Predictability of multispecies competitive interactions in three populations of Atlantic salmon Salmo salar

Juvenile Atlantic salmon Salmo salar from three allopatric populations (LaHave, Sebago and Saint‐Jean) were placed into artificial streams with combinations of four non‐native salmonids: brown trout Salmo trutta, rainbow trout Oncorhynchus mykiss, Chinook salmon Oncorhynchus tshawytscha and coho salmon Oncorhynchus kisutch. Non‐additive effects, as evidenced by lower performance than predicted from weighted summed two‐species competition trials, were detected for S. salar fork length (L_F) and mass, but not for survival, condition factor or riffle use. These data support emerging theory on niche overlap and species richness as factors that can lead to non‐additive competition effects.     

Genomic arrangement of salinity tolerance QTLs in salmonids: A comparative analysis of Atlantic salmon (Salmo salar) with Arctic charr (Salvelinus alpinus) and rainbow trout (

ABSTRACT: BACKGROUND: Quantitative trait locus (QTL) studies show that variation in salinity tolerance in Arctic charr and rainbow trout has a genetic basis, even though both these species have low to moderate salinity tolerance capacities. QTL were observed to localize to homologous linkage group segments within putative chromosomal regions possessing multiple candidate genes. We compared salinity tolerance QTL in rainbow trout and Arctic charr to those detected in a higher salinity tolerant species, Atlantic salmon. The highly derived karyotype of Atlantic salmon allows for the assessment of whether disparity in salinity tolerance in salmonids is associated with differences in genetic architecture. To facilitate these comparisons, we examined the genomic synteny patterns of key candidate genes in the other model teleost fishes that have experienced three whole-genome duplication (3R) events which preceded a fourth (4R) whole genome duplication event common to all salmonid species. RESULTS: Nine linkage groups contained chromosome-wide significant QTL (AS-2, -4p, -4q, -5, -9, -12p, -12q, -14q -17q, -22, and [MINUS SIGN]23), while a single genome-wide significant QTL was located on AS-4q. Salmonid genomes shared the greatest marker homology with the genome of three-spined stickleback. All linkage group arms in Atlantic salmon were syntenic with at least one stickleback chromosome, while 18 arms had multiple affinities. Arm fusions in Atlantic salmon were often between multiple regions bearing salinity tolerance QTL. Nine linkage groups in Arctic charr and six linkage group arms in rainbow trout currently have no synteny alignments with stickleback chromosomes, while eight rainbow trout linkage group arms were syntenic with multiple stickleback chromosomes. Rearrangements in the stickleback lineage involving fusions of ancestral arm segments could account for the 21 chromosome pairs observed in the stickleback karyotype. CONCLUSIONS: Salinity tolerance in salmonids from three genera is to some extent controlled by the same loci. Synteny between QTL in salmonids and candidate genes in stickleback suggests genetic variation at candidate gene loci could affect salinity tolerance in all three salmonids investigated. Candidate genes often occur in pairs on chromosomes, and synteny patterns indicate these pairs are generally conserved in 2R, 3R, and 4R genomes. Synteny maps also suggest that the Atlantic salmon genome contains three larger syntenic combinations of candidate genes that are not evident in any of the other 2R, 3R, or 4R genomes examined. These larger synteny tracts appear to have resulted from ancestral arm fusions that occurred in the Atlantic salmon ancestor. We hypothesize that the superior hypo-osmoregulatory efficiency that is characteristic of Atlantic salmon may be related to these clusters.     

Long‐term effects of stock transfers: synergistic introgression of allochthonous genomes in salmonids

The genus Salmo was employed as a model to study introgression of genes between species due to secondary contacts. Seven microsatellite loci, the LDH‐C1* locus and the 5S ribosomal DNA were studied. Results showed the mutually enhanced introgression of allochthonous genomes into southern European salmonids. This phenomenon appears to go beyond a simple consequence of the altered behaviour of domestic individuals. Invasions of autochthonous genomes by allochthonous genes would be enhanced by human activities such as stock transfers, which would simultaneously promote allochthonous and allospecific (from other species) introgressions in a synergistic process in Atlantic salmon Salmo salar and brown trout Salmo trutta. As a minor result, the data do not support the value of the microsatellite locus SsaD486 as a species‐specific marker.     

