A comparison of two benthic survey methods

The belt transect and the flowmeter methods, used to survey sedentary benthic organisms, were compared based on abundance estimates of tridacnid clams in the Cagayan Islands, Philippines, in April 1985. Two-way ANOVA and chi-square tests (P<0.05) show that both methods recorded similar estimates for the number of clams (regardless of species), both methods gave similar estimates for the number of individuals per species, and one or both methods may be biased for certain sizes of clams. Individuals smaller than 6 cm shell length seemed to be underestimated by the flowmeter method. Future studies must investigate the size selectivity of the method used, for instance by conducting permanent belt, transect surveys of varied belt widths (e.g. 1, 1.5,2,2.5 m) and then comparing the recorded lengths of the most abundant clams. This will aid investigators to evaluate their data properly, and enable comparison of clam-stock estimates between surveys.     

Estimating total abundance of a large temperate-reef fish using visual strip-transects

Total abundance estimates for the large, common, reef fish Cheilodactylus spectabilis (Hutton) were obtained for a marine reserve and adjacent section of coast in north-eastern New Zealand during 1985. Visual strip-transects were used to estimate abundance and size structure in both areas. The accuracy, precision and cost efficiency of five transect sizes (500, 375, 250, 100, 75 m²) were examined over three times per day (dawn, midday and dusk), by simulating transects over mapped C. spectabilis populations. Two transect sizes showed similarly high efficiency. The smaller of the two (20x5 m) was chosen for the survey because of the general advantages attributable to small sampling units. Biases related to strip-transect size are discussed. Preliminary sampling indicated that C. spectabilis was distributed heterogeneously, and that density was habitat-related. An optimal stratified-random design was employed in both locations, to obtain total abundance and size-structure estimates. This reduced the between-habitat source of variability in density. The total number of sampling units used was governed by the time available. The resulting total abundance estimates obtained were 18 338±2 886 (95% confidence limit) for the 5 km marine reserve, compared to 3 987±1 117 for an adjacent, heavily fished 4 km section of coast. When corrected for total area and habitat area sampled, this represented a 2.3-fold difference in abundance. If sampling had been designed to detect an arbitrary 10% difference in abundance within each habitat, an infeasible 440 h of sampling would have been required. Size-frequency distributions of C. spectabilis at the reserve had a larger model size class than distributions from the adjacent area. The data suggest that reserve status is causal in these differing abundance and size structure estimates.     

A Bayesian approach to line-transect analysis for estimating abundance

Line-transect analysis is a widely used method of estimating plant and animal density and abundance. A Bayesian approach to a basic line-transect analysis is developed for a half-normal detection function. We extend the model of Karunamuni and Quinn [Karunamuni, R.J., Quinn II, T.J., 1995. Bayesian estimation of animal abundance for line-transect sampling. Biometrics 51, 1325–1337] by including a binomial likelihood function for the number of objects detected. The method computes a joint posterior distribution on the effective strip width and the density of objects in the sampled area. Analytical and computational methods for binned and unbinned perpendicular distance data are provided. Existing information about effective strip width and density can be brought into the analysis via prior distributions. The Bayesian approach is compared to a standard line-transect analysis using both real and simulated data. Results of the Bayesian and non-Bayesian analyses are similar when there are no prior data on effective strip width or density, but the Bayesian approach performs better when such data are available from previous or related studies. Practical methods for including prior data on effective strip width and density are suggested. A numerical example shows how the Bayesian approach can provide valid estimates when the sample size is too small for the standard approach to work reliably. The proposed Bayesian approach can form the basis for developing more advanced analyses.     

The reflection method of line intercept sampling to eliminate boundary bias

When a line transect overlaps the boundary of the sampled region, it can be reflected back on top of itself into the region, thereby making it possible to include elements near the edge twice from the same transect. A practical advantage of doing so is the reduction of field time and effort compared to the customary procedure of folding the transect back into another part of the region. An estimator is presented which accounts for this procedure in a way that preserves design-unbiased estimation.     

