Allocation Of Sampling Effort Research Articles

Leveraging eDNA metabarcoding to characterize nearshore fish communities in Southeast Alaska: Do habitat and tide matter?

AbstractNearshore marine habitats are critical for a variety of commercially important fish species, but assessing fish communities in these habitats is costly and time‐intensive. Here, we leverage eDNA metabarcoding to characterize nearshore fish communities near Juneau, Alaska, USA, a high‐latitude environment with large tidal swings, strong currents, and significant freshwater input. We investigated whether species richness and community composition differed across three habitat types (sand beaches, eelgrass beds, and rocky shorelines) and between high and low tides. Additionally, we tested whether replication of field samples and PCR reactions influenced either species richness or composition. We amplified a 12S mitochondrial locus in our samples and identified 167 fish amplicon sequence variants, which were grouped into 24 unique taxa based on sequence similarity, with approximately half of these taxa resolved to single species. Species richness and composition inferred from eDNA differed substantially among habitats, with rock habitats containing fewer taxa and fewer overall detections than sand and eelgrass habitats. The effect of tide was not significant on its own, but a significant habitat‐tide interaction was documented, with the most pronounced differences in taxa between tides found in sand habitats. Power analyses indicated that additional field sampling is useful to detect small changes in species richness such as those due to tide. PCR replicates typically identified few additional taxa. Our results provide important information that can be used to guide future studies, most notably, that the influence of tide on eDNA results appears to be minimal and potentially isolated to certain habitats. This suggests that replication across tides may not be vital for future eDNA studies and that additional replication across space—particularly across heterogeneous environments—likely is a better allocation of sampling effort.

Sources of variability in tissue chemistry in northern hardwood species

Measurements of tree tissue chemistry are influenced by the precision and accuracy of laboratory analyses, sampling position within the tree, variation among replicate trees of the same species, and variation from year to year. We characterized these sources of uncertainty for six northern hardwood species and compared them with observed rates of long-term change. Uncertainty associated with laboratory quality control was small (1%–5%) and differed among elements, with K concentrations exhibiting the lowest accuracy and precision. Sampling position within the tree was more important for branches (the coefficient of variation was 23%) and wood (37%) than for foliage or bark (12% for both) (p < 0.001). Foliar N and P concentrations in leaves were less variable than other elements or tissue types both from tree to tree (p = 0.02) and from year to year (p = 0.03), which means that more samples would be needed to detect differences over space or time for Ca, Mg, or K in branches or wood. Concentrations of foliar N increased over 25 years at the Huntington Forest (p ≤ 0.03) by > 16%. Uncertainty analysis can be used to guide the allocation of sampling effort, depending on the elements and tissue types of interest and the objectives of the study.

Differential efficiencies of dip-net sampling versus sampling surface-floating pupal exuviae in a biodiversity survey of Chironomidae

Relative efficiencies of standard dip-net sampling (SDN) versus collections of surface-floating pupal exuviae (SFPE) were determined for detecting Chironomidae at catchment and site scales and at subfamily/tribe-, genus- and species-levels based on simultaneous, equal-effort sampling on a monthly basis for one year during a biodiversity assessment of Bear Run Nature Reserve. Results showed SFPE was more efficient than SDN at catchment scales for detecting both genera and species. At site scales, SDN sampling was more efficient for assessment of a first-order site. No consistent pattern, except for better efficiency of SFPE to detect Orthocladiinae genera, was observed at genus-level for two second-order sites. However, SFPE was consistently more efficient at detecting species of Orthocladiinae, Chironomini and Tanytarsini at the second order sites. SFPE was more efficient at detecting both genera and species at two third-order sites. The differential efficiencies of the two methods are concluded to be related to stream order and size, substrate size, flow and water velocity, depth and habitat heterogeneity, and differential ability to discriminate species among pupal exuviae specimens versus larval specimens. Although both approaches are considered necessary for comprehensive biodiversity assessments of Chironomidae, our results suggest that there is an optimal, but different, allocation of sampling effort for detecting Chironomidae across stream orders and at differing spatial and taxonomic scales.Article submitted 13. August 2014, accepted 31. October 2014, published 22. December 2014.

