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Arnaud Le Rouzic

Other affiliations: Uppsala University, University of Paris-Sud, University of Oslo  ...read more
Bio: Arnaud Le Rouzic is an academic researcher from Université Paris-Saclay. The author has contributed to research in topics: Population & Selection (genetic algorithm). The author has an hindex of 23, co-authored 62 publications receiving 1953 citations. Previous affiliations of Arnaud Le Rouzic include Uppsala University & University of Paris-Sud.


Papers
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Journal ArticleDOI
TL;DR: This review provides a synopsis of what is known about the complex interactions that exist between transposable elements and the host genome, and explores the evolutionary aspects of TEs in the light of post-Darwinian theories of evolution.
Abstract: Transposable elements (TEs) were first discovered more than 50 years ago, but were totally ignored for a long time. Over the last few decades they have gradually attracted increasing interest from research scientists. Initially they were viewed as totally marginal and anecdotic, but TEs have been revealed as potentially harmful parasitic entities, ubiquitous in genomes, and finally as unavoidable actors in the diversity, structure, and evolution of the genome. Since Darwin's theory of evolution, and the progress of molecular biology, transposable elements may be the discovery that has most influenced our vision of (genome) evolution. In this review, we provide a synopsis of what is known about the complex interactions that exist between transposable elements and the host genome. Numerous examples of these interactions are provided, first from the standpoint of the genome, and then from that of the transposable elements. We also explore the evolutionary aspects of TEs in the light of post-Darwinian theories of evolution.

224 citations

Journal ArticleDOI
TL;DR: It is argued that a common term to describe the impact of hidden genetic variation on phenotypic change is needed and will help to provide new insights into the contribution of different components of genetic architectures to the evolvability of a character.
Abstract: The ability of a population to respond to natural or artificial selection pressures is determined by the genetic architecture of the selected trait. It is now widely acknowledged that a substantial part of genetic variability can be buffered or released as the result of complex genetic interactions. However, the impact of hidden genetic diversity on phenotypic evolution is still not clear. Here, we argue that a common term to describe the impact of hidden genetic variation on phenotypic change is needed and will help to provide new insights into the contribution of different components of genetic architectures to the evolvability of a character. We introduce the 'genetic charge' concept, to describe how the architecture of a trait can be 'charged' with potential for evolutionary change that can later be 'discharged' in response to selection.

199 citations

Journal ArticleDOI
TL;DR: Evidence is reviewed for and against the allometry‐as‐a‐constraint hypothesis, which suggests that allometries have low evolvability and could constrain phenotypic evolution by forcing evolving species along fixed trajectories.
Abstract: Morphological allometry refers to patterns of covariance between body parts resulting from variation in body size. Whether measured during growth (ontogenetic allometry), among individuals at similar developmental stage (static allometry), or among populations or species (evolutionary allometry), allometric relationships are often tight and relatively invariant. Consequently, it has been suggested that allometries have low evolvability and could constrain phenotypic evolution by forcing evolving species along fixed trajectories. Alternatively, allometric relationships may result from natural selection for functional optimization. Despite nearly a century of active research, distinguishing between these alternatives remains difficult, partly due to wide differences in the meaning assigned to the term allometry. In particular, a broad use of the term, encompassing any monotonic relationship between body parts, has become common. This usage breaks the connection to the proportional growth regulation that motivated Huxley's original narrow-sense use of allometry to refer to power-law relationships between traits. Focusing on the narrow-sense definition of allometry, we review here evidence for and against the allometry-as-a-constraint hypothesis. Although the low evolvability and the evolutionary invariance of the static allometric slope observed in some studies suggest a possible constraining effect of this parameter on phenotypic evolution, the lack of knowledge about selection on allometry prevents firm conclusions.

182 citations

Journal ArticleDOI
TL;DR: Results reveal an unexpected impact of genetic drift on the “junk DNA” content of the genome and strongly question the likelihood of the sustainable long-term stable transposition-selection equilibrium on which numerous previous works were based.
Abstract: Transposable elements are often considered parasitic DNA sequences, able to invade the genome of their host thanks to their self-replicating ability. This colonization process has been extensively studied, both theoretically and experimentally, but their long-term coevolution with the genomes is still poorly understood. In this work, we aim to challenge previous population genetics models by considering features of transposable elements as quantitative, rather than discrete, variables. We also describe more realistic transposable element dynamics by accounting for the variability of the insertion effect, from deleterious to adaptive, as well as mutations leading to a loss of transposition activity and to nonautonomous copies. Individual-based simulations of the behavior of a transposable-element family over several thousand generations show different ways in which active or inactive copies can be maintained for a very long time. Results reveal an unexpected impact of genetic drift on the “junk DNA” content of the genome and strongly question the likelihood of the sustainable long-term stable transposition-selection equilibrium on which numerous previous works were based.

