Patrick Berrebi

Patrick Berrebi
Genome - Research & diagnostic

About

505
Publications
48,487
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6,513
Citations
Citations since 2016
57 Research Items
2592 Citations
20162017201820192020202120220100200300400
20162017201820192020202120220100200300400
20162017201820192020202120220100200300400
20162017201820192020202120220100200300400

Publications

Publications (505)
Article
Full-text available
The brown trout form the Salmo trutta complex, a diversified assemblage of salmonids. Its native area mainly covers Europe. It can develop three ecological forms or ecotypes, depending on its migratory behaviours: resident, anadromous (going to sea) and lacustrine (going to lakes). The sea trout is the anadromous ecotype, born up river, living at s...
Article
The association of molecular variants to phenotypic variation is a main issue in biology, often tackled with genome-wide association studies (GWAS). GWAS are challenging, with increasing, but still limited use in evolutionary biology. We used redundancy analysis (RDA) as a complimentary ordination approach to single- and multi-trait GWAS to explore...
Article
Full-text available
In Slovenia, the unique watershed naturally hosting the marble trout is the Soča River, called Isonzo in Italy. In 1993-1996 molecular data established the existence of extensive hybridization with stocked Atlantic domestic lineages which is a threat for this taxon and for the economy of the country established on the angling tourism. Different man...
Article
Full-text available
Selection, genetic drift, and gene flow affect genetic variation within populations and genetic differences among populations. Both drift and selection tend to decrease variation within populations and increase differences among populations, whereas gene flow increases variation within populations but leads to populations being related. In brown tr...
Article
Full-text available
Aim In the Mediterranean biodiversity hotspot, freshwater fishes are key biogeographic indicators, while their habitats are vulnerable to ongoing anthropogenic pressures. The freshwater blenny is a widespread endemic taxon in this area. However, our understanding of the overall diversity of specific populations and their phylogenetic relationships...
Article
Brown trout (Salmo trutta) is composed of numerous geographical forms in the wild and a multitude of stocks reared in hatcheries. One of the practices impacting this species is hatchery rearing and domestication. Thousands of hatcheries are producing domestic trout which are frequently released in the wild without real knowledge of the origin and g...
Article
Full-text available
There are particular challenges in defining the taxonomic status of recently radiated groups due to the low level of phylogenetic signal. Members of the Salmo trutta species-complex, which mostly evolved during and following the Pleistocene, show high morphological and ecological diversity that, along with their very wide geographic distribution, h...
Article
Full-text available
Pomatoschistus marmoratus and Pomatoschistus microps are small sedentary gobies inhabiting the lagoons of European Mediterranean and Atlantic coasts. Along the French Mediterranean coast their respective geographical distribution is not precisely known, in part because they are cryptic species. In this study, 512 gobies of both species were caught...
Preprint
Full-text available
Colour and pigmentation variation attracted fish biologists for a while, but high-throughput genomic studies investigating the molecular basis of body pigmentation remain still limited to few species and conservation biology issues ignored. Using 75,684 SNPs, we investigated the genomic basis of pigmentation pattern variation among individuals of t...
Article
The role of south-western Alps as a corridor for Mediterranean trout (Salmo trutta complex Linnaeus, 1758) was evaluated in order to understand the influence of the last glacial events in shaping the spatial distribution of the genetic diversity of this salmonid. For this, the allochthonous hypothesis of a man-mediated French origin (19th century)...
Article
Full-text available
The common spiny lobster (Palinurus elephas, Fabricius, 1787) is an iconic species of the Mediterranean Sea. Despite the existence of data on the artisanal fishery of P. elephas in the Mediterranean Sea and particularly in Corsica, knowledge on the biology and life history traits of this iconic species is still lacking. This paper identifies the ma...
Article
Full-text available
Brown trout Salmo trutta L. lives mainly in European rivers and is also bred in hatcheries for fishery purposes. Since the end of 19th century it has been introduced in all other continents. For the present survey most of the known self-sustaining brown trout river populations in Japan have been sampled and analyzed through sequences of the entire...
Article
Physiological plasticity gives HABs species the ability to respond to variations in the surrounding environment. The aim of this study was to examine morphological and physiological variability in Alexandrium pacificum Litaker sp. nov (Group IV) (former Alexandrium catenella) blooming in Annaba bay, Algeria. Monoclonal cultures of up to 30 strains...
Article
Full-text available
Both morphological and molecular data are presented and discussed for indigenous Salmo sp. from Corsica and Sardinia, here called Tyrrhenian trout. For comparison, morphological data obtained from museum specimens, including the Algerian S. macrostigma, are discussed in the light of recent and new molecular findings. In total, 29 measurements and 2...
Chapter
Here we summarize the current knowledge on the trout and char of central and southern Europe, including Germany, The Netherlands, Switzerland, Austria, Czech Republic, France, Spain, Portugal, Italy, the Mediterranean Islands, and northwestern Africa (Morocco and Algeria). We focus on the only two widely recognized native species: Brown Trout Salmo...
Article
Full-text available
Background: The brown trout (Salmo trutta) is an economically and ecologically important species for which population genetic monitoring is frequently performed. The most commonly used genetic markers for this species are microsatellites and mitochondrial markers that lack replicability among laboratories, and a large genome coverage. An alternati...
Article
Full-text available
The brown trout (Salmo trutta L.) is widely distributed all around Europe but its natural diversity is threatened by massive stocking with Atlantic domestic strains. Describing the remaining natural genetic diversity and the proportion of domestic hatchery strains in rivers is a prerequisite for smart conservation. The high genetic diversity of bro...
Chapter
Full-text available
