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.     

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.     

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.     

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.     

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.     

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.     

Restricted gene flow between resident Oncorhynchus mykiss and an admixed population of anadromous steelhead

The species Oncorhynchus mykiss is characterized by a complex life history that presents a significant challenge for population monitoring and conservation management. Many factors contribute to genetic variation in O. mykiss populations, including sympatry among migratory phenotypes, habitat heterogeneity, hatchery introgression, and immigration (stray) rates. The relative influences of these and other factors are contingent on characteristics of the local environment. The Rock Creek subbasin in the middle Columbia River has no history of hatchery supplementation and no dams or artificial barriers. Limited intervention and minimal management have led to a dearth of information regarding the genetic distinctiveness of the extant O. mykiss population in Rock Creek and its tributaries. We used 192 SNP markers and collections sampled over a 5‐year period to evaluate the temporal and spatial genetic structures of O. mykiss between upper and lower watersheds of the Rock Creek subbasin. We investigated potential limits to gene flow within the lower watershed where the stream is fragmented by seasonally dry stretches of streambed, and between upper and lower watershed regions. We found minor genetic differentiation within the lower watershed occupied by anadromous steelhead (F_ST = 0.004), and evidence that immigrant influences were prevalent and ubiquitous. Populations in the upper watershed above partial natural barriers were highly distinct (F_ST = 0.093) and minimally impacted by apparent introgression. Genetic structure between watersheds paralleled differences in local demographics (e.g., variation in size), migratory restrictions, and habitat discontinuity. The evidence of restricted gene flow between putative remnant resident populations in the upper watershed and the admixed anadromous population in the lower watershed has implications for local steelhead productivity and regional conservation.     

Discovery and characterization of single-nucleotide polymorphisms in steelhead/rainbow trout, Oncorhynchus mykiss

Single-nucleotide polymorphisms (SNPs) have several advantages over other genetic markers, including lower mutation and genotyping error rates, ease of inter-laboratory standardization, and the prospect of high-throughput, low-cost genotyping. Nevertheless, their development and use has only recently moved beyond model organisms to groups such as salmonid fishes. Oncorhynchus mykiss is a salmonid native to the North Pacific rim that has now been introduced throughout the world for fisheries and aquaculture. The anadromous form of the species is known as steelhead. Native steelhead populations on the west coast of the United States have declined and many now have protected status. The nonanadromous, or resident, form of the species is termed rainbow, redband or golden trout. Additional life history and morphological variation, and interactions between the forms, make the species challenging to study, monitor and evaluate. Here, we describe the discovery, characterization and assay development for 139 SNP loci in steelhead/rainbow trout. We used EST sequences from existing genomic databases to design primers for 480 genes. Sanger-sequencing products from these genes provided 130 KB of consensus sequence in which variation was surveyed for 22 individuals from steelhead, rainbow and redband trout groups. The resulting TaqMan assays were surveyed in five steelhead populations and three rainbow trout stocks, where they had a mean minor allele frequency of 0.15-0.26 and observed heterozygosity of 0.18-0.35. Mean F(ST) was 0.204. The development of SNPs for O. mykiss will help to provide highly informative genetic tools for individual and stock identification, pedigree reconstruction, phylogeography and ecological investigation.     

Nature versus nurture? Consequences of short captivity in early stages

Biological changes occurring as a consequence of domestication and/or captivity are not still deeply known. In Atlantic salmon (Salmo salar), endangered (Southern Europe) populations are enhanced by supportive breeding, which involves only 6 months of captive rearing following artificial spawning of wild‐collected adults. In this work, we assess whether several fitness‐correlated life‐history traits (migratory behavior, straying rate, age at maturity, and growth) are affected by early exposure to the captive environment within a generation, before reproduction thus before genetic selection. Results showed significant differences in growth and migratory behavior (including straying), associated with this very short period of captivity in natural fish populations, changing even genetic variability (decreased in hatchery‐reared adults) and the native population structure within and between rivers of the species. These changes appeared within a single generation, suggesting very short time of captivity is enough for initiating changes normally attributed to domestication. These results may have potential implications for the long‐term population stability/viability of species subjected to restoration and enhancement processes and could be also considered for the management of zoo populations.     

