Cortisol and Pacific Salmon: A New Look at the Role of Stress Hormones in Olfaction and Home-stream Migration

Pacific salmon (genus Oncorhynchus) exhibit an interesting anduncommon life-history pattern that combines semelparity, anadromy,and navigation (homing). During smoltification, young salmonimprint on the chemical composition of their natal stream water(the home-stream olfactory bouquet or "HSOB"); they then migrateto the ocean where they spend a few years feeding prior to migratingback to their natal freshwater stream to spawn. Upstream migrationis guided by the amazing ability to discriminate between thechemical compositions of different stream waters and thus identifyand travel to their home-stream. Pacific salmon demonstratemarked somatic and neural degeneration changes during home-streammigration and at the spawning grounds. The appearance of thesepathologies is correlated with a marked elevation in plasmacortisol levels. While the mechanisms of salmonid homing arenot completely understood, it is known that adult salmon continuouslyutilize two of their primary sensory systems, olfaction andvision, during homing. Olfaction is the primary sensory systeminvolved in freshwater homing and "HSOB" recognition, and willbe emphasized here. Previously, we proposed that the increasein plasma cortisol during Pacific salmon home-stream migrationis adaptive because it enhances the salmon's ability to recallthe imprinted memory of the "HSOB" (Carruth, 1998; Carruth etal., 2000b). Elevated plasma concentrations of cortisol couldprime the hippocampus or other olfactory regions of the brainto recall this memory and, therefore, aid in directing the fishto their natal stream. Thus, specific responses of salmon tostressors could enhance reproductive success.     

Evolution of fighting behavior under asymmetric competition: an experimental test with juvenile salmonids

Large-dominant and small-subordinate species engaging in asymmetricinterference competition may optimize behavior under differenttrade-offs between the chance of winning and the cost of fighting.If fighting behavior is heritable and under selection, theorysuggests that large-dominant and small-subordinate species shouldevolve aggressive and passive fighting behaviors, respectively.To test this prediction, I manipulated the size and competitiveasymmetry of juveniles from sympatric populations of large-dominantcoho salmon (Oncorhynchus kisutch) and small-subordinate steelheadtrout (O. mykiss) and asked whether differences in fightingbehavior persisted independently of competitive ability. I observedfighting behavior during dyadic contests in two habitats, mutuallypreferred pools and energetically demanding riffles, under eachof three size treatments: natural size asymmetry, asymmetryremoved, and reversed size asymmetry. The results supportedthe prediction. Competitive ability depended primarily on size;large individuals of both species dominated smaller heterospecifics,and neither species dominated when size matched. Fighting behaviordepended primarily on species identity; coho salmon used a higherproportion of aggressive chases, whereas steelhead trout useda higher proportion of passive displays. Large individuals weremore likely to chase, and small individuals were more likelyto display. As evidence that asymmetric competition is associatedwith behavioral divergence, these results complement previouswork on morphological divergence under asymmetric competitionand provide a richer context for other features of the coho–steelheadsystem.     

The Development of Fast-Start Performance in Fishes: Escape Kinematics of the Chinook Salmon (Oncorhynchus tshawytscha)

C-starts are high acceleration swimming movements critical forpredator avoidance by fishes. Since larval fishes are particularlyvulnerable to predation, C-start behavior is likely to be especiallyimportant during early life history stages. This paper examinesthe developmental changes in C-start performance with kinematicdata on immature chinook salmon (Oncorhynchus tshawytscha) (eleuthroembryostage, sensu Balon, 1975). The scaling of C-start kinematicsof immature fishes differs from that of adults. Adult C-startdurations increase with increasing body length while C-startdurations of immature fishes decrease (e.g., adult stage 1 duration[sec] = 0.0019.length [L] [cm] $ 0.026 [R² = 0.77] [Webb, 1978];eleuthroembryos stage 1 duration [sec] = –0.026L [cm]$ 0.100 [R² = 0.81]). Distance traveled during stage 2 alsodiffers between adult and immature fishes. Adult distance traveledscales directly with length (distance [cm] = 0.38L^1.01 [cm],R² = 0.96 [Webb, 1978]) while chinook eleuthroembryo distancetraveled is positively allometric with length (distance [cm]=0.37L¹³¹ [cm], R² = 0.83). There are similarities in the developmentof C-starts and burst swimming. For example, mean velocity scalessimilarly between the two locomotor modes (For burst swimming:U_mean [cm/sec] = 8.1 ± 1.1L [cm] $ 4.89 [R² = 0.86] [Webband Corolla, 1981]. For C-start stage 2: U_mean [cm/sec] = 10.96L[cm] - 14.09 [R² = 0.70]). This study demonstrates that C-startescape performance improves during early post-hatching development.Comparisons of immature chinook salmon fast-starts with dataon larval burst swimming and on adult C-starts suggest thatchanges specific to developing fish affect the scaling of kinematicparameters.     

