Efficiency of presence-absence sampling used to estimate the mean abundance of fish eggs

ABSTRACT:   Statistical properties of estimators relating to the mean abundance of fish eggs were investigated using the data from the presence-absence sampling (PAS) and counting sampling (CS). PAS, which focuses on the presence-absence of eggs in a sample, is more cost-effective yet is unlikely to give more precise estimates than CS, which counts the number of eggs. But when limitations are given on the sampling cost and number of sampling stations, PAS may have advantages. This study shows that the mean square error (MSE) of the maximum likelihood estimator (MLE) based on PAS may become smaller than the MSE of the MLE based on counting data when the number of observations for PAS becomes larger. The observation number for PAS is determined, which minimizes the MSE of a combined estimator from the two MLE under a restriction of the total cost of observation. A dual problem is also solved. It is shown that MSE of the MLE in PAS is a monotone increasing function of the oversight probability. PAS becomes more informative as the distribution of the number of eggs is more aggregated.     

Performance comparison of traditional sampling designs and adaptive sampling designs for fishery-independent surveys: A simulation study

We compared the performance of two traditional sampling designs with three adaptive sampling designs using simulated data based on fishery-independent surveys for yellow perch in Lake Erie. Traditionally, the fishery-independent survey has been conducted with a stratified random sampling design based on basin and depth strata; however, adaptive sampling designs are thought to be more suitable for surveying heterogeneous populations. A simulation study was conducted to compare these designs by examining the accuracy and precision of the estimators. Initially in the simulation study, we used bias, variance of the mean, and mean squared error (MSE) of the estimators to compare simple random sampling (SRS), stratified random sampling (StRS), and adaptive two-phase sampling (ATS). ATS was the best design according to these measurements. We then compared ATS, adaptive cluster sampling (ACS), adaptive two-stage sequential sampling (ATSS), and the currently used stratified random sampling design. ATS performed better than the other two approaches and the current stratified random sampling design. We concluded that ATS is preferable for yellow perch fishery-independent surveys in Lake Erie. Simulation study is a preferred approach when we seek an appropriate sampling design or evaluate the current sampling design.     

Characterizing larval swordfish habitat in the western tropical North Atlantic

Swordfish Xiphias gladius (Linnaeus, 1758) are a circumglobal pelagic fish targeted by multiple lucrative fisheries. Determining the distribution of swordfish larvae is important for indicating reproductive activity and understanding the early life history of swordfish. We identify and characterize larval swordfish distributions during peak swordfish spawning throughout the Gulf of Mexico and western Caribbean Sea with generalized additive models (GAMs) using catches of swordfish larvae during ichthyoplankton surveys in April and May of 2010, 2011, and 2012. The best fit GAM, as determined by stepwise, backward Akaike Information Criterion selection, included both physiochemical (temperature at 5 m, sea surface height anomaly (SSHA), eddy kinetic energy (EKE)), temporal (lunar illumination, hour of sampling) and spatial (location) variables, while near surface chlorophyll a concentration residuals remained as a random effect. The highest probability of larval swordfish catch occurred at sub‐surface temperatures, SSHA, and EKE values indicative of boundary currents. Standard lengths of larvae were larger further downstream in the boundary currents, despite high variability in length with location due to multiple spawning locations of swordfish near these currents. Probability of larval swordfish catch also peaked during the crescent and gibbous moons, indicating a lunar periodicity to swordfish spawning. These results suggest that swordfish may spawn during select moon phases near boundary currents that transport their larvae to larval and juvenile habitat including the northern Gulf of Mexico and coastal waters of the southeast United States.     

