Fine-scale environmentally associated spatial structure of lumpfish (Cyclopterus lumpus) across the Northwest Atlantic.

Lumpfish, Cyclopterus lumpus, have historically been harvested throughout Atlantic Canada and are increasingly in demand as a solution to controlling sea lice in Atlantic salmon farms-a process which involves both the domestication and the transfer of lumpfish between geographic regions. At present, little is known regarding population structure and diversity of wild lumpfish in Atlantic Canada, limiting attempts to assess the potential impacts of escaped lumpfish individuals from salmon pens on currently at-risk wild populations. Here, we characterize the spatial population structure and genomic-environmental associations of wild populations of lumpfish throughout the Northwest Atlantic using both 70K SNP array data and whole-genome re-sequencing data (WGS). At broad spatial scales, our results reveal a large environmentally associated genetic break between the southern populations (Gulf of Maine and Bay of Fundy) and northern populations (Newfoundland and the Gulf of St. Lawrence), linked to variation in ocean temperature and ice cover. At finer spatial scales, evidence of population structure was also evident in a distinct coastal group in Newfoundland and significant isolation by distance across the northern region. Both evidence of consistent environmental associations and elevated genome-wide variation in F ST values among these three regional groups supports their biological relevance. This study represents the first extensive description of population structure of lumpfish in Atlantic Canada, revealing evidence of broad and fine geographic scale environmentally associated genomic diversity. Our results will facilitate the commercial use of lumpfish as a cleaner fish in Atlantic salmon aquaculture, the identification of lumpfish escapees, and the delineation of conservation units of this at-risk species throughout Atlantic Canada.

Water security determines social attitudes about dams and reservoirs in South Europe.

River barriers affect river dynamics and aquatic biota, altering the entire ecosystem. Nevertheless, dams and reservoirs provide goods like water supply and low-carbon energy that are becoming increasingly critical under current climate change. To know to what extent dams and reservoirs are important to the population, we explored social attitudes towards dams and reservoirs using a face-to-face questionnaire in two regions of contrasting climate and water security in Spain, a country with one of highest densities of dams in Europe. Results (N = 613) revealed a higher support for dams, mediated by the recognition of the services they provide, in the drier Mediterranean Malaga province (Andalusia), than in the wetter Atlantic Asturias province (Bay of Biscay), where water shortages are rare. Awareness of the impacts of the dams was more pronounced in Malaga, coupled with a higher willingness to pay for reconnecting rivers. Social awareness of both impacts and services provided by dams and reservoirs may depend on local climate and water security; different dam acceptance emphasizes the need to involve local citizens in the decision-making processes about water management.

Filling the gaps: phylogeography of the self-fertilizing Kryptolebias species (Cyprinodontiformes: Rivulidae) along South American mangroves.

Mangrove killifishes of the genus Kryptolebias have been historically classified as rare because of their small size and cryptic nature. Major gaps in distribution knowledge across mangrove areas, particularly in South America, challenge the understanding of the taxonomic status, biogeographical patterns and genetic structuring of the lineages composing the self-fertilizing "Kryptolebias marmoratus species complex." In this study, the authors combined a literature survey, fieldwork and molecular data to fill major gaps of information about the distribution of mangrove killifishes across western Atlantic mangroves. They found that selfing mangrove killifishes are ubiquitously distributed across the Caribbean, Central and South American mangroves and report 14 new locations in South America, extending the range of both the "Central clade" and "Southern clade" lineages which overlap in the Amazon. Although substantial genetic differences were found between clades, the authors also found further genetic structuring within clades, with populations in Central America, north and northeast Brazil generally showing higher levels of genetic diversity compared to the clonal ones in southeast Brazil. The authors discuss the taxonomic status and update the geographical distribution of the Central and Southern clades, as well as potential dispersal routes and biogeographical barriers influencing the distribution of the selfing mangrove killifishes in the western Atlantic mangroves.

Comparative transcriptomics reveal conserved impacts of rearing density on immune response of two important aquaculture species.