A bootstrap calculation of confidence regions for proportions of sediment contributed by different source areas in a ‘fingerprinting’ model

AbstractWhen ‘fingerprinting’ is used to identify what proportions Ps (s = 1, …, g) of suspended sediment come from g different source areas, measures of the uncertainties in estimates of the Ps are also required. These uncertainties are influenced by two kinds of correlation whose effects are rarely recognized in the literature. These are (i) correlation between the estimated Ps because they must add to 1 and (ii) correlation between the geochemical tracers measured in sediment samples. This paper uses bootstrap procedures to identify joint confidence regions for the estimated proportions [responding to correlation of type (i)] and to explore alternatives to the ‘standard’ least‐squares criterion used to estimate the proportions when tracer measurements are correlated [correlation of type (ii)].Using a limited dataset with three sediment source areas for illustration (g = 3), results were obtained from 5000 bootstrap samples, using two criteria (standard and generalized least squares, GLS) with two inequality constraints: (a) 0 ≤ Ps ≤ 1, where Ps is the fraction of suspended sediment contributed by the s‐th source area (s = 1, 2, 3) and (b) 0 < Ps < 1, which, the paper argues, better represents reality. Approximate 95% confidence regions for the Ps, given by the two criteria and two inequality constraints, were compared. Using inequality constraint (a), the confidence region given by the GLS criterion was slightly smaller than that given by the standard; using constraint (b), the two confidence regions' boundaries were almost identical, suggesting that the effects of correlations between tracers were not large for the dataset used. For both criteria, the scatter amongst estimated proportions Ps obtained by bootstrapping was large, raising issues concerning the efficiency of sampling and the allocation of sampling effort, both in source areas and in transported suspended sediment. The results suggest that apparently small differences in the constraints applied to the proportions Ps can give quite different numerical results. Copyright © 2014 John Wiley & Sons, Ltd.

Evaluating gillnetting protocols to characterize lacustrine fish communities

Ecological research and monitoring of lacustrine ecosystems often requires a whole-lake assessment of fish communities. Gillnet sampling offers an efficient means of estimating abundance, biomass and fish community composition. However the choice of gillnet sampling protocol may influence lake characterization via physical properties of the nets and allocation of sampling effort between littoral, benthic and pelagic habitats. This paper compares two commonly used, whole-lake sampling protocols applied across 17 prealpine, subalpine and alpine European lakes ranging widely in size, depth and altitude to determine their relative strength for research and management applications. Effort-corrected estimates of abundance, biomass and species richness were correlated between the protocols and both distinguished the trout-dominated alpine communities from subalpine and prealpine lakes dominated by whitefish and perch. A considerable amount of variance remained unexplained between the two protocols however, which seemed to correspond with differences in the proportion of effort among benthic and pelagic habitats. We suggest that both the European standard (CEN) and vertical (VERT) netting protocols are suitable for assessing ecological status and monitoring changes in lake fish communities through time. However the details of each protocol should be kept in mind when comparing fish communities between lakes. Mesh sizes used in CEN nets produce a more even size frequency distribution, suggesting that this protocol is most appropriate for assessing size structure of fish assemblages. The high proportion of netting effort in benthic habitats shallower than 70m depth under the CEN protocol means that, particularly in larger lakes, outcomes will be disproportionately influenced by the ecological condition of this habitat. The VERT protocol presumably provides a more accurate estimate of whole-lake CPUE and community composition because effort, in terms of net area, is more evenly distributed across the entire volume of the lake. This is particularly important in large and deep lakes where pelagic habitats occupy a high proportion of the lake volume.

