Effective population size of steelhead trout: influence of variance in reproductive success, hatchery programs, and genetic compensation between life-history forms

The effective population size is influenced by many biological factors in natural populations. To evaluate their relative importance, we estimated the effective number of breeders per year (Nb) and effective population size per generation (Ne) in anadromous steelhead trout (Oncorhynchus mykiss) in the Hood River, Oregon (USA). Using demographic data and genetic parentage analysis on an almost complete sample of all adults that returned to the river over 15 years (>15,000 individuals), we estimated Nb for 13 run years and Ne for three entire generations. The results are as follows: (i) the ratio of Ne to the estimated census population size (N) was 0.17-0.40, with large variance in reproductive success among individuals being the primary cause of the reduction in Ne/N; (ii) fish from a traditional hatchery program (Htrad: nonlocal, multiple generations in a hatchery) had negative effects on Nb, not only by reducing mean reproductive success but also by increasing variance in reproductive success among breeding parents, whereas no sign of such effects was found in fish from supplementation hatchery programs (Hsupp: local, single generation in a hatchery); and (iii) Nb was relatively stable among run years, despite the widely fluctuating annual run sizes of anadromous adults. We found high levels of reproductive contribution of nonanadromous parents to anadromous offspring when anadromous run size is small, suggesting a genetic compensation between life-history forms (anadromous and nonanadromous). This is the first study showing that reproductive interaction between different life-history forms can buffer the genetic impact of fluctuating census size on Ne.     

Differential Reproductive Success of Sympatric, Naturally Spawning Hatchery and Wild Steelhead, Oncorhynchus mykiss

Hatchery propagation of salmonids has been practiced in western North America for over a century. However, recent declines in wild salmon abundance and efforts to mitigate these declines through hatcheries have greatly increased the relative abundance of fish produced in hatcheries. The over-harvest of wild salmon by fishing mixed hatchery and wild stocks has been of concern for many years but genetic interactions between populations, such as hybridization, introgression and outbreeding depression, may also compromise the sustainability of wild populations. Our goal was to examine whether a newly established hatchery population of steelhead trout successfully reproduced in the wild and to compare their rate of reproductive success to that of sympatrically spawning native steelhead. We used eight microsatellite loci to create allele frequency profiles for baseline hatchery and wild populations and assigned the smolt (age 2) offspring of this parental generation to a population of origin. Adults originating from a generalized hatchery stock artificially selected for early return and spawning date were successful at reproducing in Forks Creek, Washington. Although hatchery females (N = 90 and 73 in the two consecutive years of the study) produced offspring that survived to emigrate as smolts, they produced only 4.4–7.0% the number produced per wild female (N = 11 and 10). This deficit in reproductive success implies that the proportion of hatchery genes in the mixed population may diminish since deliberate releases into the river have ceased. This hypothesis is being tested in a long-term study at Forks Creek.     

Interactions between endangered wild and hatchery salmonids: can the pitfalls of artificial propagation be avoided in small coastal streams?

Hatchery and wild juvenile populations of steelhead Oncorhynchus mykiss and coho salmon Oncorhynchus kisutch , in a small coastal watershed in central California, were sampled throughout the year in a stream and at a hatchery. Both species grew faster in captivity than in the wild. Hatchery fish of both species had elevated gill Na⁺, K⁺‐ATPase activity, and thus were ready to enter sea water when planted during the wild fish migration. Downstream migrant trapping and stream surveys indicated that hatchery smolts went to sea soon after planting, consequently avoiding the effects of competition and predation that commonly occur when hatchery‐bred juveniles are released. Adult steelhead were also sampled throughout the watershed. The return of hatchery steelhead was highly synchronized with that of wild steelhead, indicating that hatchery propagation had no adverse effects on the timing of the run. A disproportionate number of hatchery steelhead returned to the tributary where the hatchery was located, despite being planted throughout the watershed. Hatchery steelhead did not differ in mean age or size from wild steelhead. Observations of spawning indicated that hatchery and wild steelhead interbreed. Competition for mates or spawning substratum was rarely observed between hatchery and wild steelhead. Many of the problems commonly associated with artificial propagation can be avoided in small coastal watersheds when wild broodstock are used and fish are released as smolts.     

