Shipping Federation of Canada

Abstract Teleost fishes, thanks to their rapid evolution of sex determination mechanisms, provide remarkable opportunities to study the formation of sex chromosomes and the mechanisms driving the birth of new master sex determining (MSD) genes. However, the evolutionary interplay between the sex chromosomes and the MSD genes they harbor is rather unexplored. We characterized a male-specific duplicate of the anti-Müllerian hormone ( amh) as the MSD gene in Northern Pike ( Esox lucius ), using genomic and expression evidences as well as by loss-of-function and gain-of-function experiments. Using RAD-Sequencing from a family panel, we identified Linkage Group (LG) 24 as the sex chromosome and positioned the sex locus in its sub-telomeric region. Furthermore, we demonstrated that this MSD originated from an ancient duplication of the autosomal amh gene, which was subsequently translocated to LG24. Using sex-specific pooled genome sequencing and a new male genome sequence assembled using Nanopore long reads, we also characterized the differentiation of the X and Y chromosomes, revealing a small male-specific insertion containing the MSD gene and a limited region with reduced recombination. Our study depicts an unexpected level of limited differentiation within a pair of sex chromosomes harboring an old MSD gene in a wild population of teleost fish, highlights the pivotal role of genes from the amh pathway in sex determination, as well as the importance of gene duplication as a mechanism driving the turnover of sex chromosomes in this clade. Author Summary In stark contrast to mammals and birds, teleosts have predominantly homomorphic sex chromosomes and display a high diversity of sex determining genes. Yet, population level knowledge of both the sex chromosome and the master sex determining gene is only available for the Japanese medaka, a model species. Here we identified and provided functional proofs of an old duplicate of anti-Müllerian hormone (Amh), a member of the Tgf-β family, as the male master sex determining gene in the Northern pike, Esox lucius . We found that this duplicate, named amhby (Y-chromosome-specific anti-Müllerian hormone paralog b), was translocated to the sub-telomeric region of the new sex chromosome, and now amhby shows strong sequence divergence as well as substantial expression pattern differences from its autosomal paralog, amha . We assembled a male genome sequence using Nanopore long reads and identified a restricted region of differentiation within the sex chromosome pair in a wild population. Our results provide insight on the conserved players in sex determination pathways, the mechanisms of sex chromosome turnover, and the diversity of levels of differentiation between homomorphic sex chromosomes in teleosts.

A methodology for planning an optimized river water temperature monitoring network is presented. The methodology is based on sampling of the physio-climatic variability of the region to be monitored. Physio-climatic metrics are selected to describe the study region, based on principal component analysis. The sites to be monitored are then identified based on a k-means clustering in the multidimensional space defined by the selected metrics. The methodology is validated on an existing dense water temperature network in Haute-Savoie, France. Different configurations of more or less dense network scenarios are evaluated by assessing their ability to estimate water temperature indices at ungauged locations. An optimized network containing 83 sites is found to provide satisfactory estimations for seven ecologically and biologically meaningful thermal indices defined to characterize brown trout thermal habitat.

The decline and collapse of populations have been reported for a large range of taxa. Diadromous fishes migrate between fresh water and the sea and encounter many anthropogenic pressures during their complex life cycle. In spite of being of ecological, cultural and economic interest, diadromous fishes have been in decline for decades in many parts across the world. In this study, we investigated the change in five diadromous fish counts in France over a 30-year period using 43 monitoring stations located in 29 rivers across 18 catchments. Our hypothesis was that the counts of these species evolved in a contrasting way between catchments. We also tested the effect of five drivers potentially contributing to the observed trends: catchment, latitude, presence of commercial fisheries, improvement of ecological continuity and salmon stocking. We found contrasting trends in fish counts between species at the national scale, with some taxa increasing ( Anguilla anguilla and Salmo trutta ), some showing a slight increase ( Salmo salar ) and some decreasing ( Alosa spp. and Petromyzon marinus ). For each taxon, except Anguilla anguilla , we highlighted a significant catchment effect indicating contrasting trends between catchments and stations. However, we found no significant effect of catchment characteristics for any of the studied taxa.

