Allozymic variation and differentiation in naturalized populations of rainbow trout, Oncorhynchus mykiss (Walbaum), from southern Chile

An allozyme survey was conducted in three naturalized populations of rainbow trout, Oncorhynchus mykiss (Walbaum), from rivers in two Andean lakes of southern Chile. The analysis was based on 32 presumed loci, 10 of which were variable, and revealed that the mean percentage of polymorphic loci (P= 21.8%; range = 15.6-28.1%), the mean number of alleles per locus (n=1.26; range = 1.2-1.3) and the mean observed heterozygosity (H_O=7.0%; range = 6.0-8.2%) are high, although within the range reported for rainbow trout. Although the mean genetic distance between the samples was low (D = 0.003), and only 5.2% of the total observed genetic variation can be accounted by interpopulation differences (F_ST= 0.052), eight out of 10 polymorphic loci exhibited significant allelic heterogeneity. Some loci, notably EST-1*, IDHP-3,4*, MEP-1* and PGM-1*, showed considerable discriminatory capacity among the samples. Rainbow trout has a longer history in Chilean waters since salmonid introduction started earlier this century. Under current intensive farming practices, the preliminary information provided in the present paper is likely to be helpful in setting up a baseline for further characterization and/or monitoring of naturalized populations.     

Stocking impact,population structure and conservation of wild brown trout populations in inner Galicia (NW Spain), an unstable hydrologic region

1. Brown trout (Salmo trutta) is an important conservation resource in the Iberian Peninsula. The Atlantic is considered the most hydrologically stable region for the species, although inner Galicia (NW Spain) shows Mediterranean (unstable) climatic conditions. The Galician region, threatened by past releases of brown trout individuals from central European origin, harbours two native lineages, one of them endemic to the Iberian Peninsula. These populations are thus highly valuable for conservation, as well as being important for recreational fisheries. 2. In total, 546 individuals from 16 sampling sites (15 natural locations from inner Galicia and one from a central European hatchery stock) were genotyped for 11 nuclear markers (10 microsatellite loci and the LDH‐C* locus) to analyse genetic variability, population structure and introgression impact from stocking in order to assess the conservation status of brown trout in the region. Moreover, correlation among hatchery introgression and environmental variables relevant for species population dynamics was also investigated. 3. Genetic variability was within the range of Iberian brown trout (He = 0.500–0.600). Stocking impact was higher than previously reported values for the Atlantic region and was related to environmental instability. Highly significant native population differentiation was observed in the whole region (F_ST = 0.283), at least four main genetic groups being detected across the geographic distribution studied. 4. Conservation strategies at local level (including the creation of genetic refuges and temporal monitoring of genetic composition) are suggested to agencies and administrations for the sustainable management of brown trout.     

Genetic variation and population structure of the caramote prawn Penaeus kerathurus (Forskäl) from the eastern and western Mediterranean coasts in Tunisia

Ten populations of Penaeus kerathurus (Forskäl), a prawn of high commercial value, were sampled from the eastern and western Mediterranean coastal waters of Tunisia and screened electrophoretically for genetic variation at 13 allozyme loci. Four among the six polymorphic loci were out of Hardy–Weinberg equilibrium (H–WE) in at least one population. In the same way, the multilocus test showed deviation from H–WE in six populations. These populations showed heterozygote deficiency whereas the average heterozygosity for the four remaining ones is quite similar to the expected levels. Genetic variability was low. The number of alleles per locus ranged from 1.2 to 1.5 (average=1.3), and the observed heterozygosity varied between 0.010 and 0.048 (average=0.021). Significant population differentiation (F_ST=0.076, P<0.05) in the total data set reflected the differentiation of the two populations, which were at the margins of the range sampled, from all the others (Pairwise F_ST values ranged from 0.035 to 0.208). Although there was no significant differentiation among the other populations (pairwise F_ST values ranged from ?0.006 to 0.201, P>0.05). Our data suggest a population structure consistent with separation by Mediterranean Sea basins that might reflect different local biogeographical zones.     

