Lessons for stock assessment from the northern cod collapse

Fisheries assessment scientists can learn at least three lessons from the collapse of the northern cod off Newfoundland: (1) assessment errors can contribute to overfishing through optimistic long-term forecasts leading to the build-up of overcapacity or through optimistic assessments which lead to TACs being set higher than they should; (2) stock size overestimation is a major risk when commercial catch per effort is used as an abundance trend index, so there is continued need to invest in survey indices of abundance trend no matter what assessment methodology is used; and (3) the risk of recruitment overfishing exists and may be high even for very fecund species like cod. This implies that harvest rate targets should be lower than has often been assumed, especially when stock size assessments are uncertain. In the end, the high cost of information for accurate stock assessment may call for an alternative approach to management, involving regulation of exploitation rate via measures such as large-scale closures (refuges) that directly restrict the proportion of fish available to harvest. Development of predictive models for such regulatory options is a major challenge for fisheries assessment science.     

The future of fish-based ecological assessment of European rivers: from traditional EU Water Framework Directive compliant methods to eDNA metabarcoding-based approaches

Most of the present EU Water Framework Directive (WFD) compliant fish-based assessment methods of European rivers are multi-metric indices computed from traditional electrofishing (TEF) samples, but this method has known shortcomings, especially in large rivers. The probability of detecting rare species remains limited, which can alter the sensitivity of the indices. In recent years, environmental (e)DNA metabarcoding techniques have progressed sufficiently to allow applications in various ecological domains as well as eDNA-based ecological assessment methods. A review of the 25 current WFD-compliant methods for river fish shows that 81% of the metrics used in these methods are expressed in richness or relative abundance and thus compatible with eDNA samples. However, more than half of the member states' methods include at least one metric related to age or size structure and would have to adapt their current fish index if reliant solely on eDNA-derived information. Most trait-based metrics expressed in richness are higher when computed from eDNA than when computed from TEF samples. Comparable values are obtained only when the TEF sampling effort increases. Depending on the species trait considered, most trait-based metrics expressed in relative abundance are significantly higher for eDNA than for TEF samples or vice versa due to over-estimation of sub-surface species or under-estimation of benthic and rare species by TEF sampling, respectively. An existing predictive fish index, adapted to make it compatible with eDNA data, delivers an ecological assessment comparable with the current approved method for 22 of the 25 sites tested. Its associated uncertainty is lower than that of current fish indices. Recommendations for the development of future fish eDNA-based indices and the associated eDNA water sampling strategy are discussed.     

The relationship between a summer fry (0+) abundance index, derived from semi-quantitative electrofishing, and egg deposition of Atlantic salmon, in the River Bush, Northern Ireland

Atlantic salmon survival in the R. Bush (N. Ireland) from egg to summer 0+ was inversely density-dependent on egg deposition ( P <0.05). A stock-recruitment relationship derived from egg deposition and summer 0+ abundance index data was compared to that derived from adult and smolt counts based on total trapping. Fitted Ricker curves indicated maximum recruitment at around 2.35 million eggs and 2.46 million eggs for 0+ index and smolt count methods, respectively. Salmon 0+ abundance index data from semi-quantitative electrofishing could be obtained with relatively little effort, and used to derive whole-river stock-recruitment relationships on rivers where only adult count or some other estimator of parental stock is available. The derivation and expression of spawning targets from stock/recruitment relationships is discussed with reference to the R. Bush data.     

Large-scale assessments of river health using an Index of Biotic Integrity with low-diversity fish communities

