ArticleProceedings of the National Academy of Sciences of the United States of America2013
Rates and patterns of great ape retrotransposition.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 39 papers.
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39 citing papers in PubMed, 66 citations in OpenAlex.
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- The Role of Transposable Elements of the Human Genome in Neuronal Function and Pathology.International journal of molecular sciences · 2022Review
- Characterizing mobile element insertions in 5675 genomes.Nucleic acids research · 2022Article
- Population analysis of retrotransposons in giraffe genomes supports RTE decline and widespread LINE1 activity in Giraffidae.Mobile DNA · 2021Article
- Genomic approaches to trace the history of human brain evolution with an emerging opportunity for transposon profiling of ancient humans.Mobile DNA · 2021Review
- Higher Rates of Processed Pseudogene Acquisition in Humans and Three Great Apes Revealed by Long-Read Assemblies.Molecular biology and evolution · 2021Article
- Retrotransposons as Drivers of Mammalian Brain Evolution.Life (Basel, Switzerland) · 2021Review
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- An evolutionary driver of interspersed segmental duplications in primates.Genome biology · 2020Article
- Cryptic genetic variation enhances primate L1 retrotransposon survival by enlarging the functional coiled coil sequence space of ORF1p.PLoS genetics · 2020Article
- ALU non-B-DNA conformations, flipons, binary codes and evolution.Royal Society open science · 2020Review
- The Simons Genome Diversity Project: A Global Analysis of Mobile Element Diversity.Genome biology and evolution · 2020Article
- Dual Eigen-modules of Cis-Element Regulation Profiles and Selection of Cognition-Language Eigen-direction along Evolution in Hominidae.Molecular biology and evolution · 2020Article
- Developing ancestry informative marker panel for Nigeria- Cameroonian chimpanzees.Journal of genetics · 2020Article
- Contribution of retrotransposition to developmental disorders.Nature communications · 2019Article
- Retrophylogenomics in rorquals indicate large ancestral population sizes and a rapid radiation.Mobile DNA · 2019Article
- Using Ancestry Informative Markers (AIMs) to Detect Fine Structures Within Gorilla Populations.Frontiers in genetics · 2019Article
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Authors and funding
19 authors at 6 institutions in 4 countries.
Funding
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.
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