Identification of Two Channel Catfish Stocks,Ictalurus punctatus,Cultivated in Northeast Mexico

The channel catfish farming in Mexico began in the 1970s. One of the most important areas of production is its northeastern region. Traditionally, the channel catfish farmers have attempted to preserve their original genetic stock. After more than 30 yr of production, the genetic relationship between stocks has not been assessed. The goal of this study was to evaluate the genetic differentiation between five channel catfish farm populations, using 13 microsatellite markers. A total of 154 fin clip samples were collected from five channel catfish farms in Tamaulipas. We also included 31 individuals of the commercial strain NWAC103. In each population, we calculated parameter of genetic variability: inbreeding coefficient (F_IS), pairwise differentiation (F_ST), and genetic distance (D_C). For the inference of populations and individual assignment two Bayesian methods were used. Genetic variability parameters were N_A = 9.54–11.08 and A_E = 5.40–6.67. Hardy–Weinberg equilibrium deviations were observed for all farm populations examined, and a deficit of heterozygotes was found. Signals of inbreeding were observed, particularly for the ACU (Acuamex) hatchery. Populations EKA (Empresas Karol) and ACU showed higher genetic differentiation values with respect to the commercial strain (F_ST = 0.107; F_ST = 0.082, respectively). Moderated genetic differences (F_ST = 0.067; D_C = 0.080) were observed between the EKA and ACU. Clustering analysis revealed a well‐defined group between EKA and TPA (El Tiron Parejo). In the Bayesian analysis three groups were defined. The first group was formed by EKA and TPA, the second group included ACU, LAJ (La Lajilla), and PRO (Prodatec). In the third group was the commercial strain. In the assignment of individuals, EKA and ACU were represented by exclusive genotypes. Identification of two genetic stocks, one located in the EKA and the other in the ACU population, will be relevant for future management of these hatcheries. Additionally, the information from microsatellites and the statistical procedures presented will be important tools for genetic monitoring of these farm populations.     

Effects of stocking on the genetic structure of brown trout,Salmo trutta,in Central Europe inferred from mitochondrial and nuclear DNA markers

Abstract Stocking has had a considerable effect on wild brown trout, Salmo trutta L., populations throughout Europe. To elucidate this impact and to outline further management strategies, the genetic structure of 25 wild populations and five hatchery stocks from Czech Republic and Slovakia were analysed using mitochondrial (control region) and nuclear DNA (microsatellites, LDH‐C1*) markers. Stocking practices have caused massive hybridisation between the Atlantic and Danube brown trout strains in the central Danube basin and have lead to a loss of among‐population divergence in Slovakia and the eastern part of Czech Republic. Comparison with studies from neighbouring countries revealed substantial differences in haplotype, allele frequencies and genetic diversity across Central Europe. Differences in stocking management and origin of breeding stocks appear to be crucial factors for the spatial variability of the genetic structure of brown trout.     

Genetic variability in four hatchery strains of coho salmon, Oncorhynchus kisutch (Walbaum), in Chile

Coho salmon, Oncorhynchus kisutch (Walbaum), is intensively cultured in Chile. An increasing proportion of the eggs necessary to sustain the culture are locally produced by some hatcheries. However, there is no information about the origin or the genetic variability in these strains. The present study analysed allozymic variability and its distribution within and between some commercial strains of coho salmon in southern Chile. The genetic variability was estimated using horizontal starch gel electrophoresis. Samples of coho salmon were obtained randomly from four Chilean hatcheries. Twenty‐five enzymatic systems were examined, representing 51 enzymatic loci. Eight loci showed variability in at least one strain, which represented a total polymorphism (P) of 15.7%. Only the PGM‐1* locus was variable in all strains. The remaining loci were fixed in at least one strain. Total heterozygosity (H_T) and within population heterozygosity (H_S) were 0.35% and 0.36% respectively. The index of genetic diversity (G_ST) was 1.5%. The results confirm previous reports of low genetic variability in cultured strains of coho salmon in Chile, below that observed in their native range, which suggests loss of the genetic variability caused by genetic drift or other causes in these strains.     

Genetic structure of brown trout,Salmo trutta,populations from differently sized tributaries of Lake Mjøsa in south‐east Norway

This study was based on genotyping eight microsatellite loci of 463 brown trout, Salmo trutta L., sampled in nine differently sized tributaries in three areas on the eastern shore of Lake Mjøsa, south‐eastern Norway. The populations were genetically structured, and Mantel's test showed that genetic distance correlated positively with geographical distance. Temporal differentiation F_ST over a 2‐year period was estimated in five streams and was non‐significant after Bonferroni correction. Effective population size N_e was positively correlated with the habitat length available from the lake (0.3–22 km) and negatively with the number of full sib pairs in the sample. There was no correlation between N_e and genetic diversity, and private alleles were recorded in three medium‐sized streams, but not in the largest two. The importance of small spawning and nursery streams for the maintenance of genetic diversity of brown trout was demonstrated.     

