The River Axe SAP Consultation Document

This is the River Axe Salmon Action Plan Consultation document produced by the Environment Agency in 2003. The report pays attention on the external consultation of the River Axe Salmon Action Plan (SAP). This strategy represents an entirely new approach to salmon management within the UK and introduces the concept of river-specific salmon spawning targets as a salmon management tool. This document is part of a national initiative to produce action plans for the management of all the main salmon rivers of England and Wales by 2003. The aim of this plan is (i) to assess the status of the salmon stocks and fisheries of the River Axe - including the use of Conservation Limits as part of this process, (ii) to identify factors which may be limiting stock and fishery performance and (iii) to propose remedial measures address these factors. The salmon stock of the River Axe was apparently in a healthy state in the 1950s, supporting net and rod fisheries with average annual catches of around 100 and 50 fish respectively. Catches declined through the 1970s and 1980s to the extent where no salmon were recorded in the late 1980s and early 1990s. This decline was probably due largely to the effects of agricultural pollution, which virtually extinguished the salmon stock of the River Axe. Water quality has subsequently improved, but has deteriorated again in recent years.

The River Dart SAP Consultation Document

This is the River Dart Salmon Action Plan Consultation document produced by the Environment Agency in 2003. The report pays attention on the external consultation of the River Dart Salmon Action Plan (SAP). This strategy represents an entirely new approach to salmon management within the UK and introduces the concept of river-specific salmon spawning targets as a salmon management tool. The north of the River Dart catchment is included in the Dartmoor candidate Special Area of Conservation (cSAC), designated under the Council EC Directive 92/43/EEC, the “Habitats Directive”. One of the conservation objectives for the cSAC is to maintain the habitat for Atlantic Salmon, Salmo Salar in favourable condition. The River Dart is an important salmon, sea trout and brown trout fishery with no significant coarse fishery. However, eels are ubiquitous throughout the catchment and are lightly exploited. The River Dart SAP contains a description of the river catchment and highlights particular features that are relevant to the salmon population and the associated fishery.

The River Exe SAP Consultation Document

This is the River Exe Salmon Action Plan Consultation document produced by the Environment Agency in 2003. The report pays attention on the external consultation of the River Exe Salmon Action Plan (SAP). This strategy represents an entirely new approach to salmon management within the UK and introduces the concept of river-specific salmon spawning targets as a salmon management tool. The River Exe SAP follows the format of those completed for the Rivers Teign, Torridge, Taw and Dart. It is the fifth of eight action plans that will be produced for salmon rivers within Devon Area. The River Exe SAP contains a description of the river catchment and highlights particular features that are relevant to the salmon population and the associated fishery. The Exe salmon stock is judged to be meeting its Conservation Limit. However, this assessment is uncertain as it is based on an estimate of rod exploitation rate, which in itself is also uncertain. At present there is no means of accurately assessing the River Exe salmon run. In common with many other rivers, estimation of stock using catch statistics and rod exploitation rate is the model used, when direct assessment is not possible. The installation of a fish counter on the lower river, or the use of other direct counting methods, would help to provide a direct assessment of the annual run of salmon into the river. This would improve our ability to estimate the spawning escapement and hence assess compliance with the Conservation Limit.

The River Lyn SAP Consultation Document

This is the River Lyn Salmon Action Plan Consultation document produced by the Environment Agency in 2003. The report pays attention on the external consultation of the River Lyn Salmon Action Plan (SAP). This approach to salmon management within the England and Wales introduces the concept of river-specific Conservation Limits as a method of assessing the status of the salmon stock. The River Lyn Salmon Action Plan follows the format of those completed for the Rivers Exe, Axe, Avon & Erme, Teign, Torridge, Taw and Dart. It is the last of eight action plans that have been produced for salmon rivers within Devon Area. The River Lyn Salmon Action Plan contains a description of the river catchment and highlights particular features that are relevant to the salmon population and the associated fishery. The Lyn salmon stock is judged to be meeting its Conservation Limit. However, this assessment is uncertain as it is based on an estimate of rod exploitation rate, which in itself is also uncertain.

The River Teign SAP Consultation Document

This is the River Teign Salmon Action Plan Consultation document produced by the Environment Agency in 2003. The report pays attention on the external consultation of the River Teign Salmon Action Plan (SAP). This approach to salmon management within the England and Wales introduces the concept of river-specific Conservation Limits as a method of assessing the status of the salmon stock. The River Teign Salmon Action Plan follows the format of those completed for the Rivers Torridge, Taw and Dart. It is the fourth of eight action plans that will be produced for salmon rivers within the Devon Area Fisheries, Recreation and Biodiversity Team. The River Teign SAP contains a description of the river catchment and highlights particular features that are relevant to the salmon population and the associated fishery. The Teign salmon stock is currently failing to meet its conservation limit. This failure is largely attributed to the reduction in the survival rate during the marine phase of the salmon life cycle. This is likely to constrain stocks to lower levels than have existed historically. Still further catch controls may contribute to a reduction in exploitation rates and allow stocks to recover to meet their conservation limit. Other important actions include the continuation of habitat improvement works which aim to maximise spawning habitat utilisation, spawning success, and juvenile survival and production.