Who are the missing parents? Grandparentage analysis identifies multiple sources of gene flow into a wild population

In order to increase the size of declining salmonid populations, supplementation programmes intentionally release fish raised in hatcheries into the wild. Because hatchery-born fish often have lower fitness than wild-born fish, estimating rates of gene flow from hatcheries into wild populations is essential for predicting the fitness cost to wild populations. Steelhead trout (Oncorhynchus mykiss) have both freshwater resident and anadromous (ocean-going) life history forms, known as rainbow trout and steelhead, respectively. Juvenile hatchery steelhead that 'residualize' (become residents rather than go to sea as intended) provide a previously unmeasured route for gene flow from hatchery into wild populations. We apply a combination of parentage and grandparentage methods to a three-generation pedigree of steelhead from the Hood River, Oregon, to identify the missing parents of anadromous fish. For fish with only one anadromous parent, 83% were identified as having a resident father while 17% were identified as having a resident mother. Additionally, we documented that resident hatchery males produced more offspring with wild anadromous females than with hatchery anadromous females. One explanation is the high fitness cost associated with matings between two hatchery fish. After accounting for all of the possible matings involving steelhead, we find that only 1% of steelhead genes come from residualized hatchery fish, while 20% of steelhead genes come from wild residents. A further 23% of anadromous steelhead genes come from matings between two resident parents. If these matings mirror the proportion of matings between residualized hatchery fish and anadromous partners, then closer to 40% of all steelhead genes come from wild trout each generation. These results suggest that wild resident fish contribute substantially to endangered steelhead 'populations' and highlight the need for conservation and management efforts to fully account for interconnected Oncorhynchus mykiss life histories.     

Supportive breeding boosts natural population abundance with minimal negative impacts on fitness of a wild population of Chinook salmon

While supportive breeding programmes strive to minimize negative genetic impacts to populations, case studies have found evidence for reduced fitness of artificially produced individuals when they reproduce in the wild. Pedigrees of two complete generations were tracked with molecular markers to investigate differences in reproductive success (RS) of wild and hatchery‐reared Chinook salmon spawning in the natural environment to address questions regarding the demographic and genetic impacts of supplementation to a natural population. Results show a demographic boost to the population from supplementation. On average, fish taken into the hatchery produced 4.7 times more adult offspring, and 1.3 times more adult grand‐offspring than naturally reproducing fish. Of the wild and hatchery fish that successfully reproduced, we found no significant differences in RS between any comparisons, but hatchery‐reared males typically had lower RS values than wild males. Mean relative reproductive success (RRS) for hatchery F₁ females and males was 1.11 (P = 0.84) and 0.89 (P = 0.56), respectively. RRS of hatchery‐reared fish (H) that mated in the wild with either hatchery or wild‐origin (W) fish was generally equivalent to W × W matings. Mean RRS of H × W and H × H matings was 1.07 (P = 0.92) and 0.94 (P = 0.95), respectively. We conclude that fish chosen for hatchery rearing did not have a detectable negative impact on the fitness of wild fish by mating with them for a single generation. Results suggest that supplementation following similar management practices (e.g. 100% local, wild‐origin brood stock) can successfully boost population size with minimal impacts on the fitness of salmon in the wild.     

Variation in reproductive success and effective number of breeders in a hatchery population of steelhead trout (Oncorhynchus mykiss): examination by microsatellite-based parentage analysis

Conservation programs that release captive-bred individuals into the wild to mix with naturally produced individuals are an increasingly common method of supporting or enhancing weak or reduced populations that otherwise may not be self-sustaining. Captive and supportive breeding can be important conservation tools for species with small or declining populations; however, in the case of hatcheries producing salmonid fishes, detailed evaluation of spawning programs is rare. We examined variation in reproductive success, measured by adult offspring production, from three parental generations of hatchery-bred steelhead trout (Oncorhynchus mykiss) using an exclusion-based method of genetic parentage assignment. Reproductive success varied greatly among individuals (especially males) and was correlated with fecundity and maternal spawning date. Estimates of egg to smolt survival for the population as a whole among years ranged from 64% to 95%, marine survival ranged from 0.32% to 2.30%, and the number of adults produced per female ranged from 0 to 18 and the number of adults produced per male ranged from 0 to 32. The effective number of breeders ranged from 11% to 31% of the census population size for that brood year. These ratios fell within estimates from estimates of Ne/N in chinook (O. tshawytscha) and rainbow trout (O. mykiss) hatchery populations.     