A practical guide to statistical methods for comparing means from two-stage sampling

Two-staged sampling is the method of sampling populations that occur naturally in groups and is common in ecological field studies. This sampling method requires special statistical analyses that account for this sample structure. We present and compare several analytical methods for comparing means from two-stage sampling: (1) simple ANOVA ignoring sample structure, (2) unit means ANOVA, (3) Nested Mixed ANOVA, (4) restricted maximum likelihood (REML) Nested Mixed analysis, and (5) REML Nested Mixed analysis with heteroscedasticity.We consider a fisheries survey example where the independent sampling units are subsampled (i.e., hauls are the sampling unit and fish are subsampled from hauls). To evaluate the five analytical methods, we simulated 1000 samples of fish lengths subsampled from hauls in two regions with various levels of: (1) differences between the region means, (2) unbalance among numbers of hauls within regions and numbers of fish within hauls, and (3) heteroscedasticity. For each simulated sample, we tested for a difference in mean lengths between regions using each of the five methods. The inappropriate, simple ANOVA that ignored the sample structure resulted in grossly inflated Type I errors (rejecting a true null hypothesis of no difference in the means). We labeled this analysis the Pseudoreplication ANOVA based on the term “pseudoreplication” that describes the error of using a statistical analysis that assumes independence among observations when in fact the measurements are correlated. The result of this error is artificially inflated degrees of freedom, giving the illusion of having a more powerful test than the data support.The other four analyses performed well when the data were balanced and homoscedastic. When there were unequal numbers of fish per haul, the REML Nested Mixed analyses and the Unit Means ANOVA performed best. The Unequal-Variance REML Nested Mixed analysis showed clear benefit in the presence of heteroscedasticity and unbalance in hauls. For the REML Nested Mixed analysis, we compared three software packages, S-PLUS, SAS, and SYSTAT.A second simulation that compared samples with varying ratios of among-haul to among-fish variance components showed that the Pseudoreplication ANOVA was only appropriate when the haul effect yielded a p-value >0.50.     

Effects of sampling errors on abundance estimates from virtual population analysis for walleye pollock in northern waters of Sea of Japan

ABSTRACT:   Effects of sampling errors on abundance estimates from virtual population analysis (VPA) were quantified with the bootstrap method for stock of walleye pollock in the the Sea of Japan. In the bootstrap method, individual fish measurements were resampled. A total of 1000 bootstrap samples were produced for each year from 1991 to 2001. The coefficients of variation (CV) of catch at age in 2001 ranged 6.1–33.1%. The CV of an abundance estimate in 2001 ranged 9.0–35.7%. Abundance estimates of the oldest age and the latest year, which had larger CVs than the other estimates, were sensitive to sampling errors. Effects of sampling errors became smaller when the catch at age had been accumulated over a few years. Although VPA includes various types of errors, only the sampling errors have room for improvement in reality. Quantifying the effect of sampling error on VPA estimates is essential for sound and efficient stock management, and is emphasized in this study.     

Broadbill swordfish: status of established fisheries and lessons for developing fisheries

Guidelines for the assessment and management of developing swordfish fisheries are derived through an examination of five swordfish fisheries. As they develop, swordfish fisheries may be inclined to local depletion around underwater features, such as seamounts and banks. Few nations have applied the precautionary approach in managing their developing swordfish fisheries. Without controls, swordfish fisheries expand geographically and fishing effort increases, often overshooting optimum levels. However, it is difficult to distinguish clear evidence of fishery collapse; modern longliners harvest widely distributed tuna and swordfish and they are able to relocate to distant areas or switch between target species in response to fluctuations in species abundance and price. Furthermore, the wide distribution of swordfish combined with year‐round spawning and high growth rates amongst juveniles probably contribute to the apparent resilience of swordfish stocks to intensive harvesting. Over half the world’s swordfish catch is taken as an incidental catch of longliners fishing for tuna. In several areas, such as the North Atlantic, catch quotas have sometimes caused tuna longline fishers to discard swordfish. Minimum size limits have also resulted in discarding of swordfish in tuna fisheries and in dedicated swordfish fisheries. In addition to weakening the effectiveness of those management measures, bycatch and discarding add to the complexities of managing swordfish fisheries and to uncertainties in assessing the stocks. Longliners that target swordfish often fish at high latitudes where interactions with marine wildlife, such as seabird, are generally more frequent than at low latitudes. Concern over incidental catches of marine wildlife and other species is becoming a driving force in the management of several swordfish fisheries. Fishery management organisations will need to implement management measures to protect non‐target species and gather reliable data and information on the situation by placing observers on boats fishing for swordfish.     

