Evidence of genetic and environmental influences on meristic variation in the rainbow trout,Salmo gairdneri Richardson

Synopsis An investigation of the effect of parentage and temperature on the expression of selected meristic characters of rainbow trout, Salmo gairdneri, reveals statistical differences in the number of vertebrae, dorsal fin rays and anal fin rays among test batches of progeny of different parentage. Batches of fertilized ova of the same stock or parentage, when incubated at 9.5 °C and 14.8 °C, produced lower mean dorsal and anal fin ray counts and a higher mean pectoral fin ray count at the higher temperature. Incubation temperature had no significant effect on the number of vertebrae.Significant statistical differences occurring in various characters among groups of rainbow trout of different parental origin provide convincing evidence of genetic inputs into meristic expression. However, the existence of both environmental and genetic inputs into meristic expression in rainbow trout necessitates further investigation before the meaning of observed meristic plasticity in rainbow trout can be resolved.     

Quantitative Trait Loci Analyses for Meristic Traits in Oncorhynchus mykiss

Meristic trait variation among species and populations has long been used as the basis for identification and classification of fishes. Within Oncorhynchus mykiss, there is considerable variation in meristic characters such as numbers of vertebrae, lateral line scales, fin rays, gill rakers, and pyloric caeca. In our laboratory the Oregon State University (OSU) rainbow trout and the Clearwater River (CW) steelhead trout clonal lines, produced by androgenesis, exhibit significant differences in values for meristic traits, making quantitative trait locus (QTL) analysis of these meristic characters possible. Our objective was to determine the number, location, and effects of QTL associated with meristic characters in order to test two hypotheses: (1) that QTL for different meristic traits co-localize to the same linkage group and (2) that meristic trait QTL co-localize to the same linkage group as a previously identified development rate QTL. Doubled haploid individuals, produced by androgenesis from sperm from an F₁ hybrid between the OSU and CW lines, were used to evaluate the joint segregation of each meristic phenotype and Amplified Fragment Length Polymorphic marker genotypes. Composite interval mapping revealed QTL for six of the seven traits analyzed. One QTL each for scales above the lateral line and for gill rakers co-localized to the same position. Only one QTL for scales above the lateral line co-localized to the same region as that for the development rate QTL, but a greater map resolution is necessary to determine if these loci are truly the same. We failed to detect pleiotropy for most meristic trait QTL. Our results suggest that different major loci are associated with variation in each meristic character and that the expression of these loci may be influenced by maternal and external environmental factors.     

Deviation from morphological intermediacy in interstrain hybrids of rainbow trout,Salmo gairdneri

Synopsis Deviations from morphological intermediacy in six first generation hybrids between three hatchery strains of rainbow trout, raised in a common environment, are reported. Hybrids have higher mean counts of four meristic characters than their maternal parental strain in a significantly greater number of cases (18 out of 24). Furthermore, eight of eleven hybrid indices are not intermediate. These results are discussed in reference to several mechanisms and models proposed to account for observed responses of meristic characters to environmental and genetic influences.     

Domestication shapes morphology in rainbow trout Oncorhynchus mykiss

In this study, clonal lines from North American resident and migratory populations of rainbow trout Oncorhynchus mykiss adapted to different geographical conditions and with different domestication histories were characterized morphologically. Lines reared in a common‐garden experiment were characterized for external shape and meristic values, searching for a general pattern of morphological variation due to exposure to captive conditions. A sharp distinction was identified between wild and captive lines. The body profile was deeper in captive lines, with longer dorsal and anal fins and shorter and deeper caudal peduncles. Highly significant differences were also identified in meristic values among the lines but no consistent relation between meristic values and domestication status was detected. This morphological characterization will facilitate the selection of lines with divergent phenotypes for subsequent quantitative trait loci analysis, aimed at identifying genome regions linked with morphological adaptive response to captive conditions.     

Developmental stability in brown trout: are there any effects of heterozygosity or environmental stress?

