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Rates and patterns of great ape retrotransposition

AuthorsHormozdiari, Fereydoun; Prado-Martinez, Javier ; Hernando-Herraez, Irene ; Marqués-Bonet, Tomàs ; Eichler, Evan E.
Structural variation
Genetic diversity
Issue Date2013
PublisherNational Academy of Sciences (U.S.)
CitationProceedings of the National Academy of Sciences 110(33): 13457-13462 (2013)
AbstractWe 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.
DescriptionHormozdiari, Fereydoun et al.-- Great Ape Genome Project
Publisher version (URL)http://dx.doi.org/10.1073/pnas.1310914110
Identifiersdoi: 10.1073/pnas.1310914110
issn: 0027-8424
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