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The article discusses the study which investigates the significant connection between genetic variation at circadian clock gene (OtsClock1b) and run-time phenotype in Atlantic salmon. Topics discussed include microsatellites variability, genetic drift, and fish population. The study found that there is a significant connection between OtsClock1b variation and Atlantic salmon or Salmo salar L.

Major histocompatibility complex (MHC) class I-linked microsatellite data and parental assignment data for a group of wild brown trout (Salmo trutta L.) provide evidence of closer spatial aggregation among fry sharing greater numbers of MHC class I alleles under natural conditions. This result confirms predictions from laboratory experiments demonstrating a hierarchical preference for association of fry sharing MHC alleles. Full-siblings emerge from the same nest (redd), and a passive kin association pattern arising from limited dispersal from the nest (redd effect) would predict that all such pairs would have a similar distribution. However, this study demonstrates a strong, significant trend for reduced distance between pairs of full-sibling fry sharing more MHC class I alleles reflecting their closer aggregation (no alleles shared, 311.5±(s.e.)21.03m; one allele shared, 222.2±14.49m; two alleles shared, 124.9±23.88m; P<0.0001). A significant trend for closer aggregation among fry sharing more MHC class I alleles was also observed in fry pairs, which were known to have different mothers and were otherwise unrelated (ML-r=0) (no alleles: 457.6±3.58m; one allele (422.4±3.86 m); two alleles (381.7±10.72 m); P<0.0001). These pairs are expected to have emerged from different redds and a passive association would then be unlikely. These data suggest that sharing MHC class I alleles has a role in maintaining kin association among full-siblings after emergence. This study demonstrates a pattern consistent with MHC-mediated kin association in the wild for the first time. [ABSTRACT FROM AUTHOR]

Abstract Background Anadromous migratory fish species such as Atlantic salmon (Salmo salar) have significant economic, cultural and ecological importance, but present a complex case for management and conservation due to the range of their migration. Atlantic salmon exist in rivers across the North Atlantic, returning to their river of birth with a high degree of accuracy; however, despite continuing efforts and improvements in in-river conservation, they are in steep decline across their range. Salmon from rivers across Europe migrate along similar routes, where they have, historically, been subject to commercial netting. This mixed stock exploitation has the potential to devastate weak and declining populations where they are exploited indiscriminately. Despite various tagging and marking studies, the effect of marine exploitation and the marine element of the salmon lifecycle in general, remain the "black-box" of salmon management. In a number of Pacific salmonid species and in several regions within the range of the Atlantic salmon, genetic stock identification and mixed stock analysis have been used successfully to quantify exploitation rates and identify the natal origins of fish outside their home waters - to date this has not been attempted for Atlantic salmon in the south of their European range. Results To facilitate mixed stock analysis (MSA) of Atlantic salmon, we have produced a baseline of genetic data for salmon populations originating from the largest rivers from Spain to northern Scotland, a region in which declines have been particularly marked. Using 12 microsatellites, 3,730 individual fish from 57 river catchments have been genotyped. Detailed patterns of population genetic diversity of Atlantic salmon at a sub-continent-wide level have been evaluated, demonstrating the existence of regional genetic signatures. Critically, these appear to be independent of more commonly recognised terrestrial biogeographical and political boundaries, allowing reporting regions to be defined. The implications of these results on the accuracy of MSA are evaluated and indicate that the success of MSA is not uniform across the range studied; our findings indicate large differences in the relative accuracy of stock composition estimates and MSA apportioning across the geographical range of the study, with a much higher degree of accuracy achieved when assigning and apportioning to populations in the south of the area studied. This result probably reflects the more genetically distinct nature of populations in the database from Spain, northwest France and southern England. Genetic stock identification has been undertaken and validation of the baseline microsatellite dataset with rod-and-line and estuary net fisheries of known origin has produced realistic estimates of stock composition at a regional scale. Conclusions This southern European database and supporting phylogeographic and mixed-stock analyses of net samples provide a unique tool for Atlantic salmon research and management, in both their natal rivers and the marine environment. However, the success of MSA is not uniform across the area studied, with large differences in the relative accuracy of stock composition estimates and MSA apportioning, with a much higher degree of accuracy achieved when assigning and apportioning to populations in the south of the region. More broadly, this study provides a basis for long-term salmon management across the region and confirms the value of this genetic approach for fisheries management of anadromous species.

