Correlations between fitness and heterozygosity at allozyme and microsatellite loci in the Atlantic salmon, Salmo salar L

The relationship between heterozygosity at genetic markers (six allozyme and eight microsatellite loci), and fluctuating asymmetry (FA), length and weight was investigated in two samples of Atlantic salmon (Salmo salar L.) with different timings of first active feeding (early (EA) and late (LA) salmon). This trait had previously been related to fitness. EA fish show smaller values of FA, are longer, heavier and are more heterozygous at allozyme loci than are conspecific LA fish. Also within both samples, heterozygosity at allozyme loci was inversely related to FA and was positively related to weight and length. However, no significant differences in microsatellite diversity (heterozygosity and mean d2 measurements) were observed between samples (EA vs LA). Furthermore, no association was observed between the variability at microsatellite loci and FA, weight or length within each sample. These results suggest that allozyme loci, in themselves, influence fitness components, rather than associations arising from associative overdominance.     

Genetic diversity and structure in a natural Elymus caninus population from Denmark based on microsatellite and isozyme analyses

 Genetic diversity in a natural Elymus caninus population from Denmark was assessed using isozyme and microsatellite markers. A total of 119 individuals from 46 maternal plants were assayed. Microsatellite loci are shown to display higher levels of variation than isozyme loci. The mean number of alleles per locus was 1.04 for isozymes and 1.38 for microsatellites. The percentage of polymorphic loci for isozymes and microsatellites was 4.7% and 23.6% across the maternal plant, respectively. The genetic diversity at population level was 0.1 for isozymes, and 0.63 for microsatellites. The mean genetic diversity at maternal plant level was 0.027 for isozyme loci and 0.117 for microsatellite loci. The average of total allozyme diversity (H_T) was 0.22. The average of total microsatellite diversity was 0.56. Isozyme and microsatellite variation showed the same pattern of differentiation between maternal plants. More than 75% total genetic diversity was found among maternal plants. About 25% total genetic diversity was detected within maternal plants. Ten (22.7%) maternal plants produced heterozygous offspring at allozyme loci, and 30 (68.2%) maternal plants gave heterozygous offspring at microsatellite loci. Both types of markers revealed a relatively high genetic diversity in this population. Received November 7, 2000 Accepted February 15, 2001     

Individual‐level analysis of pre‐ and post first‐feed growth and development in Atlantic salmon

Atlantic salmon Salmo salar were followed from egg to smoltification using genetic analysis to identify individuals and to link observations from pre‐ and post first feeding. Egg size and hatch timing significantly influenced alevin size at first feed but neither egg size, hatch timing or alevin sizes were correlated to size, condition factor or smolt status post first feed. In a hatchery environment the potential advantage gained by early hatching, larger alevin does not persist after first feeding. Different physiological and genetic complexes appear to influence growth in these two distinct phases of the Atlantic salmon's life‐cycle.     

Genetic differentiation of pink salmon oncorhynchus gorbuscha Walbaum in the Asian part of the range

Genetic variation at 19 allozyme (including 11 polymorphic) and 10 microsatellite loci was examined in the population samples of odd- and even-broodline pink salmon from the southern part of Sakhalin Island, Southern Kuril Islands, and the northern coast of the Sea of Okhotsk. The estimates of relative interpopulation component of genetic variation over the allozyme loci, per broodline, were on average 0.43% (GST), while over the microsatellite loci it was 0.26% (the theta(ST) coefficient, F-statistics based on the allele frequency variance), and 0.90% (the rho(ST) coefficient, R-statistics based on the allele size variance). The values of interlinear component constituted 2.34, 0.31, and 1.05% of the total variation, respectively. Using the allozyme loci, statistically significant intralinear heterogeneity was demonstrated among the regions, as well as among the populations of Southern Sakhalin Island. Multivariate scaling based on the allozyme data demonstrated regional clustering of the sample groups, representing certain populations during the spawning run or in different years. Most of the microsatellite loci examined were found to be highly polymorphic (mean heterozygosity > 0.880). The estimates of interlinear, interregional, and interpopulation variation over these loci in terms of theta(ST) values were substantially lower than in terms of rho(ST) values. Regional genetic differentiation, mostly expressed at the allozyme loci among the populations from the northern and southern parts of the Sea of Okhotsk (i.e., between the Sakhalin and Kuril populations), was less expressed at the microsatellite loci. The differentiation between these regions observed can be considered as the evidence in favor of a large-scale isolation by distance characterizing Asian pink salmon. It is suggested that in pink salmon, low genetic differentiation at neutral microsatellite loci can be explained by extremely high heterozygosity,of the loci themselves, as well as by the migration gene exchange among the populations (the estimate of the genetic migration coefficient inferred from the "private" allele data constituted 2.6 to 3.4%), specifically, by the ancient migration exchange, which occurred during postglacial colonization and colonization of the range.     

