Effective population size and temporal genetic change in stream resident brown trout (Salmo trutta, L.)

Temporal genetic data may be used forestimating effective population size (N _e) and for addressing the `temporal stability' of population structure, two issues of central importance for conservation and management. In this paper we assess the amount of spatio-temporal genetic variation at 17 di-allelic allozyme loci and estimate current N _e in two populations of stream resident brown trout (Salmo trutta) using data collected over 20 years. The amount ofpopulation divergence was found to bereasonably stable over the studied time period.There was significant temporal heterogeneitywithin both populations, however, and N _e was estimated as 19 and 48 for the twopopulations. Empirical estimates of theprobability of detecting statisticallysignificant allele frequency differencesbetween samples from the same populationseparated by different numbers of years wereobtained. This probability was found to befairly small when comparing samples collectedonly a few years apart, even for theseparticular populations that exhibit quiterestricted effective sizes. We discuss someimplications of the present results for browntrout population genetics and conservation, andfor the analysis of temporal genetic change inpopulations with overlapping generations ingeneral.     

Spatial and temporal genetic differentiation and effective population size of brown trout (<Emphasis Type="Italic">Salmo trutta</Emphasis>, L.) in small Danish rivers

The spatial and temporal genetic structure of brown trout populations from three small tributaries of Lake Hald, Denmark, was studied using analysis of variation at eight microsatellite loci. From two of the populations temporal samples were available, separated by up to 13 years (3.7 generations). Significant genetic differentiation was observed among all samples, however, hierarchical analysis of molecular variance (AMOVA) showed that differentiation among populations accounted for a non-significant amount of the genetic differentiation, whereas differentiation among temporal samples within populations was highly significant (0.0244, P<0.001). Estimates of effective population size (N _e) using a maximum-likelihood based implementation of the temporal method, yielded small values (N _e ranging from 33 to 79). When a model was applied that allows for migration among populations, N _e estimates were even lower (24–54), and migration rates were suggested to be high (0.13–0.36). All samples displayed a clear signal of a recent bottleneck, probably stemming from a period of unfavourable conditions due to organic pollution in the 1970–1980’s. By comparison to other estimates of N _e in brown trout, Lake Hald trout represent a system of small populations linked by extensive gene flow, whereas other populations in larger rivers exhibit much higher N _e values and experience lower levels of immigration. We suggest that management considerations for systems like Lake Hald brown trout should focus both on a regional scale and at the level of individual populations, as the future persistence of populations depends both on maintaining individual populations and ensuring sufficient migration links among these populations.     

A population analysis of Robertsonian and Ag-NOR polymorphisms in brown trout (Salmo trutta)

An analysis of Robertsonian polymorphism and variation in the number of active NORs has been carried out in several populations of brown trout (Salmo trutta) from Northwestern Spain. The karyotype of this species appears to be soundly established, and essentially no variation has been found in chromosome number. Interindividual and interpopulation variation in arm number was detected, with figures ranging between 100 and 102 among individuals, and between 100.10 and 100.80 among populations. This variation in arm number is solely attributable to the polymorphism of the short arm of the main NOR-bearing pair 11, which can appear from acrocentric to metacentric in different individuals. Most populations analyzed showed the standard distribution of active NORs previously observed in this species. The Miño drainage basin, and specially the Chamoso population, showed a multi-chromosomal distribution of active NORs, with several new locations, always telomeric. In most cases no concordance was observed between previously detected rDNA sites in S. trutta and the new Ag-NOR locations. This fact suggests a transposition mechanism rather than an activation of silent rDNA sites to explain this multichromosomal NOR pattern.     