Skin morphology and humoral non-specific defence parameters of mucus and plasma in rainbow trout,coho and Atlantic salmon

Susceptibility to different diseases among related species, such as coho salmon (Oncorhynchus kisutch), rainbow trout (Oncorhyncus mykiss) and Atlantic salmon (Salmo salar), is variable. The prominence of these species in aquaculture warrants investigation into sources of this variability to assist future disease management. To develop a better understanding of the basis for species variability, several important non-specific humoral parameters were examined in juvenile fish of these three economically important species. Mucous protease, alkaline phosphatase and lysozyme, as well as plasma lysozyme activities and histological parameters (epidermal thickness and mucous cell density, and size) were characterized and compared for three salmonids: rainbow trout, Atlantic salmon and coho salmon. Rainbow trout had a thicker epidermis and significantly more mucous cells per cross-sectional area than the other two species. Rainbow trout also had significantly higher mucous protease activity than Atlantic salmon and significantly higher lysozyme (plasma and mucus) activities than coho and Atlantic salmon, in seawater. Atlantic salmon, on the other hand, had the lowest activities of mucous lysozyme and proteases, the thinnest epidermal layer and the sparsest distribution of mucous cells, compared with the two other salmonids in seawater. Only coho salmon had sacciform cells. Atlantic and coho salmon had higher mucous lysozyme activities in freshwater as compared to seawater. There was no significant difference between mucous lysozyme activities in any of the three species reared in freshwater; however, rainbow trout still had a significantly higher plasma lysozyme activity compared with the other two species. All three species exhibited significantly lower mucous alkaline phosphatase and protease activities in freshwater than in seawater. Our results demonstrate that there are significant histological and biochemical differences between the skin and mucus of these three salmonid species, which may change as a result of differing environments. Variation in these innate immune factors is likely to have differing influences on each species response to disease processes.     

Characterization of 38 polymorphic microsatellite markers for rainbow trout (Oncorhynchus mykiss)

Thirty‐eight new microsatellite markers were developed for genome mapping and population genetics studies in rainbow trout (Oncorhynchus mykiss). The amount of polymorphism, percentage of heterozygosity and ability of each marker to amplify genomic DNA from other salmonids were recorded. Five markers were observed to be duplicated in the rainbow trout genome by containing more than one allele in homozygous (clonal) fish.     

Characterization of twenty‐four microsatellite markers for rainbow trout (Oncorhynchus mykiss)

Twenty‐four new microsatellite markers were developed for genome mapping and population genetics studies in rainbow trout (Oncorhynchus mykiss). The amount of polymorphism, percentage heterozygosity and ability of each marker to amplify genomic DNA from other salmonids were recorded. Seven markers were observed to be duplicated in the rainbow trout genome by containing more than one allele in homozygous (clonal) fish.     

Comparison of competitive ability between native and introduced salmonids: evidence from pairwise contests

Brown trout, Salmo trutta, and rainbow trout, Oncorhynchus mykiss, have been introduced to freshwaters in Hokkaido, Japan. Today, it is recognized that these introduced salmonids have negative impacts on native salmonids such as white-spotted charr, Salvelinus leucomaenis, and masu salmon, O. masou. In particular, interspecific competition may be an important mechanism that could contribute to the exclusion for native salmonids. In this study, experimental pairwise contests were conducted to compare interference competitive ability between native and introduced salmonids. We demonstrated that brown trout were competitively superior to white-spotted charr and masu salmon whereas rainbow trout were superior to white-spotted charr. We suggest that introduced brown trout negatively impact both white-spotted charr and masu salmon, and introduced rainbow trout negatively impact white-spotted charr.     

