Interlocus variance of F(ST) provides evidence for directional selection over an olfactory receptor gene in Coho salmon (Oncorhynchus kisutch) populations

Coho salmon (Oncorhynchus kisutch) utilize olfactory cues to recognize and home to natal streams during spawning migrations. Chemically distinct river systems may promote directional selection for appropriately tuned olfactory receptor repertoires among Coho populations. Here, we use F_ST outlier methods to test for a signal of selection over olfactory receptor gene-linked markers, characterized in Coho populations from four geographically proximate, but ecologically distinct rivers. We report evidence for directional selection over one such marker, OkiOR3001, and document substantially higher levels of genetic structure among Coho populations from Oregon coastal lakes than previously observed with putatively neutral microsatellites.     

Effect of natural selection on the duplicated lysyl oxidase gene in Atlantic salmon

We examined the polymorphism of the lysyl oxidase (LOX) locus, involved in the initiation of muscle collagen cross-linking, in three populations of Atlantic salmon with different life histories and growth rates and compared it with a closely related species (rainbow trout). Up to four alleles were observed per individual, probably as a consequence of the tetraploid origin of the salmonid genome. We found high polymorphism in the LOX locus (16 alleles expressed in total and several low frequency private alleles) in two natural Atlantic salmon populations and extremely reduced diversity in a farmed population (3 alleles) with low density of collagen crosslinks. We also assessed the relative role of selection in maintaining LOX genetic variability in Atlantic salmon. Results from several neutrality tests suggest that selection is playing a role in shaping diversity at the LOX locus. Positive selection was inferred by three different likelihood phylogeny-based methods and one selected site, identified by all three different methods (PAML, FEL and REL) was located within the “copper-talon” characteristic of LOX proteins. We suggest that the retention of four alleles in the salmon LOX locus could be related to its multiple functions.     

Cloning of the Atlantic salmon (Salmo salar) estrogen receptor-alpha gene

A cDNA clone encoding most of an Atlantic salmon (Salmo salar) estrogen receptor (ER) was obtained from a liver cDNA library and the remainder of the coding sequence from the gene was isolated from a genomic library. Sequence comparisons showed that the cloned gene represents ER-alpha. Expression of the ER-alpha gene in male and female salmon parr was analysed by RT-PCR. Highest expression was found in brain and liver, with lower levels of ER-alpha mRNA present in all other tissues tested. There was little difference in expression of ER-alpha between male and female.     

Genomic signatures of local directional selection in a high gene flow marine organism; the Atlantic cod (Gadus morhua)

Background  

Marine fishes have been shown to display low levels of genetic structuring and associated high levels of gene flow, suggesting shallow evolutionary trajectories and, possibly, limited or lacking adaptive divergence among local populations. We investigated variation in 98 gene-associated single nucleotide polymorphisms (SNPs) for evidence of selection in local populations of Atlantic cod (Gadus morhua L.) across the species distribution.     

Natural selection acts on Atlantic salmon major histocompatibility (MH) variability in the wild

Pathogen-driven balancing selection is thought to maintain polymorphism in major histocompatibility (MH) genes. However, there have been few empirical demonstrations of selection acting on MH loci in natural populations. To determine whether natural selection on MH genes has fitness consequences for wild Atlantic salmon in natural conditions, we compared observed genotype frequencies of Atlantic salmon (Salmo salar) surviving in a river six months after their introduction as eggs with frequencies expected from parental crosses. We found significant differences between expected and observed genotype frequencies at the MH class II alpha locus, but not at a MH class I-linked microsatellite or at seven non-MH-linked microsatellite loci. We therefore conclude that selection at the MH class II alpha locus was a result of disease-mediated natural selection, rather than any demographic event. We also show that survival was associated with additive allelic effects at the MH class II alpha locus. Our results have implications for both the conservation of wild salmon stocks and the management of disease in hatchery fish. We conclude that natural or hatchery populations have the best chance of dealing with episodic and variable disease challenges if MH genetic variation is preserved both within and among populations.     