La reproduction d’une population de truite (Salmo trutta L.) de forme essentiellement méditerranéenne est décrite dans le ruisseau du Chevenne, un torrent à forte pente (10 %) entrecoupé d’obstacles et limité en substrat de frai, situé dans les Alpes savoyardes. Les reproducteurs (résidents du torrent ou migrants issus du cours principal) diffèrent en taille et sexe-ratio. La majorité (58 %) des femelles migrantes entrent dans l’affluent déjà ovulées. Il existe une fort gradient décroissant aval-amont dans la répartition des géniteurs et des frayères. Les 157 frayères décrites montrent une grande diversité de microhabitats (5 types principaux) utilisés pour la reproduction, avec un pourcentage élevé (65 %) de frayères construites dans des sites protégés ayant une faible vitesse de courant (< 20 cm/s). La reproduction débute en radier, l’habitat de frai classique, puis elle s’étend ensuite aux autres microhabitats avant que le frai en milieu radier ne soit achevé. Une évaluation de la disponibilité et de l’utilisation du substrat favorable au frai (taille de 1 à 3 cm) dans les divers microhabitats a été réalisée a posteriori. Le microhabitat « côté de pool » (inhabituel pour le frai) est autant utilisé que le milieu radier. Les lentilles de substrat favorable, abritées en bordure de berge ou dans les courants sont préférées alors que les lentilles de substrat non protégées dans les courants sont évitées. Une crue en fin de la période de frai a totalement détruit 36 % des frayères avec un taux de destruction totale très variable selon le type de microhabitat de frai. Les frayères creusées en côté de pool et en bordure de berge protégées du courant ont été moins détruites (15-17 % de destruction totale) que dans les autres microhabitats (50 à 67 % de destruction totale). La diversité des sites de frai pourrait donc être une composante essentielle à la survie de la population de truite en milieu « torrent exposé à des crues hivernales ».

A multidisciplinary study was made of brown trout Salmo trutta in the Borne River, a typical fast-flowing mountain stream in the Northern French Alps, in the geographical range of the Mediterranean lineages (ML). Information on (1) the proportion of stocked fluoro-marked fish in the angling harvest, (2) the introgression of introduced DNA microsatellite alleles into the native gene pool and (3) the demography of the population in situ in autumn revealed two contrasting populations separated by a physical barrier to upstream migration. A native S. trutta population (c. 10 000 adults) lives downstream of the barrier and is characterized by a large frequency of ML alleles (82-97%) and high densities (43-55 fish 100 m(-2)). This population is maintained predominantly by natural recruitment of juveniles (51-82%). In contrast, the upstream population is characterized by a large frequency of Atlantic lineage (AL) alleles (78-100%) and low densities (1-2 fish 100 m(-2)) and appears to be maintained by restocking (90-100%). The origins of these sharply contrasting populations appear to reflect isolation by an impassable barrier, catastrophic flooding, a downstream gradient in water quality, stocking and fishing pressure. The native downstream population has been resilient to large sudden floods and to intensive stockings of domesticated AL fish. The results of this study justify a shift in management towards conservation and rehabilitation of the native population.

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 20 meristic characters were taken from each specimen. Out of the meristic characters, 12 were obtained by means of X-ray. One important morphometric character in the present study is the size of the head measured from premaxilla to posterior margin of preoperculum. This character was particularly stable in all Tyrrhenian trout, showing relatively large head compared to Atlantic trout and to S . macrostigma . On the contrary, other characters like body punctuations, black and white edges of fins, body depth or number of epurals in the caudal skeleton are quite polymorphic. In certain meristic characters, range of variation of Tyrrhenian trout even exceeds that of the extensive comparative material. Each trout has been genetically characterized. New haplotypes from Tyrrhenian trout were discovered, belonging to three mitochondrial lineages viz. Adriatic, marble and Mediterranean, however, Adriatic haplotypes are dominant. Comparing morphological and genetic data, observed morphology lacks any obvious correlation to mitochondrial lineages and it is concluded that Tyrrhenian trout show no particular affinity to S . macrostigma from Algeria.