169 citations

Journal ArticleDOI
01 Feb 2005-Genetics
TL;DR: This work proposes modeling the first steps of TE invasion, i.e., just after a horizontal transfer, when a single copy is present in the genome of one individual.
Abstract: Transposable elements are often considered as selfish DNA sequences able to invade the genome of their host species. Their evolutive dynamics are complex, due to the interaction between their intrinsic amplification capacity, selection at the host level, transposition regulation, and genetic drift. Here, we propose modeling the first steps of TE invasion, i.e., just after a horizontal transfer, when a single copy is present in the genome of one individual. If the element has a constant transposition rate, it will disappear in most cases: the elements with low-transposition rate are frequently lost through genetic drift, while those with high-transposition rate may amplify, leading to the sterility of their host. Elements whose transposition rate is regulated are able to successfully invade the populations, thanks to an initial transposition burst followed by a strong limitation of their activity. Self-regulation or hybrid dysgenesis may thus represent some genome-invasion parasitic strategies.

154 citations


Cited by
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Journal Article
TL;DR: For the next few weeks the course is going to be exploring a field that’s actually older than classical population genetics, although the approach it’ll be taking to it involves the use of population genetic machinery.
Abstract: So far in this course we have dealt entirely with the evolution of characters that are controlled by simple Mendelian inheritance at a single locus. There are notes on the course website about gametic disequilibrium and how allele frequencies change at two loci simultaneously, but we didn’t discuss them. In every example we’ve considered we’ve imagined that we could understand something about evolution by examining the evolution of a single gene. That’s the domain of classical population genetics. For the next few weeks we’re going to be exploring a field that’s actually older than classical population genetics, although the approach we’ll be taking to it involves the use of population genetic machinery. If you know a little about the history of evolutionary biology, you may know that after the rediscovery of Mendel’s work in 1900 there was a heated debate between the “biometricians” (e.g., Galton and Pearson) and the “Mendelians” (e.g., de Vries, Correns, Bateson, and Morgan). Biometricians asserted that the really important variation in evolution didn’t follow Mendelian rules. Height, weight, skin color, and similar traits seemed to

9,847 citations

Journal ArticleDOI
TL;DR: The basic components and the underlying philosophy of ADMB are described, with an emphasis on functionality found in no other statistical software, and the main advantages are flexibility, speed, precision, stability and built-in methods to quantify uncertainty.
Abstract: Many criteria for statistical parameter estimation, such as maximum likelihood, are formulated as a nonlinear optimization problem. Automatic Differentiation Model Builder (ADMB) is a programming framework based on automatic differentiation, aimed at highly nonlinear models with a large number of parameters. The benefits of using AD are computational efficiency and high numerical accuracy, both crucial in many practical problems. We describe the basic components and the underlying philosophy of ADMB, with an emphasis on functionality found in no other statistical software. One example of such a feature is the generic implementation of Laplace approximation of high-dimensional integrals for use in latent variable models. We also review the literature in which ADMB has been used, and discuss future development of ADMB as an open source project. Overall, the main advantages of ADMB are flexibility, speed, precision, stability and built-in methods to quantify uncertainty.

1,753 citations

Book ChapterDOI
01 Jan 1976
TL;DR: A positive temperature coefficient is the term which has been used to indicate that an increase in solubility occurs as the temperature is raised, whereas a negative coefficient indicates a decrease in Solubility with rise in temperature.
Abstract: A positive temperature coefficient is the term which has been used to indicate that an increase in solubility occurs as the temperature is raised, whereas a negative coefficient indicates a decrease in solubility with rise in temperature.

1,573 citations

Journal ArticleDOI
TL;DR: The computational problems surrounding repeats are discussed and strategies used by current bioinformatics systems to solve them are described.
Abstract: Repetitive DNA sequences are abundant in a broad range of species, from bacteria to mammals, and they cover nearly half of the human genome. Repeats have always presented technical challenges for sequence alignment and assembly programs. Next-generation sequencing projects, with their short read lengths and high data volumes, have made these challenges more difficult. From a computational perspective, repeats create ambiguities in alignment and assembly, which, in turn, can produce biases and errors when interpreting results. Simply ignoring repeats is not an option, as this creates problems of its own and may mean that important biological phenomena are missed. We discuss the computational problems surrounding repeats and describe strategies used by current bioinformatics systems to solve them.

1,451 citations