Large‐scale parentage analysis reveals reproductive patterns and heritability of spawn timing in a hatchery population of steelhead (Oncorhynchus mykiss)

Understanding life history traits is an important first step in formulating effective conservation and management strategies. The use of artificial propagation and supplementation as such a strategy can have numerous effects on the supplemented natural populations and minimizing life history divergence is crucial in minimizing these effects. Here, we use single nucleotide polymorphism (SNP) genotypes for large‐scale parentage analysis and pedigree reconstruction in a hatchery population of steelhead, the anadromous form of rainbow trout. Nearly complete sampling of the broodstock for several consecutive years in two hatchery programmes allowed inference about multiple aspects of life history. Reconstruction of cohort age distribution revealed a strong component of fish that spawn at 2 years of age, in contrast to programme goals and distinct from naturally spawning steelhead in the region, which raises a significant conservation concern. The first estimates of variance in family size for steelhead in this region can be used to calculate effective population size and probabilities of inbreeding, and estimation of iteroparity rate indicates that it is reduced by hatchery production. Finally, correlations between family members in the day of spawning revealed for the first time a strongly heritable component to this important life history trait in steelhead and demonstrated the potential for selection to alter life history traits rapidly in response to changes in environmental conditions. Taken together, these results demonstrate the extraordinary promise of SNP‐based pedigree reconstruction for providing biological inference in high‐fecundity organisms that is not easily achievable with traditional physical tags.     

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.     

Fluvial rainbow trout contribute to the colonization of steelhead (Oncorhynchus mykiss) in a small stream

Life history polymorphisms provide ecological and genetic diversity important to the long term persistence of species responding to stochastic environments. Oncorhynchus mykiss have complex and overlapping life history strategies that are also sympatric with hatchery populations. Passive integrated transponder (PIT) tags and parentage analysis were used to identify the life history, origin (hatchery or wild) and reproductive success of migratory rainbow/steelhead for two brood years after barriers were removed from a small stream. The fluvial rainbow trout provided a source of wild genotypes to the colonizing population boosting the number of successful spawners. Significantly more parr offspring were produced by anadromous parents than expected in brood year 2005, whereas significantly more parr offspring were produced by fluvial parents than expected in brood year 2006. Although hatchery steelhead were prevalent in the Methow Basin, they produced only 2 parr and no returning adults in Beaver Creek. On average, individual wild steelhead produced more parr offspring than the fluvial or hatchery groups. Yet, the offspring that returned as adult steelhead were from parents that produced few parr offspring, indicating that high production of parr offspring may not be related to greater returns of adult offspring. These data in combination with other studies of sympatric life histories of O. mykiss indicate that fluvial rainbow trout are important to the conservation and recovery of steelhead and should be included in the management and recovery efforts.     

Temporal Comparisons of Genetic Diversity in Lake Michigan Steelhead, Oncorhynchus mykiss, Populations: Effects of Hatchery Supplementation

Steelhead, Oncorhynchus mykiss, were first introduced into the Great Lakes in the late 1800s. Subsequently, natural recruitment across the Lake Michigan basin has been regularly supplemented by primarily one hatchery strain. Recently, multiple strains derived from locations across the species native range along the west coast of the United States have also been stocked by different management agencies. Prior to 1983, hatchery supplementation of Lake Michigan steelhead populations in Michigan was largely unsuccessful due to low smolting rates of small (<120 mm) hatchery yearlings (estimated survival 0.01%). Accordingly, contributions of hatchery fish to historical adult spawning runs in Michigan tributaries were low (0–30%) across six major drainages. Large yearlings of different hatchery strains (>150 mm) have been stocked exclusively since 1983, increasing estimates of survival to smolting (90%). Consequently, the proportion of hatchery adults in spawning runs increased to 13–79%. We examined the effects of changes in stocking practices on straying rates of hatchery steelhead and to temporal changes in levels of genetic diversity and relationships among populations. We used microsatellite loci to estimate allele frequencies for six populations sampled for two time periods (1983–1984 and 1998–1999). Measures of inter-population divergence (mean F_ST) were not significant for either time period. However, spatial genetic relationships among historical and contemporary populations were significantly correlated with geographic distance; a result not expected if gene flow (natural straying) among populations was mediated solely by hatchery supplementation. Increased numbers of alleles in spawning adults from populations can be attributed to alleles specific to recently introduced hatchery strains.     

