The tempo and mode of evolution of transposable elements as revealed by molecular phylogenies reconstructed from mosquito genomes

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).

Figure 1

Nonparametric demographic history inferred from the phylogeny tree reconstructed by BEAST for each of the TE families studied (Table 1). Thick lines indicate central estimates (median) and were used to fit the models given by models (1) and (2). Thin lines indicate 95% limits sampled from the posterior distribution by the rjMCMC procedure. The classic skyline plots are depicted by dashed lines. Logarithmic scale is used for the y-axis.

Figure 2

Parametric trajectories described by models (1) (thin line) and (2) (thick line) fitted to the nonparametric demographic history (dashed lines) reconstructed from Tc3 phylogenies. Logarithmic scale is used for the y-axes in (A), and linear scale is used for the y-axes in (B). (C) and (D), Individual parametric trajectories of active (dot only), inactive (dot and dash) and total (continuous) elements under models (1) and (2) for Tc3 family. Continuous line describing total elements was omitted from (C) for clarity.

Figure 3

Parametric trajectories described by models (1) (thin line) and (2) (thick line) fitted to the nonparametric demographic history (dashed lines) reconstructed from Mighty phylogenies. Logarithmic scale is used for the y-axes in(A), and linear scale is used for the y-axes in (B). (C) and (D), Individual parametric trajectories of active (dot only), inactive (dot and dash) and total (continuous) elements under models (1) and (2) for Mighty family. Continuous line describing total elements was omitted from (D) for clarity.