We studied the developmental stability of brown trout, Salmo trutta L., in 10 populations (five acidified, five control) in Norway, measured as fluctuating asymmetry (FA) and departure from the morphological norm. We measured four meristic and four morphometric characters, and scored the level of biochemical heterozygosity at 49 loci (20 polymorphic). We reared eggs of a single population in a hatchery using four different water qualities (three replicates of each treatment) to test the effect of acidification stress on developmental instability. There were no significant differences in the level of FA, in departure from the morphological norm between brown trout sampled from lakes with acidified or control water qualities, or in brown trout hatched at different water qualities. There was no correlation between level of heterozygosity and FA or departure from the morphological norm, either when tested within populations or among populations. There were no single-locus effects on developmental stability tested for 11 loci. We conclude that measures of developmental stability or morphological variability are not useful for detecting acidification stress in brown trout. Furthermore, we conclude that developmental stability in our material varies independently of heterozygosity.     

Morphological differences among three color morphotypes of Sebastes inermis (Scorpaenidae)

 Morphological differences among three color morphotypes occurring almost sympatrically (A, reddish type; B, blackish type; C, brownish type) of Sebastes inermis are clarified. Twenty-six morphometric characters and seven meristic characters were examined on about 20 specimens of each morphotype, 15 of the morphometric characters differing significantly. Principal component analysis (PCA) of the morphometric characters showed morphotype C to differ from the other two morphotypes. Canonical discriminant analysis (CDA) of the morphometric characters showed clear separation of each morphotype. Four meristic characters also differed significantly. Modes of pectoral fin ray counts of morphotypes A, B, and C were 15, 16, and 17, respectively, and the modes of anal fin ray counts of morphotypes B and C were 7 and 8, respectively. Many individuals of morphotype A had seven or eight anal fin rays. These differences suggested that the three morphotypes may be reproductively isolated from each other. Received: October 15, 2001 / Revised: March 14, 2002 / Accepted: April 9, 2002     

Use of shape analysis in the investigation of disputable meristic characters for Ameiurus melas (Rafinesque, 1820) and Ameiurus nebulosus (Lesueur, 1819)

The aim of this paper was to use geometric morphometry as a helpful tool to clarify the overlap between meristic characters (such as the number of anal fin rays) of different fish identification keys employed for the two sister species, Ameiurus melas and Ameiurus nebulosus. Geometric morphometry included shape analysis of 15 landmarks on 432 specimens. The analyses showed significant differences among groups based on the sampling site, while there was no difference among groups based on the number of anal fin rays (used to distinguish species). This suggests that the use of meristic characters for the determination of these two sister species is rather questionable.     

Morphological variations among four riverine populations (Bangladesh) of endangered catfish Rita rita (Hamilton, 1822)

The morphological variation of the endangered catfish Rita rita was studied based on meristic, length–weight relationship (LWR), traditional (TRA) and truss (TRU) distance based morphometric analysis of 200 juveniles collected from the Old Brahmaputra, Jamuna, Meghna and Kangsa rivers. Data were subjected to Kruskal–Wallis test for meristic counts, t test for LWR, univariate ANOVA, multivariate discriminant function analysis and canonical analysis (CA) both for TRA and TRU morphometric characters to discriminate the populations. Kruskal–Wallis test denoted that only one (caudal fin rays) out of six meristic counts was significantly (p < .05) variable among the stocks. One sample t test clarified that all parameters of LWR were significantly (p < .05) differentiated in all stocks. Univariate ANOVA revealed significant (p < .001, p < .01, and p < .05) differences among the four stocks in 14 of 15 standardized TRA traits and 17 of 25 TRU distances, respectively. The first discriminant function (DF1) explained 59.4% and 68.0% of total variance, while 30.6% and 23.1% by DF2, 10.0% and 8.9% by DF3 for TRA and TRU features, respectively among the stocks. CA showed a clear separation of the stocks both for TRA and TRU measurements. The overall random assignment of individuals into their original groups was high as 78.5% for TRA and 78.0% for TRU characters, respectively, indicating that all the four stocks are highly divergent from each other. The results exposed existence of four distinct phenotypic stocks of R. rita in the tested rivers.     