A linkage map for brown trout (Salmo trutta): chromosome homeologies and comparative genome organization with other salmonid fish

We report on the construction of a linkage map for brown trout (Salmo trutta) and its comparison with those of other tetraploid-derivative fish in the family Salmonidae, including Atlantic salmon (Salmo salar), rainbow trout (Oncorhynchus mykiss), and Arctic char (Salvelinus alpinus). Overall, we identified 37 linkage groups (2n = 80) from the analysis of 288 microsatellite polymorphisms, 13 allozyme markers, and phenotypic sex in four backcross families. Additionally, we used gene-centromere analysis to approximate the position of the centromere for 20 linkage groups and thus relate linkage arrangements to the physical morphology of chromosomes. Sex-specific maps derived from multiple parents were estimated to cover 346.4 and 912.5 cM of the male and female genomes, respectively. As previously observed in other salmonids, recombination rates showed large sex differences (average female-to-male ratio was 6.4), with male crossovers generally localized toward the distal end of linkage groups. Putative homeologous regions inherited from the salmonid tetraploid ancestor were identified for 10 pairs of linkage groups, including five chromosomes showing evidence of residual tetrasomy (pseudolinkage). Map alignments with orthologous regions in Atlantic salmon, rainbow trout, and Arctic char also revealed extensive conservation of syntenic blocks across species, which was generally consistent with chromosome divergence through Robertsonian translocations.     

Genomic organization of the IGF1, IGF2, MYF5, MYF6 and GRF/PACAP genes across Salmoninae genera

Whole-genome duplication in the ancient ray-finned fish and subsequent tetraploidization in the ancestor to the salmonids have complicated genomic and candidate gene studies in these organisms as many genes with multiple copies are present throughout their genomes. In an attempt to identify genes with a potential influence on growth and development, we investigated the genomic positions of insulin-like growth factors 1 and 2 (IGF1, IGF2), myogenic factors 5 and 6 (MYF5, MYF6) and growth hormone-releasing factor/pituitary adenylate cyclase-activating polypeptide (GRF/PACAP) in three salmonid species: rainbow trout (Oncorhynchus mykiss), Atlantic salmon (Salmo salar) and Arctic charr (Salvelinus alpinus). Our results suggest a tight association between the IGF1, MYF5 and MYF6 genes in all three species. We further localized the duplicated copies of IGF1 to the homeologous linkage groups RT-7/15 in rainbow trout and AC-3/24 in Arctic charr, and the two copies of MYF6 to homeologous linkage groups AS-22/24 in Atlantic salmon. Localization of GRF/PACAP to RT-7, AS-31 and AC-27 and IGF2 to RT-27, AS-2 and AC-4 in rainbow trout, Atlantic salmon and Arctic charr respectively is consistent with previously reported homologies among these chromosomal segments identified using other genetic markers. However, localization of the second copy of GRF/PACAP to RT-19 and AC-14 and the duplicated copy of IGF2 to AC-19 suggest a possible new homology/homeology between these chromosomes. These results might also be an indication of a more ancient polyploidization event that occurred deep in the ray-finned fish lineage.     

Discrimination between farmed and free-living invasive salmonids in Chilean Patagonia using stable isotope analysis