1. Effective tools are needed to measure the ‘health’ of rivers at scales large enough to be useful for management. Indicators for assessing the complex of variables that constitutes river health need to be ecologically based, efficient, rapid and consistently applicable in different ecological regions. 2. A large-scale survey of rivers in New South Wales, Australia provided data to test the Index of Biotic Integrity (IBI). The IBI employs the fish-community attributes, identified using regional and river-size data, expected for a river reach of excellent environmental quality. It uses metrics based on species richness, abundance, community structure and the health of individual fish. IBI metrics were established to suit a relatively low-diversity and unspecialized freshwater fish fauna in south-eastern Australia, totalling 55 species. 3. The IBI was able to discriminate between relative levels of environmental quality within a diverse set of stream systems and four presumptive ecological regions. The index was validated by testing the repeatability of scores, and by comparison of IBI scores at eighty sites with an independent measure of potential catchment condition, the River Disturbance Index. 4. Assessments of metric performance showed that eleven of the twelve metrics contributed satisfactorily. One metric based on trophic guild performed poorly and should be deleted from the index. Six other recommendations are made to enhance the performance of the IBI. 5. Results show that, while all large rivers have been disturbed, rivers in the Murray region and those in many coastal montane areas are particularly degraded. 6. The IBI results presented here demonstrate a validated method for large-scale monitoring of river health based on a fish fauna of limited diversity, in the absence of suitable reference sites.     

Assessing the effects of sewage effluents in a Mediterranean creek: fish population features and biotic indices

Sewage effluents are one of the main anthropogenic stressors in Mediterranean rivers. The establishment of a cause?Ceffect relationship is hindered in natural systems by the existence of confounding factors (i.e. biotic interactions). Here we analysed the effects that anthropogenic stressors have on a mono-specific fish community (Iberian redfin barbel population, Barbus haasi) inhabiting the northern edge of its distribution range. In Spring 2004, a total of 40 consecutive sampling sites were surveyed in Vallvidrera creek, and 1,331 specimens were measured and weighed. A principal component analysis was performed to synthesize the information provided by 22 environmental variables. Analysis of variance, bivariate correlation analyses and multiple linear regressions were then used to determine the influence of the environmental gradients built (water quality, hydromorphology, woods and macrophytes, and degree of silting) on fish population features (fish size, body condition status, density and biomass). The findings revealed that water quality was the most significant environmental gradient for this fish population. In particular, fish density decreases and fish length increases in those sites exposed to sewage. Additionally, our results showed the best body condition of those specimens inhabiting fast flow reaches which confirms the rheophilous condition of B. haasi. However, these findings were unnoticed for the current version of the index of biotic integrity using fish as bioindicators in Catalonia. Resource managers need to refine diagnostic tools in order to detect subtle deleterious changes on fish communities before they become evident at population scale. Conservation measures should be focused in these small streams in where the best preserved native fish populations usually inhabit. This study suggests the need to change water management policies in Mediterranean rivers to improve the water quality of sewage effluents and increase the dilution power of these rivers.     

Alternative models for species replacement of pelagic fishes

It is well known that the stock abundance of a pelagic fish usually fluctuates and a species of pelagic fish which was dominant in abundance is often taken over by another species. Several alternative models for species replacement among pelagic fishes are presented and analyzed: (A) environmental fluctuation, (B) strong density-dependent reproduction rate, (C) a two-species system with phase variation (density-dependent change of life history traits), (D) a two-species competition system with environmental fluctuation, (E) cyclic advantage relationship among three competitive species, and (F) a two-prey, one-predator system. Different model requires different number of species for the occurrence of species replacement. Three criteria to test each hypothesis from qualitative properties of species replacement are proposed. Possible management policies to decrease the amplitude of stock fluctuations are discussed. As a result, if the catching effort to mackerels which is rare now is large, or if the catching effort to the sardine is still large when it begins to decline in stock abundance, fisheries may be strong destabilizing effect on the stock abundance.     

Recruitment variability of resident brown trout in peripheral populations from southern Europe