DESCRIPTION OF A NEW SPECIES OF PHYLLIDIOPSIS BERGH (NUDIBRANCHIA: DORIDOIDEA: PHYLLIDIIDAE) FROM THE TROPICAL WESTERN PACIFIC, WITH COMMENTS ON THE ATLANTIC SPECIES

A new species of phyllidiid nudibranch, Phyllidiopsis shireenae,is described. The new species has a middorsal crest insteadof being flattened dorso-ventrally like most phyllidiids. Itsbody is a very pale shade of pink with black bands, and itsrhinophores are salmon pink. The anatomy of the alimentary systemand reproductive system are described. Characters originallyused by Bergh (1875) to differentiate the genus are supportedby this new species. Phyllidiopsis shi-reenae is presently knownfrom coral reef habitats in the extreme western Pacific Ocean.A review of the taxonomic status of the Atlantic specis of Phyllidiopsisis required. ^*Present address: Australian Biological and Environmental Survey.Australian National Parks and Wildlife Service, GPO Box 1383,Canberra. ACT 2601. Australia. (Received 15 August 1989; accepted 8 January 1990)     

Protandry models and their application to salmon

Mating systems characterized by restricted breeding seasons,male polygamy, and female monogamy are common among animals.In such systems (e.g., butterflies), the earlier emergenceof males than females to breeding areas (protandry) is a typicalphenological pattern. Protandry likely results from a timingstrategy that maximizes mating opportunities by males. In Pacific salmon (Oncorhynchus spp.), males typically arrive at the spawning grounds in advance of females. Using arrival-timing models,I found that under the mate-opportunity hypothesis, the matingsystem of salmon favors protandry. Protandry is predicted undera range of competitive scenarios, and the degree of protandryis especially sensitive to the duration of male spawning activity.Greater protandry is expected with increasing population sexratio (i.e., more males) when there is mate guarding, but lowerprotandry is expected with increasing population sex ratiowhen interference competition among males reduces male longevity.The timing of unequal competitors is expected to be similar,but among years, protandry may be less variable in the bettercompetitor.     

Mixing an enclosed, 1300m3 water column: effects on the planktonic food web

The nutrient, phytoplankton, and zooplankton dynamics in threeenclosed water columns (1300 m³) are described. Two of the enclosureswere mixed using a bubbling chamber at depth. Young chum salmon(Oncorhynchus keta) were added to one of the mixed enclosuresand the unmixed enclosure. No other manipulations were imposed.Copepods appeared in large numbers (e.g. especially Pseudocalanusminutus s.l. and Paracalanus parvus) and population growth rateswere estimated. Ctenophora did not appear in large numbers despitepresumably ideal food environments; it is suggested that inone enclosure this is a consequence of fish predation on thectenophores. The fish experienced high mortalities and low growthrates presumably due to unsuitable prey size. Weekly collectionsof sediment permitted isolation of two major sediment contributors,the first from phytoplankton sinking and the second from biogenkfallout associated with herbivore production. It was found thatthe more oligotrophic enclosure (unmixed) experienced proportionallyhigher utilization of organic carbon. Some of these resultsare explained by our data while others require more sophisticatedexperimentation, both in the design of the containers and inthe types of observations.     

Predator-limited population growth of the copepod Pseudocalanus sp.

