Rates and patterns of great ape retrotransposition

Fereydoun Hormozdiari, Miriam K. Konkel, Javier Prado-Martinez, Giorgia Chiatante, Irene Hernando Herraez, Jerilyn A. Walker, Benjamin Nelson, Can Alkan, Peter H. Sudmant, John Huddleston, Claudia R. Catacchio, Arthur Ko, Maika Malig, Carl Baker, Tomas Marques-Bonet, Mario Ventura, Mark A. Batzer, Evan E. Eichler

Research output: Contribution to journalArticle

29 Scopus citations

Abstract

We analyzed 83 fully sequenced great ape genomes for mobile element insertions, predicting a total of 49,452 fixed and polymorphic Alu and long interspersed element 1 (L1) insertions not present in the human reference assembly and assigning each retrotransposition event to a different time point during great ape evolution. We used these homoplasy-free markers to construct a mobile element insertions-based phylogeny of humans and great apes and demonstrate their differential power to discern ape subspecies and populations. Within this context, we find a good correlation between L1 diversity and single-nucleotide polymorphism heterozygosity (r2 =0.65) in contrast to Alu repeats, which show little correlation (r2 =0.07). We estimate that the rate of Alu retrotransposition has differed by a factor of 15-fold in these lineages. Humans, chimpanzees, and bonobos show the highest rates of Alu accumulation-the latter two since divergence 1.5 Mya. The L1 insertion rate, in contrast, has remained relatively constant, with rates differing by less than a factor of three. We conclude that Alu retrotransposition has been the most variable form of genetic variation during recent human-great ape evolution, with increases and decreases occurring over very short periods of evolutionary time.

Original languageEnglish (US)
Pages (from-to)13457-13462
Number of pages6
JournalProceedings of the National Academy of Sciences of the United States of America
Volume110
Issue number33
DOIs
StatePublished - Aug 13 2013
Externally publishedYes

Keywords

  • Genetic diversity
  • Genomics
  • Retrotransposon
  • Structural variation

ASJC Scopus subject areas

  • General

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  • Cite this

    Hormozdiari, F., Konkel, M. K., Prado-Martinez, J., Chiatante, G., Herraez, I. H., Walker, J. A., Nelson, B., Alkan, C., Sudmant, P. H., Huddleston, J., Catacchio, C. R., Ko, A., Malig, M., Baker, C., Marques-Bonet, T., Ventura, M., Batzer, M. A., & Eichler, E. E. (2013). Rates and patterns of great ape retrotransposition. Proceedings of the National Academy of Sciences of the United States of America, 110(33), 13457-13462. https://doi.org/10.1073/pnas.1310914110