The interaction of an array of volatile organic compounds (VOCs) termed bacterial volatile compounds (BVCs) with plants is now a major area of study under the umbrella of plant-microbe interactions. Many growth systems have been developed to determine the nature of these interactions in vitro . However, each of these systems have their benefits and drawbacks with respect to one another and can greatly influence the end-point interpretation of the BVC effect on plant physiology. To address the need for novel growth systems in BVC-plant interactions, our study investigated the use of a passively ventilated growth system, made possible via Microbox ® growth chambers, to determine the effect of BVCs emitted by six bacterial isolates from the genera Bacillus , Serratia , and Pseudomonas . Solid-phase microextraction GC/MS was utilized to determine the BVC profile of each bacterial isolate when cultured in three different growth media each with varying carbon content. 66 BVCs were identified in total, with alcohols and alkanes being the most abundant. When cultured in tryptic soy broth, all six isolates were capable of producing 2,5-dimethylpyrazine, however BVC emission associated with this media were deemed to have negative effects on plant growth. The two remaining media types, namely Methyl Red-Voges Proskeur (MR-VP) and Murashige and Skoog (M + S), were selected for bacterial growth in co-cultivation experiments with Solanum tuberosum L. cv. 'Golden Wonder.' The BVC emissions of Bacillus and Serratia isolates cultured on MR-VP induced alterations in the transcriptional landscape of potato across all treatments with 956 significantly differentially expressed genes. This study has yielded interesting results which indicate that BVCs may not always broadly upregulate expression of defense genes and this may be due to choice of plant-bacteria co-cultivation apparatus, bacterial growth media and/or strain, or likely, a complex interaction between these factors. The multifactorial complexities of observed effects of BVCs on target organisms, while intensely studied in recent years, need to be further elucidated before the translation of lab to open-field applications can be fully realized., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2021 Heenan-Daly, Coughlan, Dillane and Doyle Prestwich.)

The occurrence of alternative morphs within populations is common, but the underlying molecular mechanisms remain poorly understood. Many animals, for example, exhibit facultative migration, where two or more alternative migratory tactics (AMTs) coexist within populations. In certain salmonid species, some individuals remain in natal rivers all their lives, while others (in particular, females) migrate to sea for a period of marine growth. Here, we performed transcriptional profiling ("RNA-seq") of the brain and liver of male and female brown trout to understand the genes and processes that differentiate between migratory and residency morphs (AMT-associated genes) and how they may differ in expression between the sexes. We found tissue-specific differences with a greater number of genes expressed differentially in the liver ( n  = 867 genes) compared with the brain ( n  = 10) between the morphs. Genes with increased expression in resident livers were enriched for Gene Ontology terms associated with metabolic processes, highlighting key molecular-genetic pathways underlying the energetic requirements associated with divergent migratory tactics. In contrast, smolt-biased genes were enriched for biological processes such as response to cytokines, suggestive of possible immune function differences between smolts and residents. Finally, we identified evidence of sex-biased gene expression for AMT-associated genes in the liver ( n  = 12) but not the brain. Collectively, our results provide insights into tissue-specific gene expression underlying the production of alternative life histories within and between the sexes, and point toward a key role for metabolic processes in the liver in mediating divergent physiological trajectories of migrants versus residents., Competing Interests: The authors declare no conflict of interest., (© 2021 The Authors. Ecology and Evolution published by John Wiley & Sons Ltd.)