Infectious diseases represent an important barrier to sustainable aquaculture development. Rearing density can substantially impact fish productivity, health and welfare in aquaculture, including growth rates, behaviour and, crucially, immune activity. Given the current emphasis on aquaculture diversification, stress-related indicators broadly applicable across species are needed. Utilising an interspecific comparative transcriptomic (RNAseq) approach, we compared gill gene expression responses of Atlantic salmon (Salmo salar) and Nile tilapia (Oreochromis niloticus) to rearing density and Saprolegnia parasitica infection. Salmon reared at high-density showed increased expression of stress-related markers (e.g. c-fos and hsp70), and downregulation of innate immune genes. Upon pathogen challenge, only salmon reared at low density exhibited increased expression of inflammatory interleukins and lymphocyte-related genes. Tilapia immunity, in contrast, was impaired at low-density. Using overlapping gene ontology enrichment and gene ortholog analyses, we found that density-related stress similarly impacted salmon and tilapia in key immune pathways, altering the expression of genes vital to inflammatory and Th17 responses to pathogen challenge. Given the challenges posed by ectoparasites and gill diseases in fish farms, this study underscores the importance of optimal rearing densities for immunocompetence, particularly for mucosal immunity. Our comparative transcriptomics analyses identified density stress impacted immune markers common across different fish taxa, providing key molecular targets with potential for monitoring and enhancing aquaculture resilience in a wide range of farmed species.

Effect of artificial barriers on the distribution of the invasive signal crayfish and Chinese mitten crab.

The role of river obstacles in preventing or facilitating the dispersal and establishment of aquatic invasive species is controversial. Novel detection tools like environmental DNA (eDNA) can be used for monitoring aquatic invasive species (AIS) such as the American signal crayfish (Pacifastacus leniusculus) and the Chinese mitten crab (Eriocheir sinensis), providing information on the effect of barriers on their distribution. We analysed eDNA from both water and surface sediment in three river catchments (Medway, Dee and Stour; Great Britain), with differing levels of connectivity, to determine spatial distribution of the two species, and assessed the effect of barriers on their eDNA detection. Positive eDNA detections were obtained within confirmed sites for both species in all catchments, with evidence of species overlap in the River Medway. Upstream barriers in the Medway positively influenced detection success of mitten crab lower in the catchment while detection success of signal crayfish was higher in the highly fragmented catchment (River Medway). This information on the role of river barriers on AIS distribution and eDNA detection is important for management strategies and for predicting both future dispersal and likelihood of new colonisations in previously uninvaded fragmented catchments.

Patterns of natural selection acting on the mitochondrial genome of a locally adapted fish species.

BACKGROUND: Mitochondrial DNA (mtDNA) is frequently used in population genetic studies and is usually considered as a neutral marker. However, given the functional importance of the proteins encoded by the mitochondrial genome, and the prominent role of mitochondria in cellular energy production, the assumption of neutrality is increasingly being questioned. RESULTS: We tested for evidence of selection on the mitochondrial genome of the Atlantic salmon, which is a locally adapted and widely farmed species and is distributed across a large latitudinal cline. We analysed 20 independent regions of the salmon mtDNA that represented nine genes (ND1, ND2, ND3, COX1, COX2, ATP6, ND4, ND5, and CYTB). These 20 mtDNA regions were sequenced using a 454 approach from samples collected across the entire European range of this species. We found evidence of positive selection at the ND1, ND3 and ND4 genes, which is supported by at least two different codon-based methods and also by differences in the chemical properties of the amino acids involved. The geographical distribution of some of the mutations indicated to be under selection was not random, and some mutations were private to artic populations. We discuss the possibility that selection acting on the Atlantic salmon mtDNA genome might be related to the need for increased metabolic efficiency at low temperatures. CONCLUSIONS: The analysis of sequences representing nine mitochondrial genes that are involved in the OXPHOS pathway revealed signatures of positive selection in the mitochondrial genome of the Atlantic salmon. The properties of the amino acids involved suggest that some of the mutations that were identified to be under positive selection might have functional implications, possibly in relation to metabolic efficiency. Experimental evidence, and better understanding of regional phylogeographic structuring, are needed to clarify the potential role of selection acting on the mitochondrial genome of Atlantic salmon and other locally adapted fishes.

Shrinking fish: comparisons of prehistoric and contemporary salmonids indicate decreasing size at age across millennia.