Phylogenetic effects on functional traits and life history strategies of Australian freshwater fish

Understanding the biogeographic and phylogenetic basis to interspecific differences in species’ functional traits is a central goal of evolutionary biology and community ecology. We quantify the extent of phylogenetic influence on functional traits and life‐history strategies of Australian freshwater fish to highlight intercontinental differences as a result of Australia's unique biogeographic and evolutionary history. We assembled data on life history, morphological and ecological traits from published sources for 194 Australian freshwater species. Interspecific variation among species could be described by a specialist–generalist gradient of variation in life‐history strategies associated with spawning frequency, fecundity and spawning migration. In general, Australian fish showed an affinity for life‐history strategies that maximise fitness in hydrologically unpredictable environments. We also observed differences in trait lability between and within life history, morphological and ecological traits where in general morphological and ecological traits were more labile. Our results showed that life‐history strategies are relatively evolutionarily labile and species have potentially evolved or colonised in freshwaters frequently and independently allowing them to maximise population performance in a range of environments. In addition, reproductive guild membership showed strong phylogenetic constraint indicating that evolutionary history is an important component influencing the range and distribution of reproductive strategies in extant species assemblages. For Australian freshwater fish, biogeographic and phylogenetic history contribute to broad taxonomic differences in species functional traits, while finer scale ecological processes contribute to interspecific differences in smaller taxonomic units. These results suggest that the lability or phylogenetic relatedness of different functional traits affects their suitability for testing hypothesis surrounding community level responses to environmental change.     

Validation of daily increment formation in otoliths for Gymnocypris selincuoensis in the Tibetan Plateau,China

Daily increment validation in fish otolith is fundamental to studies on fish otolith microstructure, age determination and life history traits, and thus is critical for species conservation and fishery management. However, it has never been done for Schizothoracine fish, which is the dominant component of fish fauna in the Tibetan Plateau. This study validated the daily increment formation of Gymnocypris selincuoensis, as a representative of Schizothoracine fish, by monitoring the growth of hatchery‐reared larvae group and wild‐caught post‐yolk‐sac larvae group under controlled experiments. The results from monitoring the hatchery‐reared larvae group showed that sagittae and lapilli were found in yolk‐sac larvae, and formed 5–7 days before hatching, but asterisci were not found until 11 days post‐hatching. The first increment in sagittae and lapilli was formed in the first day after hatching. The daily periodicity of increment formation was examined and confirmed in sagittae and lapilli of both larvae groups. However, sagittae were better for age determination than lapilli for larvae at earlier days. For larval G. selincuoensis older than 50 days, lapilli were the only otolith pair suitable for larvae daily age determination. This study validated the daily increment formation in Schizothoracine fish for the first time has primary implications to other fishes from this subfamily.     

Role of parasite transmission in promoting inbreeding: II. Pedigree reconstruction reveals sib‐transmission and consequent kin‐mating

Even though parasitic flatworms are one of the most species‐rich groups of hermaphroditic organisms, we know virtually nothing of their mating systems (selfing or kin‐mating rates) in nature. Hence, we lack an understanding of the role of inbreeding in parasite evolution. The natural mating systems of parasitic flatworms have remained elusive due to the inherent difficulty in generating progeny‐array data in many parasite systems. New developments in pedigree reconstruction allow direct inference of realized selfing rates in nature by simply using a sample of genotyped individuals. We built upon this advancement by utilizing the closed mating systems, that is, individual hosts, of endoparasites. In particular, we created a novel means to use pedigree reconstruction data to estimate potential kin‐mating rates. With data from natural populations of a tapeworm, we demonstrated how our newly developed methods can be used to test for cosibling transmission and inbreeding depression. We then showed how independent estimates of the two mating system components, selfing and kin‐mating rates, account for the observed levels of inbreeding in the populations. Thus, our results suggest that these natural parasite populations are in inbreeding equilibrium. Pedigree reconstruction analyses along with the new companion methods we developed will be broadly applicable across a myriad of parasite species. As such, we foresee that a new frontier will emerge wherein the diverse life histories of flatworm parasites could be utilized in comparative evolutionary studies to broadly address ecological factors or life history traits that drive mating systems and hence inbreeding in natural populations.     