In Chilean Patagonia relatively pristine aquatic environments are being modified by the introduction of exotic salmonids, initially through their deliberate release for sport fishing since the early twentieth century, and more recently via the accidental escape from fish farms. There is therefore a need to reliably distinguish between naturally reproducing and fugitive salmonids associated with the Chilean salmonid farming industry, the second largest in the world. We tested the ability of stable isotope analysis (SIA) and analysis of scale growth profiles to discriminate between farmed and free-living salmonids sampled around the Island of Chiloé. Juvenile Atlantic salmon (Salmo salar) and rainbow trout (Oncorhynchus mykiss) from aquaculture facilities were significantly more enriched in δ¹⁵N and lipid-corrected δ¹³C than river-caught individuals. Scale growth slopes during the first year in freshwater were significantly higher in farmed than in wild-caught rainbow trout, indicating faster somatic growth under hatchery conditions. Stable isotopes analysis classified 94% of juvenile Atlantic salmon and rainbow trout to their correct farm or free-living groups. Our results, therefore, can help to elucidate the origin and spread of exotic invasive salmonids in Chile, and address one of the biggest threats to native freshwater fishes in Patagonia and other temperate zones of the Southern Hemisphere.     

A microsatellite linkage map for Atlantic salmon (Salmo salar)

A linkage map of the Atlantic salmon is described here consisting of 15 linkage groups containing 50 microsatellite loci with a 14 additional unlinked markers (including three allozymes). The map shows the largest sex-specific recombination rate differences so far found in any vertebrate species (3.92:1 female:male). Homologies with previous linkage mapping studies of Atlantic salmon and rainbow trout are described. An in silico search of the Genbank database carried out using the microsatellites used in the mapping process identified significant matches between the flanking regions of the microsatellite SS11 and the calcium-binding mitochondrial carrier protein, 'Aralar1'.     

Varying effects of anadromous sockeye salmon on the trophic ecology of two species of resident salmonids in southwest Alaska

1. Anadromous salmon transport marine‐derived nutrients and carbon to freshwater and riparian ecosystems upon their return to natal spawning systems. The ecological implications of these subsidies on the trophic ecology of resident fish remain poorly understood despite broad recognition of their potential importance. 2. We studied the within‐year changes in the ration size, composition and stable isotope signature of the diets of two resident salmonids (rainbow trout, Oncorhynchus mykiss; Arctic grayling, Thymallus arcticus) before and after the arrival of sockeye salmon (Oncorhynchus nerka) to their spawning grounds in the Bristol Bay region of southwest Alaska. 3. Ration size and energy intake increased by 480–620% for both species after salmon arrived. However, the cause of the increases differed between species such that rainbow trout switched to consuming salmon eggs, salmon flesh and blowflies that colonized salmon carcasses, whereas grayling primarily ate more benthic invertebrates that were presumably made available because of physical disturbances by spawning salmon. 4. We also observed an increase in the δ¹⁵N of rainbow trout diets post‐salmon, but not for grayling. This presumably led to the observed increase in the δ¹⁵N of rainbow trout with increasing body mass, but not for grayling. 5. Using a bioenergetics model, we predicted that salmon‐derived resources contributed a large majority of the energy necessary for growth in this resident fish community. Furthermore, the bioenergetics model also showed how seasonal changes in diet affected the stable isotope ratios of both species. These results expand upon a growing body of literature that highlights the different pathways whereby anadromous salmon influence coastal ecosystems, particularly resident fish.     

Type I microsatellite markers from Atlantic salmon (Salmo salar) expressed sequence tags

The detection of simple sequence repeats (SSRs) within expressed sequence tags (ESTs) connects potential microsatellite markers with specific genes, generating Type I markers. Using an in silico approach, we identified 1975 SSRs from the Genome Research on Atlantic Salmon Project EST database. We designed primers to amplify 158 SSRs, of which 65 amplified 76 loci (including 11 duplicated loci). Sixty‐one of the 76 loci were variable in 24 Atlantic salmon from seven populations, and 96% of these markers also amplify DNA from other salmonids. Functions for 16 of the SSR associated ESTs have been determined, confirming them as Type I markers.     

