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.2016-02-082016-02-0820130027-8424http://hdl.handle.net/11693/20852We 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.EnglishGenetic diversityGenomicsRetrotransposonStructural variationLong Interspersed Nucleotide ElementsArticle10.1073/pnas.1310914110