Determining Optimal Population Monitoring for Rare Butterflies

Abstract: Determining population viability of rare insects depends on precise, unbiased estimates of population size and other demographic parameters. We used data on the endangered St. Francis' satyr butterfly (Neonympha mitchellii francisci) to evaluate 2 approaches (mark–recapture and transect counts) for population analysis of rare butterflies. Mark–recapture analysis provided by far the greatest amount of demographic information, including estimates (and standard errors) of population size, detection, survival, and recruitment probabilities. Mark–recapture analysis can also be used to estimate dispersal and temporal variation in rates, although we did not do this here. Models of seasonal flight phenologies derived from transect counts (Insect Count Analyzer) provided an index of population size and estimates of survival and statistical uncertainty. Pollard–Yates population indices derived from transect counts did not provide estimates of demographic parameters. This index may be highly biased if detection and survival probabilities vary spatially and temporally. In terms of statistical performance, mark–recapture and Pollard–Yates indices were least variable. Mark–recapture estimates were less likely to fail than Insect Count Analyzer, but mark–recapture estimates became less precise as sampling intensity decreased. In general, count‐based approaches are less costly and less likely to cause harm to rare insects than mark–recapture. The optimal monitoring approach must reconcile these trade‐offs. Thus, mark–recapture should be favored when demographic estimates are needed, when financial resources enable frequent sampling, and when marking does not harm the insect populations. The optimal sampling strategy may use 2 sampling methods together in 1 overall sampling plan: limited mark–recapture sampling to estimate survival and detection probabilities and frequent but less expensive transect counts.     

Estimation of the mean in line intercept sampling

Ratio estimation of the parametric mean for a characteristic measured on plants sampled by a line intercept method is presented and evaluated via simulation using different plant dispersion patterns (Poisson, regular cluster, and Poisson cluster), plant width variances, and numbers of lines. The results indicate that on average the estimates are close to the parametric mean under all three dispersion patterns. Given a fixed number of lines, variability of the estimates is similar across dispersion patterns with variability under the Poisson pattern slightly smaller than varia-bility under the cluster patterns. No variance estimates were negative under the Poisson pattern, but some estimates were negative under the cluster patterns for smaller numbers of lines. Variance estimates become closer to zero similarly for all spatial patterns as the number of lines increases. Ratio estimation of the parametric mean in line intercept sampling works better, from the viewpoint of approximate unbiasedness and variability of estimates, under the Poisson pattern with larger numbers of lines than other combinations of spatial patterns, plant width variances and numbers of lines.     

Method of estimating the standing stock of Trochus niloticus incorporating Landsat satellite data,with application to the trochus resources of the Bourke Isles,Torres Strait,Australia

The habitat of Trochus niloticus in the Bourke Isles, Torres Strait, was classified into areas of a Landsat image, using high-ratio values of green (Band 2) to red (Band 3) light, along the windward reef margins. These shallow-water (< 15 m) areas have a coral and rubble/algal pavement cover, which constitutes the optimal habitat for this gastropod. The habitat was sampled to estimate the abundance of T. niloticus. The proportion of commercial-sized individuals was estimated by measuring the basal width of all individuals in a sample. A multistage sample design incorporating three spatial scales -100 m² (transect), 1500 m² (site) and 1 km² (reef) — was used to provide variance estimates for sample-design optimisation and to provide data on the spatial variation of abundance. Most variation (68%) in abundance was within reefs and was attributable to differences in reef cover. Variations in abundance and time costs for sampling 2 and 4 m transects were compared; the 2 m transect was more efficient than the 4 m transect. The abundance estimates were combined with habitat-area estimates and the proportion of commerical-sized individuals was estimated at a standing stock of 186000 (24% precision), or 14 t of commerical-sized T. niloticus.     

