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The blue shark Prionace glauca is a top predator with one of the widest geographic distributions of any shark species, yet classified as critically endangered in the Mediterranean Sea, and Near Threatened globally. Previous genetic studies did not reject the null hypothesis of a single global population across the worldwide species range. Blue shark situation was proposed as a possible archetype of the ‘grey zone of population differentiation’, coined to designate cases where population structure may be too recent or too faint to be detected using a limited set of markers. Here, blue shark samples collected throughout its global range were sequenced using a specific ddRAD method (DArTseq; Georges et al. 2018), which recovered 37,655 genome-wide single nucleotide polymorphisms (SNPs). Two main groups emerged, with Mediterranean Sea and Northern Atlantic samples significantly differentiated from the Indo-west Pacific samples. Significant pairwise FST values indicated further genetic differentiation within the Atlantic Ocean, and between the Atlantic Ocean and the Mediterranean Sea. Reconstruction of recent demographic history suggested the divergence between northern and southern oceanic populations emerged about 500 generations ago and revealed a drastic reduction in effective population size from a large ancestral population. Our results illustrate the power of high-density genome scans to detect population structure and reconstruct demographic history in highly migratory marine species. As the management of the blue shark fishery, either as target or as bycatch, does not account for this delineation, we strongly recommend that the results presented here be considered in future stock assessment and management plans.

The great physiological, behavioral and morphological plasticity of salmonids contributed to the success of their introduction into a wide range of habitats. However, rainbow trout (Oncorhynchus mykiss) is the only salmonid species to live in the tropics. Like for any cold-water species, water temperature is assumed to be a major constraint to the presence and expansion of rainbow trout. In this study, we collected detailed records of the introduction history of rainbow trout at 35 sites across the island over 80 years, and we document the presence of self-sustainable trout at each site. We explored the linear relationship between water temperature and elevation.

International audience; Tunas are the focus of significant fisheries in the Pacific Ocean, where landings of four species - skipjack tuna (Katsuwonus pelamis), yellowfin tuna (Thunnus albacares), bigeye tuna (Thunnus obesus) and albacore tuna (Thunnus alalunga) - constitute approximately 70 % of the global tuna catch. Stock assessments for skipjack, yellowfin and bigeye tunas in the Pacific Ocean currently assume eastern and western stocks. For albacore tuna, separate North Pacific Ocean and South Pacific Ocean stocks are currently assumed. In each case, these geographic definitions reflect the historical development of fisheries management across the Pacific rather than biological considerations. There is widespread agreement that uncertainties surrounding the stock structures of these four tuna species could have important impacts on the population dynamics models used to assess their status and inform management options. Knowledge of stock structure is also essential for improved modelling of the effects of climate change on tuna distribution and abundance and associated implications for fisheries. This paper reviews current knowledge and understanding of the stock structures of skipjack, yellowfin, bigeye and South Pacific albacore tunas in the Pacific Ocean, by exploring available literature relating to their biology, movement and spatial dynamics. As a guide for future research in this area, we identify the main uncertainties in defining the stock structure of these four tunas in the Pacific, including i) spawning dynamics; ii) the degree of spawning area fidelity and localised residency; iii) the provenance of individuals in, and proportional contributions of self-replenishing populations to, fishery catches within the Pacific Ocean; iv) linkages with adjacent 'stocks', v) the effects of climate change on stock structure and proportional contributions of self-replenishing populations to fisheries; and vi) the implications of improved knowledge of tuna stock structure for stock assessment and climate change model assumptions and fisheries management. We also briefly propose some approaches that future studies could use to address these uncertainties.

