I have a particular interest in phenotypic plasticity, more precisely in the capacity of the organisms to modify their phenotype in response to an environmental stimulus. This capacity has a substantial impact on the evolutionary history of the species because i) it is heritable and responds to evolutionary forces, ii) it increase the fitness of the individuals by allowing quick adjustment in response to environmental changes and iii) it facilitates the dispersion and colonization of organisms to new environments. Therefore, evaluating the plastic capacity of different phenotypic traits in different environments is a major asset in the goal of increasing our knowledge of the evolutionary history of different populations or genetically related species.
During my post-doctorate, I will evaluate the importance of the phenotypic plasticity in the origin of the "dwarf" morph of the white fish (Coregonus cupleaformis). This species is separated into two ecotypes, "normal" and "dwarf". It is now recognized that the "dwarf" morph, living in a limnetic habitat, derived from the "normal" morph, living in a benthic habitat. We will compare the phenotypic plasticity of the "normal" and "dwarf" forms on several phenotypic traits (e.g.: morphology, gene expression, physiology, mitochondrial activity...) in different water velocities as a first step, but also in different anoxic conditions. We chose these environmental conditions because it is considered that a higher necessity to swim and anoxia level are present in limnetic habitats when compared to benthic habitats. The results will allow us to verify if the plastic capacity of the "normal" morph of the white fish allowed the colonization of the limnetic habitat. We also predict that the plastic capacity of the "dwarf" morph have been lost during the specialization process to the limnetic habitat. Supervisors: Louis Bernatchez
Freshwater eels (Anguilla sp.) have large economic, cultural, ecological and aesthetic
importance... more Freshwater eels (Anguilla sp.) have large economic, cultural, ecological and aesthetic importance worldwide, but they suffered more than 90% decline in global stocks over the past few decades. Proper genetic resources, such as sequenced, assembled and annotated genomes, are essential to help plan sustainable recoveries by identifying physiological, biochemical and genetic mechanisms that caused the declines or that may lead to recoveries. Here, we present the first sequenced genome of the American Eel. This genome contained 305,043 contigs (N50 = 7,397) and 79,209 scaffolds (N50 = 86,641) for a total size of 1.41 Gb, which is in the middle of the range of previous estimations for this species. In addition, protein coding regions, including introns and flanking regions, are very well represented in the genome, as 95.2% of the 458 core eukaryotic genes and 98.8% of the 248 ultra-conserved subset were represented in the assembly. and a total of 24,564 genes were annotated for future functional genomics studies. We performed a candidate gene analysis to compare three genes among all three freshwater eel species and, congruent with the phylogenetic relationships, Japanese eel (A. japanica) exibited the most divergence. Overall, the sequenced genome presented in this study is a crucial addition to the presently available genetic tools to help guide future conservation efforts of Freshwater eels
Repeated adaptive ecological diversification has commonly been reported in fish and has often bee... more Repeated adaptive ecological diversification has commonly been reported in fish and has often been associated with trophic niche diversity. The main goal of this study was to investigate the extent of parallelism in the genomic and phenotypic divergence between piscivorous and planktivorous lake trout ecotypes from Laurentian Shield lakes, Canada. This was achieved by documenting the extent of morphological differentiation using geometric morphometrics and linear measurements as well as the pattern of genomic divergence by means of RADseq genotyping (3925 filtered SNPs) in 12 lakes. Our results indicate that the two ecotypes evolved distinct body shape and several linear measurements in parallel. Neutral genetic differentiation was pronounced between all isolated populations (Mean F ST = 0.433), indicating no or very limited migration and pronounced genetic drift. Significant genetic differentiation also suggested partial reproductive isolation between ecotypes in the two lakes where they are found in sympatry. Combining different outlier detection methods, we identified 48 SNPs putatively under divergent selection between ecotypes, among which 10 could be annotated and related to functions such as developmental processes and ionic regulation. Finally, our results indicate that parallel morphological divergence is accompanied by both parallel and nonparallel genomic divergence, which is associated with the use of different trophic niches between ecotypes. The results are also discussed in the context of management and conservation of this highly exploited species throughout northern North America.
Investigating how environmental features shape the genetic structure of populations is crucial fo... more Investigating how environmental features shape the genetic structure of populations is crucial for understanding how they are potentially adapted to their habitats, as well as for sound management. In this study, we assessed the relative importance of spatial distribution , ocean currents and sea surface temperature (SST) on patterns of putatively neutral and adaptive genetic variation among American lobster from 19 locations using population differentiation (PD) approaches combined with environmental association (EA) analyses. First, PD approaches (using BAYESCAN, ARLEQUIN and OUTFLANK) found 28 outlier SNPs putatively under divergent selection and 9770 neutral SNPs in common. Redundancy analysis revealed that spatial distribution, ocean current-mediated larval connectiv-ity and SST explained 31.7% of the neutral genetic differentiation, with ocean currents driving the majority of this relationship (21.0%). After removing the influence of spatial distribution, no SST were significant for putatively neutral genetic variation whereas minimum annual SST still had a significant impact and explained 8.1% of the putatively adap-tive genetic variation. Second, EA analyses (using Pearson correlation tests, BAYESCENV and LFMM) jointly identified seven SNPs as candidates for thermal adaptation. Covariation at these SNPs was assessed with a spatial multivariate analysis that highlighted a significant temperature association, after accounting for the influence of spatial distribution. Among the 505 candidate SNPs detected by at least one of the three approaches, we discovered three polymorphisms located in genes previously shown to play a role in thermal adaptation. Our results have implications for the management of the American lobster and provide a foundation on which to predict how this species will cope with climate change.
Background: Improved performance in a given ecological niche can occur through local adaptation, ... more Background: Improved performance in a given ecological niche can occur through local adaptation, phenotypic plasticity, or a combination of these mechanisms. Evaluating the relative importance of these two mechanisms is needed to better understand the cause of intra specific polymorphism. In this study, we reared populations of Lake Whitefish (Coregonus clupeaformis) representing the'normal' (benthic form) and the 'dwarf' (derived limnetic form) ecotypes in two different conditions (control and swim-training) to test the relative importance of adaptation and acclimation in the differentiation of traits related to swimming capacity. The dwarf whitefish is a more active swimmer than the normal ecotype, and also has a higher capacity for aerobic energy production in the swimming musculature. We hypothesized that dwarf fish would show changes in morphological and physiological traits consistent with reductions in the energetic costs of swimming and maintenance metabolism. Results: We found differences in traits predicted to decrease the costs of prolonged swimming and standard metabolic rate and allow for a more active lifestyle in dwarf whitefish. Dwarf whitefish evolved a more streamlined body shape, predicted to lead to a decreased drag, and a smaller brain, which may decrease their standard metabolic rate. Contrary to predictions, we also found evidence of acclimation in liver size and metabolic enzyme activities. Conclusion: Results support the view that local adaptation has contributed to the genetically-based divergence of traits associated with swimming activity. Presence of post-zygotic barriers limiting gene flow between these ecotype pairs may have favoured repeated local adaptation to the limnetic niches.
