Rates and patterns of great ape retrotransposition
dc.citation.epage | 13462 | en_US |
dc.citation.issueNumber | 33 | en_US |
dc.citation.spage | 13457 | en_US |
dc.citation.volumeNumber | 110 | en_US |
dc.contributor.author | Hormozdiari, F. | en_US |
dc.contributor.author | Konkel, M. K. | en_US |
dc.contributor.author | Prado-Martinez, J. | en_US |
dc.contributor.author | Chiatante, G. | en_US |
dc.contributor.author | Herraez, I. H. | en_US |
dc.contributor.author | Walker, J. A. | en_US |
dc.contributor.author | Nelson, B. | en_US |
dc.contributor.author | Alkan, C. | en_US |
dc.contributor.author | Sudmant, P. H. | en_US |
dc.contributor.author | Huddleston, J. | en_US |
dc.contributor.author | Catacchio, C. R. | en_US |
dc.contributor.author | Ko, A. | en_US |
dc.contributor.author | Malig, M. | en_US |
dc.contributor.author | Baker, C. | en_US |
dc.contributor.author | Marques-Bonet, T. | en_US |
dc.contributor.author | Ventura, M. | en_US |
dc.contributor.author | Batzer, M. A. | en_US |
dc.contributor.author | Eichler, E. E. | en_US |
dc.date.accessioned | 2016-02-08T09:36:32Z | |
dc.date.available | 2016-02-08T09:36:32Z | |
dc.date.issued | 2013 | en_US |
dc.department | Department of Computer Engineering | en_US |
dc.description.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 (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. | en_US |
dc.description.provenance | Made available in DSpace on 2016-02-08T09:36:32Z (GMT). No. of bitstreams: 1 bilkent-research-paper.pdf: 70227 bytes, checksum: 26e812c6f5156f83f0e77b261a471b5a (MD5) Previous issue date: 2013 | en |
dc.identifier.doi | 10.1073/pnas.1310914110 | en_US |
dc.identifier.issn | 0027-8424 | |
dc.identifier.uri | http://hdl.handle.net/11693/20852 | |
dc.language.iso | English | en_US |
dc.publisher | National Academy of Sciences | en_US |
dc.relation.isversionof | http://dx.doi.org/10.1073/pnas.1310914110 | en_US |
dc.source.title | Title National Academy of Sciences. Proceedings | en_US |
dc.subject | Genetic diversity | en_US |
dc.subject | Genomics | en_US |
dc.subject | Retrotransposon | en_US |
dc.subject | Structural variation | en_US |
dc.subject | Long Interspersed Nucleotide Elements | en_US |
dc.title | Rates and patterns of great ape retrotransposition | en_US |
dc.type | Article | en_US |
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