Optimal Allocation of Sampling Effort in Depletion Surveys

We consider the problem of designing a depletion or removal survey as part of estimating animal abundance for populations with imperfect capture or detection rates. In a depletion survey, animals are captured from a given area, counted, and withheld from the population. This process is then repeated some number of times at the same location and the decreasing catches of the local population inform jointly local abundance and the capture or detection rate, which we call catchability. The aim of such a survey may be to learn about the catchability process, and this information may then be applied to a broader survey of the population so as to accurately estimate total abundance. In this manuscript we consider the problem of how to optimally allocate sampling effort at the depletion sites. Allocating sampling effort involves determining how many times to repeat the depletion process at a given site versus how many different sites to include in the sampling. By maximizing the Fisher information of the parameter describing catchability as a function of the survey design, we attempt to estimate the optimal number of depletions per site, which depends on the catchability value itself. We also discuss other aspects of depletion sampling apparent from the derivation of Fisher information, including the difficulties of sampling with low catchability values (e.g. below 0.15), and we consider our results with respect to the annual Chesapeake Bay blue crab abundance survey conducted by the Maryland Department of Natural Resources.

Detection and stratification approaches for aerial surveys of deer in prairie–parklands

Context For management decisions that require accurate and precise estimates of large mammal population numbers, aerial surveys are considered reliable despite their cost. However, aerial surveys may still suffer from underestimation because of undetected animals and low precision as a result of inefficient sampling designs. Aims We assess detection of two species of deer in prairie-parkland communities of western Canada and evaluate a suite of survey design features for improving the accuracy and precision of population estimates from aerial surveys. Methods Modelling detection of deer was based on 100 sightability trials involving 54 radio-collared white-tailed and 46 mule deer. We used empirical survey data to simulate surveys under three alternative stratification approaches, schemes for grouping strata, and allocations of survey effort and compared the precision and accuracy of the resulting population estimates. Key results We observed deer in 83 of the 100 trials, with detection decreasing with small group size, reduced deer activity, low snow cover, high forest cover and observer fatigue. Survey precision and accuracy were highest when stratification was based on natural breaks, calculated via Jenks optimisation, in the values of resource-selection function (RSF), although improvement was less pronounced for estimates of mule deer abundance. Optimal or equal allocation of sampling effort among strata outperformed proportional allocation of sampling effort. Use of RSF for stratification reduced the coefficient of variation (CV) in estimates of deer numbers from 38% to 23% for white-tailed deer and from 33% to 27% for mule deer compared with past approaches. Conclusions Stratification based on RSF values improved precision of deer surveys the most; however, using even simple measures related to habitat selection can improve population estimates. Where deer are highly aggregated, reliably recording all variables needed to implement sightability models can prove problematic; however, survey detection adjustments are nevertheless important to account for the relatively small, but still significant, proportion of missed animals in open prairie–parkland environments. Implications Field experiments to assess aerial survey design are impractical because of cost. We illustrate how simulated surveys using empirical data can be useful to evaluate alternative survey designs to improve population estimates in a region when high accuracy or precision are needed to address management questions or to calibrate more cost-effective approaches.

Two-phase sampling to estimate river-wide populations of freshwater mussels

Two-phase sampling provides a statistical framework for combining data from qualitative and quantitative sampling methods. It is a useful approach when the survey objective is a drainage-wide estimate of mussel density and the cost of qualitative sampling is small relative to the cost of quantitative sampling. This survey design has several advantages including: 1) no need for a priori classification of stream reaches into sampling strata, 2) allocation of sampling effort so that more time is spent sampling where mussels are at higher density and less time is spent sampling where mussels are not present, 3) the ability to evaluate the relationship between qualitative and quantitative estimates of density, and 4) efficient allocation of effort so that more stream reaches can be surveyed compared to quantitative-only sampling designs with similar effort. The survey design consists of sampling as many sites as possible during a qualitative 1st phase and sampling far fewer sites during a quantitative 2nd phase. In 1995, we used a 2-phase sampling design to estimate the distribution and abundance of freshwater mussels in riffle habitat in the Cacapon River, West Virginia. Our estimate of river-wide surface density of freshwater mussels in riffles was 0.59/m2 (SE = 0.14). We used resampling simulation based on our data and determined that the most effective 2nd-phase sampling strategy was to sample a low to moderate proportion of low-density sites and a high proportion of high-density sites.