The functioning of marine protected areas (MPAs) designated for marine megafauna has been criticized due to the high mobility and dispersal potential of these taxa. However, dispersal within a network of small MPAs can be beneficial as connectivity can result in increased effective population size, maintain genetic diversity, and increase robustness to ecological and environmental changes making populations less susceptible to stochastic genetic and demographic effects (i.e., Allee effect). Here, we use both genetic and photo-identification methods to quantify gene flow and demographic dispersal between MPAs of a highly mobile marine mammal, the bottlenose dolphin Tursiops truncatus . We identify three populations in the waters of western Ireland, two of which have largely nonoverlapping core coastal home ranges and are each strongly spatially associated with specific MPAs. We find high site fidelity of individuals within each of these two coastal populations to their respective MPA. We also find low levels of demographic dispersal between the populations, but it remains unclear whether any new gametes are exchanged between populations through these migrants (genetic dispersal). The population sampled in the Shannon Estuary has a low estimated effective population size and appears to be genetically isolated. The second coastal population, sampled outside of the Shannon, may be demographically and genetically connected to other coastal subpopulations around the coastal waters of the UK. We therefore recommend that the methods applied here should be used on a broader geographically sampled dataset to better assess this connectivity.

Understanding the extent, scale and genetic basis of local adaptation (LA) is important for conservation and management. Its relevance in salmonids at microgeographic scales, where dispersal (and hence potential gene flow) can be substantial, has however been questioned. Here, we compare the fitness of communally reared offspring of local and foreign Atlantic salmon Salmo salar from adjacent Irish rivers and reciprocal F1 hybrid crosses between them, in the wild 'home' environment of the local population. Experimental groups did not differ in wild smolt output but a catastrophic flood event may have limited our ability to detect freshwater performance differences, which were evident in a previous study. Foreign parr exhibited higher, and hybrids intermediate, emigration rates from the natal stream relative to local parr, consistent with genetically based behavioural differences. Adult return rates were lower for the foreign compared to the local group. Overall lifetime success of foreigners and hybrids relative to locals was estimated at 31% and 40% (mean of both hybrid groups), respectively. The results imply a genetic basis to fitness differences among populations separated by only 50 km, driven largely by variation in smolt to adult return rates. Hence even if supplementary stocking programs obtain broodstock from neighbouring rivers, the risk of extrinsic outbreeding depression may be high.

We tested how variation at a gene of adaptive importance, MHC class I (UBA), in a wild, endemic Salmo trutta population compared to that in both a previously studied non-native S. trutta population and a co-habiting Salmo salar population (a sister species). High allelic diversity is observed and allelic divergence is much higher than that noted previously for co-habiting S. salar. Recombination was found to be important to population-level divergence. The α1 and α2 domains of UBA demonstrate ancient lineages but novel lineages are also identified at both domains in this work. We also find examples of recombination between UBA and the non-classical locus, ULA. Evidence for strong diversifying selection was found at a discrete suite of S. trutta UBA amino acid sites. The pattern was found to contrast with that found in re-analysed UBA data from an artificially stocked S. trutta population.

The analysis of stranding events and the application of molecular markers can be powerful tools to study cryptic biological aspects of delphinid species that occur mainly in open ocean habitat. In the present study, we investigated nuclear and mitochondrial genetic variability of Atlantic white-sided dolphins that stranded from 1990 to 2006 (n = 42) along the west coast of Ireland, using 8 microsatellite loci and 599 bp of the mitochondrial DNA control region. Results from both classes of markers are concordant with the hypothesis of a large random-mating population of white-sided dolphins along the west coast of Ireland. In addition, the analyses of 2 live mass stranding events (19 and 5 individuals, respectively) revealed that dolphins within each group were mainly unrelated to each other, suggesting dispersal of both sexes from the natal group (i.e., no natal phylopatry). Parentage analyses allowed the identification of mother-offspring pairs but ruled out all adult males as possible fathers. In combination with data on age of individuals, these results confirmed previous knowledge on life-history parameters, with sexually mature females ranging between 11 and 15 years of age and an interbirth interval of at least 2 years. The present study provides novel information on population and group composition of Atlantic white-sided dolphins along the west coast of Ireland, where population and social structure of the species are still poorly understood.

