Population Structure In Atlantic Salmon Research Articles

Co-diversification of an intestinal Mycoplasma and its salmonid host

Understanding the evolutionary relationships between a host and its intestinal resident bacteria can transform how we understand adaptive phenotypic traits. The interplay between hosts and their resident bacteria inevitably affects the intestinal environment and, thereby, the living conditions of both the host and the microbiota. Thereby this co-existence likely influences the fitness of both bacteria and host. Whether this co-existence leads to evolutionary co-diversification in animals is largely unexplored, mainly due to the complexity of the environment and microbial communities and the often low host selection. We present the gut metagenome from wild Atlantic salmon (Salmo salar), a new wild organism model with an intestinal microbiota of low complexity and a well-described population structure, making it well-suited for investigating co-evolution. Our data reveal a strong host selection of a core gut microbiota dominated by a single Mycoplasma species. We found a clear co-diversification between the population structure of Atlantic salmon and nucleotide variability of the intestinal Mycoplasma populations conforming to expectations from co-evolution between host and resident bacteria. Our results show that the stable microbiota of Atlantic salmon has evolved with its salmonid host populations while potentially providing adaptive traits to the salmon host populations, including defence mechanisms, biosynthesis of essential amino acids, and metabolism of B vitamins. We highlight Atlantic salmon as a novel model for studying co-evolution between vertebrate hosts and their resident bacteria.

Population genetic structure of Atlantic salmon, Salmo salar L., in the River Tamar, southwest England

Abstract Population genetic studies can be useful for informing conservation and management. In Atlantic salmon, Salmo salar L., population structuring frequently occurs between river systems, but contrasting patterns occur within rivers, highlighting the need for catchment-specific studies to inform management. Here, population structure of Atlantic salmon was examined in the River Tamar, United Kingdom, using 12 microsatellite loci. Gene diversity and allelic richness ranged from 0.80 to 0.84 and from 8.96 to 10.24, respectively. Some evidence of genetic structure was found, including significant genetic differentiation between samples in different subcatchments (pairwise θ and tests of genic differentiation), results from assignment tests and a pattern of isolation by distance. Conversely, structure revealed only one population cluster, and an analysis of molecular variance showed no significant variation between subcatchments. Evidence of population bottlenecks depended on the mutation model assumed and is discussed with reference to catchment-specific studies of stock abundance. Implications for implementing management actions are considered.

Demographics and landscape features determine intrariver population structure in Atlantic salmon (Salmo salar L.): the case of the River Moy in Ireland

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.

Loss of regional population structure in Atlantic salmon, Salmo salar L., following stocking

Abstract Many wild Atlantic salmon populations have been stocked with cultured fish during the past century. To evaluate the degree and the direction of the resulting genetic changes in wild southern European populations of Atlantic salmon, the variation at microsatellite loci was examined in historical and modern scale samples from five Spanish and two French rivers. Significant genetic differentiation between neighbouring rivers, which is typical of Atlantic salmon and which existed before stocking, appears to have been lost after only a decade of stocking with fish of foreign origin. Apparent introgression of foreign-origin genes into local gene pools was detected in the populations studied. These results indicate that stocking risks the loss of genetic diversity in wild salmon populations.

Atlantic salmon change the expression of odorant receptor genes to learn the smell of home

The ability of salmon to home to their natal stream to spawn has long intrigued biologists. It is known that olfaction is crucial to accurate homing, and that the transition between freshwater and marine environments (the parr‐smolt transformation; PST) is a period of increased olfactory sensitivity and learning, resulting in a permanent memory of natal site odours that is retained in peripheral sensory neurons. These odours are then used as cues by sexually maturing fish on their homeward migration. We have used molecular techniques to demonstrate transient increases in expression of odourant receptor transcripts coincident with PST. Both olfactory and vomeronasal receptors are involved, which suggests that the fish learn both environmental odours and semiochemicals (pheromones). Receptor expression varies between families and changes over time indicating both genetic differences in odour stimuli and multiple periods of olfactory sensitivity. We hypothesise that changes in gene expression may have a role in maintaining population structure in Atlantic salmon.