A non-random association between an environmental factor and a given trait could be explained by ... more 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 expectations. The objective of this study was to test whether this relationship could be explained by phenotypic plasticity. Salaria fluviatilis from a Corsican stream were placed in four experimental channels with different water velocities (0, 10, 20 and 30 cm s −1) to test whether there was a morphological response associated with this environmental factor. After 28 days, fish shape changed in response to water velocity without any significant growth. Fish in higher water velocities exhibited a more slender body shape and longer anal and caudal fins. These results indicate a high degree of morphological plasticity in riverine populations of S. fluviatilis and suggest that the previous relationship between morphology and water velocity observed in the field may largely be due to an environmental determinism.
Measuring the effects of selection on the genome imposed by human-altered environment is currentl... more Measuring the effects of selection on the genome imposed by human-altered environment is currently a major goal in ecological genomics. Given the polygenic basis of most phenotypic traits, quantitative genetic theory predicts that selection is expected to cause subtle allelic changes among covarying loci rather than pronounced changes at few loci of large effects. The goal of this study was to test for the occurrence of polygenic selection in both North Atlantic eels (European Eel, Anguilla anguilla and American Eel, A. rostrata), using a method that searches for covariation among loci that would discriminate eels from “control” vs. “polluted” environments and be associated with specific contaminants acting as putative selective agents. RAD-seq libraries resulted in 23,659 and 14,755 filtered loci for the European and American Eels respectively. A total of 142 and 141 covarying markers discriminating European and American Eels from “control” vs. “polluted” sampling localities were obtained using the Random Forest algorithm. Distance-based redundancy analyses (db-RDAs) were used to assess the relationships between these covarying markers and concentration of 34 contaminants measured for each individual eel. PCB153, 4'4'DDE and selenium were associated with covarying markers for both species, thus pointing to these contaminants as major selective agents in contaminated sites . Gene enrichment analyses suggested that sterol regulation plays an important role in the differential survival of eels in “polluted” environment. This study illustrates the power of combining methods for detecting signals of polygenic selection and for associating variation of markers with putative selective agents in studies aiming at documenting the dynamics of selection at the genomic level, and particularly so in human altered environments.
Genetic diversity is the raw material for evolutionary change, so a species’ capacity to maintain... more 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 study was to infer potential connectivity among isolated-by-sea populations of the vulnerable freshwater blenny (Salaria fluviatilis) and to determine if gene flow could contribute to maintaining genetic diversity in connected populations. Four genetic clusters (one small at the North, one large at the South for both East and West coasts) were detected with different clustering methods (FLOCK, STUCTURE, UPGMA, AMOVA). The two larger genetic clusters with higher migration-rate estimates among localities had higher genetic diversity and allelic richness and lower relatedness between individuals, compared to isolated localities found in smaller clusters. Our results also suggest that sea currents may facilitate fish movements among neighbouring rivers. Overall, gene flow among isolated-by-sea but close rivers could maintain the evolutionary potential of freshwater blenny populations. This finding should be considered when elaborating a conservation program for this species.
The physiological mechanisms underlying local adaptation in natural populations of animals, and w... more The physiological mechanisms underlying local adaptation in natural populations of animals, and whether the same mechanisms contribute to adaptation and acclimation, are largely unknown. Therefore, we tested for evolutionary divergence in aerobic exercise physiology in laboratory bred, size-matched crosses of ancestral, benthic, normal Lake Whitefish (Coregonus clupeaformis) and derived, limnetic, more actively-swimming ‘dwarf’ ecotypes. We acclimated fish to constant swimming (emulating limnetic foraging) and control conditions (emulating normal activity levels) to simultaneously study phenotypic plasticity. We found extensive divergence between ecotypes: dwarf fish generally had constitutively higher values of traits related to oxygen transport (ventricle size) and use by skeletal muscle (percent oxidative muscle, mitochondrial content), and also evolved differential plasticity of mitochondrial function (Complex I activity and flux through Complexes I-IV and IV). The effects of swim-training were less pronounced than differences among ecotypes and the traits which had a significant training effect (ventricle protein content, ventricle MDH activity and muscle Complex V activity) did not differ among ecotypes. Only one trait, ventricle mass, varied in a similar manner with acclimation and adaptation and followed a pattern consistent with genetic accommodation. Overall, the physiological and biochemical mechanisms underlying acclimation and adaptation to swimming activity in Lake Whitefish generally differ.
Parallel changes in body shape may evolve in response to similar environmental conditions, but wh... more 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 evidence for parallelism in fish shape using geometric morphometrics among 300 fish representing five species pairs of Lake Whitefish. Using a genetic map comprising 3438 RAD-seq SNPs, we then identified quantitative trait loci (QTL) underlying body shape traits in a backcross family reared in the laboratory. A total of 138 body shape QTL were identified in this cross, thus revealing a highly polygenic architecture of body shape in Lake Whitefish. Thirdly, we tested for evidence of genetic parallelism among independent wild populations using both a single-locus method (outlier analysis) and a polygenic approach (analysis of co-variation among markers). The single-locus approach provided limited evidence for genetic parallelism. However, the polygenic analysis revealed genetic parallelism for three of the five lakes, which differed from the two other lakes. These results provide evidence for both genetic parallelism and multiple genetic routes underlying parallel phenotypic evolution in fish shape among populations occupying similar ecological niches.
The freshwater blenny (Salaria fluviatilis), an endemic fish to the tributaries of the Mediterran... more The freshwater blenny (Salaria fluviatilis), an endemic fish to the tributaries of the Mediterranean and Black seas, is considered endangered in five of the nine Mediterranean-European countries. Substantial effort has recently been made to improve our understanding of its biology (i.e., habitat modelling, morphology, behaviour), but developing a conservation program for a species is less effective without a thorough knowledge of its genetic heterogeneity. The goal of this study was to assess the existence and boundaries of freshwater blenny genetic clusters in the occidental basin of the Mediterranean Sea. Our results suggest a genetic structure at two levels. The first is a range-wide product of two different glacial refuges, potentially the Iberian Peninsula (South of Spain; the origin of the "western" group) and Corsica (the "eastern" group). Subsequent northward migration likely took place along the Mediterranean coasts from these two glacial refuges to the southern part of mainland France, where a second contact zone potentially occurred. The second level is a fine-scale genetic structure corresponding to eight genetic groups—four to the west from the "western" refuge and four to the east from the "eastern" refuge. Furthermore, we demonstrate that population differentiation between the western and eastern groups had occurred far enough in the past that new mutations and not solely drift effects were detectable. These results provide a foundation on which to design future conservation efforts of the freshwater blenny in the occidental basin of the Mediterranean Sea.
