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Extreme selective sweeps independently targeted the X chromosomes of the great apes.

Publication ,  Journal Article
Nam, K; Munch, K; Hobolth, A; Dutheil, JY; Veeramah, KR; Woerner, AE; Hammer, MF; Great Ape Genome Diversity Project, ; Mailund, T; Schierup, MH
Published in: Proceedings of the National Academy of Sciences of the United States of America
May 2015

The unique inheritance pattern of the X chromosome exposes it to natural selection in a way that is different from that of the autosomes, potentially resulting in accelerated evolution. We perform a comparative analysis of X chromosome polymorphism in 10 great ape species, including humans. In most species, we identify striking megabase-wide regions, where nucleotide diversity is less than 20% of the chromosomal average. Such regions are found exclusively on the X chromosome. The regions overlap partially among species, suggesting that the underlying targets are partly shared among species. The regions have higher proportions of singleton SNPs, higher levels of population differentiation, and a higher nonsynonymous-to-synonymous substitution ratio than the rest of the X chromosome. We show that the extent to which diversity is reduced is incompatible with direct selection or the action of background selection and soft selective sweeps alone, and therefore, we suggest that very strong selective sweeps have independently targeted these specific regions in several species. The only genomic feature that we can identify as strongly associated with loss of diversity is the location of testis-expressed ampliconic genes, which also have reduced diversity around them. We hypothesize that these genes may be responsible for selective sweeps in the form of meiotic drive caused by an intragenomic conflict in male meiosis.

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Published In

Proceedings of the National Academy of Sciences of the United States of America

DOI

EISSN

1091-6490

ISSN

0027-8424

Publication Date

May 2015

Volume

112

Issue

20

Start / End Page

6413 / 6418

Related Subject Headings

  • X Chromosome
  • Species Specificity
  • Selection, Genetic
  • Polymorphism, Genetic
  • Models, Genetic
  • Hominidae
  • Genetics, Population
  • Genetic Variation
  • Databases, Genetic
  • Computational Biology
 

Citation

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Nam, K., Munch, K., Hobolth, A., Dutheil, J. Y., Veeramah, K. R., Woerner, A. E., … Schierup, M. H. (2015). Extreme selective sweeps independently targeted the X chromosomes of the great apes. Proceedings of the National Academy of Sciences of the United States of America, 112(20), 6413–6418. https://doi.org/10.1073/pnas.1419306112
Nam, Kiwoong, Kasper Munch, Asger Hobolth, Julien Yann Dutheil, Krishna R. Veeramah, August E. Woerner, Michael F. Hammer, Michael F. Great Ape Genome Diversity Project, Thomas Mailund, and Mikkel Heide Schierup. “Extreme selective sweeps independently targeted the X chromosomes of the great apes.Proceedings of the National Academy of Sciences of the United States of America 112, no. 20 (May 2015): 6413–18. https://doi.org/10.1073/pnas.1419306112.
Nam K, Munch K, Hobolth A, Dutheil JY, Veeramah KR, Woerner AE, et al. Extreme selective sweeps independently targeted the X chromosomes of the great apes. Proceedings of the National Academy of Sciences of the United States of America. 2015 May;112(20):6413–8.
Nam, Kiwoong, et al. “Extreme selective sweeps independently targeted the X chromosomes of the great apes.Proceedings of the National Academy of Sciences of the United States of America, vol. 112, no. 20, May 2015, pp. 6413–18. Epmc, doi:10.1073/pnas.1419306112.
Nam K, Munch K, Hobolth A, Dutheil JY, Veeramah KR, Woerner AE, Hammer MF, Great Ape Genome Diversity Project, Mailund T, Schierup MH. Extreme selective sweeps independently targeted the X chromosomes of the great apes. Proceedings of the National Academy of Sciences of the United States of America. 2015 May;112(20):6413–6418.
Journal cover image

Published In

Proceedings of the National Academy of Sciences of the United States of America

DOI

EISSN

1091-6490

ISSN

0027-8424

Publication Date

May 2015

Volume

112

Issue

20

Start / End Page

6413 / 6418

Related Subject Headings

  • X Chromosome
  • Species Specificity
  • Selection, Genetic
  • Polymorphism, Genetic
  • Models, Genetic
  • Hominidae
  • Genetics, Population
  • Genetic Variation
  • Databases, Genetic
  • Computational Biology