title: Rates and patterns of great ape retrotransposition.
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.
authors.affiliation: Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA.
authors.forename: Fereydoun
authors.initials: F
authors.lastname: Hormozdiari
authors.forename: Miriam K
authors.initials: MK
authors.lastname: Konkel
authors.forename: Javier
authors.initials: J
authors.lastname: Prado-Martinez
authors.forename: Giorgia
authors.initials: G
authors.lastname: Chiatante
authors.forename: Irene Hernando
authors.initials: IH
authors.lastname: Herraez
authors.forename: Jerilyn A
authors.initials: JA
authors.lastname: Walker
authors.forename: Benjamin
authors.initials: B
authors.lastname: Nelson
authors.forename: Can
authors.initials: C
authors.lastname: Alkan
authors.forename: Peter H
authors.initials: PH
authors.lastname: Sudmant
authors.forename: John
authors.initials: J
authors.lastname: Huddleston
authors.forename: Claudia R
authors.initials: CR
authors.lastname: Catacchio
authors.forename: Arthur
authors.initials: A
authors.lastname: Ko
authors.forename: Maika
authors.initials: M
authors.lastname: Malig
authors.forename: Carl
authors.initials: C
authors.lastname: Baker
authors.forename: Tomas
authors.initials: T
authors.lastname: Marques-Bonet
authors.forename: Mario
authors.initials: M
authors.lastname: Ventura
authors.forename: Mark A
authors.initials: MA
authors.lastname: Batzer
authors.forename: Evan E
authors.initials: EE
authors.lastname: Eichler
mesh_terms: D020087:Alu Elements / Q000235:genetics; D000818:Animals; D016000:Cluster Analysis; D017931:DNA Primers / Q000235:genetics; D014644:Genetic Variation; D016678:Genome / Q000235:genetics*; D023281:Genomics; D015186:Hominidae / Q000145:classification / Q000235:genetics*; D006801:Humans; D016013:Likelihood Functions; D020084:Long Interspersed Nucleotide Elements / Q000235:genetics; D010802:Phylogeny; D016133:Polymerase Chain Reaction; D020641:Polymorphism, Single Nucleotide; D025341:Principal Component Analysis; D013045:Species Specificity
chemical_list: D017931:DNA Primers
keywords: genetic diversity; genomics; retrotransposon; structural variation