Evaluation of lethal and non-lethal sampling methods for the detection of white sturgeon iridovirus infection in white sturgeon, Acipenser transmontanus (Richardson)

Pectoral fin tissue of white sturgeon was investigated as a potential non-lethal sample source for the detection of white sturgeon iridovirus (WSIV) infection. Histopathology and polymerase chain reaction (PCR) results using fin tissue were compared with the standard lethal histopathology sampling method that utilizes head tissue. Tissues for each of the three sampling methods were collected weekly for 8 weeks from individual sturgeon undergoing an experimental cohabitation challenge with fish infected with the Abernathy isolate of WSIV. Non-lethal fin histopathological evaluation did not reveal infection during the first 3 weeks of sampling, while non-lethal PCR and the lethal method were variable. However, all three sampling methods were equally capable of identifying infection from 4 to 8 weeks post-exposure. Of the survivors tested, all were negative by PCR and the lethal method, and only one fish was identified as being positive by non-lethal fin histopathology. In another experiment, all three sampling methods were applied to asymptomatic WSIV carriers in a case study conducted at the Kootenai Tribal Sturgeon Conservation Hatchery. Results showed that both lethal and non-lethal fin histopathology were equally effective in detecting infection, but PCR was unable to identify this strain of WSIV. Depending on the virus isolate, these results suggest that non-lethal sampling of fin tissue (histopathology or PCR) is comparable with the lethal sampling method at identifying WSIV infection once infection is established, and under certain circumstances may provide an alternative to lethal sampling.     

Movements and behaviors of swordfish in the Atlantic and Pacific Oceans examined using pop‐up satellite archival tags

Swordfish are highly specialized top‐level predators that have been challenging to study. In this paper, data from 31 pop‐up satellite archival tags attached to swordfish from (i) the eastern Pacific, (ii) central Pacific, and (iii) western North Atlantic‐Caribbean were analyzed. Common across locations was a pronounced diel vertical pattern with daytime hours spent primarily below the thermocline and nighttime hours spent in warmer waters, close to the surface. One exception to this pattern was periodic daytime basking events which were most common in cooler waters off California. Maximum daytime depths were significantly correlated with light penetration as measured by the diffuse attenuation coefficient at 490 nm. Temperature did not appear to influence daytime depths, and swordfish tolerated both extremely low temperatures (4°C) and rapid and dramatic temperature changes (>20°C). Temperature did appear to influence the nighttime depths in the Pacific where fish typically remained in the surface mixed layer. In contrast, in the warm tropical Atlantic this was not the case, and nighttime depths were much deeper. In all areas, nighttime depth increased around the full moon. Given the parallels between the vertical movement patterns of swordfish and those of the deep sound scattering layer we suggest that swordfish vertical distribution patterns, especially during daytime, are influenced largely by resource availability. At night, when swordfish are typically targeted by fisheries, both ambient light and temperature influence movements. Understanding vertical movement patterns of swordfish can help evaluate gear vulnerability, improve population assessments, and potentially reduce fisheries bycatch.     

Comparison of two methods of sub-sea sampling of the Guernsey ormer,Haliotis tuberculata L.

Abstract The ormer, Haliotis tuberculata L., is the only abalone species found on the coasts of western Europe, its northern most limit of distribution being the Channel Islands. Previous Guernsey ormer population studies were based upon a form of catch-per-unit-effort sampling where the unit of effort was one diver, searching the substrate for 5 min continuously. An ormer population survey was carried out in the waters around Guernsey, using this former method concurrent with an alternative system of sampling by area using 10 m² quadrats at randomly selected locations. The published results of a series of earlier surveys include a measure of ormer density m^-2 which, along with knowledge of the extent of suitable substrate, allows tentatively for absolute abundance to be estimated. This study demonstrates that an estimate obtained in this way may be unreliable. Statistical comparison of the population size structures derived from the two different sampling methods also showed considerable inconsistency. The implications of this for management of the Guernsey ormer stock are considered.     