Long-term temporal changes of genetic composition in brown trout (Salmo trutta L.) populations inhabiting an unstable environment

The genetic structure of brown trout (Salmo trutta) populations inhabiting rivers on the island of Bornholm in the Baltic Sea was studied on a spatial and temporal scale. Low water levels in the rivers during the summer period are assumed to have a significant impact on the persistence of local populations, possibly resulting in a metapopulation structure. Extinctions may, however, also be buffered by a remnant strategy, whereby juveniles escape to river outlets during periods of drought. We compared polymorphism at seven microsatellite DNA loci in contemporary and past samples collected from 1944 to 1997. A principal component analysis, a hierarchical gene diversity analysis and assignment tests showed that the genetic composition of populations was not temporally stable, and that temporal genetic differentiation was much stronger than spatial differentiation. Genetic variability was high and stable over time. Effective population sizes (Ne) and migration rate (m) were estimated using a maximum-likelihood-based implementation of the temporal method. Ne estimates were low (ranging from 8.3 to 22.9) and estimates of m were high (between 0.23 and 0.99), in contrast to other Danish trout populations inhabiting larger and more environmentally stable rivers (Ne between 39.2 and 289.9 and m between 0.01 and 0.09). Thus, the observed spatio-temporal patterns of genetic differentiation can be explained by drift in small persisting populations, where levels of genetic variation are maintained by strong gene flow. However, observations of rivers devoid of trout suggested that population turnover also takes place. We suggest that Bornholm trout represent a metapopulation where the genetic structure primarily reflects strong drift and gene flow, combined with occasional extinction-recolonization events.     

Being abundant is not enough: a decrease in effective population size over eight generations in a Norwegian population of the seaweed, Fucus serratus

The brown alga Fucus serratus is a key foundation species on rocky intertidal shores of northern Europe. We sampled the same population off the coast of southern Norway in 2000 and 2008, and using 26 microsatellite loci, we estimated the changes in genetic diversity and effective population size (Ne). The unexpectedly low Ne (73-386) and Ne/N ratio (10-3-10-4), in combination with a significant decrease (14%) in allelic richness over the 8-year period, suggests an increased local extinction risk. If small Ne proves to be a common feature of F. serratus, then being abundant may not be enough for the species to weather future environmental changes.     

Spatio-temporal genetic structuring of brown trout (Salmo trutta L.) populations within the River Luga, northwest Russia

The brown trout populations of the Baltic Sea region have been drastically affected by various human activities during the past century. Due to their propensity to home to their natal site to spawn and their tendency to evolve local adaptations, populations may be genetically differentiated in water systems where no physical barriers preventing interbreeding exist. Consequently, identification of management units, a prerequisite for appropriate conservation and management planning, cannot necessarily be deduced from the physical properties of the habitat. In this study, microsatellite markers were employed to assess the spatio-temporal genetic structuring of inter-connected brown trout populations from a river-system in Northwest Russia. Populations were found to be genetically differentiated from each other (global F _ST 0.06) and the genetic structuring within the river to follow an isolation by distance pattern. Indications of temporal stability were found in some populations, however others appeared to be temporally unstable suggesting differences in the demographic forces affecting the populations. Based on the observed isolation by distance pattern of genetic differentiation, preserving several breeding sites spaced evenly throughout the river-system would appear to be more appropriate than focussing conservation effort on any single stretch of the river. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Long-term effective population sizes, temporal stability of genetic composition and potential for local adaptation in anadromous brown trout (Salmo trutta) populations

We examined the long-term temporal (1910s to 1990s) genetic variation at eight microsatellite DNA loci in brown trout (Salmo trutta L) collected from five anadromous populations in Denmark to assess the long-term stability of genetic composition and to estimate effective population sizes (Ne). Contemporary and historical samples consisted of tissue and archived scales, respectively. Pairwise thetaST estimates, a hierarchical analysis of molecular variance (amova) and multidimensional scaling analysis of pairwise genetic distances between samples revealed much closer genetic relationships among temporal samples from the same populations than among samples from different populations. Estimates of Ne, using a likelihood-based implementation of the temporal method, revealed Ne >or= 500 in two of three populations for which we have historical data. A third population in a small (3 km) river showed Ne >or= 300. Assuming a stepping-stone model of gene flow we considered the relative roles of gene flow, random genetic drift and selection to assess the possibilities for local adaptation. The requirements for local adaptation were fulfilled, but only adaptations resulting from strong selection were expected to occur at the level of individual populations. Adaptations resulting from weak selection were more likely to occur on a regional basis, i.e. encompassing several populations. Ne appears to have declined recently in at least one of the studied populations, and the documented recent declines of many other anadromous brown trout populations may affect the persistence of local adaptation.     

