The effect of genetic and environmental variation on metabolic gene expression

What is the relationship between genetic or environmental variation and the variation in messenger RNA (mRNA) expression? To address this, microarrays were used to examine the effect of genetic and environmental variation on cardiac mRNA expression for metabolic genes in three groups of Fundulus heteroclitus: (i) individuals sampled in the field (field), (ii) field individuals acclimated for 6 months to laboratory conditions (acclimated), or (iii) individuals bred for 10 successive generations in a laboratory environment (G10). The G10 individuals have significantly less genetic variation than individuals obtained in the field and had a significantly lower variation in mRNA expression across all genes in comparison to the other two groups (P = 0.001). When examining the gene specific variation, 22 genes had variation in expression that was significantly different among groups with lower variation in G10 individuals than in acclimated individuals. Additionally, there were fewer genes with significant differences in expression among G10 individuals vs. either acclimated or field individuals: 66 genes have statistically different levels of expression vs. 107 or 97 for acclimated or field groups. Based on the permutation of the data, these differences in the number of genes with significant differences among individuals within a group are unlikely to occur by chance (P < 0.01). Surprisingly, variation in mRNA expression in field individuals is lower than in acclimated individuals. Relative to the variation among individual within a group, few genes have significant differences in expression among groups (seven, 2.3%) and none of these are different between acclimated and field individuals. The results support the concept that genetic variation affects variation in mRNA expression and also suggests that temporal environmental variation associated with estuarine environments does not increase the variation among individuals or add to the differences among groups.     

Genetic variation in Atlantic salmon, Salmo salar L., within the Tamar catchment in south-west England

Electrophoretic analysis of enzymes in 383 juvenile Atlantic salmon, Salmo salar L., within the Tamar catchment (south-west England) revealed significant genetic differences at the IDHP-3* locus between the three tributaries studied. Aspects of temporal and spatial variation, and management policy within catchments, are discussed.     

Genetic isolation of populations of the gammaridean amphipod, Corophium volutator, in the Bay of Fundy, Canada

Selection experiments suggest that evolutionary modifications in amphipod demography can respond to local environmental changes and that local races of amphipods may be common. We tested this hypothesis in mudflat populations of Corophium volutator in the Bay of Fundy, Canada. Due to the unique topography of the Bay of Fundy, distinctive environmental conditions are prevalent in different branches of the Bay, while the impact of shorebird predation has also been shown to vary between populations. Several hypotheses have been suggested to explain ecological evidence which indicates that Corophium volutator (Pallas), a common amphipod crustacean, exhibits extensive life history variation in Bay of Fundy populations. We used RAPD-PCR techniques to examine populations of C. volutator in an investigation of genetic isolation in marine environments. Our data suggest that variation in selection pressures have played a significant role in the genetic divergence of populations of C. volutator in the Bay of Fundy.     

Liver-specific and seasonal expression of transgenic Atlantic salmon harboring the winter flounder antifreeze protein gene

We have analyzed the inheritance and expression of a line of transgenic salmon harboring the antifreeze protein gene from the winter flounder. The genomic clone 2A-7 coding for a major liver-type antifreeze protein gene (wflAFP-6) was integrated into the salmon genome. From a transgenic founder (# 1469), an F3 generation was produced. In this study, southern blot analysis showed that only one copy of the antifreeze protein transgene was integrated into a unique site in F3 transgenic fish. The integration site was cloned and characterized. Northern analysis indicated that the antifreeze protein mRNA was only expressed in the liver and showed seasonal variation. All of the F3 offspring contained similar levels of the antifreeze protein precursor protein in the sera and the sera of these offspring showed a characteristic hexagonal ice crystal pattern indicating the presence of antifreeze activity. In addition, the antifreeze protein precursor protein level was found to vary with the season, being highest in the month of November and lowest in May. This study had demonstrated a tissue-specific and stable expression of the antifreeze protein transgene in the F3 generation of the transgenic salmon 1469 line.     