Cloning and characterisation of a putative ST2L homologue from Atlantic salmon (Salmo salar)

The ST2L receptor is a member of the interleukin-1 (IL-1) receptor family and has previously been cloned from human, mouse, rat and chicken. This orphan receptor has no known physiological role but has been implicated in T helper cell type 2 effector function. We describe in this report the cloning and characterisation of a cDNA encoding a homologue of ST2L in Atlantic salmon (Salmo salar). The salmon ST2L cDNA is 2364bp in length and has an open reading frame encoding a polypeptide of 582 amino acids. Similar to other members of the IL-1 receptor (IL-1R) family, the predicted protein has a potential signal peptide, extracellular immunoglobulin-like domains, a short transmembrane region and a characteristic cytoplasmic Toll-IL-1R domain. The predicted protein shows 33% identity and 44% similarity to the chicken ST2L homologue. Phylogenetic analyses cluster the putative salmon ST2L with the chicken and the mammalian ST2L homologues, away from the other members of the IL-1R family. Salmon ST2L is constitutively expressed in brain, white and red blood cells, head kidney, liver, gills and muscle, with highest level of expression in spleen. In vivo stimulation of salmon with lipopolysaccaride does not appear to have a significant effect on expression of the ST2L homologue.     

Comparison of F(ST) outlier tests for SNP loci under selection

Genome scans with many genetic markers provide the opportunity to investigate local adaptation in natural populations and identify candidate genes under selection. In particular, SNPs are dense throughout the genome of most organisms and are commonly observed in functional genes making them ideal markers to study adaptive molecular variation. This approach has become commonly employed in ecological and population genetics studies to detect outlier loci that are putatively under selection. However, there are several challenges to address with outlier approaches including genotyping errors, underlying population structure and false positives, variation in mutation rate and limited sensitivity (false negatives). In this study, we evaluated multiple outlier tests and their type I (false positive) and type II (false negative) error rates in a series of simulated data sets. Comparisons included simulation procedures (FDIST2, ARLEQUIN v.3.5 and BAYESCAN) as well as more conventional tools such as global F(ST) histograms. Of the three simulation methods, FDIST2 and BAYESCAN typically had the lowest type II error, BAYESCAN had the least type I error and Arlequin had highest type I and II error. High error rates in Arlequin with a hierarchical approach were partially because of confounding scenarios where patterns of adaptive variation were contrary to neutral structure; however, Arlequin consistently had highest type I and type II error in all four simulation scenarios tested in this study. Given the results provided here, it is important that outlier loci are interpreted cautiously and error rates of various methods are taken into consideration in studies of adaptive molecular variation, especially when hierarchical structure is included.     

Stable isotope analyses of otoliths in identification of hatchery origin of Atlantic salmon (Salmo salar) in Maine

We conducted stable oxygen and carbon isotope analyses for otoliths of Atlantic salmon (Salmo salar), in an attempt to develop a reference database on isotopic variability among private and federal hatcheries in Maine which currently support the salmon aquaculture industry and recovery of endangered populations. During the first phase of our study, we collected 40–50 sagittal otoliths of juvenile Atlantic salmon from each of the five hatcheries and analyzed for stable oxygen and carbon isotope ratios (¹⁸O/¹⁶O or δ¹⁸O, and ¹³C/¹²C or δ¹³C). Combination of δ¹⁸O and δ¹³C signatures in otoliths showed that the five hatcheries can be clearly separated and chemically distinguished. By identifying stable isotopic variations of otoliths from different hatchery settings, we were able to establish some isotopic criteria or standards to assign a likelihood that an individual Atlantic salmon came from a specific hatchery within the reference database. If successful, a diagnostic tool that can provide definitive information on identification of the hatchery origin could serve as a novel marking technique, and the chemical method may provide a more effective alternative to DNA analysis for mixed stocks. Overall our isotopic data from otoliths support the hypothesis that there are detectable differences between the five hatcheries, and multiple statistical analyses indicated that we can correctly distinguish individual Atlantic salmon into a hatchery with high confidence.     

