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Histograms and spatial maps of a 30 × 30 grid of the simulated spatially random (top) and patchy (bottom) density patterns; gray areas indicate grid cells where the simulated density exceeded the 80th quantile (vertical line in histogram).
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Spatially patchy populations present challenges for precise estimation of abundance from surveys, which typically result in high estimation errors compared to surveys of more evenly distributed species. In this study, we used simulations to evaluate the performance of the Trawl and Acoustic Presence/Absence Survey design (TAPAS) in reducing the var...
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... in density can occur within the 1 km 2 cells, the simulated density values are interpreted as mean density for the cell. Survey simu- lations were conducted for multiple realizations of the two spatial patterns of density and yielded similar results; thus, the results reported in this paper are based on the two spatial patterns shown in Fig. 1. The survey simulations were scaled to have the same mean as observed values of ln(CPUE) of POP for selected trawl tows with positive POP catch from the 2007 and 2009 GOA surveys (Fig. ...
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... In that case, simulations of the sampling process were used to correct for bias and improve precision in abundance indices ( Spencer et al. 2012). Wildlife surveys are another arena where density-based sampling is common, and hierarchical models that account for fixed and random effects can reduce the associated bias ( Conn et al. 2017). ...
Hook-and-line surveys can be used to estimate population trends in fish species where conventional methods such as trawl, acoustic, visual, or pot surveys cannot be applied. Hook-and-line surveys allow for the collection of biological information, but the resultant indices of abundance may be biased. We designed simulations to address concerns around survey design, hook saturation, and competition among species and found that catch per unit effort (CPUE) declined more slowly than population size across all scenarios. This hyperstability was most prominent when fish were found in high-density patches, and these scenarios have median absolute relative error values roughly three to five times greater than those with more even distributions of fish density. Despite hyperstability, the surveys still had statistical power to detect changes in abundance. Interspecific competition for hooks caused bias in survey results when one species was more aggressive than another. Taken together, our results indicate hook-and-line surveys fill a niche in survey methodologies, but their use and interpretation can be challenged by hyperstability and competition among species.
... In contrast, a method evaluation aims to present a tangible appraisal of the sampling-induced error specific to a method, providing an evaluation of accuracy, precision and overall method performance. The recent incorporation of simulation testing in marine ecology (Dorner et al., 2013;Oken and Essington, 2015;Spencer et al., 2012) has provided a means to evaluate sampling methods despite the actual population being unknown. Simulation overcomes the uncertainty of an unknown population by generating data through an 'operating model' (Fig. 1) and evaluating candidate estimation procedures and/or methods in terms of their ability to recover operating model properties Cooke, 1999;Thorson et al., 2012). ...
... In doing so, they were able to isolate and identify the relative contribution of climatedriven variables to population fluctuations (Dorner et al., 2013). Similarly, simulation testing has been applied to evaluate the performance of the Trawl and Acoustic Presence/Absence Survey design (TAPAS) in reducing the variability in the estimated biomass of patchily distributed species (Spencer et al., 2012) and to evaluate the effects of predation on population structures (Oken and Essington, 2015). Our study reiterates the importance of simulation testing as an evaluation tool in ecological research, as it can calculate the accuracy and precision of sampling methods in a controlled environment where the 'true' dynamics of the hypothetical population are known. ...
... Previous research has focused on improving rockfish survey biomass estimates using alternate sampling designs (Quinn et al. 1999, Hanselman et al. 2001. Research on the utility of hydroacoustics in gaining survey precision was completed in 2011 (Hanselman et al. 2012b, Spencer et al. 2012) which confirmed again that there are ways to improve the precision, but all of them require more sampling effort in high POP density strata. In addition, there is a study underway exploring the density of fish in untrawlable grounds that are currently assumed to have an equal density of fish compared to trawlable grounds. ...
