Models of the population genetics of transposable elements

Abstract

Although transposable elements (TEs) have been found in all organisms in which they have been looked for, the ways in which they invade genomes and populations are still a matter of debate. By extending the classical models of population genetics, several approaches have been developed to account for the dynamics of TEs, especially in Drosophila melanogaster . While the formalism of these models is based on simplifications, they enable us to understand better how TEs invade genomes, as a result of multiple evolutionary forces including duplication, deletion, self-regulation, natural selection and genetic drift. The aim of this paper is to review the assumptions and the predictions of these different models by highlighting the importance of the specific characteristics of both the TEs and the hosts, and the host/TE relationships. Then, perspectives in this domain will be discussed.

Long-Term and Short-Term Evolutionary Impacts of Transposable Elements onDrosophila

“…Even though incidences of potentially adaptive individual TE insertions with high population frequencies have been reported (Daborn et al 2002;Aminetzach et al 2005;González et al 2008;Schmidt et al 2010), the mutagenic effects of TE insertions are typically deleterious because they disrupt gene structure and function (Finnegan 1992) and can lead to deleterious chromosomal rearrangement (Montgomery et al 1987(Montgomery et al , 1991Langley et al 1988). Supporting this, TEs in natural populations of Drosophila are generally found in intergenic regions (Aquadro et al 1986;Kaminker et al 2002;Bergman et al 2006) and present at low population frequencies (reviewed in Charlesworth and Langley 1989;Le Rouzic and Deceliere 2005;Lee and Langley 2010). Drosophila melanogaster strains with a larger copy number of several TE families surveyed also have lower fitness (Mackay 1989;Pasyukova et al 2004).…”

Population dynamics of PIWI-interacting RNAs (piRNAs) and their targets in Drosophila

“…Despite their being under strong selective pressure, TEs still persist in genomes because they replicate rapidly (Ohta 1983). Decades of theoretical and experimental research have established a framework for the population genetics of TEs, after making nearly universal assumptions of equilibrium between transposition/retrotransposition, excision, migration, recurrent horizontal transfers, genetic drift, and natural selection (Charlesworth and Charlesworth 1983;Charlesworth 1988;Charlesworth and Langley 1989;Biemont 1992;Brookfield and Badge 1997;Charlesworth et al 1997;Nuzhdin 1999;Bartolome et al 2002;Brookfield 2005;Le Rouzic and Deceliere 2005).Various mechanisms of repression of TE activities have been incorporated into our understanding of the population genetics of TEs, including self-regulation of copy number by reducing transposition rates (Charlesworth and Charlesworth 1983;Langley et al 1983), cis-acting regulation (transposition immunity) and trans-acting regulation (transposition repression) of TEs (Charlesworth and Langley 1986), regulation of transposition by host factors (Badge and Brookfield 1998), or more specifically, regulation of transposition by the interaction between TEs and the host genome such as the P-M hybrid dysgenesis system (Engels …”

“…Despite their being under strong selective pressure, TEs still persist in genomes because they replicate rapidly (Ohta 1983). Decades of theoretical and experimental research have established a framework for the population genetics of TEs, after making nearly universal assumptions of equilibrium between transposition/retrotransposition, excision, migration, recurrent horizontal transfers, genetic drift, and natural selection (Charlesworth and Charlesworth 1983;Charlesworth 1988;Charlesworth and Langley 1989;Biemont 1992;Brookfield and Badge 1997;Charlesworth et al 1997;Nuzhdin 1999;Bartolome et al 2002;Brookfield 2005;Le Rouzic and Deceliere 2005).…”

Demography and weak selection drive patterns of transposable element diversity in natural populations of Arabidopsis lyrata

“…What limits the number and population frequencies of TEs? Most models of TE population dynamics have focused on the maintenance of TE copy number via an equilibrium between transposition, which increases the abundance of TEs in a host genome, and natural selection, which removes deleterious TE insertions (8,9). However, the number and distribution of TEs in genomes are unlikely to be determined by selection and transposition alone (10); factors such as the population and life history of the host may also play significant roles (11).…”