Is scuba sampling a relevant method to study fish microhabitat in lakes? Examples and comparisons for three European species

Abstract – We compared fish microhabitat use patterns in the littoral zone of a lake using a new direct method (point abundance sampling by scuba, PASS) and the widely used point abundance sampling by electrofishing technique (PASE). We collected microhabitat data for age 0+ roach ( Rutilus rutilus L.), perch ( Perca fluviatilis L.), and pike ( Esox lucius L.). The two methods yielded different results for fish assemblage structure and microhabitat patterns. Using PASE, fish were mainly found in "shelter habitats" such as shallow waters and dense vegetation. It is likely that this behavior is caused by the disturbance of the observer stamping around. Using PASS, fish escapement behavior was rarely observed. Therefore, we concluded that this direct and nondestructive sampling technique can be used to provide an accurate microhabitat estimation of a fish community and is assumed to be more suitable than PASE for fish habitat studies.     

Geostatistics in fisheries survey design and stock assessment: models, variances and applications

Over the past 10 years, fisheries scientists gradually adopted geostatistical tools when analysing fish stock survey data for estimating population abundance. First, the relation between model‐based variance estimates and covariance structure enabled estimation of survey precision for non‐random survey designs. The possibility of using spatial covariance for optimising sampling strategy has been a second motive for using geostatistics. Kriging also offers the advantage of weighting data values, which is useful when sample points are clustered. This paper discusses, with fisheries applications, the different geostatistical models that characterise spatial variation, and their variance formulae for many different survey designs. Some anticipated developments of geostatistics related to multivariate structures, temporal variability and adaptive sampling are discussed.     

Methods for studying spatial behaviour of freshwater fishes in the natural environment

Spatial behaviour of fishes in fresh and brackish water ranges in temporal scales between localized diel movements, often associated with foraging and predator evasion, to seasonal or life‐cycle related events involving movements between freshwater habitats or freshwater and marine biotopes. Recent technological advances have resulted in dramatic improvements in the range of techniques available for the study of spatial behaviour of freshwater fishes in the natural environment, and broadly may be divided into two categories: capture dependent and capture independent. The former incorporates those methods that rely on sampling marked fish (mark–recapture) or unmarked fish (density estimates, catch per unit effort) over defined scales of time and space in order to derive information on distribution and movement. Captured fish may also be tagged with transmitters that radiate energy, enabling the fish to be tracked and/or environmental data to be gathered. Biochemical analysis of samples from fish, requiring non‐destructive sampling (genetic analysis and scale microchemistry) or destructive sampling (otolith microchemistry) may also provide information on migration and ontogenetic processes. Capture independent techniques include visual observation and video techniques, hydroacoustics and automated fish counting. Catch per unit effort and mark–recapture techniques are most efficient where long‐term fishery or monitoring studies are in place and data on crude spatial and temporal scales are acceptable. They also have the advantages of low technical requirements and low equipment costs. Where specific management or ecological questions are pertinent, recapture independent techniques may be more appropriate. Telemetric methods can provide high resolution information at the individual level, while hydroacoustics is increasingly providing information at the population level in large lake and river environments. Biochemical methods are becoming increasingly useful in determining the extent of population segregation, where DNA analysis is used, and in the study of migration and ontogenetic changes in behaviour, where otolith microchemistry and stable isotope analysis is used.     

