Pierre-Alexandre Gagnaire

Pierre-Alexandre Gagnaire
Université de Montpellier | UM1 · Institut des Sciences de l’Évolution Montpellier (ISEM)

PhD

About

67
Publications
15,558
Reads
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2,376
Citations
Introduction
Research area : Population genetics; Speciation, Adaptation; From genes to phenotypes I am interested in the adaptation of natural populations to variations in their environment, and to the genetic basis of reproductive isolation. My research is based on population genomic approaches to understand how the different evolutionary forces shape genetic variation in nature. My main species of interest are marine fishes.
Additional affiliations
October 2013 - present
CNRS
Position
  • Researcher
December 2011 - October 2013
Université de Montpellier
Position
  • PostDoc Position
October 2009 - November 2011
Laval University
Position
  • PostDoc Position

Publications

Publications (67)
Article
Full-text available
Estimating the rate of exchange of individuals among populations is a central concern to evolutionary ecology and its applications to conservation and management. For instance, the efficiency of protected areas in sustaining locally endangered populations and ecosystems depends on reserve network connectivity. The population genetics theory offers...
Article
During speciation-with-gene-flow, effective migration varies across the genome as a function of several factors, including proximity of selected loci, recombination rate, strength of selection, and number of selected loci. Genome scans may provide better empirical understanding of the genome-wide patterns of genetic differentiation, especially if t...
Article
Full-text available
The European sea bass (Dicentrarchus labrax) is a temperate zone euryhaline teleost of prime importance for aquaculture and fisheries. This species is subdivided into two naturally hybridizing lineages, one inhabiting the north-eastern Atlantic Ocean and the other the Mediterranean and Black seas. Here, we provide a high-quality chromosome-scale as...
Article
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Our understanding of the genetic basis of local adaptation has recently benefited from the increased power to identify functional variants associated with environmental variables at the genome scale. However, it often remains challenging to determine whether locally adaptive alleles are actively maintained at intermediate frequencies by spatially v...
Article
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During the early stages of speciation, interspecific gene flow may be impeded by deleterious epistatic interactions in hybrids, which maintain parental allelic combinations at the speciation genes. The resulting semipermeable nature of the barrier to interspecific gene flow provides a valuable framework to identify the genes involved in hybrid mort...
Poster
Full-text available
This poster explores the extent of introgression from domestic strains into wild editerranean populations of the brown trout (Salmo trutta L.) and how introgression may vary across the genome of the recipient populations.
Poster
Full-text available
This research explores the genomic basis of skin color variation between the Atlantic and Mediterranean lineages of the brown trout (Salmo trutta L.), and shows that wild Mediterranean populations of brown trout supplemented with the foreign Atlantic lineage have intermediate colour patterns compared to ’pure’ populations.
Article
Full-text available
Parallel divergence across replicated species pairs occurring in similar environmental contrastsmay arise through distinct evolutionary scenarios. Deciphering whether such parallelism actually reflects repeated parallel divergence driven by divergent selection or a single divergence event with subsequent gene flow needs to be ascertained. Reconstru...
Article
Full-text available
High-density linkage maps are valuable tools for conservation and eco-evolutionary issues. In salmonids, a complex rediploidization process consecutive to an ancient whole genome duplication event makes linkage maps of prime importance for investigating the evolutionary history of chromosome rearrangements. Here, we developed a high-density consens...
Article
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Understanding the evolutionary mechanisms generating parallel genomic divergence patterns among replicate ecotype pairs remains an important challenge in speciation research. We investigated the genomic divergence between the anadromous parasitic river lamprey (Lampetra fluviatilis) and the freshwater-resident non-parasitic brook lamprey (Lampetra...
Article
Full-text available
In marine fishes, the extent to which spatial patterns induced by selection remain stable across generations remains largely unknown. In the gilthead sea bream Sparus aurata, polymorphisms in the growth hormone (GH) and prolactin (Prl) genes can display high levels of differentiation between marine and lagoon habitats. These genotype-environment as...
Article
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Hybrid zones provide natural experiments where new combinations of genotypes and phenotypes are produced. Studying the reshuffling of genotypes and remodeling of phenotypes in these zones is of particular interest to document the building of reproductive isolation and the possible emergence of transgressive phenotypes that can be a source of evolut...
Article
Full-text available
A genome-wide assessment of diversity is provided for wild Mediterranean brown trout Salmo trutta populations from headwater tributaries of the Orb River and from Atlantic and Mediterranean hatchery-reared strains that have been used for stocking. Double-digest restriction-site-associated DNA sequencing (dd-RADseq) was performed and the efficiency...
Article
Full-text available
Highly fecund marine species with dispersive life-history stages often display large population sizes and wide geographic distribution ranges. Consequently, they are expected to experience reduced genetic drift, efficient selection fueled by frequent adaptive mutations, and high migration loads. This has important consequences for understanding how...
Poster
Full-text available
The brown trout Salmo trutta L. is a widely distributed Eurasian species which has been heavily impacted by human activities, including traditional stocking of hatchery strains to enhance local populations. Understanding the consequences of stocking practices needs a better characterisation of genetic variation. A genome-wide assessment of diversit...
Article
Ecophenotypic differentiation among replicate ecotype pairs within a species complex is often attributed to independent outcomes of parallel divergence driven by adaptation to similar environmental contrasts. However, the extent to which parallel phenotypic and genetic divergence patterns have emerged independently is increasingly questioned by pop...
Article