Genetic divergence in pink salmon introduced into the European north of Russia: microsatellite and allozyme variation analysis

The 1985 introduction into the European North of Russia resulted in the formation of a large stock of pink salmon of the odd-year breeding line. To assess the divergence of the new population and the role of various microevolutionary factors, variation of four microsatellite loci and fifteen genes encoding proteins (allozymes) in samples of fish, running for spawning in rivers of the new area, and in samples from the donor population of the Ola River (Magadan oblast). In the generations 8 and 9 of the introduced pink salmon of the odd-year line, the genetic diversity (the number of alleles and the mean heterozygosity) both at allozyme and at microsatellite loci was significantly lower, than that in the donor population. The explanations of the decline in diversity are discussed. The first evidence for spatial genetic divergence in transplanted fish within the new area has been obtained; the divergence level may be comparable with that characteristic of native populations.     

Genetic divergence in pink salmon introduced into the European North of Russia: Microsatellite and allozyme variation analysis

The 1985 introduction into the European North of Russia resulted in the formation of a large stock of pink salmon of the odd-year broodline. To assess the divergence of the new population and the role of various microevolutionary factors, variation of four microsatellite loci and fifteen genes encoding proteins (allozymes) in samples of fish, running for spawning in rivers of the new area, and in samples from the donor population of the Ola River (Magadan region). In the generations 8 and 9 of the introduced pink salmon of the odd-year line, the genetic diversity (the number of alleles and the mean heterozygosity) both at allozyme and at microsatellite loci was significantly lower, than that in the donor population. The explanations of the decline in diversity are discussed. The first evidence for spatial genetic divergence in transplanted fish within the new area has been obtained; the divergence level may be comparable with that characteristic of native populations.     

Interregional differentiation of chum salmon from Sakhalin and South Kurils infered from microsatellite markers

Variability at ten microsatellite loci was examined in wild and hatchery populations of chum salmon from the Sakhalin Island and Southern Kuril Islands, Iturup and Kunashir. Substantial genetic differences between Sakhalin and South Kurils chum salmon (the differentiation theta reached 6.0%) were revealed. Statistically significant differences between chum salmon from Iturup and that from Kunashir were demonstrated, as well as between the chum salmon populations from different rivers within the islands. It was shown that in different types of population comparisons, required different marker sets most informative were.     

Genetic differentiation of pink salmon Oncorhynchus gorbuscha Walbaum in the Asian part of the range

Genetic variation at 19 enzyme (including 11 polymorphic) and 10 microsatellite loci was examined in the population samples of odd-and even-broodline pink salmon from the southern part of Sakhalin Island, Southern Kuril Islands, and the northern coast of the Sea of Okhotsk. The estimates of relative interpopulation component of genetic variation for the allozyme loci, per broodline, were on average 0.43% (G _ST), while over the microsatellite loci it was 0.26% (the ?_ST coefficient, F-statistics based on the allele frequency variance), and 0.90% (the ρ_ST coefficient, R-statistics based on the allele size variance). The values of interlinear component constituted 2.34, 0.31, and 1.05% of the total variation, respectively. Using the allozyme loci, statistically significant intralinear heterogeneity was demonstrated among the regions, as well as among the populations of southern Sakhalin. Multidimensional scaling based on the allozyme data demonstrated regional clustering of the sample groups, representing certain populations during the spawning run or in different years. Most of the microsatellite loci examined were found to be highly polymorphic (mean heterozygosity > 0.880). The estimates of interlinear, interregional, and interpopulation variation over these loci in terms of ?_ST values were substantially lower than in terms of ρ_ST values. Regional genetic differentiation, mostly expressed at the allozyme loci between the populations from the northern Sea of Okhotsk and the Sakhalin and Kuril group of populations, was less expressed at the microsatellite loci. The differentiation between these regions observed can be considered as the evidence in favor of a large-scale isolation by distance characterizing Asian pink salmon. It is suggested that in pink salmon, low genetic differentiation at neutral microsatellite loci can be explained by extremely high heterozygosity of the loci themselves, as well as by the migration gene exchange among the populations (the estimate of the gene migration coefficient inferred from the “private” allele data constituted 2.6 to 3.4%), specifically, by the ancient migration exchange, which occurred during postglacial colonization of the range     