Fisheries survey of the River Otter 1978

This is the Fisheries survey of the River Otter report produced by South West Water Authority in 1979. This report focuses on the trout fishery in the River Otter and the possible effects of abstraction and/or pollution. A survey was carried out to describe the fish stocks. Trout and eels were the dominant species. The population structure of trout was peculiar, there being relatively few juveniles. Growth was good and there were numerous trout of take able size in the river at the end of the fishing season. Variations in the parameters measured are explained and nothing can be attributed to abstraction or pollution.

Seasonal and interannual variation in juvenile salmonids and associated fish assemblage in open waters of the lower Columbia River estuary

The transition between freshwater and marine environments is associated with high mortality for juvenile anadromous salmonids, yet little is known about this critical period in many large rivers. To address this deficiency, we investigated the estuarine ecology of juvenile salmonids and their associated fish assemblage in open-water habitats of the lower Columbia River estuary during spring of 2007–10. For coho (Oncorhynchus kisutch), sockeye (O. nerka), chum (O. keta), and yearling (age 1.0) Chinook (O. tshawytscha) salmon, and steelhead (O. mykiss), we observed a consistent seasonal pattern characterized by extremely low abundances in mid-April, maximum abundances in May, and near absence by late June. Subyearling (age 0.0) Chinook salmon were most abundant in late June. Although we observed interannual variation in the presence, abundance, and size of juvenile salmonids, no single year was exceptional across all species-and-age classes. We estimated that >90% of juvenile Chinook and coho salmon and steelhead were of hatchery origin, a rate higher than previously reported. In contrast to juvenile salmonids, the abundance and composition of the greater estuarine fish assemblage, of which juvenile salmon were minor members, were extremely variable and likely responding to dynamic physical conditions in the estuary. Comparisons with studies conducted 3 decades earlier suggest striking changes in the estuarine fish assemblage—changes that have unknown but potentially important consequences for juvenile salmon in the Columbia River estuary.

Examination of the foraging habits of Pacific harbor seal (Phoca vitulina richardsi) to describe their use of the Umpqua River, Oregon, and their predation on salmonids

The increase in harbor seal (Phoca vitulina richardsi) abundance, concurrent with the decrease in salmonid (Oncorhynchus spp.) and other fish stocks, raises concerns about the potential negative impact of seals on fish populations. Although harbor seals are found in rivers and estuaries, their presence is not necessarily indicative of exclusive or predominant feeding in these systems. We examined the diet of harbor seals in the Umpqua River, Oregon, during 1997 and 1998 to indirectly assess whether or not they were feeding in the river. Fish otoliths and other skeletal structures were recovered from 651 scats and used to identify seal prey. The use of all diagnostic prey structures, rather than just otoliths, increased our estimates of the number of taxa, the minimum number of individuals and percent frequency of occurrence (%FO) of prey consumed. The %FO indicated that the most common prey were pleuronectids, Pacific hake (Merluccius productus), Pacific stag-horn sculpin (Leptocottus armatus), osmerids, and shiner surfperch (Cymatogaster aggregata). The majority (76%) of prey were fish that inhabit marine waters exclusively and fish found in marine and estuarine areas (e.g. anadromous spp.) which would indicate that seals forage predominantly at sea and use the estuary for resting and opportunistic feeding. Salmonid remains were encountered in 39 samples (6%); two samples contained identifiable otoliths, which were determined to be from chi-nook salmon (O. tshawytscha). Because of the complex salmonid composition in the Umpqua River, we used molecular genetic techniques on salmonid bones retrieved from scat to discern species that were rare from those that were abundant. Of the 37 scats with salmonid bones but no otoliths, bones were identified genetically as chinook or coho (O. kisutch) salmon, or steelhead trout (O. mykiss) in 90% of the samples.