Alexandrium catenella (group IV) and A. tamarense (group III) (Dinophyceae) are two cryptic invas... more Alexandrium catenella (group IV) and A. tamarense (group III) (Dinophyceae) are two cryptic invasive phytoplankton species belonging to the A. tamarense species complex. Their worldwide spread is favored by the human activities, transportation and climate change. In order to describe their diversity in the Mediterranean Sea and understand their settlements and maintenances in this area, new microsatellite markers were developed based on Thau lagoon (France) samples of A. catenella and A. tamarense strains. In this study twelve new microsatellite markers are proposed. Five of these microsatellite markers show amplifications on A. tamarense and ten on A. catenella. Three of these 12 microsatellite markers allowed amplifications on both cryptic species. Finally, the haplotypic diversity ranged from 0.000 to 0.791 and 0.000 to 0.942 for A. catenella and A. tamarense respectively.
Incomplete knowledge of biodiversity remains a stumbling block for conservation planning, and eve... more Incomplete knowledge of biodiversity remains a stumbling block for conservation planning, and even occurs within globally important Biodiversity Hotspots. Although technical advances have boosted the power of molecular biodiversity assessments, the link between DNA sequences and species and the analytics to discriminate entities, remain crucial. Here, we present an analysis of the first DNA barcode library for the freshwater fish fauna of the Mediterranean Biodiversity Hotspot (526 spp.), with virtually complete species coverage (498 spp., 98% extant species). In order to build an identification system supporting conservation, we compared species determination by taxonomists to multiple clustering analyses of DNA barcodes for 3165 specimens. The congruence of barcode clusters with morphological determination was strongly dependent on the method of cluster delineation, but was highest with the GMYC model-based approach (83% of all species recovered as GMYC entity). Overall, genetic-morphological discontinuities suggest the existence of up to 64 previously unrecognized candidate species. We found reduced identification accuracy when using the entire DNA-barcode database, compared to analyses on databases for individual river catchments. This scale effect has important implications for barcoding assessments, and suggests that fairly simple identification pipelines provide sufficient resolution in local applications. We calculated EDGE (Evolutionarily Distinct and Globally Endangered) scores in order to identify candidate species for conservation priority, and argue that the evolutionary content of barcode data can be used to detect priority species for future IUCN assessments. We show that large-scale barcoding inventories of complex biotas are feasible and contribute directly to the evaluation of conservation priorities.
The inclusion of key environmental covariables in habitat quality models is crucial to improve th... more The inclusion of key environmental covariables in habitat quality models is crucial to improve the ability
of indicators to predict the response of aquatic organisms to anthropogenic stress. The sensitivity of
the freshwater blenny (Salaria fluviatilis) to anthropogenic factors was found to be inconsistent among
studies, and this might have been because background environmental heterogeneity was not considered.
The goal of this study was to assess whether the inclusion of key environmental variables in habitat models
would improve the ability to detect the effects of anthropogenic stress on vulnerable fishes. We used a
theoretical–information approach to rank different models intended to predict the relative abundance
of freshwater blenny in 10 Corsican rivers based on a combination of environmental and anthropogenic
indicators. The results show a clear relationship between water velocity and blenny abundance in the
studied streams. When this key variable is taken into account in the model, anthropogenic variables such
as Enterococcus spp. and Escherichia coli counts, which are indicators of fecal pollution, and the number
of competitor species also explain a significant proportion of the variation in blenny abundance. This
study reveals the importance of statistically accounting for natural environmental variability, which may
conceal other effects, when modeling anthropogenic impacts on a species
Basic text books and fish databases state that the freshwater
blenny (Salaria fluviatilis Asso, ... more Basic text books and fish databases state that the freshwater
blenny (Salaria fluviatilis Asso, 1801) has a maximum size of
150 mm (Spillman, 1961; Krupp and Schneider, 1989; Keith and
Allardi, 2001; Roché, 2001; Keith et al., 2011; Froese and Pauly,
2012). After examining the scientific literature, we found the original reference for this size limit in Les Poissons des eaux douces de la France (Roule, 1925). This reference did not report any measurements of freshwater blenny, but states that “les adultes dépassent rarement 8 ou 10 centimètres, et atteignent au plus 14 à 15 centimètres” [“adults are rarely longer than 8 or 10 cm, and reach a maximum of 14 to 15 cm”].
Roads have a severe impact on wildlife. Reptiles
are particularly susceptible due to their attra... more Roads have a severe impact on wildlife. Reptiles
are particularly susceptible due to their attraction to
roads and their low car-avoidance capacity. For example, a
high number of road killed freshwater turtles resulted from
females selecting the unpaved side of roads as nesting sites.
However, roads are harmful not only for adults, but are also
expected to affect egg survival and recruitment. In this
work, we indirectly determined whether the proximity to
roads affects the reproductive success of freshwater turtles.
The painted turtle (Chrysemys picta) was chosen for its
population density, which is higher than most turtle species
considered endangered. Locations near roads (\100 m)
and in natural areas ([500 m) were sampled in three
geographically distant ecoregions. We estimated the
diversity of microsatellite loci from nuclear and mitochondrial
genomes to assess the size of the kin groups as a
proxy of the reproductive success of females. Similar
diversity at nuclear markers suggested a comparable historical
and demographic background among populations.
However, lower mitochondrial diversity, higher mean and
variance in the size of kin groups as well as a lower number
of kin groups were strongly associated with the proximity
Journal of Experimental Marine Biology and Ecology, Dec 30, 2012
Exon-primed, intron crossing DNA markers (EPICs) were screened for Mendelian-like allele size pol... more Exon-primed, intron crossing DNA markers (EPICs) were screened for Mendelian-like allele size polymorphisms in three stingray species (Himantura gerrardi, Neotrygon kuhlii and Taeniura lymna) from the central Indo-West Pacific, where they are commercially exploited. Four to 7 size-polymorphic intron loci were selected in a species, and were subsequently tested as genetic markers of stock structure. Sharp genetic differentiation was observed between populations within each species across the Indo-Malay-Papua archipelago (Weir and Cockerham's View the MathML source-values reaching 0.153–0.557 over a few thousand kilometers). A trend of increasing genetic differentiation with increasing geographic distance was apparent in N. kuhlii, in which populations distant by 3000 km were differentiated by an estimated View the MathML source ~ 0.375. This value was an order of magnitude higher than usually reported in coastal benthic teleost fishes and indicates strong sub-population structure. This is likely, at least partly, a consequence of the sedentary benthic habits of N. kuhlii at all life stages. Because replenishment of overexploited populations of N. kuhlii and two other stingray species from the central Indo-West Pacific is unlikely at ecological timescales, management should be planned at the local geographic scale.