Linking population genetic variation to the spatial heterogeneity of the environment is of fundamental interest to evolutionary biology and ecology, in particular when phenotypic differences between populations are observed at biologically small spatial scales. Here, we applied restriction-site associated DNA sequencing (RAD-Seq) to test whether ph...
Article
Full-text available
Parallel changes in body shape may evolve in response to similar environmental conditions, but whether such parallel phenotypic changes share a common genetic basis is still debated. The goal of this study was to assess if parallel phenotypic changes could be explained by genetic parallelism, multiple genetic routes or both. We first provide eviden...
Article
Full-text available
Background The two North Atlantic eel species, the European and the American eel, represent an ideal system in which to study parallel selection patterns due to their sister species status and the presence of ongoing gene flow. A panel of 80 coding-gene SNPs previously analyzed in American eel was used to genotype European eel individuals (glass ee...
Article
Major histocompatibility (MHC) immune system genes may evolve in response to pathogens in the environment. Because they also may affect mate choice, they are candidates for having great importance in ecological speciation. Here, we use next-generation sequencing to test the general hypothesis of parallelism in patterns of MHCIIβ diversity and bacte...
Conference Paper
Full-text available
When incompletely isolated taxa coexist in a patchy environment (e.g. mosaic hybrid zones, host races), patterns of variation may differ between selected traits/genes and neutral markers. While the spatial structure of selected traits/loci tends to coincide with habitat variables (Genetic-Environment Association or GEA), genetic differentiation at...
Article
Full-text available
When incompletely isolated taxa coexist in a patchy environment (e.g. mosaic hybrid zones, host-race complexes), patterns of variation may differ between selected traits/genes and neutral markers. While the genetic structure of selected traits/loci tends to coincide with habitat variables (producing Genetic-Environment Association or GEA), genetic...
Article
We performed population genetic analyses on the American eel (Anguilla rostrata) with three main objectives. First, we conducted the most comprehensive analysis of neutral genetic population structure to date to revisit the null hypothesis of panmixia in this species. Second, we used this data to provide the first estimates of contemporary effectiv...
Article
The evolution of reproductive isolation in an ecological context may involve multiple facets of species divergence on which divergent selection may operate. These include variation in quantitative phenotypic traits, regulation of gene expression, and differential transmission of particular allelic combinations. Thus, an integrative approach to the...
Article
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The genetic basis and evolutionary implications of local adaptation in high gene flow marine organisms are still poorly understood. In several Mediterranean fish species, alternative migration patterns exist between individuals entering coastal lagoons that offer favourable conditions for growth and those staying in the sea where environmental cond...
Article
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During their larval leptocephalus phase, newly hatched American eels undergo an extensive oceanic migration from the Sargasso Sea toward coastal and freshwater habitats. Their subsequent metamorphosis into glass eel is accompanied by drastic morphological and physiological changes preceding settlement over a wide geo-graphic range. The main objecti...
Article
In the marine environment, differential gene exchange between partially reproductively isolated taxa can result in introgression that extends over long distances due to high larval dispersal potential. However, the degree to which this process contributes to interlocus variance of genetic differentiation within introgressed populations remains uncl...
Article
Aim The objective of this study was to reveal the present population structure and infer the gene-flow history of the Indo-Pacific tropical eel Anguilla bicolor. Location The Indo-Pacific region. Methods The entire mitochondrial control region sequence and the genotypes at six microsatellite loci were analysed for 234 specimens collected from eight...
Article
Full-text available
Definition of the genus Calliptamus (Orthoptera: Acrididae) has generated many taxonomic debates. Even now, the existence of different geographical morphs hinders species determination, particularly as concerns females and larvae. Some of these species are observed in southern France and are recognized as potential pests. To circumvent problems of...
Article
Full-text available
The occurrence of Alexandrium catenella related to paralytic shellfish poisoning (PSP) in the French Mediterranean Thau lagoon has been known since 1998. Blooms are recurrent and usually occur each year in spring and/or autumn. Taxonomic diversity of resting cysts and vegetative cells has been studied through morphological examination and molecular...
Article
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Two morphological characters were examined in 4099 anguillid glass eels sampled in four south-western Indian Ocean islands, and resulting identifications were tested using genetic analysis. Distance between the origin of the dorsal and anal fins as related to total length and tail and caudal fin pigmentation enabled formulation of a useful field id...
Article
Investigating patterns of genetic variation in hybridizing species provides an opportunity to understand the impact of natural selection on intraspecific genetic variability and interspecific gene exchange. The Atlantic eels Anguilla rostrata and A. anguilla each occupy a large heterogeneous habitat upon which natural selection could differentially...
Article
Full-text available
Understanding the evolutionary processes underlying population structuring of freshwater eels is an essential step toward comprehending their exceptional life cycle. However, in order to infer evolutionary scenarios that account for the genetic structure of current populations, it is necessary to unravel the history of gene flow from the onset of p...
Article
Full-text available
The oceanic early-life history of Anguilla marmorata was examined in the southwestern Indian Ocean in Mayotte, Mauritius, and Re´union islands through otolith microstructural analysis. The study of the hatching dates, the first feeding check diameter (FFD), the leptocephalus (LD) and metamorphosis (MD) durations, the age at recruitment (AR), and th...
Article
Full-text available
A total of 4,172 freshwater eels have been collected by electrofishing in upper estuaries from Madagascar (East coast), Mascarene (Réunion and Mauritius Is.), Comoros (Mayotte Is.) and Seychelles (Mahé and Praslin Is.) Archipelagos, between October 2003 and February 2006. Eel species composition in the sampling stations was contrasted between easte...