Factors that contribute to the ecological risks of salmon and steelhead hatchery programs and some mitigating strategies

State and federal agencies in the United States annually release millions of hatchery salmon and steelhead into public waters. Many of the hatchery programs are located in areas where the wild populations are now listed under the U.S. Endangered Species Act (ESA) (16 U.S.C. §§ 1531–1544). These hatchery programs pose genetic and ecological risks to wild fish populations. Genetic risks occur when hatchery and wild fish interbreed and usually occur within a taxonomic species. Ecological risks occur when the presence of hatchery fish affects how wild fish interact with their environment or with other species and may affect whole species assemblages. This paper reviews some of the factors that contribute to ecological risks. Important contributing factors include the relative abundance of hatchery and wild fish in natural production areas, hatchery programs that increase density-dependant mortality, residual hatchery fish, some physical advantages that hatchery fish can have over wild fish, and life history characteristics that may make some species especially vulnerable to the effects of ecological risks. Many of these risk factors can be mitigated by management activities that reduce the level of interactions between hatchery and wild fish. This paper concludes by recommending twelve mitigation strategies that may be useful when agencies need to bring hatchery programs into compliance with the take provisions of the ESA.     

A potential bias in the temporal method for estimating Ne in admixed populations under natural selection

Indirect genetic methods are frequently used to estimate the effective population size (N(e)) or effective number of breeders (N(b)) in natural populations. Although assumptions behind these methods are often violated, there have been few attempts to evaluate how accurate these estimates really are in practice. Here we investigate the influence of natural selection following a population admixture on the temporal method for estimating N(e). Our analytical and simulation results suggest that N(e) is often underestimated in this method when subpopulations differ substantially in allele frequencies and in reproductive success. The underestimation is exacerbated when true N(e) and the fraction of the low-fitness group are large. As an empirical example, we compared N(b) estimated in natural populations of steelhead trout (Oncorhynchus mykiss) using the temporal method (N(b[temp])) with estimates based on direct demographic methods (N(b[demo])) and the linkage disequilibrium method (N(b[LD])). While N(b[LD]) was generally in close agreement with N(b[demo]), N(b[temp]) was much lower in sample sets that were dominated by nonlocal hatchery fish with low reproductive success, as predicted by the analytical results. This bias in the temporal method, which arises when genes associated with a particular group of parents are selected against in the offspring sample, has not been widely appreciated before. Such situations may be particularly common when artificial propagation or translocations are used for conservation. The linkage disequilibrium method, which requires data from only one sample, is robust to this type of bias, although it can be affected by other factors.     

Rapid expansion of an enhanced stock of chum salmon and its impacts on wild population components

A harvested stock of chum salmon homing to Kurilskiy Bay, Iturup Island, consists of two genetically distinct river populations that reproduce in two rivers that drain into the bay and are characterized by limited gene flow. One of these is small and can be regarded as wild, whereas the other is much larger and, until recently, was composed of naturally reproducing components spawning in the river??s mainstem and tributaries, with almost no hatchery reproduction during the past two decades. The only human impact on reproduction of the chum salmon stock was regulation of the escapement, with officially accepted limits to avoid ??over-escapement??. Recently the hatchery began to release a large amount of chum salmon juveniles. As confirmed by data on variation in both age composition and microsatellite DNA, first-generation hatchery-origin fish that returned from the first large releases occupied spawning grounds and presumably competed directly with, and potentially displaced wild fish. The most dramatic example is a genetically distinct beach-spawning form of chum salmon that was swamped by much more numerous hatchery-origin fish of the river-spawning form. In order to restore and support naturally reproduced population components, careful estimation of the carrying capacity of natural spawning grounds is necessary with efforts to increase escapement to these habitats. We also recommend concerted efforts to restore and conserve a unique beach-spawning population of chum salmon. We further recommend development of a marking program for direct estimation of straying and evaluation of ecological and genetic impacts of hatchery fish on neighboring wild and natural populations.     