Summary 1. The conservation of salmonid inter‐ and intra‐specific diversity is a well‐known challenge, and general management guidelines and conservation processes are available. However, research demonstrating the outcomes of practical conservation actions is largely lacking. 2. We monitored the spatiotemporal genetic and demographic evolution of a native Mediterranean brown trout population in a river in the French Alps to assess the efficacy and early effects of genetic refuge (i.e. cessation of stocking) and wild trout translocation strategies. We also studied the use of angling as a tool to limit the introgression of the wild standing population. 3. We found that the rate of non‐native alleles in wild populations was age dependent, underpinning the importance of using age profiles in the design of genetic conservation studies. 4. Genetic refuge and direct translocation of wild trout resulted in a rapid and significant decrease in the percentages of non‐native alleles. Moreover, the genetic refuge strategy resulted in a significant reduction in the number of pure non‐native individuals, without changing trout densities, whilst direct translocations resulted in the establishment of dense, self‐sustaining native trout populations. Direct translocations changed the distribution of genotype categories and increased densities up to 55‐fold in 3 years. Our results also showed that angling resulted in a selective pressure on non‐native trout introduced at fry stage, whereas non‐native trout issued from natural recruitment were not affected. 5. Our study provides insights for improving the efficacy of practical conservation policies and can be used in other native freshwater fish conservation plans. Proactive measures such as direct translocation need to be implemented together with passive approaches such as genetic refuge policies. Before implementing such actions, accurate genetic and demographic studies at small geographical scales are essential to ensure that no self‐sustaining population of non‐native fish is present. To obtain rapid colonisation, we recommend introducing fish along whole river sections rather than concentrating on a few river stretches. Angling pressure can be used as an additional tool to improve restoration.

Dix-sept espèces étrangères à la faune insulaire ont été introduites en moins d'un siècle dans les eaux douces, dont quinze espèces de poissons. Toutes se sont acclimatées dans différents types de milieux et contribuent à enrichir la biodiversité du peuplement aquatique et plus particulièrement l'ichtyocénose des lacs naturels ou artificiels. L'impact sanitaire, peu étudié, est abordé avec mention de l'apparition récente de l'anguillicolose et l'impact génétique est traité à partir des connaissances récentes acquises sur les populations sauvages de truites.

Abstract – We studied the contribution of stocking with Mediterranean autochthonous brown trout ( Salmo trutta ) to the lake‐migratory spawners in French tributaries of Lake Geneva. This singular lake system is inhabited by both the resident and the migratory life‐history form, and by trout of Atlantic and Mediterranean origins. Using two discriminatory microsatellite loci between the Atlantic and Mediterranean alleles, we compared the genetic composition of the migratory Atlantic populations of the four main tributaries before (1999; N = 113) and after (2004, 2005 and 2006; N = 137) recent introductions of native Mediterranean trout. No significant modification of the genetic composition was detected in all four populations over time and only two individuals were statistically assigned to the Mediterranean strain by the Bayesian method implemented in the structure program. These results suggest a negligible contribution of the stockings with autochthonous Mediterranean trout to the lake‐migratory spawners migrating into the four tributaries.

Vingt mille larves de brochet (Esox lucius, L.) ont été élevées 35 jours en bac, avec une nourriture vivante (zooplancton et larves de Chaoboridés, Diptères) collectée en lagune d'épuration. Le but de cette expérience était de connaître l'influence de la densité initiale de stockage (5000 à 20000 individus/m3 ) sur la survie, la croissance et la quantité journalière de nourriture consommée au cours des phases zooplanctonophage et entomophage du stade larve en début d'alimentation exogène (10-13 mm, LT) au stade juvénile de 50 à 60 mm (LT). Les taux de survie, de cannibalisme et de croissance sont dépendants de la densité d'élevage. Le rythme alimentaire est monophasique et indépendant de la mise en charge et de la taille des brochetons. La consommation journalière, évoluant avec la taille du poisson, est peu influencée par la densité. Le taux d'évacuation gastrique est stable au cours de cet élevage. Le pourcentage du poids vif ingéré par jour par rapport au poids du poisson décroît du stade larve de 13-16 mm (30 %) au stade juvénile de 35-50 mm (20 %). Des bases de rationnement pour une production de brochetons en élevage intensif sont proposées.

BACKGROUND: ) is an anadromous migratory species adapted to cool temperatures. It is protected by the Bern convention and by the European Habitats Directive. It has been listed as vulnerable by the French IUCN Red List. Salmon decline is the result of combined and cumulated, mainly anthropic, causes: climate change, increasingly high number of impoundments, degradation of water quality and habitat and over-exploitation by fisheries. Monitoring of this species has been carried out on three rivers in France (Southern part of the distribution area) to produce data and knowledge (growth, precocious maturity, survival) for stock management.For 24 years, a specific and standardised electric fishing protocol has been used to target young-of-the-year (0+ parr) Atlantic salmon. Sampling was restricted to areas with shallow running water that flows over a coarse bottom substrate, i.e. the preferred habitat of young salmon. This monitoring and inventory of growing areas thus allows assessment of juvenile recruitment and provides baseline data required to calculate total allowable catches (TACs). NEW INFORMATION: The dataset currently consists of 47,077 occurrence data points from 105 sites spanning up to 24 years in three different watersheds in France. Beyond our project, this dataset has a clear utility to research since it associates abundance measurements with the measurement of biological traits and the collection of tissue samples. It allows for current and retrospective characterisation of individuals or populations, according to life history traits and genetic features in relation to changes in environmental conditions. The fact that the monitoring takes place in France, the southern part of the distribution area, over 24 years, makes the dataset particularly relevant for climate change studies.

