Biomedical subjects

Grégory Deceliere

Publications and source records attributed to Grégory Deceliere.

4 recordsLinked to original sources

PubMed2006

TESD: a transposable element dynamics simulation environment.

UNLABELLED: Various mathematical models have been used to explore the dynamics of transposable elements (TEs) within their host genomes. However, numerous factors can influence their dynamics, and we know only little about the dynamics of TEs when they first began to invade populations. In addition, the influence of population structuring has only recently been investigated. Transposable Element Simulator Dynamics, a population genomics simulation environment, has therefore been developed to provide a simple tool for analyzing the dynamics of TEs in a community based on (i) various TE parameters, such as the transposition and excision rates, the recombination rate and the coefficient of selection against TE insertions; and (ii) population parameters, such as population size and migration rates. The simulations can be used to illustrate the dynamic fate of TEs in structured populations, can be extended by using more specific molecular or demographic models, and can be useful for teaching population genetics and genomics. AVAILABILITY: TESD is distributed under GPL from the Pôle Bioinformatique Lyonnais (PBIL) web server at http://pbil.univ-lyon1.fr/software/TESD

Algorithms↗

PubMed2005

Models of the population genetics of transposable elements.

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.

Animals↗

PubMed2004

The dynamics of transposable elements in structured populations.

We analyzed the dynamics of transposable elements (TEs) according to Wright's island and continent-island models, assuming that selection tends to counter the deleterious effects of TEs. We showed that migration between host populations has no impact on either the existence or the stability of the TE copy number equilibrium points obtained in the absence of migration. However, if the migration rate is slower than the transposition rate or if selection is weak, then the TE copy numbers in all the populations can be expected to slowly become homogeneous, whereas a heterogeneous TE copy number distribution between populations is maintained if TEs are mobilized in some populations. The mean TE copy number is highly sensitive to the population size, but as a result of migration between populations, it decreases as the sum of the population sizes increases and tends to reach the same value in these populations. We have demonstrated the existence of repulsion between TE insertion sites, which is established by selection and amplified by drift. This repulsion is reduced as much as the migration rate is higher than the recombination rate between the TE insertion sites. Migration and demographic history are therefore strong forces in determining the dynamics of TEs within the genomes and the populations of a species.

Animal Migration↗

PubMed2003

Worldwide distribution of transposable element copy number in natural populations of Drosophila simulans.

Transposable elements (TEs), which promote various kinds of mutations, constitute a large fraction of the genome. How they invade natural populations and species is therefore of fundamental importance for understanding the dynamics of genetic diversity and genome composition. On the basis of 85 samples of natural populations of Drosophila simulans, we report the distributions of the genome insertion site numbers of nine TEs that were chosen because they have a low average number of sites. Most populations were found to have 0-3 insertion sites, but some of them had a significantly higher number of sites for a given TE. The populations located in regions outside Africa had the highest number of sites for all elements except HMS Beagle and Coral, suggesting a recent increase in the activity of some TEs associated with the colonization patterns of Drosophila simulans. The element Tirant had a very distinctive pattern of distribution: it was identified mainly in populations from East Africa and some islands in the Indian Ocean, and its insertion site number was low in all these populations. The data suggest that the genome of the entire species of Drosophila simulans may be being invaded by TEs from populations in which they are present in high copy number.

Animals↗