Genetic diversity within sea trout population from an intensively stocked southern Baltic river,based on microsatellite DNA analysis

Sea trout, Salmo trutta L., populations in the Slupia River basin have been affected by mass stocking with smolts and fry. This work is focused on a small‐scale differentiation in sea trout populations from one basin with a strong emphasis on the relationship between wild and hatchery origin fish. A total of 216 sea trout were genotyped at 10 microsatellite loci. Global F_ST obtained by amova was low at 0.0165. Pairwise F_ST were significant for all tests except wild and stocked adults. The highest pairwise difference was found between the hatchery sample and Kwacza (F_ST = 0.038). Analysis of the genetic structure revealed micro‐geographical differentiation with four subpopulations. The quality of the artificial spawning was found not to be adequate with a high risk of adverse effects to the whole population. All future stocking actions in the basin should consider the existing population structures.     

Genetic variation measured by microsatellites among three strains of domesticated rainbow trout (Oncorhynchus mykiss, Walbaum)

Genetic variation fuels selective change in natural and captive populations. In establishing a broodstock for selective improvement, the level of genetic diversity is an important consideration because it provides an indication of the scope for selective progress. Three domesticated strains of rainbow trout, Oncorhynchus mykiss (Walbaum), were examined at nine polymorphic microsatellite loci to assess detectable levels of allelic diversity and heterozygosity within and differentiation among the strains. A total of 126 alleles were observed to segregate into unique multilocus genotypes for each of the 152 individuals assayed. There was an average heterozygosity of 71.5% at these nine loci, and an average of 14 alleles at a locus. Each locus was represented by alleles unique to at least two of the three strains. Deviations from Hardy–Weinberg expectations of genotype frequencies were detected in each strain. Subsequent analysis indicated sub‐structuring within strains leading to Wahlund effects that caused these deviations. Significant differences in genotype frequencies and pairwise F_ST values demonstrated that all strains were unique. The overall F_ST of 0.089 provides additional evidence of unique genetic diversity present in each strain, and agrees well with the degree of genetic variation found in rainbow trout across broad geographical ranges. The genetic diversity contributed by each population suggests that there is greater scope for selective improvement of numerous traits within a synthetic strain combining these three strains than within any individual strain.     

Microsatellite‐based genetic and growth analysis for a diallel mating design of two stocks of the clam,Meretrix meretrix

To determine the potential for productive efficiency and genetic improvement in the clam (Meretrix meretrix), four populations were produced from a diallel mating of two different geographical stocks (SD and JS). The genetic parameters at nine novel microsatellite loci indicated that the numbers of alleles, observed heterozygosity and polymorphic information content of the reciprocal cross populations (SDJS and JSSD) were larger than those of the pure populations (JSJS and SDSD). The values of Nei's unbiased genetic distance and F_ST revealed that the largest genetic divergence was between the two pure populations (D_C=0.2993, F_ST=0.1438) and the smallest was between the two reciprocal cross populations (D_C=0.1093, F_ST=0.0583). In addition, the mean shell lengths of the reciprocal cross populations were significantly larger than that of the pure populations by 1.577 mm (P<0.05), and the same trend was observed in the other traits. A significant maternal effect was revealed after analysis of the effects of egg origin and mating strategy on the four traits. Heteroses for all the traits were detected in the reciprocal cross populations. Our research implies an extensive development potential in productive efficiency and genetic improvement for M. meretrix.     