Enhanced individual selection for selecting fast growing fish: the "PROSPER" method,with application on brown trout (Salmo trutta fario)

Growth rate is the main breeding goal of fish breeders, but individual selection has often shown poor responses in fish species. The PROSPER method was developed to overcome possible factors that may contribute to this low success, using (1) a variable base population and high number of breeders (Ne > 100), (2) selection within groups with low non-genetic effects and (3) repeated growth challenges. Using calculations, we show that individual selection within groups, with appropriate management of maternal effects, can be superior to mass selection as soon as the maternal effect ratio exceeds 0.15, when heritability is 0.25. Practically, brown trout were selected on length at the age of one year with the PROSPER method. The genetic gain was evaluated against an unselected control line. After four generations, the mean response per generation in length at one year was 6.2% of the control mean, while the mean correlated response in weight was 21.5% of the control mean per generation. At the 4th generation, selected fish also appeared to be leaner than control fish when compared at the same size, and the response on weight was maximal (≈130% of the control mean) between 386 and 470 days post fertilisation. This high response is promising, however, the key points of the method have to be investigated in more detail.     

Genetic changes in Atlantic salmon stocks since historical times and the effective population size of a long-term captive breeding programme

Human-caused genetic changes in two Atlanticsalmon (Salmo salar L.) stocks, from therivers Iijoki and Oulujoki in Finland, wereassessed by comparing the genetic parameters ofthese stocks before and after the hatcherybreeding of several successive generations,corresponding to 40 and 33 years since the wildstate. The changes were also compared withthose observed in a large wild salmon stock inthe River Teno during 56 years. In all, thevariation at seven microsatellite DNA loci wasexamined in 11 Atlantic salmon samplesoriginating from these three rivers. Theeffective population size, N_e, duringbreeding of the Iijoki broodstock and for theTeno salmon was also estimated by the temporalmethod based on allele frequency changes. Forthe Iijoki broodstock, the changes could betracked generation by generation from thefounding of the stock. Statisticallysignificant changes in allele frequencies werecommon in the hatchery stocks (F = 0.029, forIijoki), but not in the wild Teno stock, whichwas temporally very stable (F = 0.007). Allelicrichness decreased statistically significantly(24.8%) in the Oulujoki broodstock, from 62.1to 46.7 alleles at nine loci. On average, therewere 9.7 fewer alleles (15.7%) in thecontemporary broodstocks than in thecorresponding historical stocks. The meanheterozygosity was 6.6% lower in thecontemporary Oulujoki broodstock, but remainedunchanged in the Iijoki broodstock. Theestimated N_e for the Iijoki broodstock wasunder 80 for 4.5 generations from 1962 to 1995and for the wild Teno salmon over 900 for 56years from 1939 to 1995.     

Reproductive ecology and growth of a population of brown trout (Salmo trutta L.) in an aquifer-fed stream of Old Castile (Spain)

In the River Lobos-Ucero and its tributary the River Avión-Milanos (Duero basin, Old Castile, Central Spain), two limestone streams fed by aquifers, the population of brown trout, as compared with the populations of other European streams, shows a high growth rate, high condition coefficients, short life-span and early age at first maturity. Gonad cycle was also studied. Size distributions of unshed eggs exhibit a dynamic activity with a bi-modal distribution from June onwards, spawning occurred in the last days of November. Fecundity (F) can be predicted from trout length (L, mm) according to the equation: F= –646.47+5.6167 · L. Numbers and standing crop of trout range from 18 to 3903 ind. ha^–1 and 3.6 to 452.9 Kg ha^–1, reaching higher values in the sites close to the aquifers. Egg production had values of 22.4 and 18.0 eggs m^–2 in the Rivers Ucero and Avión-Milanos respectively. Some factors suggested as regulators of these demographical characteristics are discussed in the light of recent literature.     