Density estimation using ranked-set sampling data

The ranked-set sampling (RSS) is applicable in practical problems where the variable of interest for an observed item is costly or time-consuming but the ranking of a set of items according to the variable can be easily done without actual measurement. In the context of RSS, the need for density estimation arises in certain statistical procedures. The density estimation also has its own interest. In this article, we develop a method for the density estimation using RSS data. We derive the properties of the resulted density estimate and compare it with its counterpart in simple random sampling (SRS). It is shown that the density estimate using RSS data provides a better estimate of the density than the usual density estimate using SRS data. The density estimate developed in this article can well serve various purposes in the context of RSS.     

Sample based estimation of landscape metrics; accuracy of line intersect sampling for estimating edge density and Shannon’s diversity index

A recent trend is to estimate landscape metrics using sample data and cost-efficiency is one important reason for this development. In this study, line intersect sampling (LIS) was used as an alternative to wall-to-wall mapping for estimating Shannon’s diversity index and edge length and density. Monte Carlo simulation was applied to study the statistical performance of the estimators. All combinations of two sampling designs (random and systematic distribution of transects), four sample sizes, five transect configurations (straight line, L, Y, triangle, and quadrat), two transect orientations (fixed and random), and three configuration lengths were tested, each with a large number of simulations. Reference was 50 photos of size 1 km², already manually delineated in vector format by photo interpreters using GIS environment. The performance was compared by root mean square error (RMSE) and bias. The best combination for all three metrics was found to be the systematic design and as response design the straight line configuration with random orientation of transects, with little difference between the fixed and random orientation of transects. The rate of decrease of RMSE for increasing sample size and line length was studied with a mixed linear model. It was found that the RMSE decreased to a larger degree with the systematic design than the random one, especially with increasing sample size. Due to the nonlinearity in the definition of Shannon diversity estimator its estimator has a small and negative bias, decreasing with sample size and line length. Finally, a time study was conducted, measuring the time for registration of line intersections and their lengths on non-delineated aerial photos. The time study showed that long sampling lines were more cost-efficient than short ones for photo-interpretation.     

Relative Contributions of Sampling Error in Initial Population Size and Vital Rates to Outcomes of Population Viability Analysis

Abstract:  We evaluated the relative contributions of sampling error (randomly chosen standard errors applied as 0–30% of parameter estimates) in initial population size and vital rates (survival and reproduction) to the outcome of a simulated population viability analysis for grizzly bears (  Ursus arctos ). Error in initial population size accounted for the largest source of variation (model II analysis of variance, F _25,5= 10.8, p = 0.00001) in simulation outcomes, explaining 60.5% of the variance. In contrast, error in vital rates contributed little to simulation outcomes ( F _25,5= 0.61, p = 0.70), accounting for only 2.4% of model variation. Reduced global variation in vital rates, as a result of independent random sampling of annual deviates for each parameter, likely contributed to the results. Errors in estimates of initial population size, if ignored in PVA, have the potential to leave managers with estimates of population persistence that are of little value for making management decisions.     

Predicting the variation in detection function in line transect sampling through random parameter model

A method for calibrating (localizing) detection function models in line transect sampling is proposed. The method is based on a random parameter model which supplies localized predictions of detection function parameters utilizing a few sample data points from the concerned location(s). The method has the clear advantage of being able to provide density estimates based on very few observations from a location which would be impossible through traditional methods. The method is successfully illustrated using census data on sambar (Cervus unicolor) from a set of wildlife sanctuaries in Kerala, India. The need for further research in this direction is indicated.     

Line intersect sampling: Ell-shaped transects and multiple intersections

The probability of selecting a population element under line intersect sampling depends on the width of the particle in the direction perpendicular to the transect, as is well known. The consequence of this when using ell-shaped transects rather than straight-line transects are explicated, and modifications that preserve design-unbiasedness of Kaiser's (1983) conditional and unconditional estimators are presented. A case against treating multiple intersections as multiple probabilistic events is argued on the basis, also, of preserving design-unbiased estimation.     