Do dams increase genetic diversity in brown trout (Salmo trutta)? Microgeographic differentiation in a fragmented river

Abstract – Local genetic differentiation may potentially arise in recently fragmented populations. Brown trout is a polytypic species exhibiting substantial genetic differentiation, which may evolve in few generations. Movement (semi‐)barriers in rivers may cause fragmentation, isolation and genetic differentiation in fish. In the Måna River (28 km) flowing from the alpine Lake Møsvatn to the boreal Lake Tinnsjø, construction of four hydropower dams during the period 1906–1957 have fragmented the previously (since last Ice Age) continuous wild resident brown trout population. Samples from the two lakes (N = 40) and six sites in the river (N = 30) isolated at different times were analysed at nine microsatellite loci. All populations showed substantial genetic variation (mean number of alleles per locus 5.3–8.9, observed heterozygosity 0.57–0.65 per population, overall F_st = 0.032). Pairwise multilocus F_st estimates indicated no significant differentiation between populations in the two lakes, and no or little differentiation in the lower river (F_st = 0.0035–0.0091). The microgeographic differentiation among wild resident trout at these sites was less than expected based on similar previous studies. However, results from the upper river, in particular the site immediately below the Lake Møsvatn outlet and dam, indicated isolation (F_st > 0.035). Calculation of genetic distances and assignment tests corroborated these results, as did a significant correlation between years of isolation (since dam construction) and F_st. The population structuring is most likely a result of fragmentation by dams, which has increased overall genetic diversity. This increased local differentiation may be caused by natural selection, but more likely by genetic drift in small, recently fragmented populations. Increased local genetic diversity by genetic drift does not justify conservation measures aiming at preserving genetic diversity.     

Genetic diversity and differentiation of sea trout (<Emphasis Type="Italic">Salmo trutta</Emphasis>) populations in Lithuanian rivers assessed by microsatellite DNA variation

The genetic diversity and differentiation of sea trout were studied in three river basins in Lithuania: Akmena-Dane, Bartuva, and Nemunas. A total of 282 individuals were genotyped at eight microsatellite loci. A similar level of genetic diversity was found in all of the populations studied: mean allelic richness ranged from 3.64 to 5.03, and average expected heterozygosity ranged from 0.588 to 0.721. Significant genetic divergence was observed among the different river basins as well as between populations within the drainages. All pairwise F _ST values were highly significant, ranging from 0.027 to 0.197. The analysis of molecular variance showed rather weak hierarchical population structuring within the Nemunas basin, which may be explained by extensive gene flow among different river basins or, alternatively, reflect the influence of artificial breeding. Information on genetic diversity and differentiation of the Lithuanian sea trout populations will be useful for future management decisions.     

Loss of genetic variability in the captive stocks of tambaqui,Colossoma macropomum (Cuvier, 1818), at breeding centres in Brazil,and their divergence from wild populations

The loss of variability in farmed populations and the risks of interactions with wild populations support the need for the genetic monitoring of species farmed throughout the world. In Brazil, the tambaqui is the most widely farmed native fish species. Despite this, there are no data on the pedigree of the farmed stocks, and the potential for interactions with wild populations in the Amazon basin has raised concerns with regard to the genetic variability of these stocks. The present study analysed sequences of the mitochondrial Control Region and 12 microsatellites to characterize the genetic variability of seven historically important commercial tambaqui breeding centres located in four different regions of Brazil, and compared these sequences with those obtained from individuals collected from a wild population. High levels of genetic diversity were found in the wild population, whereas genetic diversity was reduced in both markers in most captive populations, except for the broodstock located near the Amazon River. High F_ST and D_EST indices were recorded between the wild population and most of the captive stocks analysed. The drastic reduction in genetic diversity found in most captive stocks and the difference between these stocks and the wild population may have been the result of the small size of the founding populations and the absence of breeding management. The renewal of the broodstocks and the application of breeding management techniques are recommended. In the Amazon region, in addition, the use of broodstocks that are genetically very different from local wild populations should be avoided.     

Genetic monitoring of broodstocks of the marine shrimp Litopenaeus vannamei in a closed rearing system in Pernambuco,Brazil

Loss of genetic variability can be detrimental to a population's survival traits and fitness. These effects are likely to be maximized in shrimp closed broodstock rearing systems where post‐larvae are often produced from crosses of breeders collected from an associated grow‐out farm after mass selection. Longtime broodstock management in closed systems is also expected to lead to reduction in or even complete eradication of genetic variability. The present work aimed at monitoring the genetic variability of a Litopenaeus vannamei hatchery in the state of Pernambuco (Brazil), during three successive replacements, using microsatellite markers. No significant genetic diversity losses have been observed through the values of mean heterozygosity (H_o=0.460 and H_e=0.660 in the first sample; H_o=0.420 and H_e=0.620 in the second sample; and H_o=0.600 and H_e=0.660 in the third sample). However, some alleles appear to have been lost after three replacements. The diversity level was considered to be high and is comparable to those reported for wild populations, suggesting that the original imported founder stock of Brazilian L. vannamei is likely to have had a high genetic diversity, possibly due to multiple origins.     