Morphological variation in a secondary contact between divergent lineages of brown trout (Salmo trutta) from the Iberian Peninsula

The aim of this study was to analyze the morphological variation of brown trout (Salmo trutta) in the Duero basin, an Atlantic river basin in the Iberian Peninsula, where a spatial segregation of two divergent lineages was previously reported, based on isozyme, microsatellite and mtDNA data. In these studies, two divergent pure regions (Pisuerga and Lower-course) and several hybrid populations between them were identified. Morphological variation was evaluated in 11 populations representative of the genetic differentiation previously observed in the Duero basin, using multivariate analysis on 12 morphometric and 4 meristic traits. A large differentiation between populations was observed (interpopulation component of variance: 41.8%), similar to that previously detected with allozymes and microsatellites. Morphometric differentiation was also reflected by the high classification success of pure and hybrid individuals to their respective populations, using multivariate discriminant functions (94.1% and 79.0%, respectively). All multivariate and clustering analyses performed demonstrated a strong differentiation between the pure regions. The hybrid populations, though showing large differentiation among them, evidenced an intermediate position between the pure samples. Head and body shape traits were the most discriminant among the morphometric characters, while pectoral rays and gillrakers were the most discriminant among the meristic traits. These results confirmed the high divergence of the brown trout from the Duero basin and suggest some traits on which selection could be acting to explain the spatial segregation observed.     

Variation in number of vertebrae and gill rakers of sockeye salmon,Oncorhynchus nerka,in North America

Synopsis The latitudinal, regional, and annual variation in number of vertebrae and number of gill rakers present in sockeye salmon, Oncorhynchus nerka, stocks in North America was examined. Stocks in more northern areas had higher numbers of vertebrae and gill rakers than did those in more southern ones. Significant annual variability in the frequencies of these meristic characters within stocks was observed. When stocks were grouped into three regions (southern, central, and northern), heterogeneity in vertebral and gill raker frequencies was greater among regions than among stocks within the regions. Similarly, heterogeneity was greater among stocks than among sampling years within stocks. Differences in vertebral and gill raker frequencies are only useful for stock identification of sockeye salmon on a broad regional basis.     

Role of genetic background in the introgressive hybridization of rainbow trout (<Emphasis Type="Italic">Oncorhynchus mykiss</Emphasis>) with Westslope cutthroat trout (<Emphasis Type="Italic">O. clarkii lewisi</Emphasis>)

Conservation and management of endemic species may increasingly involve efforts to prevent hybridization with other species. Native westslope cutthroat trout (Oncorhynchus clarkii lewisi) management in western North America is based largely on admixture estimates with introduced rainbow trout (O. mykiss), with the highest conservation priority given to cutthroat populations that do not exhibit admixture. This study examined the hypothesis that such ancestry quotients are dependent upon the genetic background of reference rainbow trout populations. We used 10 microsatellite loci to estimate admixture within westslope cutthroat trout collected from 39 sites from Alberta, Canada, using three genetically distinct (pairwise F_ST = 0.100–0.281) rainbow trout genetic backgrounds: a wild (introduced) population from Alberta, two wild (native) populations from British Columbia, and a present-day hatchery broodstock line. Ancestry quotients were significantly impacted by genetic background, whereby the extent of admixture was highest with locally introduced (wild, naturalized) rainbow trout lines and lowest with the hatchery lines. Our results suggest that future studies ought to explore the possibility that local adaptation or drift in introduced rainbow trout populations may contribute to decreased reproductive isolation with geographically proximal cutthroat trout populations.     

Geographic variation in Austrolebias luteoflamulatus Vaz‐Ferreira, Sierra & Scaglia (Cyprinodontiformes, Rivulidae)

The morphological variation in the annual killifish Austrolebias luteoflamulatus was studied using meristic and pigmentation characters analysed with univariate and multivariate analysis, and morphometric characters analysed with a geometric morphometry approach (thin plate spline). The results showed that morphological variation in this species was associated with a geographical pattern. In the case of meristic and pigmentation characters, the strongest distinction occured in males, while females were more similar among different drainages. Males from Rocha (eastern Uruguay) exhibited the greatest differences from the others. The number of dorsal fin rays and bars on the flanks were the characters that contributed most to this segregation. When morphometrics were considered, the three populations analysed could be distinguished well from each other in both sexes. Some of the characters that contributed to this pattern were dorsal fin origin, position of eyes and length of snout. Since pigmentation characteristics and some characters of the dorsal fin in males were involved in the differences observed, sexual selection could have played an important role in the differentiation of populations of this species. Since Austrolebias luteoflamulatus has a restricted geographical distribution, conservation of this species should include consideration of these populations individually since they might represent different evolutionary units.     