There is no established management protocol for stocks subject to isolation-by-distance (IBD) stock structure. This study examines several management strategies for two marine fish species subject to IBD using simulation: Pacific cod (Gadus macrocephalus) in the Aleutian Islands (AI) and northern rockfish (Sebastes polyspinis) in the Eastern Bering Sea (EBS) and AI. A one-dimensional stepping stone model was used to model IBD and was intended to mimic regions where marine species are exploited along a continental shelf. The performance of spatial assessment and management methods depended on how the range was split. Splitting anywhere within the managed area led to fewer demes falling below target and threshold biomass levels and higher yield than managing the entire area as a single unit. Equilibrium yield was maximized when each deme was assessed and managed separately and under catch cascading, in which harvest quotas within a management unit are spatially allocated based upon the distribution of survey biomass. The longer-lived rockfish declined more slowly than Pacific cod and experienced greater depletion in biomass under disproportionate fishing effort because of lower productivity. Overall, splitting a management area of the size simulated in the model improved performance measures, and the optimal management strategy grouped management units by demes with similar relative fishing effort.
... In doing so, they were able to isolate and identify the relative contribution of a climate-driven covariate to population fluctuations (Dorner et al. 2013). Similarly, simulation testing has been used to evaluate the performance of the Trawl and Acoustic Presence/Absence Survey design (TAPAS) in reducing the variability in the estimated biomass of patchily distributed species (Spencer et al. 2012). ...
Tsitsikamma National Park (TNP) possesses the oldest (established 1954), and one of the largest (350 km 2) 'no-take' marine protected areas (MPA) in South Africa. A long-term monitoring (LTM) programme to observe the subtidal reef fishes in the TNP MPA was established in 2007. To date, 243 angling replicates have been completed, and a total of 2,751 fish belonging to 41 different species have been caught and released. In an era of unprecedented global biodiversity loss, data that can be used to monitor ecosystems and gauge changes in biodiversity through time are essential. This thesis aims to improve the methodological and statistical processes currently available for LTM of subtidal reef fish by providing an evaluation of the TNP MPA LTM programme. Angling data revealed definitive spatial structuring, in the form of spatial autocorrelation, and a shift in viewing spatial dependency as a statistical obstacle to a source of ecological information created a new avenue of data inference. Species-specific distribution maps identified localized habitat as the main predictor variable for species abundance, emphasizing the need for accurate a priori bathymetric information for subtidal monitoring. 'Random forest' analyses confirmed spatial variables are more important than temporal variables in predicting species abundance. The effectiveness of Generalized Linear Mixed Models (GAMMs) to account for spatial autocorrelation was highlighted, and evidence that disregarding spatial dependencies in temporal analyses can produce erroneous results was illustrated in the case of dageraad (Chrysoblephus cristiceps). Correlograms indicated that the current sampling strategy produced spatially redundant data and the sampling unit size (150 m 2) could be doubled to optimize sampling. Temporal analyses demonstrated that after 50 years of 'no take' protection the TNP MPA ichthyofauna exhibits a high level of stability. Species-specific size structure was also found to be highly stable. Dageraad was the only species to exhibit a definitive temporal trend in their size structure, which was attributed to recruitment variation and the possibility that large individuals may migrate out of the study area. The inadequacy of angling as a method for monitoring a broad spectrum of the fish species was highlighted, particularly due to its selectivity towards large predators. As a result, a new sampling iii technique known as Stereo Baited Remote Underwater Videos (stereo-BRUVs) was introduced to the LTM programme in 2013. Stereo-BRUVs enabled sampling of 2640 fish belonging to 52 different species, from 57 samples collected in less than two years. A comparison of the sampling methods concluded that, compared to angling, stereo-BRUVs provide a superior technique that can survey a significantly larger proportion of the ichthyofauna with minimal length-selectivity biases. In addition, stereo-BRUVs possess a higher statistical power to detect changes in population abundance. However, a potential bias in the form of 'hyperstability' in sites with unusually high fish densities was identified as a possible flaw when using stereo-BRUVs. In an attempt to provide a more rigorous method evaluation, simulation testing was employed to assess the ability of angling and stereo-BRUVs to accurately describe a decreasing population. The advantage of this approach is that the simulated population abundances are known, so that each sampling method can be tested in terms of how well it tracks known abundance trends. The study established that stereo-BRUVs provided more accurate data when describing a distinct population decline of roman (Chrysoblephus laticeps) over 10-and 20-year periods. In addition, spawner-biomass was found to be a more accurate population estimate than relative abundance estimates (CPUE and MaxN) due to the inclusion of population size structure information, highlighting the importance of length-frequency data. The study illustrated that an evaluation framework that utilizes simulation testing has the potential to optimize LTM sampling procedures by addressing a number of methodological questions. This includes developing a procedure that aligns data collected from different sampling methods by applying correction factors, thus ensuring LTM programmes are able to adapt sampling strategies without losing data continuity. iv
... The use of real-time processing of acoustic backscatter to determine patches was efficient, and POP were the most commonly caught species and were found in higher densities than other fishes at patch stations. However, the conditions that make the TAPAS design more efficient than random sampling, as shown in simulation studies (Spencer et al., 2012), did not materialize in the fieldwork described here. ...