Population Structure of Atlantic Salmon in Maine with Reference to Populations from Atlantic Canada

Anadromous Atlantic salmon Salmo salar from 12 rivers in Maine, 3 rivers in New Brunswick, and 2 rivers each in Nova Scotia, Quebec, Newfoundland, and Labrador as well as 2 landlocked strains in Maine (N = 3,863) were genotyped at 11 microsatellite loci. Fish in the drainages of Maine's Kennebec and Penobscot rivers were genetically similar to those sampled from the 8 rivers recently listed as containing an endangered distinct population segment under the United States' Endangered Species Act. Genetic distance estimates confirm that Maine's Atlantic salmon, both landlocked and anadromous, represent a discrete population unit, genetically as independent from any Canadian population as the Canadian populations are from each other. Within Maine, the anadromous and landlocked populations were statistically distinct. Anadromous Atlantic salmon were more genetically similar among year-classes within rivers than among rivers, as would be expected if the river is the unit of population. The effective number of breeders estimated within each river is larger than the number of adults estimated from samples and redd counts over the 10-year period from 1991 to 2000.

Seasonal differences in the origin of Atlantic salmon ( Salmo salar L.) in the Norwegian Sea based on estimates from age structures and tag recaptures

To test if the population structure of Atlantic salmon ( Salmo salar L.) at the feeding areas in the Norwegian Sea north of the Faroes is stable throughout early (November–December) and late (February–March) winter, river and sea age distributions were estimated from 2350 scale samples obtained in the early and late winter during four consecutive fishing periods 1991/1992–1994/1995. The origin of recaptures of salmon tagged as smolts in different European countries were also compared between early and late winter. The fish were classified as being of wild or fish farm origin from scale characteristics, and farmed salmon were excluded from the analyses. Age compositions in samples from the four fishing periods showed consistent patterns. The average smolt age (±S.E.) was significantly lower in the early than in the late winter (2.5±0.04 and 2.7±0.03, range 1–5) as was average sea age (1.9±0.03 and 2.2±0.02, range 1–6). As salmon from southern European countries tend to smolt at an earlier age and produce more one sea-winter salmon than in northern Europe, we suggest that a significant proportion of the salmon caught in the Faroes area during early winter originate from southern European countries and that fish from northern regions appear to be more abundant in the late winter period. Recaptures in the Faroese fishery during early and late winter of salmon tagged as smolts in different countries support this.

Fine-scale population structure in Atlantic salmon from Maine's Penobscot River drainage

We report a survey of microsatellite DNAvariation in Atlantic salmon from theunimpounded lower reaches of Maine's PenobscotRiver. Our analysis indicates that Atlanticsalmon in the Penobscot River are distinct fromother populations that have little or nohistory of human-mediated repopulation,including two of its tributaries, Cove Brookand Kenduskeag Stream, another Maine river, theDucktrap, and Canada's Miramichi and Ganderrivers. Significant heterogeneity was detectedin allele frequency among all threesubpopulations sampled in the Penobscotdrainage. The high resolution of the 12-locussuite was quantified using maximum likelihoodassignment tests, which correctly identifiedthe source of 90.4–96.1% of individuals fromwithin the Penobscot drainage. Currentpopulations are clearly isolated from eachother, however we are unable to determine fromthe present data whether the populations inCove Brook and Kenduskeag Stream are recentlydiverged from populations stocked into thePenobscot River over the last century, or areaboriginal in origin. The degree of populationstructure identified in the Penobscot drainageis noteworthy in light of its lengthy historyof systematic restocking, the geographicproximity of the subpopulations, and the extentof the differentiation. Similar populationstructure on this extremely limited geographicscale could exist among Atlantic salmon runselsewhere in Maine and throughout the species'range and should be taken into account forfuture management decisions.

Ecological determinants and temporal stability of the within-river population structure in Atlantic salmon (Salmo salar L.).