Genetic diversity status of Pacific white shrimp (<Emphasis Type="Italic">Litopenaeus vannamei</Emphasis>) using SSR markers in Iran

Genetic diversity is vital for the maintenance of genetic pool in cultured shrimps. In order to estimate the current status of genetic diversity in Litopenaeus vannamei shrimp in Iran, as an exotic species, a total of 45 individuals from Amiri and Gorgeaj farms in Jask port of Hormozgan province and one hatchery in Gomishan city of Golestan province, were detected using four microsatellite loci. The number of alleles per locus was 5–10, and the mean effective number of alleles (N _e) across populations and loci ranged from 4.834 to 5.148. The overall mean observed heterozygosity (H _o) ranged from 0.450 to 0.479, which was lower than the expected one (0.789–0.794). There was nothing remarkable about any of the allele frequencies across populations or loci. The mean inbreeding coefficient (F _IS) and pairwise genetic differentiation (F _ST) among populations were 41.6 % and 0.133, respectively. The three studied populations departed from Hardy–Weinberg equilibrium (HWE). Analysis of molecular variance revealed 14 % variability among and 86 % within populations. However, considering departing from HWE and the high F _IS and F, the moderate pairwise F _ST values, importance of introducing genetically diverse broodstock and monitoring to control inbreeding is discussed.     

Modelling effects of climate change on Michigan brown trout and rainbow trout: Precipitation and groundwater as key predictors

Understanding how changes in stream temperature affect survival and growth of coldwater fishes, including brown trout (Salmo trutta) and rainbow trout (Oncorhynchus mykiss), is important for conserving coldwater stream fisheries in a changing climate. However, some contemporary stream temperature models assume spatially uniform (i.e. unrealistic) air–stream temperature relationships or demand hydrometeorological predictors (e.g. solar radiation and convection) that are expensive and often impractical for fisheries managers to measure. As such, we produced a relatively cost-effective, management-relevant modelling approach for predicting effects of changes in air temperature, precipitation and groundwater inputs on stream temperature and, consequently, the survival and growth of brown trout and rainbow trout in Michigan, USA. We found that precipitation- and groundwater-corrected stream temperature models (mean adjusted R² = .77, range = 0.65–0.88) performed better than linear air–stream temperature models (mean adjusted R² = .59, range = 0.21–0.80). Stream temperature was projected to increase by 0.07–3.88°C (1%–22%) with simulated changes in air temperature, precipitation and groundwater inputs. The greatest warming was predicted for surface runoff-dominated sites with limited groundwater-driven thermal buffering, where thermal habitat suitability for salmonid survival and growth declined 20%–40%. However, groundwater-dominated sites may not be immune to temperature warming, especially if groundwater temperature increases or groundwater inputs decline in a changing climate. Our modelling approach provides a reliable, cost-effective method for predicting effects of climate change on brown trout and rainbow trout survival and growth, allowing for strategic management actions to increase the thermal resilience and sustainability of salmonid populations (e.g. groundwater conservation and riparian/watershed rehabilitation).     

Electrophoretic evaluation of a supplemental stocking programme for brown trout, Salmo trutta L.

Abstract. Over a 15-year period hatchery brown trout, Salmo trutta L., have been added 10 Lower Lough Erne, Northern Ireland to supplement declining native populations. Introductions have mainly comprised eyed ova and fingerlings, stocked into a number of rivers in the Erne drainage. Utilizing a natural genetic tag an electrophoretic assessment of the stocking programme was undertaken. The percentage hatchery genetic contribution in trout populations varied widely from river to river (19%-91%). Lough-caught brown trout (3+ and older) showed a substantial (21·5%) hatchery genetic component. Introgression of native-and hatchery stocks was evident. The resultant deleterious genetic consequences for the conservation of the unique Lough Erne brown trout gene pool arc discussed and alternative management strategies are proposed.     