The impact of predators on population growth of Pseudocalanussp. was investigated in Dabob Bay, Washington. Mortality ofPseudocalanus sp. was determined from stage-specific survivorship,from seasonal changes in mortality rates of adult males andfemales and from incidence of injuries to adult copepods. Theprincipal predators of adult Pseudocalanus were identified asthe predatory copepod Euchaeta elongata, the omnivorous euphausiidEuphausia pacifica and the chaetognath Sagirta elegans. Predatorattack rates - and prey mortality rates - are highly density-dependentand thus sensitive to prey dispersion in the water column, particularlyto layering in the vertical plane. Predation rates by the threeprincipal predators exceeded 100% of the recruitment rate toadult Pseudocalanus sp. beginning in early summer, thus restrictingpopulation growth. Planktivorous fish predation (by adult three-spinestickleback, Gasterosteus aculeatus, and juvenile chum salmon,Oncorhynchus keta) on Pseudocalanus sp. adults was estimatedto be two orders of magnitude lower than consumption rates bypredatory zooplankton, at a deep water station in July. Analysisof seasonal changes in prey ingested by Sagitta elegans revealedthat Pseudocalanus sp. was the major prey item of S. elegansin April (61.0% of prey) and in June (67.0% of prey), thereafterdeclining seasonally in importance. Predation by S. elegansvaried seasonally with changes in chaetognath stage structure,vertical distribution and diapause, not size structure alone.Although chaetognath recruitment and population growth appearto be directly coupled to the abundance of Pseudocalanus sp.,predation by S. elegans has little reciprocal impact on Pseudocalanussp. population growth; hence asymmetries may occur in the interaction of planktonic prey and predators.     

Environmentally controlled Daphnia spring increase with implications for sockeye salmon fry in Lake Washington, USA

In Lake Washington, juvenile sockeye salmon (Oncorhynchus nerka)strongly prefer Daphnia over other prey, switching uniformlyto Daphnia when the threshold abundance of 0.4 Daphnia L^–1is achieved. Using long-term Lake Washington data (1978–2001)and fry trap data (1992–2001) from a major tributary,we examined the following: (i) factors that predict Daphniapulicaria and Daphnia thorata increase to this threshold "switching"abundance, (ii) trends in Daphnia dynamics that may affect sockeyeforaging and (iii) temporal correspondence of Daphnia increaseand fry arrival. The winter abundance of D. pulicaria, in combinationwith basic parameters of spring conditions, was an importantpredictor of the date of D. pulicaria spring increase, indicatinggreater reliance on pelagic population dynamics (versus diapausehatch) than D. thorata exhibited. In addition, D. pulicariawas a more consistent prey than D. thorata, the latter exhibitinglarger population fluctuations. Thus, recently increasing D.thorata prominence could decrease diet consistency for sockeyefry. Additionally, the timing of sockeye arrival to Lake Washingtonand Daphnia’s increase to the switching threshold hasbecome less concordant, so that fry in recent years have hadto rely upon less profitable prey for longer periods. Long-termtrends and species-specific differences in Daphnia phenologymay affect fry through altering diet composition, with additionalimplications for other zooplankton withstanding greater predationpressure in Daphnia’s absence. Recent decades of warmingin Lake Washington are consistent with the warming of lakesworldwide, and complex phenological responses such as thosereported here may be common as the climate continues to change.     

The effects of prior residence on behavior and growth rates in juvenile Atlantic salmon (Salmo salar)

It is well documented that prior residence confers advantagesin territorial disputes, but its impact on other aspects ofbehavior and fitness is less understood. We tested how priorresidence influences the subsequent feeding behavior and growthperformance of dispersing Atlantic salmon fry (Salmo salar)using experimental manipulations of residence in a seminaturalstream tank. In replicated trials, groups of seven "primary"fish were released into the stream tank 3 days ahead of seven"secondary" fish. Standardized behavioral observations were madeon each fish over the following 14 days, after which all fishwere removed and measured. Primaries and secondaries were initiallythe same size and body condition and exhibited the same degreeof site fidelity. However, primaries darted higher into thewater column to intercept prey items, fed at a higher rate,and subsequently grew faster. Larger fish (in terms of body length)tended to be more dominant, and dominants grew faster than subordinates.However, there was no difference in dominance between primaries andsecondaries. These results suggest that the well-documentedadvantage of early-emerging salmon fry over late-emerging frycannot be completely attributed to intrinsic differences andthat the advantage is partly mediated via a prior residenceeffect. Furthermore, prior residents gain foraging advantageswithout necessarily becoming more dominant.     

Reproductive Endocrinology of Fishes

While evidence is currently lacking for the agnatha and elasmobranchs,the release of pituitary gonadotropin by the teleost pituitaryappears to be under stimulatory control by the hypothalamus. Gonadotropin has to date only been purified from teleost pituitaryglands. Bioassay and biochemical data suggest that the teleostpituitary gland elaborates only one gonadotropin; however, thereis some conflicting histological data on this point. Salmongonadotropin has a molecular weight of approximately 29,000at neutral pH and approximately 13,000 at low pH or after treatmentwith 8M urea or 1M propionic acid. Radioimmunossays have recently been developed for carp and salmongonadotropin. Immunological techniques have also been used toidentify pituitary gonadotrops. Pharmacological treatment of fish with methallibure has permittedinhibition of gonadal development while treatment with clomiphenecitrate has stimulated ovulation. The role of corticosteroidsand other steroid hormones in ovulation is still not fully elucidated.It is possible that the control of ovulation may differ betweenspecies. Experiments are described which aim to enhance natural stocksof pink salmon by endocrine manipulation of sexual developmentin the male.     