A generalized estimating equations approach for capture–recapture closed population models

The estimation of population density animal population parameters, such as capture probability, population size, or population density, is an important issue in many ecological applications. Capture–recapture data may be considered as repeated observations that are often correlated over time. If these correlations are not taken into account then parameter estimates may be biased, possibly producing misleading results. We propose a generalized estimating equations (GEE) approach to account for correlation over time instead of assuming independence as in the traditional closed population capture–recapture studies. We also account for heterogeneity among observed individuals and over-dispersion, modelling capture probabilities as a function of covariates. The GEE versions of all closed population capture–recapture models and their corresponding estimating equations are proposed. We evaluate the effect of accounting for correlation structures on capture–recapture model selection based on the quasi-likelihood information criterion (QIC). An example is used for an illustrative application and for comparison to currently used methodology. A Horvitz–Thompson-like estimator is used to obtain estimates of population size based on conditional arguments. A simulation study is conducted to evaluate the performance of the GEE approach in capture-recapture studies. The GEE approach performs well for estimating population parameters, particularly when capture probabilities are high. The simulation results also reveal that estimated population size varies on the nature of the existing correlation among capture occasions.     

Understanding and Estimating Effective Population Size for Practical Application in Marine Species Management

Abstract: Effective population size (N_e) determines the strength of genetic drift in a population and has long been recognized as an important parameter for evaluating conservation status and threats to genetic health of populations. Specifically, an estimate of N_e is crucial to management because it integrates genetic effects with the life history of the species, allowing for predictions of a population's current and future viability. Nevertheless, compared with ecological and demographic parameters, N_e has had limited influence on species management, beyond its application in very small populations. Recent developments have substantially improved N_e estimation; however, some obstacles remain for the practical application of N_e estimates. For example, the need to define the spatial and temporal scale of measurement makes the concept complex and sometimes difficult to interpret. We reviewed approaches to estimation of N_e over both long‐term and contemporary time frames, clarifying their interpretations with respect to local populations and the global metapopulation. We describe multiple experimental factors affecting robustness of contemporary N_e estimates and suggest that different sampling designs can be combined to compare largely independent measures of N_e for improved confidence in the result. Large populations with moderate gene flow pose the greatest challenges to robust estimation of contemporary N_e and require careful consideration of sampling and analysis to minimize estimator bias. We emphasize the practical utility of estimating N_e by highlighting its relevance to the adaptive potential of a population and describing applications in management of marine populations, where the focus is not always on critically endangered populations. Two cases discussed include the mechanisms generating N_e estimates many orders of magnitude lower than census N in harvested marine fishes and the predicted reduction in N_e from hatchery‐based population supplementation.     

Propagation functions for monitoring distributional changes

In environmental assessment and monitoring, a primary objective of the investigator is to describe the changes occurring in the environmentally important variables over time. Propagation functions have been proposed to describe the distributional changes occurring in the variable of interest at two different times. McDonald et al. (1992, 1995) proposed an estimator of propagation function under the assumption of normality. We conduct a detailed sensitivity analysis of inference based on the normal model. It turns out that this model is appropriate only for small departures from normality whereas, for moderate to large departures, both estimation and testing of hypothesis break down. Non-parametric estimation of the propagation function based on kernel density estimation is also considered and the robustness of the choice of bandwidth for kernel density estimation is investigated. Bootstrapping is employed to obtain confidence intervals for the propagation function and also to determine the critical regions for testing the significance of distributional changes between two sampling epochs. Also studied briefly is the mathematical form and graphical shape of the propagation function for some parametric bivariate families of distributions. Finally, the proposed estimation techniques are illustrated on a data set of tree ring widths.     