A comparison of Upper Palaeolithic and contemporary salmonid vertebrae from the Iberian Peninsula indicates that there has been a significant decrease in the mean body size for a given age among Atlantic salmon and brown trout inhabiting the southernmost range of their endemic distribution. Mean size at age was greater in prehistoric specimens for all age classes during the freshwater phase of their life histories. Fisheries-induced evolution (selection for smaller sizes) is an obvious explanation for the observed reduction in fish body size, but recent changes in the aquatic habitat affecting density-dependent growth cannot be ruled out.

Inbred and furious: negative association between aggression and genetic diversity in highly inbred fish.

Aggressive behaviour plays an important role in securing resources, defending against predators and shaping social interactions. Although aggression can have positive effects on growth and reproductive success, it is also energetically costly and may increase injury and compromise survival. Individual genetic diversity has been positively associated with aggression, but the cause for such an association is not clear, and it might be related to the ability to recognize kin. To disentangle the relationships between genetic diversity, kinship and aggression, we quantified aggressive behaviour in a wild, self-fertilizing fish (Kryptolebias marmoratus) with naturally variable degrees of genetic diversity, relatedness and familiarity. We found that in contrast to captive fish, levels of aggression among wild K. marmoratus are positively associated with individual homozygosity, but not with relatedness or familiarity. We suggest that the higher aggression shown by homozygous fish could be related to better kin discrimination and may be facilitated by hermaphrodite competition for scarce males, given the fitness advantages provided by outcrossing in terms of parasite resistance. It seems likely that the relationship between aggression and genetic diversity is largely influenced by both the environment and population history.

Detection and mapping of mtDNA SNPs in Atlantic salmon using high throughput DNA sequencing.

BACKGROUND: Approximately half of the mitochondrial genome inherent within 546 individual Atlantic salmon (Salmo salar) derived from across the species' North Atlantic range, was selectively amplified with a novel combination of standard PCR and pyro-sequencing in a single run using 454 Titanium FLX technology (Roche, 454 Life Sciences). A unique combination of barcoded primers and a partitioned sequencing plate was employed to designate each sequence read to its original sample. The sequence reads were aligned according to the S. salar mitochondrial reference sequence (NC_001960.1), with the objective of identifying single nucleotide polymorphisms (SNPs). They were validated if they met with the following three stringent criteria: (i) sequence reads were produced from both DNA strands; (ii) SNPs were confirmed in a minimum of 90% of replicate sequence reads; and (iii) SNPs occurred in more than one individual. RESULTS: Pyrosequencing generated a total of 179,826,884 bp of data, and 10,765 of the total 10,920 S. salar sequences (98.6%) were assigned back to their original samples. The approach taken resulted in a total of 216 SNPs and 2 indels, which were validated and mapped onto the S. salar mitochondrial genome, including 107 SNPs and one indel not previously reported. An average of 27.3 sequence reads with a standard deviation of 11.7 supported each SNP per individual. CONCLUSION: The study generated a mitochondrial SNP panel from a large sample group across a broad geographical area, reducing the potential for ascertainment bias, which has hampered previous studies. The SNPs identified here validate those identified in previous studies, and also contribute additional potentially informative loci for the future study of phylogeography and evolution in the Atlantic salmon. The overall success experienced with this novel application of HT sequencing of targeted regions suggests that the same approach could be successfully applied for SNP mining in other species.

Winning the invasion roulette: escapes from fish farms increase admixture and facilitate establishment of non-native rainbow trout.

Aquaculture is a major source of invasive aquatic species, despite the fact that cultured organisms often have low genetic diversity and tend to be maladapted to survive in the wild. Yet, to what extent aquaculture escapees become established by means of high propagule pressure and multiple origins is not clear. We analysed the genetic diversity of 15 established populations and four farmed stocks of non-native rainbow trout in Chile, a species first introduced for recreational fishing around 1900, but which has in recent decades escaped in large numbers from fish farms and become widespread. Aquaculture propagule pressure was a good predictor of the incidence of farm escapees, which represented 16% of all free-ranging rainbow trout and were present in 80% of the study rivers. Hybrids between farm escapes and established trout were present in all rivers at frequencies ranging between 7 and 69%, and population admixture was positively correlated with genetic diversity. We suggest that non-native salmonids introduced into the Southern Hemisphere could benefit from admixture because local adaptations may not have yet developed, and there may be initially little fitness loss resulting from outbreeding depression.