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1 December 2009 The Tempo and Mode of Evolution of Transposable Elements as Revealed by Molecular Phylogenies Reconstructed from Mosquito Genomes
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Abstract

Although many mathematical models exist predicting the dynamics of transposable elements (TEs), there is a lack of available empirical data to validate these models and inherent assumptions. Genomes can provide a snapshot of several TE families in a single organism, and these could have their demographics inferred by coalescent analysis, allowing for the testing of theories on TE amplification dynamics. Using the available genomes of the mosquitoes Aedes aegypti and Anopheles gambiae, we indicate that such an approach is feasible. Our analysis follows four steps: (1) mining the two mosquito genomes currently available in search of TE families; (2) fitting, to selected families found in (1), a phylogeny tree under the general time-reversible (GTR) nucleotide substitution model with an uncorrelated lognormal (UCLN) relaxed clock and a nonparametric demographic model; (3) fitting a nonparametric coalescent model to the tree generated in (2); and (4) fitting parametric models motivated by ecological theories to the curve generated in (3).

© 2009 The Society for the Study of Evolution.
Claudio J. Struchiner, Eduardo Massad, Zhijian Tu, and José M. C. Ribeiro "The Tempo and Mode of Evolution of Transposable Elements as Revealed by Molecular Phylogenies Reconstructed from Mosquito Genomes," Evolution 63(12), 3136-3146, (1 December 2009). https://doi.org/10.1111/j.1558-5646.2009.00788.x
Received: 26 November 2008; Accepted: 1 June 2009; Published: 1 December 2009
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