Interregional differentiation of chum salmon from Sakhalin and South Kurils inferred from microsatellite markers

Variability at ten microsatellite loci was examined in wild and hatchery populations of chum salmon (Oncorhynchus keta Walbaum) from the Sakhalin Island and Southern Kuril Islands, Iturup and Kunashir. Substantial genetic differences between Sakhalin and South Kurils chum salmon (the differentiation reached 6.0%) were revealed. Statistically significant differences between chum salmon from Iturup and those from Kunashir were demonstrated, as well as between the chum salmon populations from different rivers within the islands. It was shown that in different types of population comparisons, different marker sets were most informative.     

Allozyme heterozygosity, date of first feeding and life history strategy in Atlantic salmon

The relations between allozyme heterozygosity, relative date of first feeding and life history strategy in juvenile Atlantic salmon Salmo salar were examined using eggs obtained from a 400 family cross (20 male × 20 female adult Atlantic salmon). Multilocus heterozygosity, through its positive associations with the timing of first feeding and growth rate, was correlated with life history strategy in juvenile Atlantic salmon, albeit under genotype × environmental (temperature, food availability) regulation. Under hatchery conditions, a 10 day difference was observed in the relative date of first feeding between early and late first feeding Atlantic salmon. Early first feeding Atlantic salmon exhibited a significantly higher mean heterozygosity, grew faster at ambient water temperature (April to November) and a significantly higher proportion adopted the early freshwater maturation (age 0+ years, male fish) or early migrant (age 1+ years, mainly female fish) strategies compared to late first feeding Atlantic salmon. Elevated water temperatures over the winter (December to April, >10·5° C) provided additional growth opportunity allowing previously mature male parr (mainly early first feeders) and lower modal group parr (mainly late first feeders) to adopt the early migrant strategy by the following spring.     

Contrasting patterns of gene diversity between microsatellites and mitochondrial SNPs in farm and wild Atlantic salmon

Levels of genetic variability at 12 microsatellite loci and 19 single nucleotide polymorphisms in mitochondrial DNA were studied in four farm strains and four wild populations of Atlantic salmon. Within populations, the farm strains showed significantly lower allelic richness and expected heterozygosity than wild populations at the 12 microsatellite loci, but a significantly higher genetic variability with respect to observed number of haplotypes and haplotype diversity in mtDNA. Significant differences in allele- and haplotype-frequencies were observed between farm strains and wild populations, as well as between different farm strains and between different wild populations. The large genetic differentiation at mitochondrial DNA between wild populations (F_ST = 0.24), suggests that the farm strains attained a high mitochondrial genetic variability when created from different wild populations seven generations ago. A large proportion of this variability remains despite an expected lower effective population size for mitochondrial than nuclear DNA. This is best explained by the particular mating schemes in the breeding programmes, with 2–4 females per male. Our observations suggest that for some genetic polymorphisms farm populations might currently hold equal or higher genetic variability than wild populations, but lower overall genetic variability. In the short-term, genetic interactions between escaped farm salmon and wild salmon might increase genetic variability in wild populations, for some, but not most, genetic polymorphisms. In the long term, further losses of genetic variability in farm populations are expected for all genetic polymorphisms, and genetic variability in wild populations will be reduced if escapes of farm salmon continue.     

