B. Crouau-Roy, L. Chikhi, E. Lecompte, A. Riberon, M. Bonhomme (ATER), E. Quéméré and P. Barazer (PhD students).Chikhi L, Crouau-Roy B, Lecompte E, Magné F, Ribéron A, Bonhomme M (ATER), Quemere E (Ph.D. student), P. Barazer (thesis)
Our research aims to describe and quantify the genetic diversity present in the genome, in populations, and in species. Both empirical and theoretical approaches are needed to understand their evolution, ancient and/or recent demographic history and the selective processes having an impact on the genetic diversity distribution. This project deals with population genetics, molecular phylogeny, molecular evolution, comparative genomics and conservation genetics.
B. Crouau-Roy, E. Lecompte, M. Bonhomme (ATER)
Collaboration: G. Marais, S. Mousset (Lyon).
Detecting the molecular signature of selection at the genome level. One of the major stakes in population genomic is the identification of chromosomal regions or loci under selection (« outlier »), followed by the identification regions or genes involved in adaptive processes. This identification, possible through the study of numerous loci, allows us to discriminate locus-specific effects (selection, mutation, recombination) from those affecting the whole genome (genetic drift, migration, inbreeding). In certain cases, statistical approaches used to detect loci under selection require the distribution of summary statistics (FST, homozygosity) under a neutral model. While others consist in the evaluation the polymorphism differences between loci using the variance in allele size. We use genomic approaches to detect the signature of selection in relation with primate pathogens or adaptation.
Sex chromosomes evolution. Mammalian sex chromosomes are good models for evolutionary studies because of their particularities (females XX and male XY). They are originated from an autosomal pair of chromosomes of which mechanisms such as translocations, duplications, inversion have conducted to a progressive stop of the recombination in the Y chromosome and to its degenerescence (Muller’s ratchet, genetic hick-jacking and background selection …). However, some rare genes on the Y are yet functional. The genic configuration of these genes is favourable to study the relative proportion between random (genetic drift) and deterministic (selection) processes. Indeed, the mutations slightly deleterious have more chance to fix into the population when the effective size is low due to the genetic drift and with a low rate of recombination. The processes at the origin of the Y degenerescence leave a trace on these genes. The hypothesis of a selection less efficiency will be tested on genes located on both sex chromosomes. An evolutionary analysis of primate amelogenin, the major protein of forming enamel, is conducted under 2 approaches: i) an intra-specific one to distinguish mutational and selective effects; ii) an inter-specific one to analyze the divergence by contrasting the synonymous and non-synonymous substitution rate of the gene, but also to identify potential variation of the evolution rate in particular lineage between the X and Y copies.
The comparison between sex chromosomes markers and autosomal ones are performed to better understand evolutionary forces which promote the evolution of the genome.
B. Crouau-Roy, L. Chikhi, E. Lecompte, A. Riberon, M. Bonhomme (ATER), E. Quéméré and P. Barazer (PhD students).
Collaborations: A. Blancher (France), M. Beaumont, B. Gossens, M. Bruford (UK)
Genetics and conservation. Habitat loss and fragmentation are among the major causes of biodiversity loss across the world. Few studies have actually managed to quantify the effect of anthropogenic fragmentation on genetic diversity patterns. In most conservation studies, one explanation is that genetic data are usually obtained after deforestation or habitat destruction has started. Since the patterns of genetic diversity and the differentiation observed today could have been produced by a wide variety of demographic processes, with or without anthropogenic perturbations, it is not always clear whether the observed patterns can be objectively linked to human activities. For instance, observing a high level of genetic differentiation between populations currently living in forest fragments could be due to (i) recent, human-caused fragmentation of the habitat, (ii) more ancient environmental/climatic changes, or (iii) the natural dynamics of species of interest (small effective population size and/or limited gene flow).
From the genotyping of a great number of molecular markers (microsatellites, sequences), we have produced enough genetic data to address issues related to demographic history of populations and species. This approach includes the detection, quantification, and dating of population collapses, expansions, or admixture processes. Applications go from human evolution (e.g. the Neolithic transition in Europe) to conservation genetics of wild primate’s populations, such as macaques and lemurs.
Fig. 1. The brown lemur, Eulemur fulvus, exhibits variation in the color of the pelage. Melanocortin and Agouti genes are good candidates to explore relationships between color coat polymorphism and genetic variation.
Modelisation. We are currently using and testing existing methods but also interested in developing new methods in population genetics. Such methods are applied to uncover demographic events (recent evolutionary history) for a wide range of species. Moreover, we aim to understand the limits of genetic data as inferential tools.
There is an urgent need of developing approaches that can separate ancient from recent events, as well as assessing and quantifying the relative contribution of anthropogenic and natural factors in the patterns observed today in wild populations. Coalescent modeling together with likelihood-based approaches have allowed the development of efficient population genetics methods to infer parameters (such as expansion or migration rates, population effective sizes, dates of expansion...) by using to-date patterns of genetic diversity. From simulation-based methods, like Approximate Bayesian Computation (simulation of data under a demographic model), we have developed an improved and quicker method that allows the estimation of admixture proportions when more than two parental populations are involved. Recently, we have developed an ABC method that allows the estimation of admixture with two parental populations. Its flexibility should allow us to analyze more complex admixture scenarios.
Fig. 2. Dating the beginning of the demographic collapse of Orang-utan populations in Borneo.
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B. Crouau-Roy, E. Lecompte, F. Magne Collaborations: A. Magro, J.-L. Hemptine (ENFA). |
Ladybirds belong to a large Coleoptera family including more than 5000 species, with several subfamilies described. Despite their diversity, and their importance as bio-control, the systematic and evolutionary history of the family is poorly known. Such situation complicates the understanding of the relationships between the ladybirds and their preys (aphids, cochineal…), or the mechanisms involved in the chemical defenses. We have reconstructed the phylogeny of the family, using a multi locus approach with mitochondrial and nuclear markers.
Within this family, we mainly focus on the seven-spot ladybird, largely distributed in palearctic region. This species was introduced in North America as bio-control where it became invasive. We search to clarify the systematic of this species in its native distribution range, based on population genetic structure and trade-off analyses,. Enlarging such approaches to the introduction area, together with a phylogeographic study, we will elucidate the origin of the invasive populations, the colonization routes, and the mechanisms at the origin of its invasive success in North America.