1. Population regulation was studied for seven consecutive years (1992–98) in five rivers at the periphery of the distribution of Salmo trutta, where the fish were living under environmental constraints quite different from those of the main distribution area. 2. Recruitment is naturally highly variable and the populations had been earlier classified as overexploited. Thus we expected that densities of young trout in most populations would be too low for density‐dependent mortality to operate. We tested this by fitting the abundance of recruits to egg densities over seven consecutive years (stock–recruitment relationship), and used the results to judge whether exploitation should be restricted in the interests of conserving the populations. 3. The density of 0+ trout in early September, as well as the initial density of eggs and parents, varied greatly among localities and years. The data for all populations fitted the Ricker stock–recruitment model. The proportion of variance explained by the population curves varied between 32% and 51%. However, in most cases the observations were in the density‐independent part of the stock–recruitment curve, where densities of the recruits increased proportionally with egg densities. 4. Our findings suggest that recruitment densities in most rivers and years were below the carrying capacity of the habitats. Although density‐dependent mechanisms seemed to regulate fish abundance in some cases, environmental factors and harvesting appeared generally to preclude populations from reaching densities high enough for negative feedbacks to operate. The findings thus lend support to Haldane’s (1956) second hypothesis that changes in population density are primarily due to density‐independent factors in unfavourable areas and areas with low density due to exploitation. Exploitation should be reduced to allow natural selection to operate more effectively.     

Electrofishing results corrected by selectivity functions in stock size estimates of brown trout (Salrno trutta L.) in brooks

To overcome the problems usually met as a consequence of small numbers of fish collected for trout stock size evaluation in small rivers, a selectivity function was developed and tested in two small rivers in western Switzerland. The function takes the form In E = bL ^−k where E is the fishing efficiency, L is the fish length in cm, k is a constant and b is the slope, estimated by regression analysis.
A good fit was obtained for k = 1 (R. Flon de Carrouge) and k = 2 (R. Cerjaule). Individual selectivity functions have to be computed for each survey, because they depend on the operators of the fishing gear and on the physical and biological conditions in the rivers.
The results are discussed in the light of the Petersen mark-recapture method and the De Lury removal method for stock evaluation. The mark-recapture method gives better results when time intervals between successive fish removals are short.     

When no catches matter: Coping with zeros in environmental assessments

The environmental legislation of many countries increasingly requires the continuous monitoring of fish assemblages to evaluate the success of river and stream restorations. Predicting species–environment relationships on the basis of monitoring data is central in the evaluation of ecological integrity and planning of rehabilitation strategies. Monitoring data are, however, often plagued by a substantial proportion of zeros (no catch at single sampling points) which are caused by relevant ecological processes, but complicate the use of commonly used statistical methods. This study compares mere count regression models, mixture and hurdle models based on Poisson and negative binomial distribution and logistic regressions with respect to their ability to cope with large zero-inflated data sets obtained by point abundance sampling of young-of-the-year fish from three large German rivers. Only mixture and hurdle models based on negative binomial distribution could satisfactorily be fitted to the zero-inflated and overdispersed count data. The logistic regression models applied to transliterated catch data simplified the computational procedure and yielded qualitative similar results to the count regression models indicating that the use of more complex count data did not generally provide better predictions. Therefore, presence/absence sampling may be a suitable and less costly alternative to abundance surveys for identifying environmental factors which affect the spatial distribution of fish populations at least if information on subtly abundance fluctuations is not needed. Mixture or hurdle models are particularly worth the additional effort if it is reasonable to distinguish between those environmental factors influencing the occurrence probability and others affecting the abundance. All models showed low sensitivity to rare guilds pointing to the need for a further development of statistical models for rare species whose management is a matter of growing environmental concern.     

Introductions of distinct stocks of chum salmon, Oncorhynchus keta (Walbaum), into natural populations of the species

Populations of chum salmon, Oncorhynchus keta , are recognizable by the allelic frequencies of allozyme loci. Identification of these was used to assess the return of spawning adults to alien rivers into which they were introduced via hatchery-reared, artificially-fertilized eggs obtained from populations elsewhere in the Soviet Far East. Coefficients of return to spawn in the alien rivers were much lower than returns for the native fish, and in succeeding generations the alien fish disappeared from the spawning runs. It is concluded that transplanting salmonid eggs between populations is ineffective as a means of establishing new stock in territory already occupied by another stock, and the practice is deplored on grounds of conserving unique gene pools within species.     

