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).

Novel transposable elements from Anopheles gambiae

“…It is apparent that the Class II elements present in the genome of An. gambiae are composed of a variety of different structurally degenerated sequences that might represent different stages in the process of deterioration of these elements, which in turn might be differentially involved in the regulation of Class II families [ 59 ].…”

Confinement of gene drive systems to local populations: A comparative analysis

“…This model does not account for the tendency of TEs to jump locally (Tower et al , 1993; Zhang et al , 2003) and to home in on certain genomic regions (Guimond et al , 2003); however this is not expected to change the overall dynamics other than by reducing the effective transposition rate (Rasgon & Gould, 2005). It also does not account for evolutionary considerations such as mutational inactivation (Struchiner et al , 2009); however, these are less relevant on the timescale of a population replacement program. The general conclusion therefore holds that any TE capable of spreading is not confineable to an isolated population.…”

Birth of Three Stowaway-like MITE Families via Microhomology-Mediated Miniaturization of a Tc1/Mariner Element in the Yellow Fever Mosquito

“…This observation further supports the order of their appearance during evolution. Based on the rough estimation of the mutation rate for the mosquito genome at 1 × 10 −7 /base/year (Haag-Liautard et al 2007; Struchiner et al 2009), the average time of appearance for these families are estimated to be 60, 164, and 242 thousand years ago. Even though Elf appears to have formed before the insertion of the two repeat elements into Ozma , it is unclear whether Gnome and Goblin arose before or after the insertion events.…”