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Remarkably little variation in proteins encoded by the Y chromosome's single-copy genes, implying effective purifying selection.

Publication ,  Journal Article
Rozen, S; Marszalek, JD; Alagappan, RK; Skaletsky, H; Page, DC
Published in: Am J Hum Genet
December 2009

Y-linked single-nucleotide polymorphisms (SNPs) have served as powerful tools for reconstructing the worldwide genealogy of human Y chromosomes and for illuminating patrilineal relationships among modern human populations. However, there has been no systematic, worldwide survey of sequence variation within the protein-coding genes of the Y chromosome. Here we report and analyze coding sequence variation among the 16 single-copy "X-degenerate" genes of the Y chromosome. We examined variation in these genes in 105 men representing worldwide diversity, resequencing in each man an average of 27 kb of coding DNA, 40 kb of intronic DNA, and, for comparison, 15 kb of DNA in single-copy Y-chromosomal pseudogenes. There is remarkably little variation in X-degenerate protein sequences: two chromosomes drawn at random differ on average by a single amino acid, with half of these differences arising from a single, conservative Asp-->Glu mutation that occurred approximately 50,000 years ago. Further analysis showed that nucleotide diversity and the proportion of variant sites are significantly lower for nonsynonymous sites than for synonymous sites, introns, or pseudogenes. These differences imply that natural selection has operated effectively in preserving the amino acid sequences of the Y chromosome's X-degenerate proteins during the last approximately 100,000 years of human history. Thus our findings are at odds with prominent accounts of the human Y chromosome's imminent demise.

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Published In

Am J Hum Genet

DOI

EISSN

1537-6605

Publication Date

December 2009

Volume

85

Issue

6

Start / End Page

923 / 928

Location

United States

Related Subject Headings

  • Sequence Analysis, DNA
  • Selection, Genetic
  • Polymorphism, Single Nucleotide
  • Nucleotides
  • Models, Genetic
  • Male
  • Introns
  • Humans
  • Genetics & Heredity
  • Genetic Variation
 

Citation

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Chicago
ICMJE
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Rozen, S., Marszalek, J. D., Alagappan, R. K., Skaletsky, H., & Page, D. C. (2009). Remarkably little variation in proteins encoded by the Y chromosome's single-copy genes, implying effective purifying selection. Am J Hum Genet, 85(6), 923–928. https://doi.org/10.1016/j.ajhg.2009.11.011
Rozen, Steve, Janet D. Marszalek, Raaji K. Alagappan, Helen Skaletsky, and David C. Page. “Remarkably little variation in proteins encoded by the Y chromosome's single-copy genes, implying effective purifying selection.Am J Hum Genet 85, no. 6 (December 2009): 923–28. https://doi.org/10.1016/j.ajhg.2009.11.011.
Rozen S, Marszalek JD, Alagappan RK, Skaletsky H, Page DC. Remarkably little variation in proteins encoded by the Y chromosome's single-copy genes, implying effective purifying selection. Am J Hum Genet. 2009 Dec;85(6):923–8.
Rozen, Steve, et al. “Remarkably little variation in proteins encoded by the Y chromosome's single-copy genes, implying effective purifying selection.Am J Hum Genet, vol. 85, no. 6, Dec. 2009, pp. 923–28. Pubmed, doi:10.1016/j.ajhg.2009.11.011.
Rozen S, Marszalek JD, Alagappan RK, Skaletsky H, Page DC. Remarkably little variation in proteins encoded by the Y chromosome's single-copy genes, implying effective purifying selection. Am J Hum Genet. 2009 Dec;85(6):923–928.
Journal cover image

Published In

Am J Hum Genet

DOI

EISSN

1537-6605

Publication Date

December 2009

Volume

85

Issue

6

Start / End Page

923 / 928

Location

United States

Related Subject Headings

  • Sequence Analysis, DNA
  • Selection, Genetic
  • Polymorphism, Single Nucleotide
  • Nucleotides
  • Models, Genetic
  • Male
  • Introns
  • Humans
  • Genetics & Heredity
  • Genetic Variation