A tool for tracking genetic contributions of wild Penaeus (Melicertus) plebejus broodstock to hatchery populations

Stock enhancement, restocking and sea ranching are being increasingly applied in both fisheries and conservation. The contribution of hatchery stock to fishery harvest and the maintenance of the genetic structure of stocked populations are both important considerations when releasing captive‐bred organisms into natural systems. Use of wild‐caught broodstock generally overcomes some of the genetic problems associated with domesticated hatchery populations, but there is still a need to ensure that a sufficient proportion of the natural population contribute to production of the stocked cohort to realise the genetic benefits of using wild‐caught broodstock. Releases of Penaeus (Melicertus) plebejus are under investigation as a means of increasing prawn production in recruitment‐limited areas. We used the highly variable mitochondrial control region (mtCR) to assign post‐larvae to maternal lineages in the hatchery and also to investigate the reproductive performance of female broodstock in terms of contribution to the production of the cohorts of post‐larvae in the hatchery. Our data showed that mtCR can be a useful tool for tracking lineages and provided genetic evidence that unequal contribution and underproducing females can occur even in wild‐caught broodstock. This work therefore highlights the importance of monitoring the genetic composition of pre‐release hatchery stocks.     

Development of natural growth regimes for hatchery-reared steelhead to reduce residualism, fitness loss, and negative ecological interactions

Wild steelhead (Oncorhynchus mykiss) typically spend two or more years in freshwater before migrating to sea, but hatchery steelhead are almost ubiquitously released as yearlings. Their large size at release coupled with life history pathways that include both male and female maturation in freshwater present ecological risks different from those posed by hatchery populations of Pacific salmon. Yearling hatchery reared steelhead that fail to attain minimum thresholds for smoltification or exceed thresholds for male maturation tend to ‘residualize’ (i.e., remain in freshwater). Residuals pose ecological risks including size-biased interference competition and predation on juvenile salmon and trout. Three hatchery populations of steelhead in Hood Canal, WA were reared under growth regimes designed to produce a more natural age at smoltification (age-2) to aid in rebuilding their respective natural populations. Mean smolt sizes and size variability at age-2 were within the range of wild smolts for two of the three populations. The third population reared at a different facility under similar temperatures exhibited high growth rate variability and high male maturation rates (20% of all released fish). Experimentally comparing age-1 and age-2 smolt programs will help identify optimal rearing strategies to reduce the genetic risk of domestication selection and reduce residualism rates and associated negative ecological effects on natural populations. Investigations of Winthrop National Fish Hatchery summer-run steelhead will measure a) selection on correlated behavioral traits (‘behavioral syndromes’), b) degree of smoltification, c) changes in hormones that regulate gonad growth at key developmental stages, and d) conduct extensive post-release monitoring of fish reared under each growth regime.     

Some consequences of Pacific salmon hatchery production in Kamchatka: changes in age structure and contributions to natural spawning populations

Aggregate hatchery production of Pacific salmon in the Kamchatka region of the Russian Federation is very low (< 0.5% of total harvest, with five hatcheries releasing approximately 41 M juvenile salmon annually), but contributions in certain rivers can be substantial. Enhancement programs in these rivers may strongly influence fitness and production of wild salmon. In this paper we document significant divergence in demographic traits in hatchery salmon populations in the Bolshaya River and we estimate the proportion of hatchery chum salmon in the total run in the Paratunka River to demonstrate the magnitude of enhancement in this system. We observed a reduction in the expression of life history types in hatchery populations (ranging from 1 to 9 types) compared to wild populations (17 types) of sockeye salmon in the Bolshaya River. We found similar trends in Chinook salmon in the same river system. This reduced life history diversity may make these fish less resilient to changes in habitat and climate. We estimate hatchery chum salmon currently contribute 17-45% to the natural spawning population in the Paratunka River. As hatchery fish increase in numbers at natural spawning sites, this hatchery production may affect wild salmon production. It is important to investigate the risk of introgression between hatchery and wild salmon that can lead to reduction in salmon fitness in Kamchatka rivers, as well as the potential of ecological interactions that can have consequences on status of wild salmon and overall salmon production in this region.     