First maturity and spawning periodicity of hatchery‐origin pallid sturgeon in the upper Missouri River above Fort Peck Reservoir,Montana

The pallid sturgeon Scaphirhynchus albus conservation propagation program has augmented declining wild populations since the 1990s and the older age classes of hatchery‐origin fish are beginning to reach sexual maturity in the wild. Currently, the majority of the information available on the age and size at first maturity and spawning periodicity for pallid sturgeon in the upper basin is from captive hatchery‐origin pallid sturgeon (i.e. age and size at first maturity and spawning periodicity) or from wild pallid sturgeon artificially spawned in the propagation program (i.e. spawning periodicity). The purpose of this study was to document age and size at first maturity and spawning periodicity of known age hatchery‐origin pallid sturgeon that have reached maturity in the wild. Radio‐tagged pallid sturgeon in the upper Missouri River upstream of Fort Peck Reservoir were serially sampled in the early‐spring over multiple years and assigned to reproductive classifications each year based on sex‐steroid concentrations. The youngest reproductively‐active male hatchery‐origin pallid sturgeon sampled was 14.5 years old and the youngest female was 18. Hatchery‐origin males were observed having annual (N = 3) and biennial (N = 2) reproductive cycles. The observed spawning periodicity was similar to what has been reported elsewhere for the species. The youngest mature fish in this study are older and larger than what has been reported for those retained in captivity, indicating that body size alone is not a reliable predictor of maturity for pallid sturgeon.     

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.     

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.     

Molecular and pedigree measures of relatedness provide similar estimates of inbreeding depression in a bottlenecked population

Individual‐based estimates of the degree of inbreeding or parental relatedness from pedigrees provide a critical starting point for studies of inbreeding depression, but in practice wild pedigrees are difficult to obtain. Because inbreeding increases the proportion of genomewide loci that are identical by descent, inbreeding variation within populations has the potential to generate observable correlations between heterozygosity measured using molecular markers and a variety of fitness related traits. Termed heterozygosity‐fitness correlations (HFCs), these correlations have been observed in a wide variety of taxa. The difficulty of obtaining wild pedigree data, however, means that empirical investigations of how pedigree inbreeding influences HFCs are rare. Here, we assess evidence for inbreeding depression in three life‐history traits (hatching and fledging success and juvenile survival) in an isolated population of Stewart Island robins using both pedigree‐ and molecular‐derived measures of relatedness. We found results from the two measures were highly correlated and supported evidence for significant but weak inbreeding depression. However, standardized effect sizes for inbreeding depression based on the pedigree‐based kin coefficients (k) were greater and had smaller standard errors than those based on molecular genetic measures of relatedness (RI), particularly for hatching and fledging success. Nevertheless, the results presented here support the use of molecular‐based measures of relatedness in bottlenecked populations when information regarding inbreeding depression is desired but pedigree data on relatedness are unavailable.     

Pedigree analysis for the genetic management of group‐living species

Captive breeding programs are an important tool for the conservation of endangered species. These programs are commonly managed using pedigrees containing information about the history of each individual's family, such as breeding pairs and parentage. However, there are some species that are kept in groups where it is hard to distinguish between particular individuals within the group, making it very difficult to record any information at an individual level. Currently, software and methods commonly used for registering and analyzing pedigrees to help manage populations at an individual level are not adequate for managing these group‐living species. Therefore, there is a need to further develop these tools and methodologies for pedigree analysis to better manage group‐living species. PMx is a program used for the management of ex situ populations in zoos and aquariums. We adapted the pedigree analysis method implemented in PMx to analyze pedigrees (records of descendant lineages) of group‐living species. In addition, we developed a group pedigree data entry sheet and group2PMx, a converter program that enables group datasets to be imported into PMx. We show how pedigree analysis of a group‐living species can be used for population management using the studbook of the endangered Texas blind cave salamander Eurycea rathbuni. Such analyses of the pedigree of groups can improve the management of group‐living species in ex situ breeding programs. Firstly, it enables better management decisions based on more accurate genetic measures between groups, allowing for greater control of inbreeding. Secondly, it can improve the conditions in which group‐living species are held by adapting husbandry practices to better reflect conditions of these species living in the wild. The use of the spreadsheet and group2PMx extends the application of PMx_, allowing conservation managers and other institutions outside the zoo and aquarium community to easily import and analyze their pedigree data.     