Genetic variation in immune parameters and associations to survival in Atlantic salmon

Lysozyme activity, haemolytic activity, total level of IgM, and levels of antibodies against A-layer from Aeromonas salmonicida and O-antigen from Vibrio salmonicida , respectively, were determined in 77 full-sib groups of Atlantic salmon in order to evaluate their possible use as immune parameters for indirect selection to improve disease resistance. Fish from parallel full-sib groups had previously been challenged with Aeromonas salmonicida (causing furunculosis), Renibacterium salmoninarum (causing bacterial kidney disease, BKD) and Vibrio salmonicida (causing cold-water vibriosis). Heritabilities were estimated for each of the immune parameters and correlations between the least square means of the full-sib groups for the different immune parameters and survival rates in the parallel full-sib groups were determined. A significant genetic variation in lysozyme activity was found, as well as an apparent genetic association between low lysozyme activity and high survival rates. Low heritabilities and low univariate correlations with survival in the full-sib groups were estimated for all of the other immune parameters. An analysis of the multivariate associations between the full-sib mean values of the complete set of immune parameters, and survival rates in the parallel full-sib groups in each of the challenge tests, revealed that, at low levels of lysozyme activity and with low antibody titres against V. salmonicida O-antigen, increased IgM levels seemed to increase survival from furunculosis.     

Genetic variation within and among domesticated Atlantic salmon broodstocks in British Columbia, Canada

Atlantic salmon have been reared in the British Columbia, Canada aquaculture industry since the early 1980s. No breeding programmes spanned the entire production period and pedigree records were not kept for broodstocks prior to or since importation. Of the three recognized industry strains, two are of European ancestry ('Mowi' from Norway and 'McConnell' from Scotland) and one is of North American heritage ('Cascade' from Gaspe, Quebec). We evaluated the amount and distribution of genetic variation within industry broodstocks by surveying microsatellite variation at 11 loci in 20 broodstock groups sampled from major production facilities. Allelic richness averaged 10.9 (range 5.8-13.8), compared with a value of 20.3 obtained for a North American wild population. Pairwise genetic distances (D(S)) between samples within strains were generally less than those between strains, with samples attributed to the same strain clustering together in a neighbour-joining dendrogram. Nevertheless, average distances between samples within the European strains were high (0.41 for Mowi; 0.71 for McConnell) but lower (0.06) for the Cascade strain. The reduced intra-sample and increased intra-strain genetic variation observed for the BC domesticated samples compared with wild populations was similar to observations for European domesticated Atlantic salmon. Evidence of introgression of the Cascade strain into European broodstocks was provided by the presence of large Ssa202 alleles (confined to North America in wild populations) in some Mowi and McConnell samples. Introgression likely also contributed to the decreased intercontinental genetic distance for the domesticated samples of this study compared with that observed for wild populations.     

Genetic variation at the Me-2 locus in the Atlantic salmon within and between rivers: evidence for its selective maintenance

Spatial variation at the diallelic Me-2 locus in the Atlantic salmon, Salmo salar L., was analysed using data from 95 river basins. Gene diversity was apportioned as follows: 63% within samples, 20% between North America and Europe, 14% between regions within continents and 3% within and among rivers within regions. On both continents the variation between rivers was clinal with latitude and highly correlated with summer temperatures. The correlation was detectable within and between rivers. These correlations strongly suggest that variation at the locus is subject to the direct or indirect effects of natural selection, and that caution is required when interpreting between-location differentiation at the locus as evidence for distinct stocks.     

Genetic variation at enzyme loci in the southernmost European populations of Atlantic salmon

Genetic variation was studied at 8 allozyme loci in six severely endangered wild Spanish populations of Salmo salar located at the southernmost geographical limit of European Atlantic salmon. Low levels of variation were detected and no significant deviations from Hardy–Weinberg equilibrium were found.     

A critical review of adaptive genetic variation in Atlantic salmon: implications for conservation

