Population Genetics Models of Competition Between Transposable Element Subfamilies

Rouzic, Arnaud Le; Capy, Pierre

doi:10.1534/genetics.105.052241

Cited by 62 publications

(68 citation statements)

References 66 publications

(57 reference statements)

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“…The maximum rate of transposition was fixed to be u 0 = 1.0 3 10 22 , which is roughly in agreement with both empirical estimations (Charlesworth et al 1992;Nuzhdin and Mackay 1995;Suh et al 1995;Maside et al 2000) and those used in previous simulation studies (Morgan 2001;NavarroQuezada and Schoen 2002;Le Rouzic and Capy 2006;Le Rouzic et al 2007). We used three different rates of excision, v = {0, 1.0 3 10 26 , 1.0 3 10 24 }.…”

Section: Simulationssupporting

confidence: 54%

“…As mentioned above, because TEs usually have harmful effects on the host genome to some extent, almost all of these models consider selection that operates to decrease the copy number of TEs. Models were further extended to explore the potential roles of other factors, such as breeding system (Hickey 1982;Charlesworth and Charlesworth 1995;Wright and Schoen 1999;Morgan 2001), migration between subpopulations (Deceliere et al 2005), competition between subfamilies (Le Rouzic and Capy 2006), and activity decay by point mutations (Le Rouzic and Capy 2006;Le Rouzic et al 2007). However, these models focus only on the copy number dynamics and did not consider the sequences of TEs.…”

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confidence: 99%

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Population Genetics and Molecular Evolution of DNA Sequences in Transposable Elements. I. A Simulation Framework

Kijima

Innan

2013

Genetics

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A population genetic simulation framework is developed to understand the behavior and molecular evolution of DNA sequences of transposable elements. Our model incorporates random transposition and excision of transposable element (TE) copies, two modes of selection against TEs, and degeneration of transpositional activity by point mutations. We first investigated the relationships between the behavior of the copy number of TEs and these parameters. Our results show that when selection is weak, the genome can maintain a relatively large number of TEs, but most of them are less active. In contrast, with strong selection, the genome can maintain only a limited number of TEs but the proportion of active copies is large. In such a case, there could be substantial fluctuations of the copy number over generations. We also explored how DNA sequences of TEs evolve through the simulations. In general, active copies form clusters around the original sequence, while less active copies have long branches specific to themselves, exhibiting a star-shaped phylogeny. It is demonstrated that the phylogeny of TE sequences could be informative to understand the dynamics of TE evolution.

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Section: Simulationssupporting

confidence: 54%

mentioning

confidence: 99%

Population Genetics and Molecular Evolution of DNA Sequences in Transposable Elements. I. A Simulation Framework

Kijima

Innan

2013

Genetics

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“…TE/host coevolution is an intriguing topic that has received little attention in theoretical population genetics, with models focusing instead on mobile element gain and loss. (48)(49)(50)(51)(52) The models do, however, predict a declining trajectory in transposition rate, as TEs become established in host populations. Colonizing TEs require high intrinsic amplification rates to overcome elimination by drift and selection against deleterious insertions.…”

Section: Transposable Elements Drive the Evolution Of Epigenetic Silementioning

confidence: 97%

Transposable elements and an epigenetic basis for punctuated equilibria

2009

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Evolution is frequently concentrated in bursts of rapid morphological change and speciation followed by longterm stasis. We propose that this pattern of punctuated equilibria results from an evolutionary tug-of-war between host genomes and transposable elements (TEs) mediated through the epigenome. According to this hypothesis, epigenetic regulatory mechanisms (RNA interference, DNA methylation and histone modifications) maintain stasis by suppressing TE mobilization. However, physiological stress, induced by climate change or invasion of new habitats, disrupts epigenetic regulation and unleashes TEs. With their capacity to drive non-adaptive host evolution, mobilized TEs can restructure the genome and displace populations from adaptive peaks, thus providing an escape from stasis and generating genetic innovations required for rapid diversification. This ''epi-transposon hypothesis'' can not only explain macroevolutionary tempo and mode, but may also resolve other long-standing controversies, such as Wright's shifting balance theory, Mayr's peripheral isolates model, and McClintock's view of genome restructuring as an adaptive response to challenge.