Multidirectional movements of sportfish species between an estuarine no-take zone and surrounding waters of the Indian River Lagoon, Florida

We examined movement patterns of sportfish that were tagged in the northern Indian River Lagoon, Florida, between 1990 and 1999 to assess the degree of fish exchange between an estuarine no-take zone (NTZ) and surrounding waters. The tagged f ish were from seven species: red drum (Sciaenops ocellatus); black drum (Pogonias cromis); sheepshead (Archosargus probatocephalus); common snook (Centropomus undecimalis); spotted seatrout (Cynoscion nebulosus); bull shark (Carcharhinus leucas); and crevalle jack (Caranx hippos). A total of 403 tagged fish were recaptured during the study period, including 65 individuals that emigrated from the NTZ and 16 individuals that immigrated into the NTZ from surrounding waters of the lagoon. Migration distances between the original tagging location and the sites where emigrating fish were recaptured were from 0 to 150 km, and these migration distances appeared to be influenced by the proximity of the NTZ to spawning areas or other habitats that are important to specific life-history stages of individual species. Fish that immigrated into the NTZ moved distances ranging from approximately 10 to 75 km. Recapture rates for sportfish species that migrated across the NTZ boundary suggested that more individuals may move into the protected habitats than move out. These data demonstrated that although this estuarine no-take reserve can protect species from fishing, it may also serve to extract exploitable individuals from surrounding fisheries; therefore, if the no-take reserve does function to replenish surrounding fisheries, then increased egg production and larval export may be more important mechanisms of replenishment than the spillover of excess adults from the reserve into fishable areas.

The geographic basis for population structure in Fraser River chinook salmon (Oncorhynchus tshawytscha)

We surveyed variation at 13 microsatellite loci in approximately 7400 chinook salmon sampled from 52 spawning sites in the Fraser River drainage during 1988–98 to examine the spatial and temporal basis of population structure in the watershed. Genetically discrete chinook salmon populations were associated with almost all spawning sites, although gene flow within some tributaries prevented or limited differentiation among spawning groups. The mean FST value over 52 samples and 13 loci surveyed was 0.039. Geographic structuring of populations was apparent: distinct groups were identified in the upper, middle, and lower Fraser River regions, and the north, south, and lower Thompson River regions. The geographically and temporally isolated Birkenhead River population of the lower Fraser region was sufficiently genetically distinctive to be treated as a separate region in a hierarchial analysis of gene diversity. Approximately 95% of genetic variation was contained within populations, and the remainder was accounted for by differentiation among regions (3.1%), among populations within regions (1.3%), and among years within populations (0.5%).Analysis of allelic diversity and private alleles did not support the suggestion that genetically distinctive populations of chinook salmon in the south Thompson were the result of postglacial hybridization of ocean-type and stream-type chinook in the Fraser River drainage. However, the relatively small amount of differentiation among Fraser River chinook salmon populations supports the suggestion that gene flow among genetically distinct groups of postglacial colonizing groups of chinook salmon has occurred, possibly prior to colonization of the Fraser River drainage.

Evaluation and application of microsatellites for population identification of Fraser River chinook salmon (Oncorhynchus tshawytscha)

Variation at 13 microsatellite loci was previously surveyed in approximately 7400 chinook salmon (Oncorhynchus tshawytscha) sampled from 50 localities in the Fraser River drainage in southern British Columbia. Evaluation of the utility of the microsatellite variation for population-specific stock identification applications indicated that the accuracy of the stock composition estimates generally improved with an increasing number of loci used in the estimation procedure, but an increase in accuracy was generally marginal after eight loci were used. With 10–14 populations in a simulated fishery sample, the mean error in population-specific estimated stock composition with a 50-popula-tion baseline was <1.4%. Identification of individuals to specific populations was highest for lower Fraser River and lower and North Thompson River populations; an average of 70% of the individual fish were correctly assigned to specific populations. The average error of the estimated percentage for the seven populations present in a coded-wire tag sample was 2% per population. Estimation of stock composition in the lower river commercial net fishery prior to June is of key local fishery management interest. Chinook salmon from the Chilcotin River and Nicola River drainages were important contributors to the early commercial fishery in the lower river because they comprised approximately 50% of the samples from the net fishery prior to mid April.

Modeling the effect of striped bass (Morone saxatilis) on the population viability of Sacramento River winter-run chinook salmon (Onchorhynchus tshawytscha)

We estimated the impact of striped bass (Morone saxatilis) predation on winter-run chinook salmon (Oncorhynchus tshawytscha) with a Bayesian population dynamics model using striped bass and winter-run chinook salmon population abundance data. Winter-run chinook salmon extinction and recovery probabilities under different future striped bass abundance levels were estimated by simulating from the posterior distribution of model parameters. The model predicts that if the striped bass population declines to 512,000 adults as expected in the absence of stocking, winter-run chinook salmon will have about a 28% chance of quasi-extinction (defined as three consecutive spawning runs of fewer than 200 adults) within 50 years. If stocking stabilizes the striped bass population at 700,000 adults, the predicted quasi-extinction probability is 30%. A more ambitious stocking program that maintains a population of 3 million adult striped bass would increase the predicted quasi-extinction probability to 55%. Extinction probability, but not recovery probability, was fairly insensitive to assumptions about density dependence. We conclude that winter-run chinook salmon face a serious extinction risk without augmentation of the striped bass population and that substantial increases in striped bass abundance could significantly increase the threat to winter-run chi-nook salmon if not mitigated by increasing winter chinook salmon survival in some other way.