Ten new microsatellite markers were isolated
from the freshwater blenny, Salaria fluviatilis. Th... more Ten new microsatellite markers were isolated
from the freshwater blenny, Salaria fluviatilis. These loci
were characterised for three distinct populations (Var
River and Lake Bourget in France, and Lake Kinneret in
Israel). S. fluviatilis populations in the North-West of the
Mediterranean Sea are all polymorphic and under Hardy–
Weinberg equilibrium. These microsatellite markers are
suggested for studying the genetic structure in this area.
Seven of the ten microsatellite markers are applicable for
all the freshwater blenny populations of the entire Mediterranean
basin. Cross-species characterisation was also
performed on the peacock blenny, Salaria pavo. Seven of
the ten microsatellite loci exhibited successful PCR
amplification on this latter species. Polymorphism is
observed on four of these seven loci.
Phenotypic change in closely related lineages frequently follows a common pathway in response to ... more Phenotypic change in closely related lineages frequently follows a common pathway in response to similar environmental conditions. This process, termed parallel evolution, results in the evolution of similar but independentlyderived ecotypes. Individuals with a blue phenotype are observed in some populations of walleye (Sander vitreus) from Laurentian Shield lakes. The blue phenotype may represent a case of parallel evolution: previous morphological studies revealed significant differences compared with the yellow phenotype as well as numerous lake-specific characteristics among blue individuals. The genetic variability of blue and yellow walleye phenotypes from 6 Laurentian Shield lakes was estimated using AFLP. Results clearly indicate that, whatever their phenotype, individuals from a given lake were more similar genetically than those from other lakes. However, blue and yellow phenotypes represent different populations with in each lake. These results suggest the colonization of each lake by a single group of walleye followed by the parallel origin of the blue phenotype. The parallel evolution of the blue walleye phenotype could represent an excellent model for studying mechanisms underlying divergent selection and reproductive isolation
Freshwater eels (Anguilla sp.) have large economic, cultural, ecological and aesthetic
importance... more Freshwater eels (Anguilla sp.) have large economic, cultural, ecological and aesthetic importance worldwide, but they suffered more than 90% decline in global stocks over the past few decades. Proper genetic resources, such as sequenced, assembled and annotated genomes, are essential to help plan sustainable recoveries by identifying physiological, biochemical and genetic mechanisms that caused the declines or that may lead to recoveries. Here, we present the first sequenced genome of the American Eel. This genome contained 305,043 contigs (N50 = 7,397) and 79,209 scaffolds (N50 = 86,641) for a total size of 1.41 Gb, which is in the middle of the range of previous estimations for this species. In addition, protein coding regions, including introns and flanking regions, are very well represented in the genome, as 95.2% of the 458 core eukaryotic genes and 98.8% of the 248 ultra-conserved subset were represented in the assembly. and a total of 24,564 genes were annotated for future functional genomics studies. We performed a candidate gene analysis to compare three genes among all three freshwater eel species and, congruent with the phylogenetic relationships, Japanese eel (A. japanica) exibited the most divergence. Overall, the sequenced genome presented in this study is a crucial addition to the presently available genetic tools to help guide future conservation efforts of Freshwater eels
Repeated adaptive ecological diversification has commonly been reported in fish and has often bee... more Repeated adaptive ecological diversification has commonly been reported in fish and has often been associated with trophic niche diversity. The main goal of this study was to investigate the extent of parallelism in the genomic and phenotypic divergence between piscivorous and planktivorous lake trout ecotypes from Laurentian Shield lakes, Canada. This was achieved by documenting the extent of morphological differentiation using geometric morphometrics and linear measurements as well as the pattern of genomic divergence by means of RADseq genotyping (3925 filtered SNPs) in 12 lakes. Our results indicate that the two ecotypes evolved distinct body shape and several linear measurements in parallel. Neutral genetic differentiation was pronounced between all isolated populations (Mean F ST = 0.433), indicating no or very limited migration and pronounced genetic drift. Significant genetic differentiation also suggested partial reproductive isolation between ecotypes in the two lakes where they are found in sympatry. Combining different outlier detection methods, we identified 48 SNPs putatively under divergent selection between ecotypes, among which 10 could be annotated and related to functions such as developmental processes and ionic regulation. Finally, our results indicate that parallel morphological divergence is accompanied by both parallel and nonparallel genomic divergence, which is associated with the use of different trophic niches between ecotypes. The results are also discussed in the context of management and conservation of this highly exploited species throughout northern North America.
Investigating how environmental features shape the genetic structure of populations is crucial fo... more Investigating how environmental features shape the genetic structure of populations is crucial for understanding how they are potentially adapted to their habitats, as well as for sound management. In this study, we assessed the relative importance of spatial distribution , ocean currents and sea surface temperature (SST) on patterns of putatively neutral and adaptive genetic variation among American lobster from 19 locations using population differentiation (PD) approaches combined with environmental association (EA) analyses. First, PD approaches (using BAYESCAN, ARLEQUIN and OUTFLANK) found 28 outlier SNPs putatively under divergent selection and 9770 neutral SNPs in common. Redundancy analysis revealed that spatial distribution, ocean current-mediated larval connectiv-ity and SST explained 31.7% of the neutral genetic differentiation, with ocean currents driving the majority of this relationship (21.0%). After removing the influence of spatial distribution, no SST were significant for putatively neutral genetic variation whereas minimum annual SST still had a significant impact and explained 8.1% of the putatively adap-tive genetic variation. Second, EA analyses (using Pearson correlation tests, BAYESCENV and LFMM) jointly identified seven SNPs as candidates for thermal adaptation. Covariation at these SNPs was assessed with a spatial multivariate analysis that highlighted a significant temperature association, after accounting for the influence of spatial distribution. Among the 505 candidate SNPs detected by at least one of the three approaches, we discovered three polymorphisms located in genes previously shown to play a role in thermal adaptation. Our results have implications for the management of the American lobster and provide a foundation on which to predict how this species will cope with climate change.
Background: Improved performance in a given ecological niche can occur through local adaptation, ... more Background: Improved performance in a given ecological niche can occur through local adaptation, phenotypic plasticity, or a combination of these mechanisms. Evaluating the relative importance of these two mechanisms is needed to better understand the cause of intra specific polymorphism. In this study, we reared populations of Lake Whitefish (Coregonus clupeaformis) representing the'normal' (benthic form) and the 'dwarf' (derived limnetic form) ecotypes in two different conditions (control and swim-training) to test the relative importance of adaptation and acclimation in the differentiation of traits related to swimming capacity. The dwarf whitefish is a more active swimmer than the normal ecotype, and also has a higher capacity for aerobic energy production in the swimming musculature. We hypothesized that dwarf fish would show changes in morphological and physiological traits consistent with reductions in the energetic costs of swimming and maintenance metabolism. Results: We found differences in traits predicted to decrease the costs of prolonged swimming and standard metabolic rate and allow for a more active lifestyle in dwarf whitefish. Dwarf whitefish evolved a more streamlined body shape, predicted to lead to a decreased drag, and a smaller brain, which may decrease their standard metabolic rate. Contrary to predictions, we also found evidence of acclimation in liver size and metabolic enzyme activities. Conclusion: Results support the view that local adaptation has contributed to the genetically-based divergence of traits associated with swimming activity. Presence of post-zygotic barriers limiting gene flow between these ecotype pairs may have favoured repeated local adaptation to the limnetic niches.