The Effects of NPY and Insulin on Food Intake Regulation in Fish

Recent abundant studies report that in rodents starvation inducesincreased neuropeptide Y (NPY) mRNA expression and peptide secretionin the hypothalamus which reduces autonomic nervous activityand promotes food intake, and intracerebroventricular (ICV)injection of NPY has potent orexigenic effects. Conversely,the effect of insulin in the central nervous system is to inhibitfood intake and NPY biosynthesis and secretion. In mammals bodyfatness is regulated and insulin acts as one intake inhibitorysignal related to fatness. In salmon (Oncorhynchus sp.) we havedemonstrated a rise in NPY-like mRNA expression and a coincidentdecrease in plasma insulin levels during 2 to 3 weeks of starvation.Additionally, experimentally manipulating body fatness withhigh and low fat diets has demonstrated that body fatness affectsfood intake in teleost fishes, raising the possibility thatNPY and insulin act to regulate their food intake. Therefore,we hypothesized that as in rodents, ICV treatment with NPY wouldstimulate food intake while ICV insulin would reduce food intake.Preliminary results suggest that ICV NPY administration doesstimulate food intake in channel catfish (Ictalurus punctatus),but central injection of insulin has no effect. Results of treatmentswith the sulfated octapeptide of cholecystokinin and the recombinantfragment of rat leptin 22–56 are also discussed.     

Base-Specific Endo-Exonucleolytic Activity of Chlamydomonas Nuclease C1&2

The reaction kinetics of nuclease C1&2 from Chlamydomonasreinhardtii were studied. It showed endo-exonucleolytic activitywith sugar non-specificity. The relative rates of RNA breakdownwere in order of poly(U) > poly(A) > yeast sRNA. In contrast,poly(G) and poly(C) released almost no acid-soluble materialsafter reacting with nuclease C1&2. The major products ofa 100% limit digest of synthetic RNA homopolymers were mononucleotideswith 3'-phosphate termini. Large oligonucleotides produced duringendo-exonucleolytic degradation also appeared carrying 3'-phosphatetermini. Nuclease C1&2 hydrolyzed single stranded DNA 20times faster than double stranded DNA by endo-exonucleolyticaction, releasing acid-soluble materials. High performance liquidchromatography of a 100% limit digest of salmon testes DNA demonstratedthat the major products were deoxymononucleotides with phosphateat 3'-position. Furthermore, the level of 3'-dCMP among themwas found to be extremely low. Poly(dC) and poly(me⁵dC) werehydrolyzed much more slowly than single stranded (or denatured)DNA, releasing acid-soluble materials. The present results suggestthat nuclease C1&2 is a base-specific nucleate 3'-oligonucleotidohydrolasedifferent from the restriction enzymes. (Received January 13, 1986; Accepted March 25, 1986)     

Straying of hatchery salmon in Prince William Sound,Alaska

The straying of hatchery salmon may harm wild salmon populations through a variety of ecological and genetic mechanisms. Surveys of pink (Oncorhynchus gorbuscha), chum (O. keta) and sockeye (O. nerka) salmon in wild salmon spawning locations in Prince William Sound (PWS), Alaska since 1997 show a wide range of hatchery straying. The analysis of thermally marked otoliths collected from carcasses indicate that 0–98% of pink salmon, 0–63% of chum salmon and 0–93% of sockeye salmon in spawning areas are hatchery fish, producing an unknown number of hatchery-wild hybrids. Most spawning locations sampled (77%) had hatchery pink salmon from three or more hatcheries, and 51% had annual escapements consisting of more than 10% hatchery pink salmon during at least one of the years surveyed. An exponential decay model of the percentage of hatchery pink salmon strays with distance from hatcheries indicated that streams throughout PWS contain more than 10% hatchery pink salmon. The prevalence of hatchery pink salmon strays in streams increased throughout the spawning season, while the prevalence of hatchery chum salmon decreased. The level of hatchery salmon strays in many areas of PWS are beyond all proposed thresholds (2–10%), which confounds wild salmon escapement goals and may harm the productivity, genetic diversity and fitness of wild salmon in this region     

