Population Genetics and Molecular Evolution of DNA Sequences in Transposable Elements. II. Accumulation of Variation and Evolution of a New Subfamily

Abstract

In order to understand how DNA sequences of transposable elements (TEs) evolve, extensive simulations were carried out. We first used our previous model, in which the copy number of TEs is mainly controlled by selection against ectopic recombination. It was found that along a simulation run, the shape of phylogeny changes quite much, from monophyletic trees to dimorphic trees with two clusters. Our results demonstrated that the change of the phase is usually slow from a monomorphic phase to a dimorphic phase, accompanied with a growth of an internal branch by accumulation of variation between two types. Then, the phase immediately changes back to a monomorphic phase when one group gets extinct. Under this condition, monomorphic and dimorphic phases arise repeatedly, and it is very difficult to maintain two or more different types of TEs for a long time. Then, how a new subfamily can evolve? To solve this, we developed a new model, in which ectopic recombination is restricted between two types under some condition, for example, accumulation of mutations between them. Under this model, because selection works on the copy number of each types separately, two types can be maintained for a long time. As expected, our simulations demonstrated that a new type arises and persists quite stably, and that it will be recognized as a new subfamily followed by further accumulation of mutations. It is indicated that how ectopic recombination is regulated in a genome is an important factor for the evolution of a new subfamily.

Patterns of piRNA Regulation in Drosophila Revealed through Transposable Element Clade Inference

“…Early in the P -element and hobo invasions, variant lineages emerged and rose to high copy number, entirely replacing the wild-type TE in some populations within a decade ( Black et al 1987 ; Periquet et al 1989 ). These dynamics may reflect selection acting at the level of TEs, with variants outcompeting the ancestral lineage ( Le Rouzic and Capy 2006 ; Robillard et al 2016 ; Iwasaki et al 2020 ). The clades we identified provide an opportunity to catch such events in progress.…”

“…Ultimately the TE copy number may reach a steady state, with the rate of transposition dampened by piRNA silencing as well as selection against the deleterious consequences to reproductive fitness of the host organism ( Charlesworth and Charlesworth 1983 ; Lee and Langley 2010 ; Kelleher et al 2020 ). However, as TEs expand in copy number, they also acquire polymorphisms in their sequences, which may lead to the formation of new lineages or subfamilies ( Moody 1988 ; Kimmel and Mathaes 2010 ; Kijima and Innan 2013 ; Iwasaki et al 2020 ). Multiple lineages of a TE will compete with each other, as long as their polymorphisms are not deactivating ( Abrusán and Krambeck 2006 ; Le Rouzic and Capy 2006 ; Iwasaki et al 2020 ).…”

“…However, as TEs expand in copy number, they also acquire polymorphisms in their sequences, which may lead to the formation of new lineages or subfamilies ( Moody 1988 ; Kimmel and Mathaes 2010 ; Kijima and Innan 2013 ; Iwasaki et al 2020 ). Multiple lineages of a TE will compete with each other, as long as their polymorphisms are not deactivating ( Abrusán and Krambeck 2006 ; Le Rouzic and Capy 2006 ; Iwasaki et al 2020 ). Much in the same way individuals within an ecological system are constrained by a carrying capacity, variants of the same TE may be constrained by the copy-number carrying capacity of the host ( Brookfield 2005 ; Le Rouzic and Capy 2006 ).…”

Patterns of piRNA regulation inDrosophilarevealed through transposable element clade inference

“…Early in the P -element and hobo invasions, variant lineages emerged and rose to high copy-number, entirely replacing the wild-type TE in some populations within a decade (Black et al 1987; Periquet et al 1989). These dynamics may reflect selection acting at the level of TEs, with variants outcompeting the ancestral lineage (Le Rouzic and Capy 2006; Robillard et al 2016; Iwasaki et al 2020). The clades we identified provide an opportunity to catch such events in progress.…”