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

Elhaik, Eran LU orcid ; Tatarinova, Tatiana V ; Klyosov, Anatole A and Graur, Dan (2014) In European Journal of Human Genetics 22(9). p.1111-1116
Abstract

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 338,000 years ago (95% CI=237,000-581,000). Such an extraordinarily early estimate contradicts all previous estimates in the literature and is over a 100,000 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... (More)

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 338,000 years ago (95% CI=237,000-581,000). Such an extraordinarily early estimate contradicts all previous estimates in the literature and is over a 100,000 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 208,300 (95% CI=163,900-260,200) years ago.

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author
; ; and
publishing date
type
Contribution to journal
publication status
published
keywords
Chromosomes, Human, X/genetics, Chromosomes, Human, Y/genetics, Evolution, Molecular, Fossils, Haplotypes, Humans, Mutation, Polymorphism, Genetic
in
European Journal of Human Genetics
volume
22
issue
9
pages
1111 - 1116
publisher
Nature Publishing Group
external identifiers
  • pmid:24448544
  • scopus:84906276648
ISSN
1476-5438
DOI
10.1038/ejhg.2013.303
language
English
LU publication?
no
id
71f0743f-70b2-415c-8ba4-a404ba8d1c61
date added to LUP
2019-11-10 16:58:13
date last changed
2024-05-29 03:32:51
@article{71f0743f-70b2-415c-8ba4-a404ba8d1c61,
  abstract     = {{<p>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 338,000 years ago (95% CI=237,000-581,000). Such an extraordinarily early estimate contradicts all previous estimates in the literature and is over a 100,000 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 208,300 (95% CI=163,900-260,200) years ago.</p>}},
  author       = {{Elhaik, Eran and Tatarinova, Tatiana V and Klyosov, Anatole A and Graur, Dan}},
  issn         = {{1476-5438}},
  keywords     = {{Chromosomes, Human, X/genetics; Chromosomes, Human, Y/genetics; Evolution, Molecular; Fossils; Haplotypes; Humans; Mutation; Polymorphism, Genetic}},
  language     = {{eng}},
  number       = {{9}},
  pages        = {{1111--1116}},
  publisher    = {{Nature Publishing Group}},
  series       = {{European Journal of Human Genetics}},
  title        = {{The 'extremely ancient' chromosome that isn't : a forensic bioinformatic investigation of Albert Perry's X-degenerate portion of the Y chromosome}},
  url          = {{http://dx.doi.org/10.1038/ejhg.2013.303}},
  doi          = {{10.1038/ejhg.2013.303}},
  volume       = {{22}},
  year         = {{2014}},
}