNA (mtDNA) and paternally-inherited non-recombining Y chromosome (NRY) variation have provided important insights into the impact of sex-biased processes (such as migration, residence pattern, and so on) on human genetic variation. However, such comparisons have been limited by the different molecular methods typically used to assay mtDNA and NRY variation (for example, sequencing hypervariable segments of the control region for mtDNA vs. genotyping SNPs and/or STR loci for the NRY). Here, we report a simple capture array method to enrich Illumina sequencing libraries for approximately 500 kb of NRY sequence, which we use to generate NRY sequences from 623 males from 51 populations in the CEPH Human Genome Diversity Panel (HGDP). We also obtained complete mtDNA genome sequences from the same individuals, allowing us to compare maternal and paternal histories free of any ascertainment bias.
    Investigative genetics. 01/2014; 5:13.
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Y chromosome is a superb tool for inferring human evolution and recent demographic history from a paternal perspective. However, Y chromosomal substitution rates obtained using different modes of calibration vary considerably, and have produced disparate reconstructions of human history. Here, we discuss how substitution rate and date estimates are affected by the choice of different calibration points. We argue that most Y chromosomal substitution rates calculated to date have shortcomings, including a reliance on the ambiguous human-chimpanzee divergence time, insufficient sampling of deep-rooting pedigrees, and using inappropriate founding migrations, although the rates obtained from a single pedigree or calibrated with the peopling of the Americas seem plausible. We highlight the need for using more deep-rooting pedigrees and ancient genomes with reliable dates to improve the rate estimation.
    Investigative Genetics. 08/2014; 5(12).
  • [Show abstract] [Hide abstract]
    ABSTRACT: Hominins from Europe and Africa shed light on functional adaptations and other aspects of lifeways during the Middle Paleolithic. By the end of that time span, Neanderthals and modern humans clearly differed physically and perhaps behaviorally. Explanations of the anatomical differences have largely focused on adaptation (directional selection) to climate and habitual activity, but it is hard to rule out the alternative of genetic drift. Drift would have accelerated during periods of low population numbers, while selection operates best when populations are large and expanding. Demographic changes almost certainly tracked climatic conditions in both continents. Environmental and genetic data suggest that European hominins were primarily shaped by drift, while both factors operated in Africa.
    Current Anthropology 12/2013; 54(S8):S221-S233. · 2.93 Impact Factor

Full-text

Download
59 Downloads
Available from
Jun 4, 2014