Genome Evolution

Brookfield, John F. Y.

doi:10.1002/9780470061619.ch13

Cited by 1 publication

(1 citation statement)

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“…Nonequilibrium conditions for the majority of LTR elements may explain why no single selective mechanism appears to be sufficient to explain the distribution of all LTR families (43). Recent LTR insertion may also explain the observation that levels of nucleotide diversity within full-length LTR elements are much lower than expected (44) relative to predictions of models that assume copy number and coalescent equilibrium (45,46).…”

Section: Discussionmentioning

confidence: 70%

Recent LTR retrotransposon insertion contrasts with waves of non-LTR insertion since speciation in Drosophila melanogaster

Bergman

Bensasson

2007

Proc. Natl. Acad. Sci. U.S.A.

128

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LTR and non-LTR retrotransposons exhibit distinct patterns of abundance within the Drosophila melanogaster genome, yet the causes of these differences remain unknown. Here we investigate whether genomic differences between LTR and non-LTR retrotransposons reflect systematic differences in their insertion history. We find that for 17 LTR and 10 non-LTR retrotransposon families that evolve under a pseudogene-like mode of evolution, most elements from LTR families have integrated in the very recent past since colonization of non-African habitats (Ϸ16,000 years ago), whereas elements from non-LTR families have been accumulating in overlapping waves since the divergence of D. melanogaster from its sister species, Drosophila simulans (Ϸ5.4 Mya). LTR elements are significantly younger than non-LTR elements, individually and by family, in regions of high and low recombination, and in genic and intergenic regions. We show that analysis of transposable element (TE) nesting provides a method to calculate transposition rates from genome sequences, which we estimate to be one to two orders of magnitude lower than those that are based on mutation accumulation studies. Recent LTR integration provides a nonequilibrium alternative for the low population frequency of LTR elements in this species, a pattern that is classically interpreted as evidence for selection against the transpositional increase of TEs. Our results call for a new class of population genetic models that incorporate TE copy number, allele frequency, and the age of insertions to provide more powerful and robust inferences about the forces that control the evolution of TEs in natural populations. genome evolution ͉ mutation ͉ transposable element ͉ mobile DNA ͉ transposition-selection balance R etrotransposons are a taxonomically widespread class of transposable elements (TEs) that transpose via an RNA intermediate and comprise significant fractions of most multicellular eukaryotic genomes. Much is known about the molecular mechanisms governing the retrotransposition cycle (transcription, reverse transcription and insertion) because they were among the very first eukaryotic DNA sequences to be characterized at the molecular level (1). However, as with most kinds of mobile DNA, less is known about the evolutionary mechanisms that control their abundance, distribution, and diversity. A more detailed understanding of these mechanisms will provide insight into the causes and consequences of retrotransposition, one of the major forces that shape eukaryotic genome organization and evolution.In Drosophila melanogaster, as in other metazoans, retrotransposons can be subdivided into two major subclasses that are based on the presence or absence of LTRs. LTR and non-LTR (or LINE-like) retrotransposons share many basic structural features, such as encoding a reverse transcriptase gene and the use of internal, TATA-less RNA polymerase II promoters (1). However, there are important differences among them as well, most notably in their mechanisms of reverse transcription and i...

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Section: Discussionmentioning

confidence: 70%