A non-random association between an environmental factor and a given trait could be explained by ... more 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 expectations. The objective of this study was to test whether this relationship could be explained by phenotypic plasticity. Salaria fluviatilis from a Corsican stream were placed in four experimental channels with different water velocities (0, 10, 20 and 30 cm s −1) to test whether there was a morphological response associated with this environmental factor. After 28 days, fish shape changed in response to water velocity without any significant growth. Fish in higher water velocities exhibited a more slender body shape and longer anal and caudal fins. These results indicate a high degree of morphological plasticity in riverine populations of S. fluviatilis and suggest that the previous relationship between morphology and water velocity observed in the field may largely be due to an environmental determinism.
Measuring the effects of selection on the genome imposed by human-altered environment is currentl... more Measuring the effects of selection on the genome imposed by human-altered environment is currently a major goal in ecological genomics. Given the polygenic basis of most phenotypic traits, quantitative genetic theory predicts that selection is expected to cause subtle allelic changes among covarying loci rather than pronounced changes at few loci of large effects. The goal of this study was to test for the occurrence of polygenic selection in both North Atlantic eels (European Eel, Anguilla anguilla and American Eel, A. rostrata), using a method that searches for covariation among loci that would discriminate eels from “control” vs. “polluted” environments and be associated with specific contaminants acting as putative selective agents. RAD-seq libraries resulted in 23,659 and 14,755 filtered loci for the European and American Eels respectively. A total of 142 and 141 covarying markers discriminating European and American Eels from “control” vs. “polluted” sampling localities were obtained using the Random Forest algorithm. Distance-based redundancy analyses (db-RDAs) were used to assess the relationships between these covarying markers and concentration of 34 contaminants measured for each individual eel. PCB153, 4'4'DDE and selenium were associated with covarying markers for both species, thus pointing to these contaminants as major selective agents in contaminated sites . Gene enrichment analyses suggested that sterol regulation plays an important role in the differential survival of eels in “polluted” environment. This study illustrates the power of combining methods for detecting signals of polygenic selection and for associating variation of markers with putative selective agents in studies aiming at documenting the dynamics of selection at the genomic level, and particularly so in human altered environments.
Genetic diversity is the raw material for evolutionary change, so a species’ capacity to maintain... more 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 study was to infer potential connectivity among isolated-by-sea populations of the vulnerable freshwater blenny (Salaria fluviatilis) and to determine if gene flow could contribute to maintaining genetic diversity in connected populations. Four genetic clusters (one small at the North, one large at the South for both East and West coasts) were detected with different clustering methods (FLOCK, STUCTURE, UPGMA, AMOVA). The two larger genetic clusters with higher migration-rate estimates among localities had higher genetic diversity and allelic richness and lower relatedness between individuals, compared to isolated localities found in smaller clusters. Our results also suggest that sea currents may facilitate fish movements among neighbouring rivers. Overall, gene flow among isolated-by-sea but close rivers could maintain the evolutionary potential of freshwater blenny populations. This finding should be considered when elaborating a conservation program for this species.
The physiological mechanisms underlying local adaptation in natural populations of animals, and w... more The physiological mechanisms underlying local adaptation in natural populations of animals, and whether the same mechanisms contribute to adaptation and acclimation, are largely unknown. Therefore, we tested for evolutionary divergence in aerobic exercise physiology in laboratory bred, size-matched crosses of ancestral, benthic, normal Lake Whitefish (Coregonus clupeaformis) and derived, limnetic, more actively-swimming ‘dwarf’ ecotypes. We acclimated fish to constant swimming (emulating limnetic foraging) and control conditions (emulating normal activity levels) to simultaneously study phenotypic plasticity. We found extensive divergence between ecotypes: dwarf fish generally had constitutively higher values of traits related to oxygen transport (ventricle size) and use by skeletal muscle (percent oxidative muscle, mitochondrial content), and also evolved differential plasticity of mitochondrial function (Complex I activity and flux through Complexes I-IV and IV). The effects of swim-training were less pronounced than differences among ecotypes and the traits which had a significant training effect (ventricle protein content, ventricle MDH activity and muscle Complex V activity) did not differ among ecotypes. Only one trait, ventricle mass, varied in a similar manner with acclimation and adaptation and followed a pattern consistent with genetic accommodation. Overall, the physiological and biochemical mechanisms underlying acclimation and adaptation to swimming activity in Lake Whitefish generally differ.
Parallel changes in body shape may evolve in response to similar environmental conditions, but wh... more 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 evidence for parallelism in fish shape using geometric morphometrics among 300 fish representing five species pairs of Lake Whitefish. Using a genetic map comprising 3438 RAD-seq SNPs, we then identified quantitative trait loci (QTL) underlying body shape traits in a backcross family reared in the laboratory. A total of 138 body shape QTL were identified in this cross, thus revealing a highly polygenic architecture of body shape in Lake Whitefish. Thirdly, we tested for evidence of genetic parallelism among independent wild populations using both a single-locus method (outlier analysis) and a polygenic approach (analysis of co-variation among markers). The single-locus approach provided limited evidence for genetic parallelism. However, the polygenic analysis revealed genetic parallelism for three of the five lakes, which differed from the two other lakes. These results provide evidence for both genetic parallelism and multiple genetic routes underlying parallel phenotypic evolution in fish shape among populations occupying similar ecological niches.
The freshwater blenny (Salaria fluviatilis), an endemic fish to the tributaries of the Mediterran... more The freshwater blenny (Salaria fluviatilis), an endemic fish to the tributaries of the Mediterranean and Black seas, is considered endangered in five of the nine Mediterranean-European countries. Substantial effort has recently been made to improve our understanding of its biology (i.e., habitat modelling, morphology, behaviour), but developing a conservation program for a species is less effective without a thorough knowledge of its genetic heterogeneity. The goal of this study was to assess the existence and boundaries of freshwater blenny genetic clusters in the occidental basin of the Mediterranean Sea. Our results suggest a genetic structure at two levels. The first is a range-wide product of two different glacial refuges, potentially the Iberian Peninsula (South of Spain; the origin of the "western" group) and Corsica (the "eastern" group). Subsequent northward migration likely took place along the Mediterranean coasts from these two glacial refuges to the southern part of mainland France, where a second contact zone potentially occurred. The second level is a fine-scale genetic structure corresponding to eight genetic groups—four to the west from the "western" refuge and four to the east from the "eastern" refuge. Furthermore, we demonstrate that population differentiation between the western and eastern groups had occurred far enough in the past that new mutations and not solely drift effects were detectable. These results provide a foundation on which to design future conservation efforts of the freshwater blenny in the occidental basin of the Mediterranean Sea.
