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National Academy of Sciences, Proceedings of the National Academy of Sciences, 33(110), p. 13457-13462, 2013

DOI: 10.1073/pnas.1310914110

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Rates and patterns of great ape retrotransposition

Journal article published in 2013 by Fereydoun Hormozdiari, Miriam K. Konkel, Javier Prado-Martinez ORCID, Giorgia Chiatante, Irene Hernando Herraez, Jerilyn A. Walker, Benjamin Nelson, Can Alkan, Peter H. Sudmant ORCID, John Huddleston, Claudia R. Catacchio, Arthur Ko, Maika Malig, Carl Baker, Great Ape Genome Project and other authors.
This paper is made freely available by the publisher.
This paper is made freely available by the publisher.

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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 ( 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.