Effects of environmental variables on fish feeding ecology: implications for the performance of baited fishing gear and stock assessment

The effectiveness of baited fishing gear ultimately depends upon behaviour of the target species – activity rhythms, feeding motivation, and sensory and locomotory abilities. While any environmental parameter that mediates feeding or locomotion can have an important influence on the active space presented by the bait and fish catchability, few biologists have considered how such variation in behaviour might affect catch per unit effort (CPUE) and the resultant stock abundance estimates or population parameters. This review reveals that environment‐related variation in feeding behaviour can act through four different mechanisms: metabolic processes, sensory limitations, social interactions and direct impacts. Water temperature, light level, current velocity and ambient prey density are likely to have largest effects on fish catchability, potentially affecting variation in CPUE by a factor of ten. Feeding behaviour is also density‐dependent, with both positive and negative effects. Over time and geographic space a target species can occupy wide ranges of environmental conditions, and in certain cases, spatial and temporal variation in feeding biology could have a larger impact on CPUE than patterns of abundance. Temperature, light and current can be measured with relative facility and corrections to stock assessment models are feasible. Making corrections for biological variables such as prey density and bait competitors will be more difficult because the measurements are often not practical and relationships to feeding catchability are more complex and poorly understood. There is a critical need for greater understanding of how environmental variables affect feeding‐related performance of baited fishing gear. A combination of field observations and laboratory experiments will be necessary to parameterize stock assessment models that are improved to accommodate variation in fish behaviour. Otherwise, survey data could reveal more about variation in behaviour than abundance trends.     

Pacific sardine (<Emphasis Type="Italic">Sardinops melanostictus</Emphasis>) migrations to the shores of Sakhalin Island in the 20th–early 21st centuries

Historical data for the period 1929?2011 were used to generalize information on the seasonal feeding migrations of Pacific sardine to the shores of Sakhalin Island. In the 20th century, the cyclicity of sardine occurrence in the Tatar Strait and southwestern part of the Sea of Okhotsk appeared to have a similar character. Sardine distribution patterns are considered in connection with the oceanological characteristics on these areas. A close correlated relationship was revealed between the SST anomalies and northern boundary of distribution of this subtropical fish. Besides the water temperature, Pacific sardine northern migrations have been formed under the influence of many other factors (by origin and impact), including fluctuations in abundance, index of stock biomass, food supply, state of marine ecosystems, and climatic conditions.     

VIS – A database on the distribution of fishes in inland and estuarine waters in Flanders,Belgium

The Research Institute for Nature and Forest (INBO) has been performing standardized fish stock assessments in Flanders, Belgium. This Flemish Fish Monitoring Network aims to assess fish populations in public waters at regular time intervals in both inland waters and estuaries. This monitoring was set up in support of the Water Framework Directive, the Habitat Directive, the Eel Regulation, the Red List of fishes, fish stock management, biodiversity research, and to assess the colonization and spreading of non-native fish species. The collected data are consolidated in the Fish Information System or VIS. From VIS, the occurrence data are now published at the INBO IPT as two datasets: ‘VIS - Fishes in inland waters in Flanders, Belgium’ and ‘VIS - Fishes in estuarine waters in Flanders, Belgium’. Together these datasets represent a complete overview of the distribution and abundance of fish species pertaining in Flanders from late 1992 to the end of 2012. This data paper discusses both datasets together, as both have a similar methodology and structure. The inland waters dataset contains over 350,000 fish observations, sampled between 1992 and 2012 from over 2,000 locations in inland rivers, streams, canals, and enclosed waters in Flanders. The dataset includes 64 fish species, as well as a number of non-target species (mainly crustaceans). The estuarine waters dataset contains over 44,000 fish observations, sampled between 1995 and 2012 from almost 50 locations in the estuaries of the rivers Yser and Scheldt (“Zeeschelde”), including two sampling sites in the Netherlands. The dataset includes 69 fish species and a number of non-target crustacean species. To foster broad and collaborative use, the data are dedicated to the public domain under a Creative Commons Zero waiver and reference the INBO norms for data use.     