A gene diversity analysis was performed using microsatellite loci in order to (i) describe the extent and pattern of population structure in Atlantic salmon (Salmo salar L.) within a river system; (ii) establish the importance of quantifying the signal:noise ratio in accurately estimating population structure; and (iii) assess the potential usefulness of two evolutionary models in explaining within-river population structure from the ecological and habitat characteristics of Atlantic salmon. We found weak, yet highly significant microscale spatial patterning after accounting for variance among temporal replicates within sites. Lower genetic distances were observed among temporal samples at four sampling sites whereas no evidence for temporal stability was observed at the other three locations. The component of genetic variance attributable to either temporal instability and/or random sampling errors was almost three times more important than the pure spatial component. This indicates that not considering signal:noise ratio may lead to an important overestimation of genetic substructuring in situations of weak genetic differentiation. This study also illustrates the usefulness of the member-vagrant hypothesis to generate a priori predictions regarding the number of subpopulations that should compose a species, given its life-history characteristics and habitat structure. On the other hand, a metapopulation model appears better suited to explain the extent of genetic divergence among subpopulations, as well as its temporal persistence, given the reality of habitat patchiness and environment instability. We thus conclude that the combined use of both models may offer a promising avenue for studies aiming to understand the dynamics of genetic structure of species found in unstable environments.

Population structure of Atlantic salmon from the Conne River, Newfoundland as determined from microsatellite DNA

Variation at four microsatellite loci was examined for three populations of Atlantic salmon Salmo salar from the Conne River, Newfoundland. Samples of wild parr were collected from the mainstem Conne River during 4 years, and from tributaries Twillick Brook and Bernard Brook during 2 years. No significant temporal variation was observed in allele frequencies at the Ssal4, Ssal97, Ssa202, and Ssa289 loci. No difference in allele frequencies was observed between parr from Bernard and Twillick brooks at any locus, but allele frequencies of mainstem Conne River parr were significantly different from those of the tributaries at Ssal4 and Ssa202, indicative of differentiation among local populations. Atlantic salmon from the Conne River system were well differentiated from those in Nova Scotia, Canada and from those in Europe.

Population structure of Atlantic salmon from the Conne River, Newfoundland as determined from microsatellite DNA

Population structure of Atlantic salmon from the Conne River, Newfoundland as determined from microsatellite DNA

Allozyme variation in populations of Atlantic salmon located throughout Europe: diversity that could be compromised by introductions of reared fish

A comprehensive understanding of the population structure of Atlantic salmon (Salmo salar L.) throughout the species range would help to determine the impact that cultured fish could have on wild populations. To help achieve this aim, Atlantic salmon samples were obtained from 14 locations throughout Europe (including Iceland) and screened for variation at 32 allozyme loci. A sample was also obtained from Canada to serve as an out-group. Seventeen allozyme loci were found to be variable in one or more of the populations studied and three, s AAT-4 * , IDDH-2 * , and m MEP-2 * were variable across the range. This is the widest-ranging study to include ESTD-2 * , FBALD-3 * , and TPI-3 * , which combined contributed 28% to the total genetic diversity detected. Genotype frequencies complied with Hardy-Weinberg expected proportions. Over all loci, highly significant heterogeneity was observed between samples. Alternate alleles segregating at ESTD-2 * were found to be largely exclusive to Europe or North America. A neighbour-joining dendrogram was constructed to visualize relationships between populations and was consistent with previous findings that revealed Baltic and European clusters, with the Canadian population being the most genetically distinct. A significant association was observed between geographic and genetic distance, which suggests the potential for local adaptation, thus highlighting the need for conservation of wild populations.

Alternative reproductive tactics in atlantic salmon: factors affecting mature parr success

In Atlantic salmon, as in most salmonids, males can mature early in the life cycle, as small freshwater fish, termed parr, and/or undergo a sea migration before maturing as full–size adults. The alternative life histories are contingent on environmental and social circumstances, such as growth rate, territory quality or any other factor that affects the individual9s state. In order to model the choice of life history in this group of commercially valuable species, it is necessary to understand not only the relative contribution of the different male types to subsequent generations, but also to know the factors that affect reproductive success in each type. In this paper we present the results of a study designed to investigate the factors that affect the reproductive success of mature parr. We used highly polymorphic minisatellite DNA markers to analyse paternity in a series of mating experiments where the number and body size of parr were manipulated. The fraction of eggs fertilized by mature parr ranged from 26 to 40 per cent, with individual parr fertilizing up to 26 per cent of the eggs. A strong positive correlation was found between parr size and reproductive success. The relative success of parr decreased with increasing parr number. Data from this and other studies on variation in the timing and degree of parr reproductive success are discussed in relation to the evolution of male mating strategies and life history in salmonids.