An African American paternal lineage adds an extremely ancient root to the human y chromosome phylogenetic tree

Fernando L. Mendez, Thomas Krahn, Bonnie Schrack, Astrid Maria Krahn, Krishna R. Veeramah, August E. Woerner, Forka Leypey Mathew Fomine, Neil Bradman, Mark G. Thomas, Tatiana Karafet, Michael F Hammer

Research output: Contribution to journalArticle

74 Citations (Scopus)

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.

Original languageEnglish (US)
Pages (from-to)454-459
Number of pages6
JournalAmerican Journal of Human Genetics
Volume92
Issue number3
DOIs
StatePublished - Mar 7 2013

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Y Chromosome
Human Chromosomes
African Americans
Central Africa
Geographic Locations
Fossils
Africa South of the Sahara
Mitochondrial DNA
Population
Single Nucleotide Polymorphism
Chromosomes
Databases
Confidence Intervals
Mutation

ASJC Scopus subject areas

  • Genetics
  • Genetics(clinical)

Cite this

An African American paternal lineage adds an extremely ancient root to the human y chromosome phylogenetic tree. / Mendez, Fernando L.; Krahn, Thomas; Schrack, Bonnie; Krahn, Astrid Maria; Veeramah, Krishna R.; Woerner, August E.; Fomine, Forka Leypey Mathew; Bradman, Neil; Thomas, Mark G.; Karafet, Tatiana; Hammer, Michael F.

In: American Journal of Human Genetics, Vol. 92, No. 3, 07.03.2013, p. 454-459.

Research output: Contribution to journalArticle

Mendez, FL, Krahn, T, Schrack, B, Krahn, AM, Veeramah, KR, Woerner, AE, Fomine, FLM, Bradman, N, Thomas, MG, Karafet, T & Hammer, MF 2013, 'An African American paternal lineage adds an extremely ancient root to the human y chromosome phylogenetic tree', American Journal of Human Genetics, vol. 92, no. 3, pp. 454-459. https://doi.org/10.1016/j.ajhg.2013.02.002
Mendez, Fernando L. ; Krahn, Thomas ; Schrack, Bonnie ; Krahn, Astrid Maria ; Veeramah, Krishna R. ; Woerner, August E. ; Fomine, Forka Leypey Mathew ; Bradman, Neil ; Thomas, Mark G. ; Karafet, Tatiana ; Hammer, Michael F. / An African American paternal lineage adds an extremely ancient root to the human y chromosome phylogenetic tree. In: American Journal of Human Genetics. 2013 ; Vol. 92, No. 3. pp. 454-459.
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