Dynamic micro-geographic and temporal genetic diversity in vertebrates: the case of lake-spawning populations of brown trout (Salmo trutta)

Conservation of species should be based on knowledge of effective population sizes and understanding of how breeding tactics and selection of recruitment habitats lead to genetic structuring. In the stream‐spawning and genetically diverse brown trout, spawning and rearing areas may be restricted source habitats. Spatio–temporal genetic variability patterns were studied in brown trout occupying three lakes characterized by restricted stream habitat but high recruitment levels. This suggested non‐typical lake‐spawning, potentially representing additional spatio–temporal genetic variation in continuous habitats. Three years of sampling documented presence of young‐of‐the‐year cohorts in littoral lake areas with groundwater inflow, confirming lake‐spawning trout in all three lakes. Nine microsatellite markers assayed across 901 young‐of‐the‐year individuals indicated overall substantial genetic differentiation in space and time. Nested gene diversity analyses revealed highly significant (≤P = 0.002) differentiation on all hierarchical levels, represented by regional lakes (F_LT = 0.281), stream vs. lake habitat within regional lakes (F_HL = 0.045), sample site within habitats (F_SH = 0.010), and cohorts within sample sites (F_CS = 0.016). Genetic structuring was, however, different among lakes. It was more pronounced in a natural lake, which exhibited temporally stable structuring both between two lake‐spawning populations and between lake‐ and stream spawners. Hence, it is demonstrated that lake‐spawning brown trout form genetically distinct populations and may significantly contribute to genetic diversity. In another lake, differentiation was substantial between stream‐ and lake‐spawning populations but not within habitat. In the third lake, there was less apparent spatial or temporal genetic structuring. Calculation of effective population sizes suggested small spawning populations in general, both within streams and lakes, and indicates that the presence of lake‐spawning populations tended to reduce genetic drift in the total (meta‐) population of the lake.     

Glucose metabolism by trout (Salmo trutta) red blood cells

Summary Glucose metabolism has been studied in Salmo trutta red blood cells. From non-metabolizable analogue (3-O-methyl glucose and l-glucose) uptake experiments it is concluded that there is no counterpart to the membrane transport system for glucose found in mammalian red blood cells. Once within the cells, glucose is directed to CO₂ and lactate formation through both the Embden-Meyerhoff and hexose monophosphate shunts; lactate appears as the most important endproduct of glucose metabolism in these cells. From experiments under anaerobic conditions, and in the presence of an inhibitor of pyruvate transfer to mitochondria, most of the CO₂ formed appears to derive from the hexose monophosphate pathway. Appreciable O₂ consumption has been detected, but there is no clear relationship between this and substrate metabolism. Key enzymes of glucose metabolism hexokinase, fructose-6-phosphate kinase and, probably, pyruvate kinase are out of equilibrium, confirming their regulatory activity in Salmo trutta red blood cells. The presence of isoproterenol, a catecholamine analogue, induces important changes in glucose metabolism under both aerobic and anaerobic conditions, and increases the production of both CO₂ and lactate. From the data presented, glucose appears to be the major fuel for Salmo trutta red blood cells, showing a slightly different pattern of glucose metabolism from rainbow trout red blood cells.Abbreviations EM Embden-Meyerhoff pathway - G6D glucose-6-phosphate dehydrogenase - GOT glutamate oxalacetate transaminase - GPI glucose phosphate isomerase - HK hexokinase - HMS hexose monophosphate shunt - IP isoproterenol - LDH lactate dehydrogenase - MCB modified Cortland buffer - OMG 3-O-methyl glucose - PFK fructose-6-phosphate kinase - PK pyruvate kinase - RBC red blood cells - TAC tricarboxylic acid cycle     

Food availability and growth rate in natural populations of the brown trout (Salmo trutta) in Corsican streams