Carry-over effect of captive breeding reduces reproductive fitness of wild-born descendants in the wild

Supplementation of wild populations with captive-bred organisms is a common practice for conservation of threatened wild populations. Yet it is largely unknown whether such programmes actually help population size recovery. While a negative genetic effect of captive breeding that decreases fitness of captive-bred organisms has been detected, there is no direct evidence for a carry-over effect of captive breeding in their wild-born descendants, which would drag down the fitness of the wild population in subsequent generations. In this study, we use genetic parentage assignments to reconstruct a pedigree and estimate reproductive fitness of the wild-born descendants of captive-bred parents in a supplemented population of steelhead trout (Oncorhynchus mykiss). The estimated fitness varied among years, but overall relative reproductive fitness was only 37 per cent in wild-born fish from two captive-bred parents and 87 per cent in those from one captive-bred and one wild parent (relative to those from two wild parents). Our results suggest a significant carry-over effect of captive breeding, which has negative influence on the size of the wild population in the generation after supplementation. In this population, the population fitness could have been 8 per cent higher if there was no carry-over effect during the study period.     

Breeding success of male brook trout (Salvelinus fontinalis) in the wild

Competition for females generally results in some males adopting alternative reproductive tactics to acquire matings. For fish, the ecological and evolutionary consequences of these tactics are not well understood because of an inability to link directly the interactions of individuals on the breeding grounds with genetic data. This study combines behavioural observations with genetic estimates of male reproductive success within an intensively studied wild population of lacustrine brook trout (Salvelinus fontinalis). Male brook trout exhibit a conditional reproductive strategy with small males adopting a peripheral position to that of larger dominant males in their proximity to spawning females. Parentage analysis of eggs collected from wild redds confirmed the reproductive success of individual males. Males relegated to peripheral positions during spawning participated frequently in spawning events, but in most cases the first male to spawn was the sole contributor, and no more than two males contributed successfully to a single brood. While behavioural observations of salmonines suggests that reproduction is partitioned among males in a manner dependent upon body size and proximity to spawning females, the genetic evidence from this study suggests a more limited distribution of reproductive success in the field. The genetic contributions of male brook trout are highly skewed towards larger males for this population. A review of the salmonine literature suggests little difference in individual reproductive success for males exhibiting size-related tactics within a conditional mating strategy vs. precocial maturation. Collectively, these genetic studies provide new insights on the evolution of alternative life histories among salmonines.     

Genetic monitoring of the Amazonian fish matrinchã (Brycon cephalus) using RAPD markers: insights into supportive breeding and conservation programmes

The importance of genetic evaluations in aquaculture programmes has been increased significantly not only to improve effectiveness of hatchery production but also to maintain genetic diversity. In the present study, wild and captive populations of a commercially important neotropical freshwater fish, Brycon cephalus (Amazonian matrinchã), were analyzed in order to evaluate the levels of genetic diversity in a breeding programme at a Brazilian research institute of tropical fish. Random Amplified Polymorphic DNA fingerprinting was used to access the genetic variability of a wild stock from the Amazon River and of three captive stocks that correspond to consecutive generations from the fishery culture. Although farmed stocks showed considerably lower genetic variation than the wild population, a significantly higher level of polymorphism was detected in the third hatchery generation. The results seem to reflect a common breeding practice on several hatchery fish programmes that use a small number of parents as broodstocks, obtaining reproductive success with few non‐identified mating couples. The obtained data were useful for discussing suitable strategies for the genetic management and biodiversity conservation of this species.     

Isolation of 15 single nucleotide polymorphisms from coastal steelhead, Oncorhynchus mykiss (Salmonidae)

We describe 15 single nucleotide polymorphisms (SNPs) isolated in coastal California populations of steelhead (Oncorhynchus mykiss). SNP loci were developed using a 'gene-targeted' approach, which involved the development of primers from functional genes in O. mykiss that were deposited in GenBank or in the published literature. These markers show a wide range of variability in three coastal steelhead populations, and will be useful in population genetic studies and in pedigree reconstruction. Potential applications include evaluation of population structure, introgression between native and hatchery trout, and evaluating reproductive success.