A survey of genes in the Atlantic salmon (Salmo salar) as identified by expressed sequence tags

We describe the construction and quality analysis of six cDNA libraries from the liver, ovary, testis, brain, spleen and muscle tissues of adult Atlantic salmon. The cDNA libraries were then screened with total cDNA probes to catalogue clones representing the abundant and rare mRNA populations in each tissue. Subsequently, the 5'-terminal DNA sequences of 1152 cDNA clones, composed of 96 clones from each of the abundant and rare mRNA populations in the six tissues, were determined. Bioinformatic analysis revealed that 510 (50%) of the salmon expressed sequence tags (ESTs) of sufficient length showed significant homology to previously identified genes from salmonid and other species, while 517 (50%) of salmon ESTs were unidentified or novel. After accounting for multi-EST redundancy, the 510 identified ESTs provided DNA sequence markers for 178 salmon genes which are listed in terms of tissue of origin and mRNA abundance class.     

Beyond MHC: signals of elevated selection pressure on Atlantic salmon (Salmo salar) immune‐relevant loci

Using Atlantic salmon (Salmo salar) as a model system, we investigated whether 18 microsatellites tightly linked to immune‐relevant genes have experienced different selection pressures than 76 loci with no obvious association with immune function. Immune‐relevant loci were identified as outliers by two outlier tests significantly more often than nonimmune linked loci (22% vs. 1.6%). In addition, the allele frequencies of immune relevant markers were more often correlated with latitude and temperature. Combined, these results support the hypothesis that immune‐relevant loci more frequently exhibit footprints of selection than other loci. They also indicate that the correlation between immune‐relevant loci and latitude may be due to temperature‐induced differences in pathogen‐driven selection or some other environmental factor correlated with latitude.     

Predictions of response to selection caused by angling in a wild population of Atlantic salmon (Salmo salar)

1. Recreational angling activities in wild populations of Atlantic salmon may induce a selection pressure towards a reduction in body size and length if the angling season coincides with the return of the largest sea age fish class. 2. Using estimates of heritability for growth traits and estimates of the selection pressure from angling operating on growth, we predicted the response to selection expected to occur in a wild population of Atlantic salmon. 3. The dataset used here comprised individuals from two consecutive generations (parents and offspring) from the River Bidasoa (NW Spain). Offspring were assigned to parents using six highly polymorphic microsatellite loci. Use of restricted maximum likelihood methodology and the animal model allowed us to estimate the heritability for body length and body weight as well as their genetic correlation. 4. Estimated heritabilities (0.32 ± 0.12 for length and 0.32 ± 0.11 for weight) and selection pressure caused by angling were used to obtain predictions of response to selection because of angling. Our results suggested a decline of 1.9 mm in body length and 103.3 g in body weight per generation because of angling pressure. 5. The results derived from this study suggest that the angling season should be annually delayed in order to avoid selective angling of the multi‐year class and further reductions in body weight and length.     

Genetic stock identification of Atlantic salmon (Salmo salar) populations in the southern part of the European range

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 two myostatin genes of Atlantic salmon (Salmo salar) are expressed in a variety of tissues.