Interspecific habitat associations of juvenile salmonids in Lake Ontario tributaries: implications for Atlantic salmon restoration

Diel variation in habitat use of subyearling Chinook salmon (Oncorhynchus tshawytscha), subyearling coho salmon (O. kisutch), yearling steelhead (O. mykiss), and yearling Atlantic salmon (Salmo salar) was examined during the spring in two tributaries of Lake Ontario. A total of 1318 habitat observations were made on juvenile salmonids including 367 on steelhead, 351 on Chinook salmon, 333 on Atlantic salmon, and 261 on coho salmon. Steelhead exhibited the most diel variation in habitat use and Chinook the least. Juvenile salmonids were generally associated with more cover and larger substrate during the day in both streams. Interspecific differences in habitat use in both streams occurred with Atlantic salmon (fast velocities) and coho salmon (pools) using the least similar habitat. Chinook salmon and Atlantic salmon used similar habitat in both streams. These findings should help guide future management actions specific to habitat protection and restoration of Atlantic salmon in Lake Ontario tributaries.     

Effects of Pacific salmon spawning and carcass availability on the caddisfly Ecclisomyia conspersa (Trichoptera: Limnephilidae)

1. The effects of spawning coho (Oncorhynchus kisutch) and chum salmon (Oncorhynchus keta) on the limnephilid caddisfly Ecclisomyia conspersa were evaluated by experimentally excluding salmon from the upper 14‐m stretch of a spawning channel by a wire‐meshed fence. Density, and development and growth rates, of larvae upstream of the fence (without salmon) were compared with those downstream (with salmon). 2. Larval density in the stretch with salmon declined during spawning, but increased again after spawning subsided and the carcasses of dead fish became available. In the stretch with salmon, larval density on salmon carcasses was seven to 37 times greater than on the adjacent channel substratum. The rate of larval development in the stretch with salmon was greater than that in the stretch without salmon. Two months after carcasses became available, 98% of larvae sampled from the stretch with salmon were in the fifth instar, compared to only 23% from the stretch without salmon. Body weight of E. conspersa in the stretches with and without salmon increased by an average of 3.04 and 2.38 mg, respectively, over a 6‐month period. 3. ¹⁵N values of larvae from the stretch with salmon increased following the arrival of the fish, suggesting that the larvae were feeding on salmon‐derived material, such as eggs and carcasses, which contain a high proportion of the heavier stable isotope. In contrast, ¹⁵N values of larvae from the stretch without salmon remained relatively constant throughout the experiment. The availability of salmon carcasses as a high‐quality food source late in larval development may increase survival and fecundity of E. conspersa. 4. These substantial differences were consistent with the view that they were due to the experimental exclusion of salmon and salmon carcasses from the upstream stretch, though the study was un‐replicated and thus precludes ascribing causation more definitely.     

Occupancy dynamics of escaped farmed Atlantic salmon in Canadian Pacific coastal salmon streams: implications for sustained invasions

Farmed non-native Atlantic salmon (Salmo salar) is the largest agriculture export product of British Columbia, Canada. Chronic low-volume escapes of salmon from farms into Pacific waters (“leakage”) are typically undetectable (Britton et al. 2011). Analysis of escape-reporting from farmers indicates that reports greatly underestimate the true number of Atlantic salmon inadvertently released from open-net pen rearing sites (Morton and Volpe 2002). To quantify the spatial extent of escaped Atlantic salmon in Canadian Pacific rivers, we systematically snorkel-surveyed 41 known Pacific salmon (Oncorhynchus spp.)-supporting rivers and creeks on Vancouver Island over a span of 3 years. We estimated and accounted for imperfect detections using multi-season occupancy models. We detected Atlantic salmon in 36.6 % of surveyed rivers. After accounting for imperfect detection, occupancy models estimated that over half of surveyed streams across the study area contained Atlantic salmon, and that 97 % of streams with high native salmon diversity were occupied by Atlantic salmon. Even in intensive snorkel surveys, Atlantic salmon are detected in occupied streams only 2/3 the time, suggesting abundance and distribution of non-native salmon is greater than indicated by the only existing data. Further, Atlantic salmon are more likely to occupy streams with high native Pacific salmon diversity—and more likely to maintain occupancy across years—potentially increasing competitive pressure on native salmonids. Understanding local biotic and abiotic predictors of Atlantic salmon occupancy, stream colonization, and local extinction requires more data; the same is true for the effects of escaped Atlantic salmon on local salmon diversity and sustainability. These data for the first time show that Atlantic salmon occupy Pacific coastal rivers for multiple years. The impact of Atlantic salmon occupancy in British Columbia rivers must be factored into policy decisions regarding the future of salmon farming in the provincial waters.     