Distribution pattern, endemism, threat status and conservation measures of fishes in the Tunga and Bhadra rivers of Western Ghats, India

This study documents the distribution patterns, endemism and uniqueness (species richness) of fishes in the Tunga and Bhadra rivers of Western Ghats, India. We recorded 77 species represented by 7 orders, 16 families and 44 genera, of which 36 species are endemic to Western Ghats, 12 species endemic to India and 26 species endemic to the Indian Subcontinent. Based on our analysis on the distribution patterns, the Tunga River is richer in diversity and higher in endemism than the Bhadra. We calculated the similarity of the species composition among sites within these two rivers using the Jacquard index. The similarity index between the sampling sites of these rivers revealed that the similarity decreases with increasing distance between the sampling sites. Of the 77 fish species we collected, 8 species (11.1%) are in the Critical category, 10 species (13.8%) are in the High Risk category, 36 species (50%) are in the Moderate category and the remaining 18 species (25%) are at lower risk. The threat status of fishes found in the Tunga and Bhadra rivers strongly suggests the need for effective conservation measures to conserve the fish species richness of these rivers.     

River fish assemblages along an elevation gradient in the eastern extremity of Europe

Studies on assemblages of freshwater fishes along elevational gradients of rivers are lacking, even in Europe. In this paper we have explored the entire range of elevational gradients existing in the European part of Russia. We analyzed how fish biodiversity (species richness, abundance, diversity indices) at 435 river sites differed by elevation. The impact of elevation on the distribution of freshwater fish species was analyzed using regression and ordination methods. For the first time for a large area of Eastern Europe, optimum points and niche breadth for fish species along altitude gradients were estimated. Our analyses showed: (1) species richness and Shannon index decreased in the upper part of the gradient; fish abundance showed a unimodal response to elevation; highest numbers were found at elevations between 250 and 500 m; (2) ordination analysis demonstrated an upstream-downstream gradient of the fish assemblages; (3) regression analysis showed significant preferences for elevation by 19 species, all of which were monotonic; (4) optimum and niche breadth (tolerance) were highly variable between species; only five species (brown trout, grayling, common minnow, bullhead and stone loach) were encountered at elevations above 650 m; and (5) in our region, the habitat of grayling was higher in the mountains, and its abundance (numbers) at extreme elevations was greater, than brown trout. These results show how fish assemblages differ with elevation. Our findings identify the data that can be used for regional environmental monitoring of the state of small rivers and for aquatic conservation.     

Development and validation of a fish-based index for the assessment of 'river health' in France

SUMMARY 1. In Europe, water policy is currently undergoing considerable change as emphasised by the recent European Water Framework Directive (WFD), which requires the restoration and maintenance of 'healthy' aquatic ecosystems by the assessment of their hydromorphological, chemical and biological characteristics. If the requirements of the WFD are to be met, effective biological tools are needed to measure the 'health' of rivers at scales large enough to be useful for management. These tools need to be ecologically based, efficient, rapid and applicable in different ecological regions. Among potential indicators, fish assemblages are of particular interest because of their ability to integrate environmental variability at different spatial scales. To meet the goals of the WFD, the French Water Agencies and the Ministry of the Environment initiated a research programme to develop a fish-based index that would be applicable nationwide.
2. A variety of metrics based on occurrence and abundance data and reflecting different aspects of the fish assemblage structure and function were selected from available literature and for their potential to indicate degradation.
3. Logistic and multiple linear regression procedures were applied, using an initial data set of 650 reference sites fairly evenly distributed across French rivers and defined by some easily measured regional and local characteristics, to elaborate the simplest possible response model that adequately explained the observed patterns of each metric for a given site.
4. Models obtained for each metric were validated using two independent data sets of 88 reference sites and 88 disturbed sites. These procedures allowed us to select the most effective metrics in discriminating between reference and disturbed sites.     