Effective size of a wild salmonid population is greatly reduced by hatchery supplementation

Many declining and commercially important populations are supplemented with captive-born individuals that are intentionally released into the wild. These supplementation programs often create large numbers of offspring from relatively few breeding adults, which can have substantial population-level effects. We examined the genetic effects of supplementation on a wild population of steelhead (Oncorhynchus mykiss) from the Hood River, Oregon, by matching 12 run-years of hatchery steelhead back to their broodstock parents. We show that the effective number of breeders producing the hatchery fish (broodstock parents; N(b)) was quite small (harmonic mean N(b)=25 fish per brood-year vs 373 for wild fish), and was exacerbated by a high variance in broodstock reproductive success among individuals within years. The low N(b) caused hatchery fish to have decreased allelic richness, increased average relatedness, more loci in linkage disequilibrium and substantial levels of genetic drift in comparison with their wild-born counterparts. We also documented a substantial Ryman-Laikre effect whereby the additional hatchery fish doubled the total number of adult fish on the spawning grounds each year, but cut the effective population size of the total population (wild and hatchery fish combined) by nearly two-thirds. We further demonstrate that the Ryman-Laikre effect is most severe in this population when (1) >10% of fish allowed onto spawning grounds are from hatcheries and (2) the hatchery fish have high reproductive success in the wild. These results emphasize the trade-offs that arise when supplementation programs attempt to balance disparate goals (increasing production while maintaining genetic diversity and fitness).     

Population genetic structure and ancestry of steelhead/rainbow trout (<Emphasis Type="Italic">Oncorhynchus mykiss</Emphasis>) at the extreme southern edge of their range in North America

Steelhead (Oncorhynchus mykiss) populations have declined dramatically in many parts of their range in North America, most critically in Southern California, where these anadromous trout are now classified as ‘Endangered’ under the United States Endangered Species Act. The widespread introduction of hatchery rainbow trout, the domesticated freshwater resident form of the species O. mykiss, is one factor threatening the long-term persistence of native steelhead and other trout populations. To identify where native fish of coastal steelhead lineage remained, we performed a population genetic analysis of microsatellite and SNP genotypes from O. mykiss populations at the extreme southern end of their range in Southern California, USA and Baja California, Mexico. In the northern part of this region, nearly all populations appeared to be primarily descendants of native coastal steelhead. However, in the southern, more urbanized part of this region, the majority of the sampled populations were derived primarily from hatchery trout, indicating either complete replacement of native fish or a strong signal of introgression overlaying native ancestry. Nevertheless, these genetically introgressed populations represent potentially critical genetic resources for the continued persistence of viable networks of O. mykiss populations, given the limited native ancestry uncovered in this region and the importance of genetic variation in adaptation. This study elucidates the geographic distribution of native trout populations in this region, and serves as a baseline for evaluating the impacts of hatchery trout on native O. mykiss populations and the success of steelhead conservation and recovery efforts.     

Long-term captive breeding does not necessarily prevent reestablishment: lessons learned from Eagle Lake rainbow trout

Captive breeding of animals is often cited as an important tool in conservation, especially for fishes, but there are few reports of long-term (<50 years) success of captive breeding programs, even in salmonid fishes. Here we describe the captive breeding program for Eagle Lake rainbow trout, Oncorhynchus mykiss aquilarum, which is endemic to the Eagle Lake watershed of northeastern California. The population in Eagle Lake has been dependent on captive breeding for more than 60 years and supports a trophy fishery in the lake. Nevertheless, the basic life history, ecological, and genetic traits of the subspecies still seem to be mostly intact. Although management has apparently minimized negative effects of hatchery rearing, reestablishing a wild population would ensure maintenance of its distinctive life history and its value for future use as a hatchery fish. An important factor that makes reestablishment possible is that the habitat in Eagle Lake is still intact and that Pine Creek, its major spawning stream, is recovering as habitat. With the exception of an abundant alien brook trout (Salvelinus fontinalis) population in Pine Creek, the habitat factors that led to the presumed near-extinction of Eagle Lake rainbow trout in the early twentieth century have been ameliorated, although the final stages of reestablishment (eradication of brook trout, unequivocal demonstration of successful spawning migration) have still not been completed. The Eagle Lake rainbow trout story shows that long-term captive breeding of migratory salmonid fishes does not necessarily prevent reestablishment of wild populations, provided effort is made to counter the effects of hatchery selection and that natural habitats are restored for reintroduction. Long-term success, however, ultimately depends upon eliminating hatchery influences on wild-spawning populations. Extinction of Eagle Lake rainbow trout as a wild species becomes increasingly likely if we fail to act boldly to protect it and the Eagle Lake watershed.