Alexandrium catenella (group IV) and A. tamarense (group III) (Dinophyceae) are two cryptic invas... more Alexandrium catenella (group IV) and A. tamarense (group III) (Dinophyceae) are two cryptic invasive phytoplankton species belonging to the A. tamarense species complex. Their worldwide spread is favored by the human activities, transportation and climate change. In order to describe their diversity in the Mediterranean Sea and understand their settlements and maintenances in this area, new microsatellite markers were developed based on Thau lagoon (France) samples of A. catenella and A. tamarense strains. In this study twelve new microsatellite markers are proposed. Five of these microsatellite markers show amplifications on A. tamarense and ten on A. catenella. Three of these 12 microsatellite markers allowed amplifications on both cryptic species. Finally, the haplotypic diversity ranged from 0.000 to 0.791 and 0.000 to 0.942 for A. catenella and A. tamarense respectively.
Incomplete knowledge of biodiversity remains a stumbling block for conservation planning, and eve... more Incomplete knowledge of biodiversity remains a stumbling block for conservation planning, and even occurs within globally important Biodiversity Hotspots. Although technical advances have boosted the power of molecular biodiversity assessments, the link between DNA sequences and species and the analytics to discriminate entities, remain crucial. Here, we present an analysis of the first DNA barcode library for the freshwater fish fauna of the Mediterranean Biodiversity Hotspot (526 spp.), with virtually complete species coverage (498 spp., 98% extant species). In order to build an identification system supporting conservation, we compared species determination by taxonomists to multiple clustering analyses of DNA barcodes for 3165 specimens. The congruence of barcode clusters with morphological determination was strongly dependent on the method of cluster delineation, but was highest with the GMYC model-based approach (83% of all species recovered as GMYC entity). Overall, genetic-morphological discontinuities suggest the existence of up to 64 previously unrecognized candidate species. We found reduced identification accuracy when using the entire DNA-barcode database, compared to analyses on databases for individual river catchments. This scale effect has important implications for barcoding assessments, and suggests that fairly simple identification pipelines provide sufficient resolution in local applications. We calculated EDGE (Evolutionarily Distinct and Globally Endangered) scores in order to identify candidate species for conservation priority, and argue that the evolutionary content of barcode data can be used to detect priority species for future IUCN assessments. We show that large-scale barcoding inventories of complex biotas are feasible and contribute directly to the evaluation of conservation priorities.
The inclusion of key environmental covariables in habitat quality models is crucial to improve th... more The inclusion of key environmental covariables in habitat quality models is crucial to improve the ability
of indicators to predict the response of aquatic organisms to anthropogenic stress. The sensitivity of
the freshwater blenny (Salaria fluviatilis) to anthropogenic factors was found to be inconsistent among
studies, and this might have been because background environmental heterogeneity was not considered.
The goal of this study was to assess whether the inclusion of key environmental variables in habitat models
would improve the ability to detect the effects of anthropogenic stress on vulnerable fishes. We used a
theoretical–information approach to rank different models intended to predict the relative abundance
of freshwater blenny in 10 Corsican rivers based on a combination of environmental and anthropogenic
indicators. The results show a clear relationship between water velocity and blenny abundance in the
studied streams. When this key variable is taken into account in the model, anthropogenic variables such
as Enterococcus spp. and Escherichia coli counts, which are indicators of fecal pollution, and the number
of competitor species also explain a significant proportion of the variation in blenny abundance. This
study reveals the importance of statistically accounting for natural environmental variability, which may
conceal other effects, when modeling anthropogenic impacts on a species
Basic text books and fish databases state that the freshwater
blenny (Salaria fluviatilis Asso, ... more Basic text books and fish databases state that the freshwater
blenny (Salaria fluviatilis Asso, 1801) has a maximum size of
150 mm (Spillman, 1961; Krupp and Schneider, 1989; Keith and
Allardi, 2001; Roché, 2001; Keith et al., 2011; Froese and Pauly,
2012). After examining the scientific literature, we found the original reference for this size limit in Les Poissons des eaux douces de la France (Roule, 1925). This reference did not report any measurements of freshwater blenny, but states that “les adultes dépassent rarement 8 ou 10 centimètres, et atteignent au plus 14 à 15 centimètres” [“adults are rarely longer than 8 or 10 cm, and reach a maximum of 14 to 15 cm”].
Roads have a severe impact on wildlife. Reptiles
are particularly susceptible due to their attra... more Roads have a severe impact on wildlife. Reptiles
are particularly susceptible due to their attraction to
roads and their low car-avoidance capacity. For example, a
high number of road killed freshwater turtles resulted from
females selecting the unpaved side of roads as nesting sites.
However, roads are harmful not only for adults, but are also
expected to affect egg survival and recruitment. In this
work, we indirectly determined whether the proximity to
roads affects the reproductive success of freshwater turtles.
The painted turtle (Chrysemys picta) was chosen for its
population density, which is higher than most turtle species
considered endangered. Locations near roads (\100 m)
and in natural areas ([500 m) were sampled in three
geographically distant ecoregions. We estimated the
diversity of microsatellite loci from nuclear and mitochondrial
genomes to assess the size of the kin groups as a
proxy of the reproductive success of females. Similar
diversity at nuclear markers suggested a comparable historical
and demographic background among populations.
However, lower mitochondrial diversity, higher mean and
variance in the size of kin groups as well as a lower number
of kin groups were strongly associated with the proximity
Journal of Experimental Marine Biology and Ecology, Dec 30, 2012
Exon-primed, intron crossing DNA markers (EPICs) were screened for Mendelian-like allele size pol... more Exon-primed, intron crossing DNA markers (EPICs) were screened for Mendelian-like allele size polymorphisms in three stingray species (Himantura gerrardi, Neotrygon kuhlii and Taeniura lymna) from the central Indo-West Pacific, where they are commercially exploited. Four to 7 size-polymorphic intron loci were selected in a species, and were subsequently tested as genetic markers of stock structure. Sharp genetic differentiation was observed between populations within each species across the Indo-Malay-Papua archipelago (Weir and Cockerham's View the MathML source-values reaching 0.153–0.557 over a few thousand kilometers). A trend of increasing genetic differentiation with increasing geographic distance was apparent in N. kuhlii, in which populations distant by 3000 km were differentiated by an estimated View the MathML source ~ 0.375. This value was an order of magnitude higher than usually reported in coastal benthic teleost fishes and indicates strong sub-population structure. This is likely, at least partly, a consequence of the sedentary benthic habits of N. kuhlii at all life stages. Because replenishment of overexploited populations of N. kuhlii and two other stingray species from the central Indo-West Pacific is unlikely at ecological timescales, management should be planned at the local geographic scale.