Delineating the stock structure of highly-mobile, wide-ranging fishes subject to exploitation is a challenging task, yet one that is fundamental to optimal fisheries management. A case in point are stocks of skipjack tuna (Katsuwonus pelamis), yellowfin tuna (Thunnus albacares), bigeye tuna (Thunnus obesus) and albacore tuna (Thunnus alalunga) in the Pacific Ocean, which support important commercial, artisanal, subsistence, and recreational fisheries, and contribute roughly 70 % of global commercial tuna catches. Although some spatial and temporal structuring is recognised within these stocks, growing evidence from a range of approaches suggests that the stock structure of each tuna species is more complex than is currently assumed in both stock assessment and climate change models, and in management regimes. In a move towards improving understanding of the stock structure of skipjack, yellowfin, bigeye and South Pacific albacore tunas in the Pacific Ocean, an international workshop was held in Nouméa, New Caledonia, in October 2018 to review knowledge about their movement and stock structure in the region, define and discuss the main knowledge gaps and uncertainties concerning their stock structure, and develop biological sampling approaches to support the provision of this information. Here, we synthesise the discussions of this latter component. For each tuna species, we identify several general sampling considerations needed to reduce uncertainty, including i) the need for broadscale sampling in space, ideally covering each species’ distribution, targeting adults in spawning condition and adopting a phased approach; ii) the need for temporally-repeated sampling of the same geographical areas to assess stability in observed patterns over time; iii) the need to resolve patterns in spatial dynamics, such as those resulting from movements associated with the seasonal extensions of poleward flowing currents, from underlying stock structure, iv) the importance of adopting a multidisciplinary approach to stock identification, and v) the need for careful planning of logistics and coordination of sampling efforts across agencies. Finally, we present potential sampling designs that could be adopted to help overcome uncertainties around the initial identification of stocks and the provenance, mixing and proportional contributions of individuals in harvested assemblages, as well as how these uncertainties could be accounted for in fisheries management via the use of management strategy evaluation., Funding support for the workshop was provided by Conservation International as part of the GEF-funded, World Bank-implemented Ocean Partnerships for sustainable fisheries and biodiversity conservation (OPP), a sub-project of the Common Oceans ABNJ Program led by UN-FAO.

Shark species have undergone drastic population declines in recent decades due to overfishing and habitat destruction; thus, establishing connectivity among the populations of various shark species is important to determine the appropriate units and spatial scale for conservation and management, particularly as this group is long-lived with late age of maturation. Consequently, we used DNA variation at 1,317 putatively neutral and 25 potentially adaptive single nucleotide polymorphisms (SNPs) to analyze population genetic structure among 174 unrelated individuals of scalloped hammerhead sharks (Sphyrna lewini) from the Rewa Delta and the Ba Estuary, where documented aggregations of neonates and young-of-the-year occur in the island of Viti Levu, Republic of Fiji. Results of the pairwise F analysis for the neutral loci revealed a small but significant genetic differentiation (F: 0.004; P-value = 0.0009). Furthermore, the 25 potentially adaptive loci (i.e., under putative selection) revealed a magnitude of differentiation four times bigger than the estimate obtained using neutral genetic diversity (F: 0.017; P-value = 0.0009). Interestingly, population assignment tests, using the neutral SNP data set and two different software packages, Admixture and assignPOP, provided evidence for the existence of up to four genetically differentiated populations among our samples. Assignment probabilities ranged from 0.98 ± 0.01 to 0.81 ± 0.03. Admixture and assignPOP assigned the same individuals to the same putative populations for all sampled neonates. Thus, our results provide unequivocal evidence that adult females from multiple genetically differentiated breeding populations contribute to these juvenile aggregation sites., The work was supported by the University of the South Pacific, SRT project F1006-R1001-71502-621.