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“…where +s i is the sum of the selective effects (s i < 0) of all the retrotransposons carried on one chromosome (Le Rouzic and Capy 2006), or modeled by an exponential quadratic function,…”

Section: Forward Simulations Of the Population Genetics Of Pirts And mentioning

confidence: 99%

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

Lü¹,

Clark²

2009

Genome Res.

102

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Transposable elements (TEs) are mobile DNA sequences that make up a large fraction of eukaryotic genomes. Recently it was discovered that PIWI-interacting RNAs (piRNAs), a class of small RNA molecules that are mainly generated from transposable elements, are crucial repressors of active TEs in the germline of fruit flies. By quantifying expression levels of 32 TE families in piRNA pathway mutants relative to wild-type fruit flies, we provide evidence that piRNAs can severely silence the activities of retrotransposons. We incorporate piRNAs into a population genetic framework for retrotransposons and perform forward simulations to model the population dynamics of piRNA loci and their targets. Using parameters optimized for Drosophila melanogaster, our simulation results indicate that (1) piRNAs can significantly reduce the fitness cost of retrotransposons; (2) retrotransposons that generate piRNAs (piRTs) are selectively more advantageous, and such retrotransposon insertions more easily attain high frequency or fixation; (3) retrotransposons that are repressed by piRNAs (targetRTs), however, also have an elevated probability of reaching high frequency or fixation in the population because their deleterious effects are attenuated. By surveying the polymorphisms of piRT and targetRT insertions across nine strains of D. melanogaster, we verified these theoretical predictions with population genomic data. Our theoretical and empirical analysis suggests that piRNAs can significantly increase the fitness of individuals that bear them; however, piRNAs may provide a shelter or Trojan horse for retrotransposons, allowing them to increase in frequency in a population by shielding the host from the deleterious consequences of retrotransposition.[Supplemental material is available online at http://www.genome.org.] Like other kinds of mutations, however, most mutations created by TE insertions are deleterious to the host and are thus selected against. Approximately 50%-80% of mutations arising in D. melanogaster can be attributed to TEs (Finnegan 1992;Ashburner et al. 2004). Based on the copy number of TEs in D. melanogaster, it was estimated that TEs can decrease the fitness of hosts by 0.4%-5% (Eanes et al. 1987;Charlesworth and Langley 1989;Mackay et al. 1992;Pasyukova et al. 2004). The fitness costs of TEs are generally mediated through the following mechanisms: (1) TE insertions disrupt genes (Charlesworth and Charlesworth 1983;Finnegan 1992;McDonald et al. 1997); (2) transcription and translation of TE-encoded genes are costly (Brookfield 1991; Nuzhdin 1999); and (3) ectopic recombination among dispersed and heterozygous TEs creates deleterious chromosomal rearrangements (Montgomery et al. 1987;Langley et al. 1988;Charlesworth and Langley 1989;Petrov et al. 2003). It has been demonstrated that different TE families are regulated by different mechanisms, although these mechanisms are not mutually exclusive (Biemont et al. 1994;Carr et al. 2002;Petrov et al. 2003). Despite their being under strong selective pressure, TEs ...

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Population Genetics Models of Competition Between Transposable Element Subfamilies

Cited by 62 publications

References 66 publications

Population Genetics and Molecular Evolution of DNA Sequences in Transposable Elements. I. A Simulation Framework

Population Genetics and Molecular Evolution of DNA Sequences in Transposable Elements. I. A Simulation Framework

Transposable elements and an epigenetic basis for punctuated equilibria

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

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