Comparative diets and foraging strategies of subyearling Atlantic salmon,brown trout,and rainbow trout during winter

Over‐winter survival of salmonids in streams is thought to be an important population regulation mechanism. Yet because of the difficulty of conducting field studies due to adverse weather or ice conditions, compared to other seasons, salmonid ecology during winter is least understood. Consequently, we sought to examine interspecific feeding associations of an important salmonid stream assemblage in the Lake Ontario watershed during winter. The diets of Atlantic salmon (Salmo salar) parr, brown trout (S. trutta) parr, and rainbow trout (Oncorhynchus mykiss) parr were significantly different in February but not in March. Salmonid diets differed from the benthos and the drift during both months. Dipterans (chironomids, simuliids, and tipulids) and ephemerellids were the major prey taxa consumed. All three species fed more heavily on prey items from the benthos than from the drift. The diet of Atlantic salmon had the highest similarity to the benthos whereas the diet of brown trout had the lowest similarity to the drift. All three salmonid species generally selected ephemerellids, limnephilids, and chironomids and avoided elmids. These winter feeding observations are the first reported for this specific salmonid assemblage and will help managers better understand interspecific associations during this critical period.     

水产养殖动物遗传连锁图谱及QTL定位研究进展

自1997年美国农业部启动5种水产养殖动物基因组计划以来,在不到10年的时间里,世界各国都相继开展了本国主要水产养殖动物基因组研究。截至2005年底,有近17种海淡水养殖动物公布了遗传连锁图谱：属于高密度连锁图谱的有虹鳟和大西洋鲑（标记数超过1000）;属于中密度遗传连锁图谱的有罗非鱼、沟鲶、黑虎虾、日本牙鲆和欧洲海鲈（标记数为400-1000）;属于低密度遗传连锁图谱的有泰国的胡鲶,中国的栉孔扇贝、鲤鱼,日本的黄尾鲕,美国的牡蛎等近10种养殖种类（标记数少于400）。水产养殖动物遗传连锁图谱的构建和发展,促进了一些与经济性状（如生长、抗逆、发育等）相关的数量性状位点（QTL）的定位研究。然而,QTL定位研究目前只在具有中高密度遗传连锁图谱的鲑科鱼类（虹鳟、大西洋鲑和北极嘉鱼）、罗非鱼、沟鲶和日本牙鲆等种类中开展,而且定位研究仍处在初级水平。遗传连锁图谱的高分辨率和QTL在图谱上的精确定位,是今后能否实现对主要水产养殖动物的经济性状进行遗传操作的技术保证,同时也是实现分子标记或基因辅助育种在水产养殖动物中成功运用的制胜法宝。     

Tissue astaxanthin and canthaxanthin distribution in rainbow trout (Oncorhynchus mykiss) and Atlantic salmon (Salmo salar)

A comparative investigation of tissue carotenoid distribution between rainbow trout, Oncorhynchus mykiss, and Atlantic salmon, Salmo salar, was undertaken to identify the relative efficiency of utilization of astaxanthin and canthaxanthin. Higher apparent digestibility coefficients (ADCs) (96% in trout vs. 28-31% in salmon; P<0.05), and pigment retention efficiencies (11.5-12.5% in trout vs. 5.5% in salmon; P<0.05), for both astaxanthin and canthaxanthin, were observed for rainbow trout. Astaxanthin deposition was higher than canthaxanthin in rainbow trout, while the reverse was true for Atlantic salmon, suggesting species-specificity in carotenoid utilization. The white muscle (95% in trout vs. 93% in salmon) and kidneys (0.5% in trout vs. 0.2% in salmon) represented higher proportions of the total body carotenoid pool in rainbow trout than in Atlantic salmon (P<0.05), whereas the liver was a more important storage organ in Atlantic salmon (2-6% in salmon vs. 0.2% in trout; P<0.05). The liver and kidney appeared to be important sites of carotenoid catabolism based on the relative proportion of the peak chromatogram of the fed carotenoid in both species, with the pyloric caecae and hind gut being more important in Atlantic salmon than in the rainbow trout. Liver catabolism is suspected to be a critical determinant in carotenoid clearance, with higher catabolism expected in Atlantic salmon than in rainbow trout.