Population declines in shark species have been reported on local and global scales, with overfishing, habitat destruction and climate change posing severe threats. The lack of species-specific baseline data on ecology and distribution of many sharks, however, makes conservation measures challenging. Here, we present a fisheries-independent shark survey from the Fiji Islands, where scientific knowledge on locally occurring elasmobranchs is largely still lacking despite the location’s role as a shark hotspot in the Pacific. Juvenile shark abundance in the fishing grounds of the Ba Estuary (north-western Viti Levu) was assessed with a gillnet-and longline-based survey from December 2015 to April 2016. A total of 103 juvenile sharks identified as blacktip Carcharhinus limbatus (n = 57), scalloped hammerhead Sphyrna lewini (n = 35), and great hammerhead Sphyrna mokarran (n = 11) sharks were captured, tagged, and released. The condition of umbilical scars (68% open or semihealed), mean sizes of individuals (±SD) (C. limbatus: 66.5 ± 3.8 cm, S. lewini: 51.8 ± 4.8 cm, S. mokarran 77.4 ± 2.8 cm), and the presence of these species over recent years (based on fishermen interviews), suggest that the Ba Estuary area is a critical habitat for multiple species that are classified as “Near Threatened” or “Endangered.” Specifically, the area likely acts as a parturition ground over the studied period, and potentially as a subsequent nursery area. We identified subareas of high abundance and found that temperature, salinity and depth acted as small-scale environmental drivers of shark abundance. The data suggests a tendency for species-specific spatial use, both horizontally (i.e., between sampling areas) and vertically (i.e., across the water column). These results enhance the understanding of shark ecology in Fiji and provide a scientific basis for the implementation of local conservation strategies that contribute to the protection of these threatened species

Sharp declines in numerous shark populations around the world have generated considerable interest in better understanding and characterising their biology, ecology and critical habitats. The scalloped hammerhead shark (SHS, Sphyrna lewini) is subject to a multitude of natural and anthropogenic threats that are often exacerbated within the coastal embayments and estuaries used during SHS early life stages. In this study, we describe the temporal and spatial distribution, age class composition, and reproductive biology of SHS in the Rewa Delta (RD), Fiji. A total of 1054 SHS (including 796 tagged individuals; 101 of which were recaptured) were captured from September 2014 to March 2016 in the RD. A majority of the captures in this area were neonates and young-of-the-year (YOY) (99.8%). Significant seasonality in patterns of occurrence of both neonates and YOY individuals suggests a defined parturition period during the austral summer. Between the seven sampling sites in the RD we also found significant differences in SHS neonate catch per unit of effort, and average total length of individuals. According to the data, the RD is likely to represent an important nursery area for SHS up to one year of age.

Organisms develop local adaptations to cope with spatially and temporally variable environments such as estuarine habitats, where abiotic parameters such as salinity and temperature fluctuate continuously. Studying the regulation of gene expression in a variable environment allows us to understand the underlying molecular mechanisms of these adaptations and the relative roles of the genetic and plastic response. The transcriptomes of the European native Palaemon longirostris (PL) and the introduced P. macrodactylus (PM) shrimps are described and compared after an experiment simulating summer conditions in the Guadalquivir Estuary, Spain. Specimens, collected in the Guadalquivir Estuary, were maintained at a temperature and salinity of 20 °C and 5 ppt for the control, and 30 °C and 15 ppt for the stress treatment. A large amount of differential gene expression was observed: 16,013 and 2,594 for PL and PM respectively. Functionally annotated unigenes revealed some differences, with PL seemingly having to face stronger physiological stress than PM. Thus, PM seems to have greater resistance than PL under conditions of high temperature and salinity. These results constitute a step forward in the understanding of the underlying molecular mechanisms of genetic adaptation of native invertebrates, and alien taxa that have successfully invaded estuaries in temperate regions around the world.

20 páginas, 1 figura, 3 tablas., Recent studies have reported an unusually high frequency of nonamplifying alleles at microsatellite loci in bivalves. Null alleles have been associated with heterozygous deficits in many studies. While several studies have tested for its presence using different analytical tools, few have empirically tested for its consequences in estimating population structure and differentiation. We characterised 16 newly developed microsatellite loci and show that null alleles are ubiquitous in the wedge clam, Donax trunculus. We carried out several tests to demonstrate that the large heterozygous deficits observed in the newly characterised loci were most likely due to null alleles.Wetested the robustness of microsatellite genotyping for population assignment by showing that well-recognised biogeographic regions of the south Atlantic and south Mediterranean coast of Spain harbour genetically different populations., CR was supported by the Spanish Ministry of Education (Grant no PR2010-0601) and the Spanish Scientific Research Council (CSIC). This research was financially supported by Organismo Autonomo de Parque Nacionales Grant OAPN122_2010 to CR, EM, JAC and PD. ADM was supported by the Strategic Research Themes of the University of the South Pacific.