Here we summarize the current knowledge on the trout and char of central and southern Europe, including Germany, The Netherlands, Switzerland, Austria, Czech Republic, France, Spain, Portugal, Italy, the Mediterranean Islands, and northwestern Africa (Morocco and Algeria). We focus on the only two widely recognized native species: Brown Trout Salmo...
Article
Full-text available
The common dentex, Dentex dentex, is a fish species which inhabits marine environments in the Mediterranean and Northeast Atlantic regions. This is an important species from an ecological, economic and conservation perspective, however critical information on its population genetic structure is lacking. Most samples were obtained from the Mediterra...
Data
Information on the eight microsatellite loci used in the present study and the PCR conditions. (CL168 and CL1014 [72]; Ds33 and Dxd16 [73]; SaGT41b [74]; SaI19 [75]; SauE82INRA and SauI41INRA [76]). (DOCX)
Data
D-loop haplotypes for each individual. (DOCX)
Data
Dentex dentex genotypes at 8 microsatellites. (0 = no amplification). (DOCX)
Data
Diagram from Structure Harvester expressing Delta K according to K. (TIFF)
Data
All information used for COI gene sequence analyses in Figs 2 and 3. np: not published. (DOCX)
Data
Factorial Correspondences Analysis (FCA) of the whole Dentex dentex specimens. In the blue envelope are the very homogeneous samples of Mediterranean and Bay of Biscay origin. The red envelope gathers the Bargelloni et al. 2003 Portugal samples. Clearly, Bargelloni's Portuguese fish are heterogeneous (at least three clouds) and do not belong to D....
Data
Diagram from Structure Harvester expressing likelihood according to K. Standard error bars are also indicated. (TIFF)
Data
COI and D-loop sequences included in mtDNA analyses. (DOCX)
Data
Mismatch distribution for D-loop haplotypes of Dentex dentex. (TIFF)
Data
Heat-map of D-loop pairwise Fst's between all pairs of localities. Asterisk indicates P≤ 0.05 in terms of statistical significance. (TIFF)
Article
We examined specimens of the macrostigma trout Salmo macrostigma , which refers to big black spots on the flanks, to assess whether it is an example of taxonomic inflation within the brown trout Salmo trutta complex. Using new specimens, publicly available data and a mitogenomic protocol to amplify the control and cytochrome b regions of the mitoch...
Article
We examined specimens of the macrostigma trout Salmo macrostigma, which refers to big black spots on the flanks, to assess whether it is an example of taxonomic inflation within the brown trout Salmo trutta complex. Using new specimens, publicly available data and a mitogenomic protocol to amplify the control and cytochrome b regions of the mitocho...
Article
Full-text available
Understanding the evolutionary consequences of human‐mediated introductions of domesticated strains into the wild and their subsequent admixture with natural populations is of major concern in conservation biology. However, the genomic impacts of stocking from distinct sources (locally‐derived vs divergent) on the genetic integrity of wild populati...
Preprint
Full-text available
Understanding the evolutionary consequences of human-mediated introductions of domestic strains into the wild and their subsequent admixture with natural populations is of major concern in conservation biology. In the brown trout Salmo trutta , decades of stocking practices have profoundly impacted the genetic makeup of wild populations. Small loca...
Article
Aim The European sturgeon, Acipenser sturio, was classified as “Critically Endangered” in 1996. Its last natural population is currently living in the Gironde Estuary (French Atlantic coastal region) but has a low level of genetic diversity and is on the brink of extinction. In order to reconstitute the genetic structure, migrations and hybridizati...
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
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
Full-text available
The endemic marble trout, Salmo trutta marmoratus, suffered massive stocking with brown trout in Slovenia and Italy. In the Soča River (Slovenia) long-term surveys have evidenced Danubian and Atlantic introgressions. The observation of discrepancies between introgression frequencies when using morphology, mitochondrial sequences, allozymes, or micr...
Preprint
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
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
The only remaining population of the critically endangered European sturgeon, Acipenser sturio, is located in the Gironde basin (France). A restoration program initiated 20 years ago has allowed more than one and a half million individuals to be stocked. Effective monitoring of this population is a key prerequisite in ensuring the sustainability of...
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
Full-text available
Genetic diversity is the raw material for evolutionary change, so a species' capacity to maintain its genetic diversity is a major concern in conservation genetics. Although genetic diversity within a population is reduced through time by genetic drift, gene flow among populations can act to recover or add new genetic variants. The goal of this stu...
Article
Animals in captivity are subject to similar evolutionary forces that act on natural populations, which can facilitate the generation of population genetic structure. Understanding the extent of genetic differentiation among captive populations provides insights into industry practices and the domestication process. We investigated the genetic struc...
Article
A non-random association between an environmental factor and a given trait could be explained by directional selection (genetic determinism) and by phenotypic plasticity (environmental determinism). A previous study showed a significant relationship between morphology and water velocity in Salaria fluviatilis that conformed to functional expectatio...
Article
The European sturgeon (Acipenser sturio) was once a common species throughout Europe, but the sole remaining natural population presently inhabits the Gironde Estuary in France (Atlantic coast). The species was classified as 'Critically Endangered' in 1996, and the Gironde population is now on the verge of extinction. In this setting, and for the f...
Article
Full-text available
Indonesian waters, have been proposed by biologists to be the origin of freshwater eel anguillid. The objective of this study was to investigate molecular phylogenetic relationships and genetic diversity of the seven Indonesian eel taxa based on the cyt b gene. Each eel species was identified by comparison with published sequences, namely Anguilla...
Article
Full-text available
The short-finned eel Anguilla bicolor is known to be subdivided in two distinct subspecies (i.e. A. bicolor bicolor and A. bicolor pacifica), each subspecies being geographically distributed in allopatry. The present survey intends to describe genetic differentiation, population structure, molecular variance and phylogeny of both subspecies of A. b...