Here we critically review the scale and extent of adaptive genetic variation in Atlantic salmon (Salmo salar L.), an important model system in evolutionary and conservation biology that provides fundamental insights into population persistence, adaptive response and the effects of anthropogenic change. We consider the process of adaptation as the end product of natural selection, one that can best be viewed as the degree of matching between phenotype and environment. We recognise three potential sources of adaptive variation: heritable variation in phenotypic traits related to fitness, variation at the molecular level in genes influenced by selection, and variation in the way genes interact with the environment to produce phenotypes of varying plasticity. Of all phenotypic traits examined, variation in body size (or in correlated characters such as growth rates, age of seaward migration or age at sexual maturity) generally shows the highest heritability, as well as a strong effect on fitness. Thus, body size in Atlantic salmon tends to be positively correlated with freshwater and marine survival, as well as with fecundity, egg size, reproductive success, and offspring survival. By contrast, the fitness implications of variation in behavioural traits such as aggression, sheltering behaviour, or timing of migration are largely unknown. The adaptive significance of molecular variation in salmonids is also scant and largely circumstantial, despite extensive molecular screening on these species. Adaptive variation can result in local adaptations (LA) when, among other necessary conditions, populations live in patchy environments, exchange few or no migrants, and are subjected to differential selective pressures. Evidence for LA in Atlantic salmon is indirect and comes mostly from ecological correlates in fitness-related traits, the failure of many translocations, the poor performance of domesticated stocks, results of a few common-garden experiments (where different populations were raised in a common environment in an attempt to dissociate heritable from environmentally induced phenotypic variation), and the pattern of inherited resistance to some parasites and diseases. Genotype x environment interactions occurr for many fitness traits, suggesting that LA might be important. However, the scale and extent of adaptive variation remains poorly understood and probably varies, depending on habitat heterogeneity, environmental stability and the relative roles of selection and drift. As maladaptation often results from phenotype-environment mismatch, we argue that acting as if populations are not locally adapted carries a much greater risk of mismanagement than acting under the assumption for local adaptations when there are none. As such, an evolutionary approach to salmon conservation is required, aimed at maintaining the conditions necessary for natural selection to operate most efficiently and unhindered. This may require minimising alterations to native genotypes and habitats to which populations have likely become adapted, but also allowing for population size to reach or extend beyond carrying capacity to encourage competition and other sources of natural mortality.     

Population genetic variation in genome-wide gene expression

Evolutionary biologists seek to understand which traits display variation, are heritable, and influence differential reproduction, because such traits respond to natural selection and underlie organic evolution. Selection acts upon individual differences within a population. Whether individual differences within a natural population include variation in gene expression levels has not yet been addressed on a genome-wide scale. Here we use DNA microarray technology for measuring comparative gene expression and a refined statistical analysis for the purpose of comparing gene expression levels in natural isolates of the wine yeast Saccharomyces cerevisiae. A method for the Bayesian analysis of gene expression levels is used to compare four natural isolates of S. cerevisiae from Montalcino, Italy. Widespread variation in amino acid metabolism, sulfur assimilation and processing, and protein degradation-primarily consisting of differences in expression level smaller than a factor of 2-is demonstrated. Genetic variation in gene expression among isolates from a natural population is present on a genomic scale. It remains to be determined what role differential gene expression may play in adaptation to new or changing environments.     

A study of temporal genetic variation in a natural population of Atlantic salmon in the River Bush, Northern Ireland

Temporal genetic variation in River Bush Atlantic salmon was low and much less than among geographically discrete samples reported from elsewhere.     

Temporal and spatial variation in growth of juvenile Atlantic salmon

Spatial and temporal variation in length‐at‐age and environmental factors affecting variation in growth rate of juvenile Atlantic salmon Salmo salar were studied using data from a long‐term study in the River Stjørdalselva, central Norway. Mean annual instantaneous growth rate among 1+ and 2+year juvenile Atlantic salmon varied between 0·59 and 1·50 g g⁻¹ year⁻¹ and mean instantaneous daily growth rate of young‐of‐the‐year (YOY) varied between 0·013 and 0·033 g g⁻¹ day⁻¹. Between year variation in growth was larger than the within year intra‐watercourse spatial variation. For YOY and 1+year Atlantic salmon, a major part of the observed between year variation in growth rates was explained by variation in mean daily water discharge and spring temperature. For 2+year juvenile Atlantic salmon, mean daily water discharge and cohort density were the only variables to significantly explain variation in growth rates. A large part of the within water‐course spatial variation could not be explained by temperature variations and juvenile Atlantic salmon in the uppermost areas of the river, experiencing the lowest ambient temperatures during the growth period, displayed the highest growth rates. Within the baselines set by temperature, biotic and abiotic factors connected to water flow regime and variation in food availability are suggested to be a major determinants of the temporal and spatial variation in juvenile Atlantic salmon growth rates.     

