European Journal of Human Genetics (2014) 22, 1111–1116; doi:10.1038/ejhg.2013.303; published online 22 January 2014

The ‘extremely ancient’ chromosome that isn’t: a forensic bioinformatic investigation of Albert Perry’s X-degenerate portion of the Y chromosome

Eran Elhaik1,2, Tatiana V Tatarinova3, Anatole A Klyosov4 and Dan Graur5

  1. 1Department of Mental Health, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, USA
  2. 2Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield, UK
  3. 3Department of Pediatrics, Children's Hospital Los Angeles and Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
  4. 4The Academy of DNA Genealogy, Newton, MA, USA
  5. 5Department of Biology & Biochemistry, University of Houston, Houston, TX, USA

Correspondence: Dr E Elhaik, Department of Mental Health, Johns Hopkins University, 615 North Wolfe Street, Baltimore, MD 21205, USA. E-mail:

Received 27 August 2013; Revised 21 November 2013; Accepted 27 November 2013
Advance online publication 22 January 2014



Mendez and colleagues reported the identification of a Y chromosome haplotype (the A00 lineage) that lies at the basal position of the Y chromosome phylogenetic tree. Incorporating this haplotype, the authors estimated the time to the most recent common ancestor (TMRCA) for the Y tree to be 338000 years ago (95% CI=237000–581000). Such an extraordinarily early estimate contradicts all previous estimates in the literature and is over a 100000 years older than the earliest fossils of anatomically modern humans. This estimate raises two astonishing possibilities, either the novel Y chromosome was inherited after ancestral humans interbred with another species, or anatomically modern Homo sapiens emerged earlier than previously estimated and quickly became subdivided into genetically differentiated subpopulations. We demonstrate that the TMRCA estimate was reached through inadequate statistical and analytical methods, each of which contributed to its inflation. We show that the authors ignored previously inferred Y-specific rates of substitution, incorrectly derived the Y-specific substitution rate from autosomal mutation rates, and compared unequal lengths of the novel Y chromosome with the previously recognized basal lineage. Our analysis indicates that the A00 lineage was derived from all the other lineages 208300 (95% CI=163900–260200) years ago.


A00 haplotype; Y chromosome; Albert Perry; Y-chromosomal Adam; TMRCA; interbreeding