Population genomics of transposable elements in Drosophila melanogaster

Transposable elements (TEs) are the primary contributors to the genome bulk in many organisms and are major players in genome evolution. A clear and thorough understanding of the population dynamics of TEs is therefore essential for full comprehension of the eukaryotic genome evolution and function....

Full description

Saved in:
Bibliographic Details
Published in:Molecular biology and evolution 2011-05, Vol.28 (5), p.1633-1644
Main Authors: Petrov, Dmitri A, Fiston-Lavier, Anna-Sophie, Lipatov, Mikhail, Lenkov, Kapa, González, Josefa
Format: Article
Language:English
Subjects:
Animal populations
Animals
DNA Transposable Elements - genetics
Drosophila melanogaster - genetics
Eukaryotes
Evolution
Gene Expression
Gene Frequency
Genetic Variation
Genomes
Genomics
Insects
Metagenomics
Models, Genetic
Population dynamics
Recombination, Genetic
Selection, Genetic
Sequence Analysis, DNA
Statistical models
Terminal Repeat Sequences
Citations: Items that this one cites
Items that cite this one
Online Access:Get full text
Tags: Add Tag
No Tags, Be the first to tag this record!
Description
Summary:Transposable elements (TEs) are the primary contributors to the genome bulk in many organisms and are major players in genome evolution. A clear and thorough understanding of the population dynamics of TEs is therefore essential for full comprehension of the eukaryotic genome evolution and function. Although TEs in Drosophila melanogaster have received much attention, population dynamics of most TE families in this species remains entirely unexplored. It is not clear whether the same population processes can account for the population behaviors of all TEs in Drosophila or whether, as has been suggested previously, different orders behave according to very different rules. In this work, we analyzed population frequencies for a large number of individual TEs (755 TEs) in five North American and one sub-Saharan African D. melanogaster populations (75 strains in total). These TEs have been annotated in the reference D. melanogaster euchromatic genome and have been sampled from all three major orders (non-LTR, LTR, and TIR) and from all families with more than 20 TE copies (55 families in total). We find strong evidence that TEs in Drosophila across all orders and families are subject to purifying selection at the level of ectopic recombination. We showed that strength of this selection varies predictably with recombination rate, length of individual TEs, and copy number and length of other TEs in the same family. Importantly, these rules do not appear to vary across orders. Finally, we built a statistical model that considered only individual TE-level (such as the TE length) and family-level properties (such as the copy number) and were able to explain more than 40% of the variation in TE frequencies in D. melanogaster.
ISSN:0737-4038
1537-1719
DOI:10.1093/molbev/msq337