Les pratiques de repeuplement en truite à des stades précoces (alevins nourris et truitelles 3-5 cm) ont été évaluées par la technique de fluoromarquage des otolithes sur le bassin amont du Fier pour trois cohortes (1995, 1996, 1997).

Aquitanian pike, Esox aquitanicus , is a new esocid species described in 2014 and endemic to Southwestern France. The four main goals of the present study were to (i) obtain the first morphological data on the early life stages, (ii) test the effects of temperature on their survival and development, (iii) compare the results with the Northern pike, and (iv) produce a few individuals to exhibit them at the Aquarium of Limoges. Eggs are yellowish, demersal, and sticky. The mean diameter was 2.73 ± 0.08 mm ( n = 174). The larval size at hatching was 9.09 ± 0.24 mm ( n = 14). The morphological development of 15 larvae was followed during 11 weeks as well as the snout growth in relation to eye size. It appeared that already after three weeks, slight differences between the two species were apparent, and after nine weeks, this snout/eye ratio was twice greater for Northern pike than Aquitanian pike. At the end of the yolk-feeding period, which lasted from 12 days at 18 °C to 36 days at 6 °C, the overall survival rate was over 85% and larvae were of similar size, except at 6 °C. After three months, the best results in term of survival were obtained at 12 °C (60%) and for growth at 15 °C (34.11 mm), followed at 12 °C (27.85 mm). Based on these results, we were able to rear Aquitanian pike for more than 2 years in the Aquarium of Limoges in order to promote the conservation of the species to the public.

La station de contrle des migrations de saumon du Moulin des Princes Pont-Scorff, proprit de la Fdration du Morbihan pour la pche et la protection des milieux aquatiques, a t mise en service en mai 1994 afin d'tudier la dynamique de population chez le saumon atlantique.L'Institut national de recherche pour l'alimentation, l'agriculture et l'environnement (INRAE) et l'Office Franais pour la Biodiversit (OFB) sont responsables du programme de recherche, bas sur les donnes rcoltes la station du Moulin des Princes sur les adultes et les juvniles migrants (smolts), mais aussi par pche lectrique sur l'ensemble du rseau hydrographique pour les juvniles rsidants.Ce programme permet d'avoir aujourd'hui des sries chronologiques longues, acquises diffrents stades du cycle biologique.Les suivis mis en place sur le stock du saumon du Scorff depuis 1994 mettent en vidence que le nombre de smolts dvalants est trs fluctuant d'une anne l'autre, mais ces fluctuations sont beaucoup moins fortes depuis le dbut des annes 2000.A partir de 2003, on note une production de smolts en moyenne de prs de 8657 alors que la production moyenne des annes prcdentes tait seulement de 5200 smolts.En 2020, on ne dispose pas des donnes concernant la dvalaison des smolts puisque les oprations de pigeage n'ayant pu tre conduites en raison de la crise sanitaire.Les adultes quant eux reviennent prfrentiellement comme castillons ; ceux-ci reprsentent en moyenne 86% des effectifs totaux d'adultes.On observe une augmentation des effectifs de saumons de printemps depuis 2005 : les effectifs moyens estims sont de 115 depuis 2005, alors qu'ils taient de 62 entre 1995 et 2004.Cependant, comme en 2019, l'anne 2020 ne suit pas ce patron avec un retour de saumons de printemps nettement plus faible que les dernires annes, en-dessous de la moyenne interannuelle.Les effectifs de castillons sont variables d'une anne l'autre, mais sans qu'on puisse observer de tendance l'augmentation ou la baisse depuis 1994.Avec 441 castillons, l'anne 2020 est en augmentation par rapport 2019 mais reste en dessous du niveau moyen.Le nombre de poissons de 2 nd retour, en nette augmentation entre 2004 et 2014, est nouveau plus faible ces dernires annes.En 2020, comme en 2019, seuls 2 poissons de 2 nd retour ont t observs.Si le nombre total de saumons adultes ne montre pas de tendance particulire, on note en revanche une diminution sensible de leur taille et de leur poids, avec une tendance la stabilit des niveaux bas ces dernires annes.Les valeurs observes en 2020 dnotent par rapport ce patron gnral ; elles sont en forte augmentation par rapport la moyenne des annes les plus rcentes.Aprs avoir fortement dcru, l'embonpoint (rapport longueur poids) des adultes semble s'amliorer pour les saumons de printemps ou se stabiliser pour les castillons au cours des 10 dernires annes.Ces volutions sont le reflet des changements des conditions de croissance en mer sans que l'on connaisse ce jour les causes exactes.Paralllement, un retard progressif des retours de saumons de printemps et des castillons a t observ, qui s'est cependant invers au cours des dernires annes.Les donnes ne sont pas disponibles en 2020 pour les saumons de printemps pour cause d'arrt du pigeage en lien avec la situation sanitaire.Pour les castillons elles confirment le retour des entres en eau douce prcoces.Le taux de survie oeufs/smolts s'est globalement amlior par rapport au dbut de la priode de suivi, mais il tend quand mme rgresser ces dernires annes.Les taux de survie en mer montrent eux de plus fortes fluctuations avec un point exceptionnellement bas enregistr pour l'anne de dvalaison 2008 (retours d'adultes en 2009 et 2010) et une tendance l'amlioration depuis.La dernire cohorte de smolt observe (2018) montre cependant une survie en mer assez faible.Face ces fluctuations ocaniques plus fortes, la prservation d'un environnement en eau douce favorable la survie des juvniles est particulirement importante pour la prennit de la population de saumon du Scorff.