10 páginas, 2 figuras, 5 tablas., In a resource management perspective, the understanding of the relative influence of the physical factors on species connectivity remains a major challenge and is also of great ecological and conservation biology interest. Despite the overfishing threat on the wedge clam Donax trunculus in Europe, relatively little information is known about its population genetic structure and connectivity and their consequences on conservation policies. We employed 16 microsatellite loci to characterise the genetic diversity and population structure of D. trunculus. A total of 514 samples from seven different localities along the Atlantic-Mediterranean transition, from the Atlantic (Gulf of Cádiz) to the north-western Mediterranean were genotyped. The analysis of the population genetic structure displayed a clear distinction along the Atlantic-Mediterranean transition with different clusters in the Atlantic Ocean, the Alboran Sea and the northwestern Mediterranean. Consequently, we recommend that these three areas should be considered as different management units. We showed that all populations seem to be at high long-term risk of extinction with the exception of the protected Doñana National Park population which still seems to have evolutionary potential. Therefore, our results emphasized the necessity of protection of this economic resource and the validity of molecular tools to evaluate the population dynamics., This research was financially supported by Organismo Autónomo de Parques Nacionales Grant OAPN122_2010 to C.R., E.M., J.A.C. and P.D.

Recent studies have reported an unusually high frequency of nonamplifying alleles at microsatellite loci in bivalves. Null alleles have been associated with heterozygous deficits in many studies. While several studies have tested for its presence using different analytical tools, few have empirically tested for its consequences in estimating population structure and differentiation. We characterised 16 newly developed microsatellite loci and show that null alleles are ubiquitous in the wedge clam, Donax trunculus. We carried out several tests to demonstrate that the large heterozygous deficits observed in the newly characterised loci were most likely due to null alleles. We tested the robustness of microsatellite genotyping for population assignment by showing that well-recognised biogeographic regions of the south Atlantic and south Mediterranean coast of Spain harbour genetically different populations.

Salmonid fishes rank among species being most severely affected by introgressive hybridization as a result of a long tradition of stocking with hatchery-reared conspecifics. The objectives of this study were (i) to evaluate the genetic consequences of stocking and resulting introgression rates on the genetic integrity of natural populations of brook charr, (ii) to identify genomic regions potentially associated with adaptation to natural and artificial rearing environments, and (iii) to test the null hypothesis that introgression from domesticated brook charr into wild populations is homogeneous among loci. A total of 336 individuals were sampled from nine lakes, which were stocked at different intensities with domestic fish. Individuals were genotyped at 280 SNPs located in transcribed regions and developed by means of next-generation sequencing. As previously reported with microsatellites, we observed a positive relationship between stocking intensity and genetic diversity among stocking groups, and a decrease in population differentiation. Individual admixture proportions also increased with stocking intensity. Moreover, genomic cline analysis revealed 27 SNPs, seven of which were also identified as outliers in a genome scan, which showed an introgression rate either more restricted or enhanced relative to neutral expectations. This indicated that selection, mainly for growth-related biological processes, has favored or hampered the introgression of genomic blocks into the introgressed wild populations. Overall, this study highlights the usefulness of investigating the impact of stocking on the dynamics of introgression of potentially adaptive genetic variation to better understand the consequences of such practice on the genomic integrity of wild populations.

Stocking wild populations with domesticated fish is a common practice that promotes variable levels of introgression depending on the stocking intensity. The detection of hybridization and introgression has recently benefited from the application of Bayesian techniques implemented in various software. However, few studies have assessed their efficiency under various scenarios of stocking in the wild. The objective of this study is to assess quantitatively the effects of using two of the most widely distributed software, Structure and NewHybrids, on the level of introgression detected in wild brook charr (Salvelinus fontinalis) subjected to variable stocking intensities. We first found differences in the efficiency of software assignments based on simulated individuals, with Structure performing better than NewHybrids. However, NewHybrids showed higher assignments accuracy than Structure for the same sets of individuals. Thus, our results suggest that these software should be used in combination to assess the effects of stocking. Indeed, Structure is particularly relevant to evaluate the presence of hybrids in wild populations, whereas NewHybrids might be preferred to accurately assess the number of hybrids present in a sample. When applied to wild populations, Structure assigned more individuals than NewHybrids to the wild category. Moreover, the proportions of assigned domestic and hybrid individuals were higher in more intensively stocked lakes, whereas the opposite trend was observed for wild individuals.