Testing the relationship between domestication and developmental instability in rainbow trout,Oncorhynchus mykiss (Teleostei,Salmonidae)

Fish domestication is an evolutionary process arising in captivity through genetic and developmental mechanisms, producing organisms performing more poorly than wild conspecifics in the natural environment. Culture conditions could be suboptimal for fish at particular life cycle stages, presenting environmental disturbances leading to developmental instability. The limited size of captive lots, moreover, can result in the loss of genetic variation, and the resulting homozygosity (as well as hybridization and mutation) could have strong harmful effects on developmental stability. Rainbow trout are the most widely‐cultured species in Europe and North America, having been in culture for more than a century. Prolonged artificial selection for desired traits and incidental effects of domestication has led to the development of a ‘farmed type’. Fluctuating asymmetry, variations in meristic counts, and skeletal anomalies were examined in several rainbow trout captive and wild clonal lines as indicators of developmental instability. Differences in developmental stability were identified among lines and correlated with different degrees of exposure to captivity. Some relationship between meristic counts and domestication level was found in the present study, with the number of vertebrae and of dorsal pterygiophores and rays being the strongest predictors of the domestication level. However, the occurrence of skeletal anomalies and fluctuating asymmetry were apparently not related to the level of exposure to captivity. The findings of the present study will facilitate the selection of clonal lines with divergent phenotypes for subsequent quantitative trait loci analyses aimed at identifying genome regions linked with morpho‐anatomical and physiological adaptive responses to captivity. © 2015 The Linnean Society of London, Biological Journal of the Linnean Society, 2015, 114 , 608–628.     

A genetic analysis of the London strain of rainbow trout

The London strain of rainbow trout (Oncorhynchus mykiss) was created by interbreeding three other strains of rainbow trout and therefore was expected to have higher levels of genetic variation than other strains of rainbow trout. We examined 129 London strain rainbow trout from Indiana by allozyme electrophoresis to assess levels of genetic variation and to examine the relationship between the London strain and other hatchery strains. When using the same loci to compare with other hatchery strains the London strain showed levels of genetic variation within the range of other hatchery strains: mean heterozygosity of 0.053 (0.031-0.099), 1.27 (1.20-1.60) alleles per locus and 20.0% (20.0-40.0%) of the loci were polymorphic. The London strain is somewhat distinct from other hatchery strains (D=0.009-0.072), in part because of the high frequency of the sIDHP*40 allele.     

Skeletal characterization of wild and reared zebrafish: anomalies and meristic characters

Among two groups of wild and reared zebrafishes (zf) Danio rerio, all meristic characters considered were variable except the numbers of rays and pterygophores of the dorsal fin and the principal caudal fin rays, which tended to be canalized. Wild and reared individuals differed in the number of intervertebrae and anal pterygophores, and the dorsal and anal fin insertion. There were some skeletal anomalies of vertebrae and fins, particularly the caudal fin. Cephalic and Weber-apparatus anomalies were rare. Types and frequencies of anomalies were quite similar in the two zf groups, but differences emerged for several less frequent anomalies. Such differences and the phenotypic variability of D. rerio make this species a perfect teleost model for investigating the influence of experimental or unfavourable environmental conditions on skeletal development of both domesticated and wild fish.     

A genetically distinct wild redband trout (<Emphasis Type="Italic">Oncorhynchus mykiss gairdneri</Emphasis>) population in Crane Prairie Reservoir,Oregon, persists despite extensive stocking of hatchery rainbow trout (<Emphasis Type="Italic">O. m. irideus</Emphasis>)