Variation within and among species in gene expression: raw material for evolution

Heritable variation in regulatory or coding regions is the raw material for evolutionary processes. The advent of microarrays has recently promoted examination of the extent of variation in gene expression within and among taxa and examination of the evolutionary processes affecting variation. This review examines these issues. We find: (i) microarray-based measures of gene expression are precise given appropriate experimental design; (ii) there is large inter-individual variation, which is composed of a minor nongenetic component and a large heritable component; (iii) variation among populations and species appears to be affected primarily by neutral drift and stabilizing selection, and to a lesser degree by directional selection; and (iv) neutral evolutionary divergence in gene expression becomes nonlinear with greater divergence times due to functional constraint. Evolutionary analyses of gene expression reviewed here provide unique insights into partitioning of regulatory variation in nature. However, common limitations of these studies include the tendency to assume a linear relationship between expression divergence and species divergence, and failure to test explicit hypotheses that involve the ecological context of evolutionary divergence.     

Amount and distribution of biochemical-genetic variation among wild populations and a hatchery stock of Atlantic salmon, Salmo salar L., from north-east Ireland

The effects of tributyltin (TBT) compounds on gill morphology were examined in the mummichog, Fundulus heteroclitus , in 96-h LC50 and 6-week sublethal exposures. Morphometry was used for the identification and quantification of effects with the light microscope. A 96-h LC50 of 17.2 μg 1 ¹ was determined. Morphometric analysis of gill tissues revealed hypertrophy of the lamellar epithelium in fish exposed to 17.2 μg 1–1. Relative diffusing capacity was significantly decreased (−41 %); ( P <0.05, ANOVA, Bonferroni t -test). At 35.6 μg 1⁻¹, TBT exposure resulted in a significant reduction (− 40%) in the volume of the lamellar blood channels. Both of these observations occurred in fish that showed signs of acute poisoning including loss of equilibrium. In fish exposed to sublethal concentrations of 0.105–2.000 μg TBT 1⁻¹ for 6 weeks, there were no pathological changes in the gill. There were no treatment-related changes in the surface morphology of the gills of fish from both experiments upon scanning electron microscopic examination. Although gill pathology was observed in acutely toxic exposures, it does not appear to be a major mechanism of TBT toxicity.     

Conservation of gene function in behaviour

Behaviour genetic research has shown that a given gene or gene pathway can influence categorically similar behaviours in different species. Questions about the conservation of gene function in behaviour are increasingly tractable. This is owing to the surge of DNA and 'omics data, bioinformatic tools, as well as advances in technologies for behavioural phenotyping. Here, we discuss how gene function, as a hierarchical biological phenomenon, can be used to examine behavioural homology across species. The question can be addressed independently using different levels of investigation including the DNA sequence, the gene's position in a genetic pathway, spatial-temporal tissue expression and neural circuitry. Selected examples from the literature are used to illustrate this point. We will also discuss how qualitative and quantitative comparisons of the behavioural phenotype, its function and the importance of environmental and social context should be used in cross-species comparisons. We conclude that (i) there are homologous behaviours, (ii) they are hard to define and (iii) neurogenetics and genomics investigations should help in this endeavour.     

Genetic analysis of fish genomes and populations: allozyme variation within and among Atlantic salmon from Downeast rivers of Maine

Analysis of genetic variation within and among samples of naturally produced Atlantic salmon ( n  = 372) from 7 Maine (U.S.A.) and one Canadian river were conducted based on 54 allozyme loci. Eight of the 54 loci proved polymorphic, and estimated heterozygosities ( H _S) based on all loci ranged from 0·012 to 0·026 (mean = 0·021, s . e . = 0·002). Only one of 56 tests revealed genotypic proportions that deviated significantly from Hardy–Weinberg expectations. Genetic distances ( D ) between samples ranged from 0·002 to 0·022. No obvious association existed between genetic and geographic distances. Cluster analysis of genetic distances revealed the Dennys River sample as the most differentiated when all samples were included in the analysis, though bootstrap support of the cluster analysis was generally weak. G ‐tests revealed significant differences in allele frequencies among samples at five of the polymorphic loci, and the G ‐value summed over all loci also indicated significant differences among samples. F _ST values indicated that 3·4% of the total genetic diversity was due to variability among samples, while 96·6% was due to variability within samples. These results indicate that the Atlantic salmon analyzed in this study had levels of genetic variability and differentiation among samples comparable to native populations from other areas collected across a similar geographic range.