Larval development of the southern sea garfish (Hyporhamphus melanochir) and the river garfish (H. regularis) (Beloniformes: Hemiramphidae) from South Australian waters

Larval development of the southern sea garfish (Hyporhamphus melanochir) and the river garfish (H. regularis) is described from specimens from South Australian waters. Larvae of H. melanochir and H. regularis have completed notochord flexion at hatching and are characterized by an elongate body with distinct rows of melanophores along the dorsal, lateral, and ventral surfaces; a small to moderate head; a heavily pigmented and long straight gut; a persistent pre-anal finfold; and an extended lower jaw. Fin formation occurs in the following sequence: caudal, dorsal and anal (almost simultaneously), pectoral, and pelvic. Despite the similarities between both species and among hemiramphid larvae in general, H. melanochir larvae are distinguishable from H. regularis by 1) having 58–61 vertebrae (vs. 51–54 for H. regularis); 2) having 12–15 melanophore pairs in longitudinal rows along the dorsal margin between the head and origin of the dorsal fin (vs. 19–22 for H. regularis); and 3) the absence of a large ventral pigment blotch anteriorly on the gut and isthmus (present in H. regularis). Both species can be distinguished from similar larvae of southern Australia (other hemiramphids and a scomberosocid) by differences in meristic counts and pigmentation.

Genetic analysis of juvenile coho salmon (Oncorhynchus kisutch) off Oregon and Washington reveals few Columbia River wild fish

Little is known about the ocean distributions of wild juvenile coho salmon off the Oregon-Washington coast. In this study we report tag recoveries and genetic mixed-stock estimates of juvenile fish caught in coastal waters near the Columbia River plume. To support the genetic estimates, we report an allozyme-frequency baseline for 89 wild and hatchery-reared coho salmon spawning populations, extending from northern California to southern British Columbia. The products of 59 allozyme-encoding loci were examined with starch-gel electrophoresis. Of these, 56 loci were polymorphic, and 29 loci had P0.95 levels of polymorphism. Average heterozygosities within populations ranged from 0.021 to 0.046 and averaged 0.033. Multidimensional scaling of chord genetic distances between samples resolved nine regional groups that were sufficiently distinct for genetic mixed-stock analysis. About 2.9% of the total gene diversity was due to differences among populations within these regions, and 2.6% was due to differences among the nine regions. This allele-frequency data base was used to estimate the stock proportions of 730 juvenile coho salmon in offshore samples collected from central Oregon to northern Washington in June and September-October 1998−2000. Genetic mixed-stock analysis, together with recoveries of tagged or fin-clipped fish, indicates that about one half of the juveniles came from Columbia River hatcheries. Only 22% of the ocean-caught juveniles were wild fish, originating largely from coastal Oregon and Washington rivers (about 20%). Unlike previous studies of tagged juveniles, both tag recoveries and genetic estimates indicate the presence of fish from British Columbia and Puget Sound in southern waters. The most salient feature of genetic mixed stock estimates was the paucity of wild juveniles from natural populations in the Columbia River Basin. This result reflects the large decrease in the abundances of these populations in the last few decades.

Longitudinal logbook survey designs for estimating recreational fishery catch, with application to ayu (Plecoglossus altivelis)

Longitudinal surveys of anglers or boat owners are widely used in recreational fishery management to estimate total catch over a fishing season. Survey designs with repeated measures of the same random sample over time are effective if the goal is to show statistically significant differences among point estimates for successive time intervals. However, estimators for total catch over the season that are based on longitudinal sampling will be less precise than stratified estimators based on successive independent samples. Conventional stratified variance estimators would be negatively biased if applied to such data because the samples for different time strata are not independent. We formulated new general estimators for catch rate, total catch, and respective variances that sum across time strata but also account for correlation stratum samples. A case study of the Japanese recreational fishery for ayu (Plecoglossus altivelis) showed that the conventional stratified variance estimate of total catch was about 10% of the variance estimated by our new method. Combining the catch data for each angler or boat owners throughout the season reduced the variance of the total catch estimate by about 75%. For successive independent surveys based on random independent samples, catch, and variance estimators derived from combined data would be the same as conventional stratified estimators when sample allocation is proportional to strata size. We are the first to report annual catch estimates for ayu in a Japanese river by formulating modified estimators for day-permit anglers.