Variations in energy storage metabolism discriminate fresh and brackish/saltwater ecotypes in American glass eels

International audienceRecently, different ecotypes characterized by their migration form, have been genetically documented in the American eel, Anguilla rostrata. The aim of this study was to verify if energy status and differential abilities in mobilizing energy reserves could discriminate freshwater and brackish/saltwater ecotypes. To do so, analyses were done on glass eels at recruitment according to location of capture, date and salinity preference using eco-physiological and molecular tools. Salinity preference did not differ between ecotypes. Instead, we observed spatial and temporal variations adding to the body of evidence of genetic and environmental controls in the differentiation of ecotypes. Compared to the brackish/saltwater ecotype, the freshwater ecotype was larger and more pigmented, had 73.8 % lesser triacylglycerol content and 67,7 % higher glycogen content, and overexpressed 7.65 and 3.25 times respectively the transcripts of bile salt activated and triacylglycerol lipases. No variation in transcripts of glycogen phosphorylase, leptin and ghrelin was observed between ecotypes. For both ecotypes, level of pigmentation was higher and energetic reserves were lesser in glass eels arriving two weeks later. Our results suggest the existence of differential regulation mechanisms relative to energy metabolism between ecotypes and allow us to propose a new model of the physiological mechanisms underlying the recruitment of freshwater and brackish/saltwater ecotype in American glass eel. This new biological information contributes to the building knowledge on the distribution of ecotypes and on the internal factors involved in glass eel migration regulation, giving new indications to improve conservation measure for this species declared “threatened” in Canada

Divergence in gene regulation at young life history stages of whitefish (Coregonus sp.) and the emergence of genomic isolation

<p>Abstract</p> <p>Background</p> <p>The evolution of barriers to reproduction is of key interest to understand speciation. However, there may be a current bias towards studying intrinsic postzygotic isolation in old species pairs as compared to the emergence of barriers to gene flow through adaptive divergence. This study evaluates the relative importance of both processes in the evolution of genomic isolation in incipient species of whitefish (<it>Coregonus clupeaformis</it>) for which preliminary data suggest that postzygotic isolation emerges with intrinsic factors acting at embryo stages but also due to extrinsic factors during adult life.</p> <p>Results</p> <p>Gene expression data were screened using cDNA microarrays to identify regulatory changes at embryo and juvenile stages that provide evidence for genomic divergence at the underlying genetic factors. A comparison of different life history stages shows that 16-week old juvenile fish have 14 times more genes displaying significant regulatory divergence than embryos. Furthermore, regulatory changes in juvenile fish match patterns in adult fish suggesting that gene expression divergence is established early in juvenile fish and persists throughout the adult phase. Comparative analyses with results from previous studies on dwarf-normal species pairs show that at least 26 genetic factors identified in juvenile fish are candidate traits for adaptive divergence in adult fish. Eight of these show parallel directions of gene expression divergence independent of tissue type or age of the fish. The latter are associated with energy metabolism, a complex trait known to drive adaptive divergence in dwarf and normal whitefish.</p> <p>Conclusion</p> <p>Although experimental evidence suggests the existence of genetic factors that cause intrinsic postzygotic isolation acting in embryos, the analysis presented here provided few candidate genes in embryos, which also corroborate previous studies showing a lack of ecological divergence between sympatric dwarf and normal whitefish at the larval stage. In contrast, gene expression divergence in juveniles can be linked to adaptive traits and seems to be driven by positive selection. The results support the idea that adaptive differentiation may be more important in explaining the emergence of barriers to gene flow in an early phase of speciation by providing a broad genomic basis for extrinsic postzygotic isolation rather than intrinsic barriers.</p

The influence of gene-environment interactions on GHR and IGF-1 expression and their association with growth in brook charr, Salvelinus fontinalis (Mitchill)