Supportive breeding and stocking performed with non-native or domesticated fish to support sport fishery industry is a common practice throughout the world. Such practices are likely to modify the genetic integrity of natural populations depending on the extent of genetic differences between domesticated and wild fish and on the intensity of stocking. The purpose of this study is to assess the effects of variable stocking intensities on patterns of genetic diversity and population differentiation among nearly 2000 brook charr (Salvelinus fontinalis) from 24 lakes located in two wildlife reserves in Quebec, Canada. Our results indicated that the level of genetic diversity was increased in more intensively stocked lakes, mainly due to the introduction of new alleles of domestic origin. As a consequence, the population genetic structure was strongly homogenized by intense stocking. Heavily stocked lakes presented higher admixture levels and lower levels of among lakes genetic differentiation than moderately and un-stocked lakes. Moreover, the number of stocking events explained the observed pattern of population genetic structure as much as hydrographical connections among lakes in each reserve. We discuss the implications for the conservation of exploited fish populations and the management of stocking practices.

Thaumatocotyle pseudodasybatis Hargis, 1955, has previously been described from Aetobatus narinari in the Atlantic and subsequently recorded from the Pacific. Aetobatus cf. narinari is now considered a species complex; as monocotylids are often strictly species specific, we test the hypothesis that detailed examination of specimens of monocotylids from rays from various localities could reveal morphological differences and eventually help our understanding of the systematics of the host. T. pseudodasybatis, previously known from seven specimens only, is redescribed from an additional 26 specimens from the South Pacific (off New Caledonia, Australia and Ranguiroa, French Polynesia), all from Aetobatus cf. narinari. The female reproductive organs are described in detail. The distal extremity of the male sclerotised copulatory organ, described in detail for the first time, shows a characteristic pattern of longitudinal striations on its edge that might be useful for future distinction from other species. The development of the male and female organs in juveniles is described, showing that growth of the male sclerotised copulatory organ begins with its basal part and precedes development of the ejaculatory bulb. Specimens from New Caledonia, Australia and French Polynesia had similar measurements and morphology, especially in the shape of the distal end of the male sclerotised copulatory organ; they were also similar to the holotype from the Atlantic. This suggests that all specimens from the Pacific and Atlantic belong to a single species; T. pseudodasybatis thus cannot be used to differentiate populations of Aetobatus cf. narinari, perhaps because this monocotylid is not strictly species-specific.

Four species of monocotylid monogeneans were found on a spotted eagle ray Aetobatus cf. narinari caught off Noumea, New Caledonia, South Pacific. The host is illustrated for future possible identification, because it belongs to a currently unresolved species complex. Decacotyle octona (Young, 1967) ChisholmWhittington, 1998, from the secondary gill lamellae, is figured and previously unreported details of the reproductive system are described. D. elpora n. sp. is described from numerous specimens found between the secondary gill lamellae. The new species, 780-1650 microm in body length, is smaller than D. octona, but has a longer sclerotised male copulatory organ. It is characterised by two dorsal haptoral accessory structures, each with three bumps, and a 9-shaped sclerotised male copulatory organ 240-290 microm in length. D. octona and Clemacotyle australis Young, 1967, both from the branchial cavity, and Thaumatocotyle pseudodasybatis Hargis, 1955, from the nasal tissue, are new geographical records for New Caledonia. It is suggested that differences in the monocotylid fauna between the Atlantic and Indo-Pacific forms of Aetobatus cf. narinari could be of interest for the systematic status of the ray, but the sporadic nature of the sampling probably casts doubt on the usefulness of the currently available data.