Landings, logbooks and observer surveys: improving the protocols for sampling commercial fisheries

The sampling of commercial marine fisheries for management purposes often displays a key weakness in the form of poor documentation of the scientific basis of sampling and estimation, the assumptions made, and the practical constraints. This paper reviews systematically the theoretical and practical options that can remedy this situation and recommends that decisions be archived in regularly updated ‘Sampling Approach and Modifications’ (SAM) documents. Defining the target population, the observable population (usually a subset of the target), and the assumed links between them is important, along with the distinction between design‐ and model‐based sampling approaches. Fleet‐targeted and stock‐targeted sampling strategies are contrasted, the latter being much harder to implement. Sampling protocols aimed at estimating quantities of fish landed and discarded, length–frequency distributions, length‐related variables such as age, weight and maturity, and ratio variables such as catch per unit of effort and the proportions of discards are discussed, together with the raising of estimates to fleet and/or stock levels. The ideas are summarized in the specific contexts of landings sampling, logbook schemes and sea‐going observer surveys. SAMs are commended for enhancing the scientific value of fishery sampling, and for encouraging methodological discussions among users and producers of the data.     

Quantifying fish species richness and abundance in Amazonian streams: assessment of a multiple gear method suitable for Terra firme stream fish assemblages

A multigear sampling method to quantify fish richness and abundance in Amazonian Terra firme streams was assessed. This method is based on the four‐pass removal method using the combined application of different nets. The efficiency of the method was explored over 10 replicated sites along three streams over day, night and seasons. Use of four successive passes allowed both abundant and rare species to be collected and the abundance of common species to be estimated. On average, a high proportion (41%) of rare species was collected per sample (only one or two individuals) after four fishing passes. The efficiency of the sampling method to detect species richness per sample between successive passes was estimated using an autosimilarity approach. Although species richness and abundance increased with successive passes, no major differences were obtained between the third and fourth pass. A single pass considerably underestimated the richness and abundance of species in these type of streams, and night sampling also increased beta‐diversity by at least 20%. Abundance estimates demonstrated high efficiency with an overall sampling error of only 8 and 11% for samples and single species, respectively. Capture efficiency differed among fish species exhibiting different ecological traits and showed significant differences among seasons for total samples. Results supported the robustness of the method and its suitability to quantify fish richness and abundance in small, wadeable Amazonian Terra firme streams inhabited by highly diverse fish assemblages.     

Concurrent assessment of fish and habitat in warmwater streams in Wyoming

Abstract  Fisheries research and management in North America have focused largely on sport fishes, but native non-game fishes have attracted increased attention due to their declines. The Warmwater Stream Assessment (WSA) was developed to evaluate simultaneously both fish and habitat in Wyoming streams by a process that includes three major components: (1) stream-reach selection and accumulation of existing information, (2) fish and habitat sampling and (3) summarisation and evaluation of fish and habitat information. Fish are sampled by electric fishing or seining and habitat is measured at reach and channel-unit (i.e. pool, run, riffle, side channel, or backwater) scales. Fish and habitat data are subsequently summarised using a data-matrix approach. Hierarchical decision trees are used to assess critical habitat requirements for each fish species expected or found in the reach. Combined measurements of available habitat and the ecology of individual species contribute to the evaluation of the observed fish assemblage. The WSA incorporates knowledge of the fish assemblage and habitat features to enable inferences of factors likely influencing both the fish assemblage and their habitat. The WSA was developed for warmwater streams in Wyoming, but its philosophy, process and conceptual basis may be applied to environmental assessments in other geographical areas.     

Oversight probability in presence–absence sampling for detection of fish eggs

ABSTRACT:   Presence–absence sampling (PAS) is a sampling technique that observes only the presence or absence of objects, such as eggs, in sampling units. The purpose of the present paper was to study the oversight probability in a PAS study for detecting fish eggs in connection with the spatial distribution of eggs. It was shown that the oversight probability of presence of eggs under no-eggs observation is a monotone decreasing function of the parameter of the degree of contagion.     

Can fish sampling protocol (CEN, 2005) be amended for Mediterranean lakes?