Effects of melatonin feeding on smoltification in masu salmon (Oncorhynchus masou)

Influences of photoperiod on plasma melatonin profiles and effects of melatonin administration on long-day-induced smoltification in masu salmon (Oncorhynchus masou) were investigated in order to reveal the roles of melatonin in the regulation of smoltification in salmonids. Under light-dark (LD) cycles, plasma melatonin levels exhibited daily variation, with higher values during the dark phase than during the light phase. The duration of nocturnal elevation under short photoperiod (LD 8:16) was longer than that under long photoperiod (LD 16:8). Melatonin feeding (0.01, 0.1 and 1 mg/kg body weight) elevated plasma levels of melatonin in a dose-dependent manner for at least 7 h but not for 24 h. When masu salmon reared under short photoperiod were exposed to long photoperiod (LD 16:8) and fed melatonin (1 mg/kg body weight) 7 hours before the onset of darkness, a significantly smaller proportion of smolts appeared in the melatonin-fed group after 32 days than in the control group. However, after 59 days of the treatment, there was no difference in the proportion of smolts between the control and melatonin-treated groups. Thus, melatonin feeding mimicked the effects of short photoperiod, which delays but does not completely suppress smoltification. These results indicate that the day length is transduced into changes in the duration of nocturnal elevation in plasma melatonin levels, and that artificial modification of the plasma melatonin pattern possibly delays the physiological processes of smoltification induced by long-day photoperiodic treatment.     

The lipid status and feeding habits of yearlings of mykiss <Emphasis Type="Italic">Parasalmo mykiss</Emphasis> and coho salmon <Emphasis Type="Italic">Oncorhynchus kisutch</Emphasis> in autumn

Juveniles of coho salmon Oncorhynchus kisutch and mykiss Parasalmo mykiss at the age 1 + (yearlings) are differentiated by the content of different fractions of lipids (the lipid status), feeding habits, and by size-weight characteristics even eight months prior to smoltification. The juveniles of coho salmon and mykiss with high lipid status consume more calorific food items and, as a rule, have higher (on average) body length and weight. The juveniles with low lipid status consume less calorific organisms and have lower body length and weight. It is supposed that a considerable part of juveniles with high lipid status will migrate seaward the next year. The role of feeding habits in formation of this differentiation and, accordingly, in determination of timing of smoltification are discussed.     

Microsatellite Variation in Two Populations of Free-Ranging Yellow Baboons (Papio hamadryas cynocephalus)

We investigated genetic variation at six microsatellite (simple sequence repeat) loci in yellow baboons (Papio hamadryas cynocephalus) at two localities: the Tana River Primate Reserve in eastern Kenya and Mikumi National Park, central Tanzania. The six loci (D1S158, D2S144, D4S243, D5S1466, D16S508, and D17S804) were all originally cloned from and characterized in the human genome. These microsatellites are polymorphic in both baboon populations, with the average heterozygosity across loci equal to 0.731 in the Tana River sample and 0.787 in the Mikumi sample. The genetic differentiation between the two populations is substantial. Kolmogornov–Smirnov tests indicate that five of the six loci are significantly different in allele frequencies in the two populations. The mean F _ST across loci is 0.069, and Shriver's measure of genetic distance, which was developed for microsatellite loci (Shriver et al., 1995), is 0.255. This genetic distance is larger than corresponding distances among human populations residing in different continents. We conclude that (a) the arrays of alleles present at these six microsatellite loci in two geographically separated populations of yellow baboons are quite similar, but (b) the two populations exhibit significant differences in allele frequencies. This study illustrates the potential value of human microsatellite loci for analyses of population genetic structure in baboons and suggests that this approach will be useful in studies of other Old World monkeys.     

The effects of intraperitoneally implanted dummy acoustic transmitters on the behaviour and physiology of juvenile Atlantic salmon, Salmo salar L

The behavioural and physiological effects of surgical implantation of dummy miniature acoustic transmitters into the peritonealcavities ofjuvenile Atlantic salmon, Salmo salar L., were assessed. lntraperitoneal implantations had no significant effect on growth, feeding or swimming behaviour in either parr or smolts. Recovery from the surgical implantation was both rapid and total; infection was absent; and physiological processes such as smoltification and maturation of testes in precocious parr were unaffected. Expulsion of the transmitter through the body wall, not through the implantation wound, occurred in a number of fish but without adversely affecting the animals. The intraperitoneal implantation technique is discussed in relation to its use during biotelemetry studies.     