... Improved correspondence between acoustic backscatter and trawl CPUE, for example, could be obtained from better partitioning of acoustic backscatter to species and quantifying the availability and vulnerability of a fish to these 2 sampling methods. Spencer et al. (2012) showed that the highest gains in efficiency for the TAPAS design, compared with SRS in simulations, were achieved when the spatial correlation of fish density was low and there was a large number of patches of small size. Such circumstances resulted in the TAPAS design sampling a high proportion of the total area of patches in the population. ...
... Such circumstances resulted in the TAPAS design sampling a high proportion of the total area of patches in the population. In addition, Spencer et al. (2012) showed that a modified TAPAS design, in which every third patch was sampled, resulted in higher efficiency than did an SRS design. However, the situations in Spencer et al. (2012) where there were significant gains in performance relative to SRS occurred only when there was a strong relationship between S v and CPUE. ...
Biomass estimates of several species of Alaskan rockfishes exhibit large interannual variations. Because rockf ishes are long lived and relatively slow growing, large, short-term shifts in population abundance are not likely. We attribute the variations in biomass estimates to the high variability in the spatial distribution of rockf ishes that is not well accounted for by the survey design currently used. We evaluated the performance of an experimental survey design, the Trawl and Acoustic Presence/Absence Survey (TAPAS), to reduce the variability in estimated biomass for Pacif ic ocean perch (Sebastes alutus). Analysis of archived acoustic backscatter data produced an acoustic threshold for delineating potential areas of high ("patch") and low ("background") catch per unit of effort (CPUE) in real time. In 2009, we conducted a 12-day TAPAS near Yakutat, Alaska. We completed 59 trawls at 19 patch stations and 40 background stations. The design performed well logistically, and Pacific ocean perch (POP) accounted for 55% of the 31 metric tons (t) of the catch from this survey. The resulting estimates of rockfish biomass were slightly less precise than estimates from simple random sampling. This difference in precision was due to the weak relationship of CPUE to mean volume backscattering and the relatively low variability of POP CPUE encountered. When the data were re-analyzed with a higher acoustic threshold than the one used in the field study, performance was slightly better with this revised design than with the original field design. The TAPAS design could be made more effective by establishing a stronger link between acoustic backscatter and CPUE and by deriving an acoustic threshold that allows better identification of backscatter as that from the target species.
Beaked redfish inhabits North Atlantic waters in the depth range 100-950 m, over the continental shelf, slope and the open ocean. Individuals can live demersal or pelagic, at various stages of their life cycle. The geographical distribution of the species extends to most of the Atlantic waters from Newfoundland and the Labrador basin in the west to the Barents Sea in the east. Monitoring beaked redfish is challenging because of the species wide geographical distribution and large scale migrations; deep distribution, which complicates trawling and hydroacoustic surveys; difficulties with tagging; and persistent difficulties in taxonomic identification. These challenges make it a particularly problematic species to observe with conventional research methods. We review these key challenges and provide recommendations for the coordinated observation of Sebastes mentella in the North Atlantic that would best contribute to the assessment and ecological research on this species.