1980—2007年大亚湾鱼类物种多样性、区系特征和数量变化

根据2004—2005年大亚湾海域底拖网鱼类调查数据,并结合1980—2007年的历史资料,分析了该海域鱼类的种类组成、区系特征、多样性、优势种和数量变化趋势.结果表明： 2004—2005年,大亚湾海域共记录鱼类107种,分属13目50科,以中下层鱼类的种类最多,为48种,其次是中上层和底层种类,分别为37种和21种.大亚湾鱼类区系具热带和亚热带特性,以暖水性种类占绝对优势,为97种,暖温性种类为10种.多样性指数以夏季最高（3.82）,其次是冬季（3.37）和秋季（3.00）,春季最低（2.40）.Pielou均匀度指数的季节变化情况与多样性指数相似.1980—2007年大亚湾海域鱼类群落特征发生了明显的变化：鱼类种类数减少,优势种更替明显.鱼类种类数由1980年的157种减少至1990年的110种,2004—2005年继续减少至107种;鱼类优势种由1980年以带鱼和银鲳等优质鱼为主,更替为以小型和低值的小沙丁鱼、小公鱼和二长棘鲷幼鱼为主.用包含年际变化趋势和季节性周期变化的回归模型模拟1980—2007大亚湾鱼类资源密度的变化,鱼类资源密度在1980—1999年和1990—2007年两个时期均呈下降趋势,但1990—2007年间下降幅度比1980—1999年间大;1980—1999年鱼类资源密度的季节波动幅度较平缓（振幅为0.099）,而1990—2007年的季节波动较大（振幅为0.420）,说明1990—2007年阶段大亚湾鱼类数量的季节变化更为显著.     

Evaluation of pulse fishing for the walleye, Stizostedion vitreum vitreum, in Henderson Lake, Ontario

A total of 3226 walleye were removed from Henderson Lake, Ontario over 3 years (1980–2), causing the stock to collapse. This removal tested the applicability of 'pulse' fishing as a management alternative, and also provided an opportunity to determine which population characteristics might be monitored to serve as predictors of stock collapse in this species.
Following initial exploitation, increased length at age occurred only within younger age-lasses. To use this response as a predictor, one must first obtain pre-exploitation length-at-age data through using the proper gear to sample small fish. Abrosov's mean age to mean age at maturity index may also forewarn of stress (1.2 critical t value for Henderson Lake), but poor recruitment usually invalidates this index, since the lower angling vulnerability of large fish biases mean age calculations. While annual production estimates were a good indicator of the collapse, their determination required much effort. Petersen population estimates produced much more realistic estimates of population size than Schumacher–Eschmeyer estimates, but both estimates not only require much effort but also are influenced by changes in recruitment.
Poor predictors of the walleye collapse included: catch-per-unit-effort data, which, while giving some idea of fish density, were not good indices of exploitation stress; condition factors, which were not correlated to fish abundance; fecundity increases, which suffered far too much of a retarded response in Henderson Lake to serve as a predictor of stock collapse. The inability to determine accurately sex ratios of measure recruitment made these parameters unless.
At least over the short term, neither northern pike nor white sucker populations have increased following the walleye collapse. As yet, walleye have not returned to their former abundance, so the operational usefulness of 'pulse' fishing remains an unknown.     

Risk of inter-river transmission of Gyrodactylus salaris by migrating Atlantic salmon smolts, estimated by Monte Carlo simulation

The possibility of Gyrodactylus salaris infection of wild North Atlantic salmon Salmo salar spreading to new rivers poses a major threat in Norway. This freshwater parasite can survive for some time in brackish water, and it has been suggested that smolts leaving infected rivers could transport vital parasites to new rivers. A Monte Carlo simulation model was used to estimate the risk that infected smolts would ascend a new river. Data from an infected watercourse in Norway, where the salmon population is maintained constant by cultivation, were used. The model included information on prevalence of infection, hydrographical conditions, survival of G. salaris in brackish water, fish population characteristics, and smolt behaviour during seaward migration. The annual risk was estimated for 3 neighbouring rivers situated at different distances from the index river. For the nearest river, which shares the same brackish water zone with the index river, the model estimated an annual risk of 31% that at least 1 infected smolt would ascend this river. The results of the simulation were highly sensitive to the water salinity along the migration route. For the other rivers, the annual risk was lower than 0.5%. Risk was positively correlated with the number of fish leaving the index river, indicating control of this number as a possible tool in risk management.