Variability of size-age indices and genetic variability of sockeye salmon <Emphasis Type="Italic">Oncorhynchus nerka</Emphasis> from the Western Coast of Kamchatka: Comparative analysis of methods of differentiation of local populations

Study of variability of size-age indices and polymorphism of 6 microsatellite loci, 5 loci of SNP, and accidentally amplified polymorphic DNA (RAPD) of sockeye salmon Oncorhynchus nerka of three largest populations from the western coast of Kamchatka Peninsula was performed. The efficiency of using different types of markers for the differentiation of populations and determination of the population belonging of sockeye salmon from lake-river systems of western Kamchatka was analyzed. Significant interpopulation differences were revealed from the frequencies of alleles of genetic markers and from a set of biological indices. It was established that genetic markers are characterized by a better differentiating capacity, as compared to biological characteristics. The most satisfactory results during determination of population belonging of sockeye salmon were obtained using an integrated data base of allele frequencies of microsatellite and SNP loci.     

Genetic Structure of Chum Salmon (Oncorhynchus keta) Populations in the Lower Columbia River: Are Chum Salmon in Cascade Tributaries Remnant Populations?

The lower Columbia River drainage once supported a run of over a million chum salmon. By the late 1950s, the run had decreased to often a few hundred fish. With the exception of Grays River near the coast and an aggregation of chum salmon spawning in creeks and the main stem near Bonneville Dam in the Columbia Gorge, most populations were thought to be extinct. However, chum salmon consistently return in low numbers to tributaries originating in the Cascade Range: the Cowlitz, Lewis, and Washougal rivers. To assess whether Cascade spawners were strays or remnants of former populations, chum salmon from the Coastal, Cascade and Gorge ecoregional zones were characterized at 17 microsatellite loci. Significant heterogeneity in genotype distributions was detected between zones and collections formed regional groups in a neighbor-joining tree. Cascade collections had higher allelic richness and private alleles, and the Cowlitz River supported genetically divergent fall and summer runs, the only summer chum salmon run extant in the Columbia River drainage. We propose that chum salmon in the Cascade zone are remnants of original populations. We attribute the divergence between zonal groups to diverse ecological conditions in each zone, which promoted regional genetic adaptation, and to genetic drift experienced in small populations.     

Comparative mapping reveals quantitative trait loci that affect spawning time in coho salmon (Oncorhynchus kisutch)

Spawning time in salmonids is a sex-limited quantitative trait that can be modified by selection. In rainbow trout (Oncorhynchus mykiss), various quantitative trait loci (QTL) that affect the expression of this trait have been discovered. In this study, we describe four microsatellite loci associated with two possible spawning time QTL regions in coho salmon (Oncorhynchus kisutch). The four loci were identified in females from two populations (early and late spawners) produced by divergent selection from the same base population. Three of the loci (OmyFGT34TUF, One2ASC and One19ASC) that were strongly associated with spawning time in coho salmon (p < 0.0002) were previously associated with QTL for the same trait in rainbow trout; a fourth loci (Oki10) with a suggestive association (p = 0.00035) mapped 10 cM from locus OmyFGT34TUF in rainbow trout. The changes in allelic frequency observed after three generations of selection were greater than expected because of genetic drift. This work shows that comparing information from closely-related species is a valid strategy for identifying QTLs for marker-assisted selection in species whose genomes are poorly characterized or lack a saturated genetic map.     

Microsatellite variability and differentiation of hatchery stocks of chum salmon Oncorhynchus keta Walbaum in Sakhalin

Variability at eight microsatellite loci was examined in five populations of chum salmon Oncorhynchus keta Walbaum from Sakhalin hatcheries. The population of Kalinino hatchery had the lowest heterozygosity and the lowest average number of alleles per locus. The populations examined exhibited significant differentiation, theta ST = 0.026 on average per locus. The maximum genetic differences were found between the populations of the Kalinino and the Ado-Tymovo hatcheries; the latter differs from the remaining populations also by the highest number and high frequencies of specific alleles. The genetic features of the Taranai hatchery population, observed at microsatellite loci, reflect its "mixed" origin.     

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.