<p>Abstract</p> <p>Background</p> <p>Quantitative reaction norm theory proposes that genotype-by-environment interaction (GxE) results from inter-individual differences of expression in adaptive suites of genes in distinct environments. However, environmental norms for actual gene suites are poorly documented. In this study, we investigated the effects of GxE interactions on levels of gene transcription and growth by documenting the impact of rearing environment (freshwater vs. saltwater), sex and genotypic (low vs. high estimated breeding value EBV) effects on the transcription level of insulin-like growth factor (IGF-1) and growth hormone receptor (GHR) in brook charr (<it>Salvelinus fontinalis</it>).</p> <p>Results</p> <p>Males grew faster than females (μ_♀= 1.20 ± 0.07 g·d^-1, μ_♂= 1.46 ± 0.06 g·d^-1) and high-EBV fish faster than low-EBV fish (μ_LOW= 0.97 ± 0.05 g·d^-1, μ_HIGH= 1.58 ± 0.07 g·d^-1; p < 0.05). However, growth was markedly lower in saltwater-reared fish than freshwater sibs (μ_FW= 1.52 ± 0.07 g·d^-1, μ_SW= 1.15 ± 0.06 g·d^-1), yet GHR mRNA transcription level was significantly higher in saltwater than in freshwater (μ_SW= 0.85 ± 0.05, μ_FW= 0.61 ± 0.05). The ratio of actual growth to units in assayed mRNA ('individual transcript efficiency', iTE; g·d^-1·u^-1) also differed among EBV groups (μ_LOW= 2.0 ± 0.24 g·d^-1·u^-1; μ_HIGH= 3.7 ± 0.24 g·d^-1·u^-1) and environments (μ_SW= 2.0 ± 0.25 g·d^-1·u^-1; μ_FW= 3.7 ± 0.25 g·d^-1·u^-1) for GHR. Males had a lower iTE for GHR than females (μ_♂= 2.4 ± 0.29 g·d^-1·u^-1; μ_♀= 3.1 ± 0.23 g·d^-1·u^-1). There was no difference in IGF-1 transcription level between environments (p > 0.7) or EBV groups (p > 0.15) but the level of IGF-1 was four times higher in males than females (μ_♂= 2.4 ± 0.11, μ_♀= 0.58 ± 0.09; p < 0.0001). We detected significant sexual differences in iTE (μ_♂= 1.3 ± 0.59 g·d^-1·u^-1; μ_♀= 3.9 ± 0.47 g·d^-1·u^-1), salinities (μ_SW= 2.3 ± 0.52 g·d^-1·u^-1; μ_FW= 3.7 ± 0.53 g·d^-1·u^-1) and EBV-groups (μ_LOW= 2.4 ± 0.49 g·d^-1·u^-1; μ_HIGH= 3.8 ± 0.49 g·d^-1·u^-1). Interaction between EBV-group and environment was detected for both GHR (p = 0.027) and IGF-1 (p = 0.019), and for iTE in the two genes (p < 0.0001; p < 0.05, respectively), where increased divergence in levels of GHR and IGF-1 transcription occurred among EBV-groups in the saltwater environment.</p> <p>Conclusion</p> <p>Our results show that both environment and sex have major impacts on the expression of mRNA for two key genes involved in the physiological pathway for growth. We also demonstrate for the first time, at least in fish, genotype-by-environment interaction at the level of individual gene transcription. This work contributes significantly to ongoing efforts towards documenting environmentally and sexually induced variance of gene activity and understanding the resulting phenotypes.</p

Sex Chromosome Evolution, Heterochiasmy, and Physiological QTL in the Salmonid Brook Charr Salvelinus fontinalis

Whole-genome duplication (WGD) can have large impacts on genome evolution, and much remains unknown about these impacts. This includes the mechanisms of coping with a duplicated sex determination system and whether this has an impact on increasing the diversity of sex determination mechanisms. Other impacts include sexual conflict, where alleles having different optimums in each sex can result in sequestration of genes into nonrecombining sex chromosomes. Sex chromosome development itself may involve sex-specific recombination rate (i.e., heterochiasmy), which is also poorly understood. The family Salmonidae is a model system for these phenomena, having undergone autotetraploidization and subsequent rediploidization in most of the genome at the base of the lineage. The salmonid master sex determining gene is known, and many species have nonhomologous sex chromosomes, putatively due to transposition of this gene. In this study, we identify the sex chromosome of Brook Charr Salvelinus fontinalis and compare sex chromosome identities across the lineage (eight species and four genera). Although nonhomology is frequent, homologous sex chromosomes and other consistencies are present in distantly related species, indicating probable convergence on specific sex and neo-sex chromosomes. We also characterize strong heterochiasmy with 2.7-fold more crossovers in maternal than paternal haplotypes with paternal crossovers biased to chromosome ends. When considering only rediploidized chromosomes, the overall heterochiasmy trend remains, although with only 1.9-fold more recombination in the female than the male. Y chromosome crossovers are restricted to a single end of the chromosome, and this chromosome contains a large interspecific inversion, although its status between males and females remains unknown. Finally, we identify quantitative trait loci (QTL) for 21 unique growth, reproductive, and stress-related phenotypes to improve knowledge of the genetic architecture of these traits important to aquaculture and evolution

Quantifying relative fish abundance with eDNA : a promising tool for fisheries management