Background: Anadromous migratory fish species such as Atlantic salmon (Salmo salar) have significant economic, cultural and ecological importance, but present a complex case for management and conservation due to the range of their migration. Atlantic salmon exist in rivers across the North Atlantic, returning to their river of birth with a high degree of accuracy; however, despite continuing efforts and improvements in in-river conservation, they are in steep decline across their range. Salmon from rivers across Europe migrate along similar routes, where they have, historically, been subject to commercial netting. This mixed stock exploitation has the potential to devastate weak and declining populations where they are exploited indiscriminately. Despite various tagging and marking studies, the effect of marine exploitation and the marine element of the salmon lifecycle in general, remain the "black-box" of salmon management. In a number of Pacific salmonid species and in several regions within the range of the Atlantic salmon, genetic stock identification and mixed stock analysis have been used successfully to quantify exploitation rates and identify the natal origins of fish outside their home waters - to date this has not been attempted for Atlantic salmon in the south of their European range., Results: To facilitate mixed stock analysis (MSA) of Atlantic salmon, we have produced a baseline of genetic data for salmon populations originating from the largest rivers from Spain to northern Scotland, a region in which declines have been particularly marked. Using 12 microsatellites, 3,730 individual fish from 57 river catchments have been genotyped. Detailed patterns of population genetic diversity of Atlantic salmon at a sub-continent-wide level have been evaluated, demonstrating the existence of regional genetic signatures. Critically, these appear to be independent of more commonly recognised terrestrial biogeographical and political boundaries, allowing reporting regions to be defined. The implications of these results on the accuracy of MSA are evaluated and indicate that the success of MSA is not uniform across the range studied; our findings indicate large differences in the relative accuracy of stock composition estimates and MSA apportioning across the geographical range of the study, with a much higher degree of accuracy achieved when assigning and apportioning to populations in the south of the area studied. This result probably reflects the more genetically distinct nature of populations in the database from Spain, northwest France and southern England. Genetic stock identification has been undertaken and validation of the baseline microsatellite dataset with rod-and-line and estuary net fisheries of known origin has produced realistic estimates of stock composition at a regional scale., Conclusions: This southern European database and supporting phylogeographic and mixed-stock analyses of net samples provide a unique tool for Atlantic salmon research and management, in both their natal rivers and the marine environment. However, the success of MSA is not uniform across the area studied, with large differences in the relative accuracy of stock composition estimates and MSA apportioning, with a much higher degree of accuracy achieved when assigning and apportioning to populations in the south of the region. More broadly, this study provides a basis for long-term salmon management across the region and confirms the value of this genetic approach for fisheries management of anadromous species.

Contemporary genetic structure of Atlantic salmon (Salmo salar L.) in the River Moy in Ireland is shown here to be strongly related to landscape features and population demographics, with populations being defined largely by their degree of physical isolation and their size. Samples of juvenile salmon were collected from the 17 major spawning areas on the river Moy and from one spawning area in each of five smaller nearby rivers. No temporal allele frequency differences were observed within locations for 12 microsatellite loci, whereas nearly all spatial samples differed significantly, suggesting that each was a separate population. Bayesian clustering and landscape genetic analyses suggest that these populations can be combined hierarchically into five genetically informative larger groupings. Lakes were found to be the single most important determinant of the observed population structure. Spawning area size was also an important factor. The salmon population of the closest nearby river resembled genetically the largest Moy population grouping. In addition, we showed that anthropogenic influences on spawning habitats, in this case arterial drainage, can affect relationships between populations. Our results show that Atlantic salmon biodiversity can be largely defined by geography, and thus, knowledge of landscape features (for example, as characterized within Geographical Information Systems) has the potential to predict population structure in other rivers without an intensive genetic survey, or at least to help direct sampling. This approach of combining genetics and geography, for sampling and in subsequent statistical analyses, has wider application to the investigation of population structure in other freshwater/anadromous fish species and possibly in marine fish and other organisms.