The rivers of the island of Corsica, whose catchment areas are on crystalline rock, have low salt contents and their invertebrate fauna is qualitatively and quantitatively poorer than on the European mainland. The growth rate of trout in Corsica was analysed on samples from of six coastal rivers: the Tavignano, the Fium Orbo and the Golo on the west coast, the Prunelli, the Taravo and the Rizzanese on the east coast. Mesological data — conductivity, temperature, calcium content and altitude and biological data — biomass and linear growth rate of the trout, and density of benthic invertebrates — were collected at each of the sampling station.Analysis of variance of the size of three year old trout revealed three groups of rivers. The first includes the Tavignano, the Rizzanese and the Taravo, where the highest linear growth rates were recorded; the second consists of the Golo and the Prunelli, and the third, of the Fium Orbo. Principal component analysis gave two main axes on the basis of temperature and benthic invertebrate density for the first, and trout biomass for the second. Linear regression showed that benthic invertebrate density accounted for 75% of size variance of three year old trout. Evidence of the limiting role of the trophic factor is provided.     

Lack of molecular genetic divergence between sea-ranched and wild sea trout (Salmo trutta)

The supportive breeding programme for sea trout (Salmo trutta) in the River Dalälven, Sweden, is based on a sea‐ranched hatchery stock of local origin that has been kept ‘closed’ to the immigration of wild genes since the late 1960s (about seven generations). In spite of an apparent potential for substantial uni directional gene flow from sea‐ranched to wild (naturally produced) trout, phenotypic differences with a presumed genetic basis have previously been observed between the two ‘stocks’. Likewise, two previous studies of allozyme and mitochondrial DNA variation based on a single year of sampling have indicated genetic differentiation. In the present study we used microsatellite and allozyme data collected over four consecutive years, and tested for the existence of overall genetic stock divergence while accounting for temporal heterogeneity. Statistical analyses of allele frequency variation (F‐statistics) and multilocus genotypes (assignment tests) revealed that wild and sea‐ranched trout were significantly different in three of four years, whereas no overall genetic divergence could be found when temporal heterogeneity among years within stocks was accounted for. On the basis of estimates of effective population size in the two stocks, and of F_ST between them, we also assessed the level of gene flow from sea‐ranched to wild trout to be ≈ 80% per generation (with a lower confidence limit of ≈ 20%). The results suggest that the reproductive success of hatchery and naturally produced trout may be quite similar in the wild, and that the genetic characteristics of the wild stock are largely determined by introgressed genes from sea‐ranched fish.     

Temporal variations in the diet of brown trout (Salmo trutta L.) and rainbow trout (S. gairdneri R.) in Rutland Water

The diet of brown trout (Salmo trutta L.) and rainbow trout (S. gairdneri Richardson) in Rutland Water were compared during the first two fishing seasons (April–October 1977 and 1978).Fortnightly samples of approximately forty stomachs were obtained from boat and bank, rod-and-line caught trout giving a total of 1046 stomachs over the two seasons.During 1977 seasonal changes in the diet were divided into two phases; the first being a period of abundant drowned terrestrial food until June. This was followed by a period of more stable water level from July onwards when chironomid larvae and pupae were consistently the most important food items and the diversity of food also increased.In 1978 the proportion of chironomid pupae and larvae declined and they were replaced in the diet by Gammarus and Asellus.     

Effects of six trace metals on calcium fluxes in brown trout (Salmo trutta L.) in soft water

Summary Calcium fluxes were measured simultaneously in brown trout fry maintained in an artificial soft water medium of [Ca] 20 mol·l^-1 and pH 5.6, and exposed to each of six trace metals (Al, Cu, Fe, Ni, Pb, and Zn). The trace metal concentrations represented typical and maximum levels found in acid waters experiencing declining fishery status. In the absence of trace metals, evidence is presented which suggests that ca. 91% of Ca taken up from the external medium was by extraintestinal active transport. Calcium efflux was stimulated by both concentrations of Al, Cu, Fe, and Pb. Efflux was also stimulated by [Ni] 170 nmol·l^-1 and [Zn] 3000 nmol·l^-1. In some cases, response to increased efflux was stimulation of influx. Lack of stimulation of influx resulted in negative net Ca fluxes. Net Ca losses were recorded at both concentrations of Al, Pb, and Ni, lower concentrations only of Fe, and higher concentrations only of Cu and Zn.Abbreviations J _in influx - J _net net flux - J _out efflux Henceforward in this paper, chemical elements are referred to by their chemical symbols rather than by full names     