Crane Prairie Reservoir in the upper Deschutes River Basin has historically supported a wild population of migratory Deschutes River redband trout. Owing to its status as a premier destination for recreational angling in Oregon, the reservoir has been stocked with domesticated hatchery rainbow trout since 1955. In recent years the wild redband trout population has experienced a substantial decline. Effects on productivity related to genetic interaction with naturally spawning hatchery-origin fish (fitness risks) have not been determined. The species Oncorhynchus mykiss has been characterized with substantial genetic diversity throughout the Deschutes River Basin that further heightens the challenge of identifying specific conservation needs of wild populations. A conservation plan for Crane Prairie wild redband trout requires a better understanding of the natural reproductive success of out-of-basin hatchery trout in the reservoir tributaries, and the similarity between Crane Prairie redband trout with other extant redband trout populations in the basin. Using a suite of 17 microsatellite nuclear DNA markers, we evaluated the genetic structure among Crane Prairie Reservoir redband trout, hatchery rainbow trout, and two adjacent populations of redband trout from within the Upper Deschutes River Basin. We observed significant heterogeneity between the hatchery and wild Crane Prairie populations that may reflect differences in life histories, differential productivity and assortative mating. The genetic distinctions observed among the three redband trout populations suggest restricted gene flow and genetic drift within the upper basin. Temporally stratified sampling and larger numbers of samples will be necessary to confirm these conclusions.     

Body pigmentation pattern to assess introgression by hatchery stocks in native Salmo trutta from Mediterranean streams

Five qualitative and seven quantitative colouration and spotting pattern features were measured in 23 brown trout Salmo trutta populations and two hatchery stocks. Simultaneously, the LDH‐C1 *, a diagnostic locus fixed for *90 and *100 alleles in stocking and native populations from southern Europe, respectively, was analysed to classify the brown trout studied according to their origin: native, hatchery stock and hybrids. The three genotypes showed significant differences in the colouration and spotting features and a discriminant function analysis could correctly identify 79% of the individuals. The most discriminating variables were dorsal fin margin colour, number of opercular spots, presence of the preopercular mark and diameter of black spots. Given the low cost, ease and possibility of field identification of native fish, the results indicate great opportunities for the application of morphological‐based classification models on the conservation and management of native brown trout stocks.     

Erosion of interspecific reproductive barriers resulting from hatchery supplementation of rainbow trout sympatric with cutthroat trout

The frequency of hybridization between cutthroat (Onchorhynchus clarki clarki) and rainbow (O. mykiss irideus) trout from coastal habitats in British Columbia, Canada, was examined in seven populations where the two species are sympatric with no history of rainbow trout stocking and compared with areas where native rainbow trout populations have been supplemented with hatchery fish (three populations). Four nuclear markers were used to identify each species and interspecific hybrids and one mitochondrial marker showed the direction of gene exchange between species. The frequency of hybrids was significantly higher (Fisher exact test, P < 0.001) in river systems where hatchery rainbow trout have been introduced (50.6% hybrids) than in populations where the two species naturally co-occur without supplementation (9.9% hybrids).     

Genetic variability and components of fitness in hatchery strains of rainbow trout

Two fitness components, development rate and egg size, were examined in six hatchery strains of rainbow trout, Oncorhynchus mykiss (syn. Salmo gairdneri Richardson), with different amounts of enzyme heterozygosity. The average expected heterozygosities per strain ranged from 4 to 8%, based upon an electrophoretic analysis of the protein products of 42 loci. Strains with higher heterozygosities had faster development rates, as measured by hatching time, than strains with lower heterozygosity. Concordance between hatching time and another measure of development rate, degree of yolk-sac resorption, suggests that hatching time is a valid measure of embryonic development rate in salmonid fishes. Earlier-hatching embryos were longer and heavier at the time of yolk-sac resorption than later-hatching fish. Females from more-heterozygous strains also had a tendency to have larger eggs. These data suggest that genetic variation is an important biological resource to be conserved in hatchery stocks.     

Effects of Hatchery Rearing on Brain Structures of Rainbow Trout, Oncorhynchus mykiss

In this study, we contrast brain morphology from hatchery and wild reared stocks to examine the hypothesis that in salmonid fishes, captive rearing produces changes in brain development. Using rainbow trout, Oncorhynchus mykiss, as a model, we measured eight regions of the salmonid brain to examine differences between wild and hatchery reared fish. We find using multiple analysis of covariance (MANCOVA), analysis of covariance (ANCOVA) and discriminant function analysis (DFA) that the brains of hatchery reared fish are relatively smaller in several critical measures than their wild counterparts. Our work may suggest a mechanistic basis for the observed vulnerability of hatchery fish to predation and their general low survival upon release into the wild. Our results are the first to highlight the effects of hatchery rearing on changes in brain development inbreak fishes.