Rates and patterns of great ape retrotransposition

Proc Natl Acad Sci U S A. 2013 Aug 13;110(33):13457-62. doi: 10.1073/pnas.1310914110. Epub 2013 Jul 24.


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 (r(2) = 0.65) in contrast to Alu repeats, which show little correlation (r(2) = 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.

Keywords: genetic diversity; genomics; retrotransposon; structural variation.

Publication types

  • Comparative Study
  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Alu Elements / genetics
  • Animals
  • Cluster Analysis
  • DNA Primers / genetics
  • Genetic Variation*
  • Genome / genetics*
  • Genomics
  • Hominidae / classification
  • Hominidae / genetics*
  • Humans
  • Likelihood Functions
  • Long Interspersed Nucleotide Elements / genetics
  • Phylogeny*
  • Polymerase Chain Reaction
  • Polymorphism, Single Nucleotide
  • Principal Component Analysis
  • Species Specificity


  • DNA Primers