Ten new microsatellite markers were isolated
from the freshwater blenny, Salaria fluviatilis. Th... more Ten new microsatellite markers were isolated
from the freshwater blenny, Salaria fluviatilis. These loci
were characterised for three distinct populations (Var
River and Lake Bourget in France, and Lake Kinneret in
Israel). S. fluviatilis populations in the North-West of the
Mediterranean Sea are all polymorphic and under Hardy–
Weinberg equilibrium. These microsatellite markers are
suggested for studying the genetic structure in this area.
Seven of the ten microsatellite markers are applicable for
all the freshwater blenny populations of the entire Mediterranean
basin. Cross-species characterisation was also
performed on the peacock blenny, Salaria pavo. Seven of
the ten microsatellite loci exhibited successful PCR
amplification on this latter species. Polymorphism is
observed on four of these seven loci.
Phenotypic change in closely related lineages frequently follows a common pathway in response to ... more Phenotypic change in closely related lineages frequently follows a common pathway in response to similar environmental conditions. This process, termed parallel evolution, results in the evolution of similar but independentlyderived ecotypes. Individuals with a blue phenotype are observed in some populations of walleye (Sander vitreus) from Laurentian Shield lakes. The blue phenotype may represent a case of parallel evolution: previous morphological studies revealed significant differences compared with the yellow phenotype as well as numerous lake-specific characteristics among blue individuals. The genetic variability of blue and yellow walleye phenotypes from 6 Laurentian Shield lakes was estimated using AFLP. Results clearly indicate that, whatever their phenotype, individuals from a given lake were more similar genetically than those from other lakes. However, blue and yellow phenotypes represent different populations with in each lake. These results suggest the colonization of each lake by a single group of walleye followed by the parallel origin of the blue phenotype. The parallel evolution of the blue walleye phenotype could represent an excellent model for studying mechanisms underlying divergent selection and reproductive isolation
Government report for the Direction Régionale de l'Environnement, de l'Aménagement et du logement... more Government report for the Direction Régionale de l'Environnement, de l'Aménagement et du logement de la Corse (Corsica, France)
"La blennie fluviatile (Salaria fluviatilis) est une espèce qui a colonisé l'environnement dulcic... more "La blennie fluviatile (Salaria fluviatilis) est une espèce qui a colonisé l'environnement dulcicole à partir d'un ancêtre marin et habite actuellement lacs et rivières situés autour de la Méditerranée. Comment un tel changement d'environnement peut avoir affecté la structure génétique et le phénotype de cette espèce ? C'est autour de cette question centrale que s'articulent les deux principaux volets de cette thèse. Le premier s'intéresse aux conséquences d'évènements géologiques historiques, affectant la structure génétique de S. fluviatilis. Nous y verrons, entre autres, qu'à l'intérieur du bassin occidental de la Méditerranée, les localisations les plus nordiques ont été colonisées à partir de deux refuges glaciaires. Le deuxième volet est centré sur l'adaptation et l'acclimatation que nécessite un tel changement d'environnement. Il y sera révélé que les réponses de la forme du corps et la longueur des nageoires face à la vitesse du courant sont contrôlées par un déterminisme environnemental chez la blennie fluviatile. Ensemble, ces deux volets permettent de mieux comprendre les processus derrière la différenciation des populations dans un contexte de colonisation d'un nouvel environnement."
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importance worldwide, but they suffered more than 90% decline in global stocks over the past
few decades. Proper genetic resources, such as sequenced, assembled and annotated genomes,
are essential to help plan sustainable recoveries by identifying physiological, biochemical and
genetic mechanisms that caused the declines or that may lead to recoveries. Here, we present
the first sequenced genome of the American Eel. This genome contained 305,043 contigs (N50
= 7,397) and 79,209 scaffolds (N50 = 86,641) for a total size of 1.41 Gb, which is in the middle of
the range of previous estimations for this species. In addition, protein coding regions, including
introns and flanking regions, are very well represented in the genome, as 95.2% of the 458 core
eukaryotic genes and 98.8% of the 248 ultra-conserved subset were represented in the
assembly. and a total of 24,564 genes were annotated for future functional genomics studies.
We performed a candidate gene analysis to compare three genes among all three freshwater
eel species and, congruent with the phylogenetic relationships, Japanese eel (A. japanica)
exibited the most divergence. Overall, the sequenced genome presented in this study is a
crucial addition to the presently available genetic tools to help guide future conservation efforts
of Freshwater eels
(FLOCK, STUCTURE, UPGMA, AMOVA). The two larger genetic clusters with higher migration-rate estimates among localities had higher genetic diversity and allelic richness and lower relatedness between individuals, compared to isolated localities found in smaller clusters. Our results also suggest that sea currents may facilitate fish movements among neighbouring rivers. Overall, gene flow among isolated-by-sea but close rivers could maintain the evolutionary potential of freshwater blenny populations. This finding should be considered when elaborating a conservation program for this species.
of indicators to predict the response of aquatic organisms to anthropogenic stress. The sensitivity of
the freshwater blenny (Salaria fluviatilis) to anthropogenic factors was found to be inconsistent among
studies, and this might have been because background environmental heterogeneity was not considered.
The goal of this study was to assess whether the inclusion of key environmental variables in habitat models
would improve the ability to detect the effects of anthropogenic stress on vulnerable fishes. We used a
theoretical–information approach to rank different models intended to predict the relative abundance
of freshwater blenny in 10 Corsican rivers based on a combination of environmental and anthropogenic
indicators. The results show a clear relationship between water velocity and blenny abundance in the
studied streams. When this key variable is taken into account in the model, anthropogenic variables such
as Enterococcus spp. and Escherichia coli counts, which are indicators of fecal pollution, and the number
of competitor species also explain a significant proportion of the variation in blenny abundance. This
study reveals the importance of statistically accounting for natural environmental variability, which may
conceal other effects, when modeling anthropogenic impacts on a species
blenny (Salaria fluviatilis Asso, 1801) has a maximum size of
150 mm (Spillman, 1961; Krupp and Schneider, 1989; Keith and
Allardi, 2001; Roché, 2001; Keith et al., 2011; Froese and Pauly,
2012). After examining the scientific literature, we found the original reference for this size limit in Les Poissons des eaux douces de la France (Roule, 1925). This reference did not report any measurements of freshwater blenny, but states that “les adultes dépassent rarement 8 ou 10 centimètres, et atteignent au plus 14 à 15 centimètres” [“adults are rarely longer than 8 or 10 cm, and reach a maximum of 14 to 15 cm”].
are particularly susceptible due to their attraction to
roads and their low car-avoidance capacity. For example, a
high number of road killed freshwater turtles resulted from
females selecting the unpaved side of roads as nesting sites.