Managing fish populations under mosaic relationships. The case of brown trout (Salmo trutta) in peripheral Mediterranean populations

Brown trout were collected from 36 locations inthe Iberian Peninsula representing thesouthwestern extreme of this species'distribution in Mediterranean drainages.Allelic distributions among these peripheralpopulations for 26 polymorphic allozyme loci(corrected to remove effects of introgressionfrom exogenous hatchery introductions)indicated a mosaic pattern both within andamong drainages. This distribution wasinterpreted to reflect reticular evolutionaryprocesses involving multiple colonizationepisodes by distinct lineages, secondaryintergradations, and drift. Under thisscenario, management to conserve native genepools differs from that commonly used underhierarchical structures (such as in AtlanticIberian drainages) where geographic patternscould justify regional stocking of indigenousfish in adjacent unsampled areas. Because suchaction risks erosion of native populations inthe present case, remedial efforts should focuson habitat recovery and environmental educationprograms, and harvest sustained by naturalreproduction.     

Spatio-temporal genetic variability in sea trout (Salmo trutta) populations from north-western Spain

1. Genetic variation at five microsatellite loci was investigated in six sea trout ( Salmo trutta ) populations to describe their spatio-temporal genetic variation in north-western Spain. We observed significant genetic variation between river basins, and isolation by distance with restricted gene flow between neighbouring rivers, which suggests an important homing behaviour.
2. Despite these populations suffering a serious demographic decline during 1998, we did not detect any reduction in their genetic variation, suggesting a reasonably high effective population size and temporal stability.
3. Genetic differences among rivers should be taken into account in future management activities. Given the high genetic variability and the temporal stability observed, we believe that no supportive breeding programmes are presently needed in these populations.     

Demographic and genetic estimates of effective population size (Ne) reveals genetic compensation in steelhead trout

Estimates of effective population size (Ne) are required to predict the impacts of genetic drift and inbreeding on the evolutionary dynamics of populations. How the ratio of Ne to the number of sexually mature adults (N) varies in natural vertebrate populations has not been addressed. We examined the sensitivity of Ne/N to fluctuations of N and determined the major variables responsible for changing the ratio over a period of 17 years in a population of steelhead trout (Oncorhynchus mykiss) from Washington State. Demographic and genetic methods were used to estimate Ne. Genetic estimates of Ne were gained via temporal and linkage disequilibrium methods using data from eight microsatellite loci. DNA for genetic analysis was amplified from archived smolt scales. The Ne/N from 1977 to 1994, estimated using the temporal method, was 0.73 and the comprehensive demographic estimate of Ne/N over the same time period was 0.53. Demographic estimates of Ne indicated that variance in reproductive success had the most substantial impact on reducing Ne in this population, followed by fluctuations in population size. We found increased Ne/N ratios at low N, which we identified as genetic compensation. Combining the information from the demographic and genetic methods of estimating Ne allowed us to determine that a reduction in variance in reproductive success must be responsible for this compensation effect. Understanding genetic compensation in natural populations will be valuable for predicting the effects of changes in N (i.e. periods of high population density and bottlenecks) on the fitness and genetic variation of natural populations.     

Localisation of NORs and counterstain-enhanced fluorescence studies in Salmo gairdneri and Salmo trutta (Pisces,Salmonidae)

Summary The karyotypes of the rainbow trout (Salmo gairdneri R.) and the brown trout (Salmo trutta L.) were analyzed by means of silver staining and the chromomycin A₃/distamycin A/DAPI fluorescence banding technique. The nucleolus organizer regions (NORs) were localized at the secondary constrictions of chromosome no. 14 in S. gairdneri and of chromosome no. 10 in S. trutta. Additional silver positive dots were observed at or close to several centromeres in S. gairdneri. Brilliant chromomycin A₃ (CMA₃) fluorescence heterochromatin blocks were localized on both sides of the nucleolar constrictions in S. gairdneri. A polymorphic CMA₃ positive band was detected close to the NORs of S. trutta. No distamycin A/DAPI intense heterochromatin blocks were detected in the genomes of the two Salmo species investigated.