Genetic relatedness and differentiation of hatchery populations of Asian seabass (Lates calcarifer) (Bloch, 1790) broodstock in Thailand inferred from microsatellite genetic markers

After more than 20 years of hatchery production of Asian seabass in Thailand, genetic information is still lacking for effective genetic management and a selective breeding programme. This study aimed to evaluate genetic status of existing hatchery populations and genetic consequences of a selective breeding attempt. We examined genetic relatedness in seven hatchery samples, including a selectively bred population (RACF‐F1), compared with three wild samples using 11 microsatellite loci. Genetic diversity and relatedness values within most hatchery samples, except for RACF‐F1, did not differ from those of wild populations (P > 0.05). RACF‐F1 had the lowest allelic diversity and effective population size (A_r = 6.99; N_e = 7.8) and highest relatedness values (mean r_xy = 0.075–0.204). Pairwise Φ_ST values, principal component analysis and model‐based cluster analyses revealed three genetically distinct hatchery groups: Eastern Thailand (CHN, RACF, NSCF and SKCF), Southern Thailand (NICA) and the Andaman Sea (STCF). Results suggest that exiting domestic populations capture reasonable amount of genetic variation and can be useful for a base population for genetic improvement programmes. In addition, given the rapid increase in relatedness that we observed in one selectively bred population, we recommend using selection methods and hatchery practices that reduce variability in family contribution in the subsequent generations.     

Reproductive performance of cultured brown trout (Salmo trutta L.) in Chile

Data on reproductive traits in a cultured population of brown trout (Salmo trutta L.) in southern Chile were collected over three consecutive reproductive seasons: 1999, 2000 and 2001, corresponding to the first (at 3 years), second and third spawnings in females. Data were collected from individual females (n=238, 273 and 169 respectively). The reproductive season lasted mainly from June to August. The peak (July) tended to increase with each season (55.46%, 62.27% and 80.81% of total spawning fish respectively). Female body weight (470.8±102.5, 735.0±150 and 1263.9±263.4 g), total fecundity (1182±344, 1904±595 and 2744±605) and egg diameter (4.64±0.11, 4.67±0.27 and 5.24±0.12 mm) increased significantly (P<0.01) over successive reproductive seasons, particularly between the second and third spawnings. Relative fecundity, on the other hand, decreased significantly with each season (3577±471, 2591±900 and 2181±360). Following analysis of the variables over the three seasons, the correlation pattern of female body weight with total fecundity (r=0.91, n=458; P<0.001) and relative fecundity (r=?034, n=451; P<0.001) proved similar to that described in other salmonid females. Fertilization rate and survival to the eyed egg stage were also positively correlated (r=0.73, n=453; P<0.001). The systematically high values obtained for these latter variables over the seasons evaluated (consistently above 90%) are clearly greater than those we registered in other species of salmonids bred in Chile under similar conditions and suggest highly efficient biological variables that determine the gamete fertilization of this species. The brown trout is, therefore, an interesting potential aquaculture resource in Chile.     

Genetic Diversity and Population Structure in the Heavily Exploited Korean Rockfish,Sebastes schlegeli,in Korea

The Korean rockfish, Sebastes schlegeli, is a valuable and intensively exploited species in Korea. We discuss the genetic diversity and genetic structure of four Korean rockfish populations using eight microsatellite loci. In total, 161 different alleles from 138 individuals were observed. Average allele number per locus ranged from 2.5 to 23 and allelic richness varied from 13.38 to 14.63 within a population. Despite a long history of stocking practices, we found very high levels of polymorphism (mean heterozygosity = 0.810), which is comparable to other congeneric species. No significant difference in genetic diversity and molecular genetic variance (F_ST and R_ST) was observed among four local samples (P > 0.1). Little indication of contemporary inbreeding (F_IS= 0.051) or population structure (K = 1) was detected. This absence of differentiation may reflect high levels of gene flow along the coast of Korea. Our study demonstrates that rockfish in Korea should be managed as a single unit. Currently, the species does not appear to be genetically threatened, but the potential for a rapid loss of genetic diversity remains. This information on the genetic characteristics of Korean rockfish populations has important implications for fisheries management and conservation efforts, and will aid in the sustainable exploitation of the fishing resources and the preservation of biodiversity.