However, roads are harmful not only for adults, but are also
expected to affect egg survival and recruitment. In this
work, we indirectly determined whether the proximity to
roads affects the reproductive success of freshwater turtles.
The painted turtle (Chrysemys picta) was chosen for its
population density, which is higher than most turtle species
considered endangered. Locations near roads (\100 m)
and in natural areas ([500 m) were sampled in three
geographically distant ecoregions. We estimated the
diversity of microsatellite loci from nuclear and mitochondrial
genomes to assess the size of the kin groups as a
proxy of the reproductive success of females. Similar
diversity at nuclear markers suggested a comparable historical
and demographic background among populations.
However, lower mitochondrial diversity, higher mean and
variance in the size of kin groups as well as a lower number
of kin groups were strongly associated with the proximity
from the freshwater blenny, Salaria fluviatilis. These loci
were characterised for three distinct populations (Var
River and Lake Bourget in France, and Lake Kinneret in
Israel). S. fluviatilis populations in the North-West of the
Mediterranean Sea are all polymorphic and under Hardy–
Weinberg equilibrium. These microsatellite markers are
suggested for studying the genetic structure in this area.
Seven of the ten microsatellite markers are applicable for
all the freshwater blenny populations of the entire Mediterranean
basin. Cross-species characterisation was also
performed on the peacock blenny, Salaria pavo. Seven of
the ten microsatellite loci exhibited successful PCR
amplification on this latter species. Polymorphism is
observed on four of these seven loci.
importance worldwide, but they suffered more than 90% decline in global stocks over the past
few decades. Proper genetic resources, such as sequenced, assembled and annotated genomes,
are essential to help plan sustainable recoveries by identifying physiological, biochemical and
genetic mechanisms that caused the declines or that may lead to recoveries. Here, we present
the first sequenced genome of the American Eel. This genome contained 305,043 contigs (N50
= 7,397) and 79,209 scaffolds (N50 = 86,641) for a total size of 1.41 Gb, which is in the middle of
the range of previous estimations for this species. In addition, protein coding regions, including
introns and flanking regions, are very well represented in the genome, as 95.2% of the 458 core
eukaryotic genes and 98.8% of the 248 ultra-conserved subset were represented in the
assembly. and a total of 24,564 genes were annotated for future functional genomics studies.
We performed a candidate gene analysis to compare three genes among all three freshwater
eel species and, congruent with the phylogenetic relationships, Japanese eel (A. japanica)
exibited the most divergence. Overall, the sequenced genome presented in this study is a
crucial addition to the presently available genetic tools to help guide future conservation efforts
of Freshwater eels
(FLOCK, STUCTURE, UPGMA, AMOVA). The two larger genetic clusters with higher migration-rate estimates among localities had higher genetic diversity and allelic richness and lower relatedness between individuals, compared to isolated localities found in smaller clusters. Our results also suggest that sea currents may facilitate fish movements among neighbouring rivers. Overall, gene flow among isolated-by-sea but close rivers could maintain the evolutionary potential of freshwater blenny populations. This finding should be considered when elaborating a conservation program for this species.
of indicators to predict the response of aquatic organisms to anthropogenic stress. The sensitivity of
the freshwater blenny (Salaria fluviatilis) to anthropogenic factors was found to be inconsistent among
studies, and this might have been because background environmental heterogeneity was not considered.
The goal of this study was to assess whether the inclusion of key environmental variables in habitat models
would improve the ability to detect the effects of anthropogenic stress on vulnerable fishes. We used a
theoretical–information approach to rank different models intended to predict the relative abundance
of freshwater blenny in 10 Corsican rivers based on a combination of environmental and anthropogenic
indicators. The results show a clear relationship between water velocity and blenny abundance in the
studied streams. When this key variable is taken into account in the model, anthropogenic variables such
as Enterococcus spp. and Escherichia coli counts, which are indicators of fecal pollution, and the number
of competitor species also explain a significant proportion of the variation in blenny abundance. This
study reveals the importance of statistically accounting for natural environmental variability, which may
conceal other effects, when modeling anthropogenic impacts on a species
blenny (Salaria fluviatilis Asso, 1801) has a maximum size of
150 mm (Spillman, 1961; Krupp and Schneider, 1989; Keith and
Allardi, 2001; Roché, 2001; Keith et al., 2011; Froese and Pauly,
2012). After examining the scientific literature, we found the original reference for this size limit in Les Poissons des eaux douces de la France (Roule, 1925). This reference did not report any measurements of freshwater blenny, but states that “les adultes dépassent rarement 8 ou 10 centimètres, et atteignent au plus 14 à 15 centimètres” [“adults are rarely longer than 8 or 10 cm, and reach a maximum of 14 to 15 cm”].
are particularly susceptible due to their attraction to
roads and their low car-avoidance capacity. For example, a
high number of road killed freshwater turtles resulted from
females selecting the unpaved side of roads as nesting sites.
However, roads are harmful not only for adults, but are also
expected to affect egg survival and recruitment. In this
work, we indirectly determined whether the proximity to
roads affects the reproductive success of freshwater turtles.
The painted turtle (Chrysemys picta) was chosen for its
population density, which is higher than most turtle species
considered endangered. Locations near roads (\100 m)
and in natural areas ([500 m) were sampled in three
geographically distant ecoregions. We estimated the
diversity of microsatellite loci from nuclear and mitochondrial
genomes to assess the size of the kin groups as a
proxy of the reproductive success of females. Similar
diversity at nuclear markers suggested a comparable historical
and demographic background among populations.
However, lower mitochondrial diversity, higher mean and
variance in the size of kin groups as well as a lower number
of kin groups were strongly associated with the proximity
from the freshwater blenny, Salaria fluviatilis. These loci
were characterised for three distinct populations (Var
River and Lake Bourget in France, and Lake Kinneret in
Israel). S. fluviatilis populations in the North-West of the
Mediterranean Sea are all polymorphic and under Hardy–
Weinberg equilibrium. These microsatellite markers are
suggested for studying the genetic structure in this area.
Seven of the ten microsatellite markers are applicable for
all the freshwater blenny populations of the entire Mediterranean
basin. Cross-species characterisation was also
performed on the peacock blenny, Salaria pavo. Seven of
the ten microsatellite loci exhibited successful PCR
amplification on this latter species. Polymorphism is
observed on four of these seven loci.