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La ripisylve désigne l’ensemble des peuplements forestiers et boisements linéaires situés aux abords des cours d'eau, à l’interface entre les milieux aquatique et terrestre. Ces dernières décennies, un nombre croissant d’études scientifiques ont mis en lumière les intérêts écologiques, sociétaux et économiques de la préservation et de la restauration des ripisylves. Dans la première partie de cet article, nous synthétisons les bénéfices associés aux ripisylves. Nous présentons, dans une seconde partie, les éléments soutenant la préservation et la restauration des ripisylves comme des stratégies d’atténuation du changement climatique et d'adaptation à ses effets sur les rivières, la biodiversité et les humains. Ces caractéristiques font de la restauration de la végétation des berges des cours d’eau une mesure de gestion à développer dans les années à venir, dans un cadre réfléchi et adapté aux contraintes locales.

National audience

ABSTRACT Large alluvial plain rivers provide a complex mosaic of freshwater habitats characterised by a lateral hydrological connectivity (LHC) gradient between the main channel and floodplains. This connectivity plays a key role in structuring aquatic communities, influencing species distribution, diversity, and ecosystem processes. The aims of our study were to assess the effects of the LHC gradient on both fish taxonomic and functional diversity, and to characterise the effects of this connectivity on the distribution of non‐native species. Community data were gathered through electrofishing at five sites in the main channel of the Saône River (France), and in four permanently (parapotamic) and four occasionally (plesiopotamic) connected oxbows. Functional diversity was investigated using a trait‐based approach as surrogates of ecosystem processes. A total of 28 fish species were identified, including 14 non‐native species. Our results show that main channel and plesiopotamic oxbows exhibited distinct compositional and structural patterns of fish communities, while parapotamic oxbows displayed an intermediate composition and community structure. Taxonomic and functional diversity decreased along the lateral continuum from the main channel to plesiopotamic waterbodies. In contrast, while non‐native species richness was similar between the main channel and floodplains, their densities were higher in floodplain oxbows. These findings highlight the prominent role of hydrological connectivity in sustaining both taxonomic and functional diversity in riverine ecosystems. Fish community variations between habitats may be explained by physical changes resulting from reduced connectivity, primarily characterised by a loss of depth and surface area, which in turn affect a broad spectrum of abiotic and biotic factors. High densities of non‐native species in lentic environments like oxbows can be attributed to specific abiotic conditions (e.g., hypoxia, rapid temperature fluctuations and eutrophication) and the greater tolerance and plasticity of non‐native species compared to native species. Additionally, the absence of predators reduces top‐down control and intensifies competition with native species for resources. Conservation and management strategies should prioritise preserving and restoring connectivity to support native fish communities, limit the dominance of non‐native species, and maintain the ecological integrity of freshwater ecosystems.

Localisation Bibliothèque Aquapôle M 2137