1. Assessment and monitoring of exploited fish populations are challenged by costs, logistics and negative impacts on target populations. These factors therefore limit large-scale effective management strategies. 2. Evidence is growing that the quantity of eDNA may be related not only to species presence/absence, but also to species abundance. In this study, the concentrations of environmental DNA (eDNA) from a highly prized sport fish species, Lake Trout Salvelinus namaycush (Walbaum 1792), were estimated in water samples from 12 natural lakes and compared to abundance and biomass data obtained from standardized gillnet catches as performed routinely for fisheries management purposes. To reduce environmental variability among lakes, all lakes were sampled in spring, between ice melt and water stratification. 3. The eDNA concentration did not vary significantly with water temperature, dissolved oxygen, pH and turbidity, but was significantly positively correlated with relative fish abundance estimated as catch per unit effort (CPUE), whereas the relationship with biomass per unit effort (BPUE) was less pronounced. 4. The value of eDNA to inform about local aquatic species distribution was further supported by the similarity between the spatial heterogeneity of eDNA distribution and spatial variation in CPUE measured by the gillnet method. 5. Synthesis and applications. Large-scale empirical evidence of the relationship between the eDNA concentration and species abundance allows for the assessment of the potential to integrate eDNA within fisheries management plans. As such, the eDNA quantitative method represents a promising population abundance assessment tool that could significantly reduce the costs associated with sampling and increase the power of detection, the spatial coverage and the frequency of sampling, without any negative impacts on fish populations

Insights into the role of differential gene expression on the ecological adaptation of the snail Littorina saxatilis

<p>Abstract</p> <p>Background</p> <p>In the past 40 years, there has been increasing acceptance that variation in levels of gene expression represents a major source of evolutionary novelty. Gene expression divergence is therefore likely to be involved in the emergence of incipient species, namely, in a context of adaptive radiation. In this study, a genome-wide expression profiling approach (cDNA-AFLP), validated by quantitative real-time polymerase chain reaction (qPCR) were used to get insights into the role of differential gene expression on the ecological adaptation of the marine snail <it>Littorina saxatilis</it>. This gastropod displays two sympatric ecotypes (RB and SU) which are becoming one of the best studied systems for ecological speciation.</p> <p>Results</p> <p>Among the 99 transcripts shared between ecotypes, 12.12% showed significant differential expression. At least 4% of these transcripts still displayed significant differences after correction for multiple tests, highlighting that gene expression can differ considerably between subpopulations adapted to alternative habitats in the face of gene flow. One of the transcripts identified was Cytochrome c Oxidase subunit I (COI). In addition, 6 possible reference genes were validated to normalize and confirm this result using qPCR. α-Tubulin and histone H3.3 showed the more stable expression levels, being therefore chosen as the best option for normalization. The qPCR analysis confirmed a higher COI expression in SU individuals.</p> <p>Conclusions</p> <p>At least 4% of the transcriptome studied is being differentially expressed between ecotypes living in alternative habitats, even when gene flow is still substantial between ecotypes. We could identify a candidate transcript of such ecotype differentiation: Cytochrome c Oxidase Subunit I (COI), a mitochondrial gene involved in energy metabolism. Quantitative PCR was used to confirm the differences found in COI and its over-expression in the SU ecotype. Interestingly, COI is involved in the oxidative phosphorylation, suggesting an enhanced mitochondrial gene expression (or increased number of mitochondria) to improve energy supply in the ecotype subjected to the strongest wave action.</p

Disturbance of Social Hierarchy by an Invasive Species: A Gene Transcription Study

BACKGROUND: Ecological and evolutionary changes in native populations facing invasion by exotic species are increasingly reported. Recently, it has been shown that competition with exotic rainbow trout (Oncorhynchus mykiss) disrupts dominance hierarchies within groups of native Atlantic salmon (Salmo salar). The genetic and molecular actors underlying phenotypic plasticity are poorly understood. METHODOLOGY: Here, we aimed at identifying the genetic and molecular actors contributing to this plastic loss of dominance hierarchies as well as at identifying genes implicated in behaviours related to social dominance. By using microarrays, we compared the genome-wide gene transcription profiles in brains of dominant versus subordinate juvenile Atlantic salmon in presence or absence of a competitive rainbow trout. PRINCIPAL FINDINGS: Adding the trout competitor resulted in dominant and subordinate salmon being more similar, both behaviourally and at the level of brain gene transcription patterns. Genes for which transcription levels differed between dominant and subordinate salmon in the absence of exotic trout were mainly over-expressed in dominant salmon and included genes implicated in protein turnover, neuronal structural change and oxygen transport. CONCLUSIONS/SIGNIFICANCE: Our study provides one of the few examples demonstrating a close interplay between behavioural plasticity and gene transcription, therefore contributing to the understanding of the molecular mechanisms underlying these processes in an ecologically relevant context