Two myostatin isoforms were identified in Atlantic salmon (Salmo salar) by RT-PCR, and genomic sequences encoding this negative muscle growth factor were for the first time isolated from a nonmammalian species. Salmon myostatin isoform I is transcribed in white skeletal muscle as a 2346-nucleotide mRNA species that encodes a precursor protein of 373 amino acids. Salmon myostatin I shows 93% sequence identity with isoform II which was isolated from white muscle as a partial cDNA sequence of 1409 nucleotides. In contrast to the restricted gene expression of myostatin in mammals, salmon myostatin I and II mRNAs were identified by RT-PCR in multiple tissues, including white muscle, intestine, brain, gills, tongue and eye. In addition, isoform I mRNA was found in red skeletal muscle, heart, spleen, and ovarian tissue. Using polyclonal antibodies against both isoforms, a 55-kDa precursor protein was detected by Western blot analysis in the red and white skeletal muscle, heart, intestine, and brain. Immunoreactive peptides of 35-40 kDa were identified in the gills, tongue, spleen, and head kidney, while the 25-kDa mature myostatin was found in the eye and serum, and in vitro expressed in rabbit reticulocyte lysate. Salmon myostatin was immunohistochemically localized in the sarcoplasma of red and white muscle fibres, in intestinal epithelial cells, at the basis of the branchial primary lamellae, and in odontoblasts and ameloblasts of the tongue teeth. The results indicate that the role of fish myostatin may not be restricted to muscle growth regulation, but may have additional functions similar to the growth/differentiation factor-11 in mammals.     

Rapidly evolving mitochondrial genome and directional selection in mitochondrial genes in the parasitic wasp nasonia (hymenoptera: pteromalidae)

We sequenced the nearly complete mtDNA of 3 species of parasitic wasps, Nasonia vitripennis (2 strains), Nasonia giraulti, and Nasonia longicornis, including all 13 protein-coding genes and the 2 rRNAs, and found unusual patterns of mitochondrial evolution. The Nasonia mtDNA has a unique gene order compared with other insect mtDNAs due to multiple rearrangements. The mtDNAs of these wasps also show nucleotide substitution rates over 30 times faster than nuclear protein-coding genes, indicating among the highest substitution rates found in animal mitochondria (normally <10 times faster). A McDonald and Kreitman test shows that the between-species frequency of fixed replacement sites relative to silent sites is significantly higher compared with within-species polymorphisms in 2 mitochondrial genes of Nasonia, atp6 and atp8, indicating directional selection. Consistent with this interpretation, the Ka/Ks (nonsynonymous/synonymous substitution rates) ratios are higher between species than within species. In contrast, cox1 shows a signature of purifying selection for amino acid sequence conservation, although rates of amino acid substitutions are still higher than for comparable insects. The mitochondrial-encoded polypeptides atp6 and atp8 both occur in F0F1ATP synthase of the electron transport chain. Because malfunction in this fundamental protein severely affects fitness, we suggest that the accelerated accumulation of replacements is due to beneficial mutations necessary to compensate mild-deleterious mutations fixed by random genetic drift or Wolbachia sweeps in the fast evolving mitochondria of Nasonia. We further propose that relatively high rates of amino acid substitution in some mitochondrial genes can be driven by a "Compensation-Draft Feedback"; increased fixation of mildly deleterious mutations results in selection for compensatory mutations, which lead to fixation of additional deleterious mutations in nonrecombining mitochondrial genomes, thus accelerating the process of amino acid substitutions.     

Ubiquinone （Coenzyme Q） Biosynthesis in Chlamydophila pneumoniae AR39： Identification of the ubiD Gene

Ubiquinone is an essential electron carrier in prokaryotes.Ubiquinone biosynthesis involves atleast nine reactions in Escherichia coli.3-octaprenyl-4-hydroxybenzoate decarboxylase (UbiD) is an importantenzyme on the pathway and deletion of the ubiD gene in E.coli gives rise to ubiquinone deficiency in vivo.A protein from Chlamydophila pneumoniae AR39 had significant similarity compared with protein UbiDfrom E.coli.Based on this information,the protein-encoding gene was used to swap its counterpart inE.coli,and gene expression in resultant strain DYC was confirmed by RT-PCR.Strain DYC grew usingsuccinate as carbon source and rescued ubiquinone content in vivo,while ubiD deletion strain DYD did not.Results suggest that the chlamydial protein exerts the function of UbiD.