The CEN (2005) methodology for fish monitoring of mesotrophic to eutrophic Mediterranean lakes was evaluated. The contribution of gillnet (benthic and pelagic) and electrofishing catches on species richness was examined. Additionally, the contribution of benthic gillnet sampling effort on species richness and precision of catch‐per‐unit‐effort (CPUE) estimates, considering both number of specimens (ΝPUE) and biomass (BPUE), was assessed. Subsequently, the impact of reduction in sampling effort on the parameters mentioned above was estimated and the effort needed to acquire the desired precision level considering different NPUE values was modelled. The use of different sampling gears was found to contribute to species richness assessment, while sampling effort could be reduced in the deepest zones of the lakes. The resultant model can reliably guide assessment of the sampling effort required in the Mediterranean and central European lakes with high fish densities.     

Environmental effects on swordfish and blue shark catch rates in the US North Pacific longline fishery

Generalized additive models (GAMs) were applied to examine the relative influence of various factors on fishery performance, defined as nominal catch- per-unit-effort (CPUE) of swordfish (Xiphias gladius) and blue shark (Prionace glauca) in the Hawaii-based swordfish fishery. Commercial fisheries data for the analysis consisted of a 5 year (1991–1995) time series of 27 901 longline sets. Mesoscale relationships were analysed for seven physical variables (latitude, longitude, SST, SST frontal energy, temporal changes in SST (ΔSST), SST frontal energy (ΔSST frontal energy) and bathymetry), all of which may affect the availability of swordfish and blue shark to the fishery, and three variables (number of lightsticks per hook, lunar index, and wind velocity) which may relate to the effectiveness of the fishing gear. Longline CPUE data were analysed in relation to SST data on three spatiotemporal scales (18 km weekly, 1°-weekly, 1°-monthly). Depending on the scale of SST data, GAM analysis accounted for 39–42% and 44–45% of the variance in nominal CPUE for swordfish and blue shark, respectively. Stepwise GAM building revealed the relative importance of the variables in explaining the variance in CPUE. For swordfish, by decreasing importance, the variables ranked: (1) latitude, (2) time, (3) longitude, (4) lunar index, (5) lightsticks per hook, (6) SST, (7) ΔSST frontal energy, (8) wind velocity, (9) SST frontal energy, (10) bathymetry, and (11) ΔSST. For blue shark, the variables ranked: (1) latitude, (2) longitude, (3) time, (4) SST, (5) lightsticks per hook, (6) ΔSST, (7) ΔSST frontal energy, (8) SST frontal energy, (9) wind velocity, (10) lunar index, and (11) bathymetry. Swordfish CPUE increased with latitude to peak at 35–40°N and increased in the vicinity of temperature fronts and during the full moon. Shark CPUE also increased with latitude up to 40°N, and increased westward, but declined abruptly at SSTs colder than 16°C. As a comparison with modelling fishery performance in relation to specific environmental and fishery operational effects, fishery performance was also modelled as a function of categorical time (month) and area (2° squares) variables using a generalized linear model (GLM) approach. The variance accounted for by the GLMs was ≈ 1–3% lower than the variance explained by the GAMs. Time series of swordfish and blue shark CPUE standardized for the environmental and operational variables quantified in the GAM and for the time-area effects in the GLM are presented. For swordfish, both nominal and standardized time series indicate a decline in CPUE, whereas the opposite trend was seen for blue shark.     

Systematic point sampling of fish communities in medium‐ and large‐sized rivers: sampling procedure and effort

Compared with small rivers and streams, the study of fish communities in large rivers remains challenging as spatial and temporal data variability can be greatly influenced by sampling strategy and operator choice. In an attempt to limit this variability, a new sampling protocol for fish communities in medium‐ to large‐sized rivers was developed, based on point sampling by electric fishing and using standardised procedures and effort. Here, change in data quality (assemblage abundance, richness, structure and biotic index) with increasing sampling effort (from 1 to 100 sampling points) was evaluated. A total of 75 sampling points are proposed as the standard number of samples per site. Broadly, the results show that the application of 75 sampling points provides a reproducible representation of fish community structure in medium and large rivers, with little additional information provided by further sampling except under certain conditions, when 100 points are recommended to maintain data quality.