Optimal partition of sampling effort between observations of fish density and migration speed for a riverine hydroacoustic duration-in-beam method

The duration-in-beam model has long been used in fisheries acoustics. For instance, the Pacific Salmon Commission uses this model for the hydroacoustic data collected at Mission, BC, Canada to estimate daily salmon passages in the Fraser River for in-season salmon management. The fish flux is calculated as the product of fish density times the migration speed. These two components are measured separately with the same acoustical sampling system. As the system can only acquire either density or speed data at any given time, an optimal sampling design is needed to partition the sampling effort for acoustical measurements of fish density and migration speed. In this paper, we present a method to estimate the optimal allocation of sampling effort between the density and speed measurements. The optimum was achieved by minimizing the variance of the estimated fish flux. The theoretical optimization method was applied to the hydroacoustic data collected in the 1998 fishing season to obtain an estimated optimal sampling design. This optimal design was adopted for the hydroacoustic sampling program at Mission, BC in the 1999 salmon migration season. The statistical results from the 1999 data were examined and compared with that from the 1998 data acquired according to a non-optimized sampling plan. It was found that the optimized sampling plan reduced the relative variance by 20%. Therefore, the methodology of this optimal design for sampling effort is a useful addition to the duration-in-beam model in fisheries acoustics.

Optimizing Larval Assessment to Support Sea Lamprey Control in the Great Lakes

Elements of the larval sea lamprey ( Petromyzon marinus) assessment program that most strongly influence the chemical treatment program were analyzed, including selection of streams for larval surveys, allocation of sampling effort among stream reaches, allocation of sampling effort among habitat types, estimation of daily growth rates, and estimation of metamorphosis rates, to determine how uncertainty in each element influenced the stream selection program. First, the stream selection model based on current larval assessment sampling protocol significantly underestimated transforming sea lam-prey abundance, transforming sea lampreys killed, and marginal costs per sea lamprey killed, compared to a protocol that included more years of data (especially for large streams). Second, larval density in streams varied significantly with Type-I habitat area, but not with total area or reach length. Third, the ratio of larval density between Type-I and Type-II habitat varied significantly among streams, and that the optimal allocation of sampling effort varied with the proportion of habitat types and variability of larval density within each habitat. Fourth, mean length varied significantly among streams and years. Last, size at metamorphosis varied more among years than within or among regions and that metamorphosis varied significantly among streams within regions. Study results indicate that: (1) the stream selection model should be used to identify streams with potentially high residual populations of larval sea lampreys; (2) larval sampling in Type-II habitat should be initiated in all streams by increasing sampling in Type-II habitat to 50% of the sampling effort in Type-I habitat; and (3) methods should be investigated to reduce uncertainty in estimates of sea lamprey production, with emphasis on those that reduce the uncertainty associated with larval length at the end of the growing season and those used to predict metamorphosis.

Optimal Allocation in Stratified and Multistage Samples Using Prior Information

The author [1], [2] has given an algorithm for finding that stratified allocation which minimizes the posterior variance of the overall population mean subject to a budget constraint under a model in which a normal prior distribution and independent normal sampling distributions were assumed. The budget constraint assumed a variable per unit cost of observation. In the present paper these results are extended to cover the case where there are fixed costs, as well as variable costs, associated with sampling in the ith stratum. The resulting algorithm is noted to be applicable in finding the optimal allocation of sampling effort (with fixed and variable sampling costs) under a variety of distributional assumptions. An interpretation is also given to two and higher stage design questions when there is differential prior information regarding the first stage units.