Effects of salmon lice infection and salmon lice protection on fjord migrating Atlantic salmon and brown trout post-smolts

Effects of artificial salmon lice infection and pharmaceutical salmon lice prophylaxis on survival and rate of progression of Atlantic salmon (n = 72) and brown trout post-smolts (n = 72) during their fjord migration, were studied by telemetry. The infected groups were artificially exposed to infective salmon lice larvae in the laboratory immediately before release in the inner part of the fjord to simulate a naturally high infection pressure. Groups of infected Atlantic salmon (n = 20) and brown trout (n = 12) were also retained in the hatchery to control the infection intensity and lice development during the study period. Neither salmon lice infection nor pharmaceutical prophylaxis had any effects on survival and rate of progression of fjord migrating Atlantic salmon post-smolts compared to control fish. Atlantic salmon spent on average only 151.2 h (maximum 207.3 h) in passing the 80 km fjord system and had, thus, entered the ocean when the more pathogenic pre-adult and adult lice stages developed. The brown trout, in comparison to Atlantic salmon, remained to a larger extent than Atlantic salmon in the inner part of the fjord system. No effect of salmon lice infection, or protection, was found in brown trout during the first weeks of their fjord migration. Brown trout will, to a larger extent than Atlantic salmon, stay in the fjord areas when salmon lice infections reach the more pathogenic pre-adult and adult stages. In contrast to Atlantic salmon, they will thereby possess the practical capability of returning to freshwater when encountering severe salmon lice attacks.     

Comparative anatomy of the dorsal hump in mature Pacific salmon

Mature male Pacific salmon (Genus Oncorhynchus ) demonstrate prominent morphological changes, such as the development of a dorsal hump. The degree of dorsal hump formation depends on the species in Pacific salmon. It is generally accepted that mature males of sockeye (O. nerka ) and pink (O. gorbuscha ) salmon develop most pronounced dorsal humps. The internal structure of the dorsal hump in pink salmon has been confirmed in detail. In this study, the dorsal hump morphologies were analyzed in four Pacific salmon species inhabiting Japan, masu (O. masou ), sockeye, chum (O. keta ), and pink salmon. The internal structure of the dorsal humps also depended on the species; sockeye and pink salmon showed conspicuous development of connective tissue and growth of bone tissues in the dorsal tissues. Masu and chum salmon exhibited less‐pronounced increases in connective tissues and bone growth. Hyaluronic acid was clearly detected in dorsal hump connective tissue by histochemistry, except for in masu salmon. The lipid content in dorsal hump connective tissue was richer in masu and chum salmon than in sockeye and pink salmon. These results revealed that the patterns of dorsal hump formation differed among species, and especially sockeye and pink salmon develop pronounced dorsal humps through both increases in the amount of connective tissue and the growth of bone tissues. In contrast, masu and chum salmon develop their dorsal humps by the growth of bone tissues, rather than the development of connective tissue.     

Introgression of Oncorhynchus masou subsp. (Biwa salmon) genome into lake-run O. m. ishikawae (Amago salmon) introduced into Lake Biwa, Japan

An investigation to determine the extent of introgression between Biwa salmon Oncorhynchus masou subsp. and lake-run Amago salmon O. m. ishikawae from Lake Biwa was conducted using mtDNA sequence and amplified fragment length polymorphism (AFLP) analysis. Hatchery-reared Amago salmon from the Samegai Trout Farm, the main source of stock released into the inflowing rivers of Lake Biwa, were also investigated. The extent of mtDNA introgression between these two subspecies was quite low: an anomalous haplotype was detected in just 1 of 55 Biwa salmon and 2 of 63 lake-run Amago salmon. Many of the mtDNA haplotypes found in lake-run Amago salmon were common to those in hatchery-reared Amago salmon. In the AFLP analysis, the nuclear genome of Amago salmon was hardly detected in Biwa salmon, but the Biwa salmon genome comprised 13.4% of the total amplified fragments from lake-run Amago salmon, being detected in different proportions in 28 of the 63 investigated individuals of the latter subspecies. These results suggest that introgression has occurred between Biwa salmon and lake-run Amago salmon descending from hatchery-reared Amago salmon from the Samegai Trout Farm.