Spatial trends in abundance of long-finned pilot whales, white-beaked dolphins and harbour porpoises in West Greenland

Data from an aerial line transect survey conducted off West Greenland during August–September 2007 were used to estimate the abundance of long-finned pilot whales (Globicephala melas), white-beaked dolphins (Lagenorhynchus albirostris) and harbour porpoises (Phocoena phocoena). The abundance of each species was estimated using mark-recapture distance sampling techniques to correct for perception bias, and correction factors for time spent at the surface were applied. The fully corrected abundance estimates were 8,133 long-finned pilot whales, 11,984 white-beaked dolphins and 33,271 harbour porpoises. Based on density surface modelling methods, a count model with a generalised additive model formulation was used to relate abundance to spatial variables. Response curves indicated that the preferred habitats were deep offshore areas in Midwest Greenland for pilot whales, deep water over steep seabed slopes in South Greenland for white-beaked dolphins and relatively shallow inshore waters in Midwest–South Greenland for harbour porpoises. The abundance estimates and spatial trends for the three species are the first obtained from Greenland.     

Episodes of starvation are recorded in the otoliths of juvenile Ambassis vachelli (Chandidae), a tropical estuarine fish

Juvenile Ambassis vachelli, 40 to 50 d old, were used to test the effects of starvation and recovery-feeding on the widths of otolith increments. Three laboratory treatments (fed continuously; fed for 9d then starved for 15 d; starved for 9 d then fed for 15 d), were compared. Fish were also collected throughout the experiment from a field site to assess the natural fluctuations of increment widths. Growth, starvation and recovery were reflected in the widths of otolith increments. The width of increments deposited during starvation were similar in all fish, regardless of prior feeding history, despite the lower mortality recorded in starved fish with a history of intense feeding. Increment-width data were confounded by an ontogenetic decrease in increment widths with age. The results indicate that starvation and recovery are recorded in the increment widths of otoliths and are distinguishable from the effects of ontogenetic development. However, ontogenetic changes in the width of otolith increments confounded the interpretation of otolith-increment series. Therefore, the ontogenetic pattern of otolith increments must be known for each species before valid interpretation of otolith microstructure is possible.     

Estimating the complexity of bird song by using capture-recapture approaches from community ecology

Repertoire size, the number of unique song or syllable types in the repertoire, is a widely used measure of song complexity in birds, but it is difficult to calculate this exactly in species with large repertoires. A new method of repertoire size estimation applies species richness estimation procedures from community ecology, but such capture-recapture approaches have not been much tested. Here, we establish standardized sampling schemes and estimation procedures using capture-recapture models for syllable repertoires from 18 bird species, and suggest how these may be used to tackle problems of repertoire estimation. Different models, with different assumptions regarding the heterogeneity of the use of syllable types, performed best for different species with different song organizations. For most species, models assuming heterogeneous probability of occurrence of syllables (so-called detection probability) were selected due to the presence of both rare and frequent syllables. Capture-recapture estimates of syllable repertoire size from our small sample did not differ significantly from previous estimates using larger samples of count data. However, the enumeration of syllables in 15 songs yielded significantly lower estimates than previous reports. Hence, heterogeneity in detection probability of syllables should be addressed when estimating repertoire size. This is neglected using simple enumeration procedures, but is taken into account when repertoire size is estimated by appropriate capture-recapture models adjusted for species-specific song organization characteristics. We suggest that such approaches, in combination with standardized sampling, should be applied in species with potentially large repertoire size. On the other hand, in species with small repertoire size and homogenous syllable usage, enumerations may be satisfactory. Although researchers often use repertoire size as a measure of song complexity, listeners to songs are unlikely to count entire repertoires and they may rely on other cues, such as syllable detection probability.Communicated by A. Cockburn     

Is Chinese trade policy motivated by environmental concerns?

This paper analyses whether China's export VAT rebates and export taxes are driven by environmental concerns. Since China struggles to enforce environmental regulation, trade policy can be used as a second-best environmental policy. In a general equilibrium model it is possible to show that the second-best export tax increases in a product's pollution intensity. The empirical analysis investigates whether the export tax equivalent of partial VAT rebates and export taxes are higher for products which are more pollution intensive along several dimensions. The results indicate that the VAT rebate rates are set in a way that discourages exports of water pollution intensive, SO₂ intensive and energy intensive products from 2007 on. Moreover, the conservation of natural resources such as minerals, metals, wood products and precious stones seems to be a key determinant of China's export VAT rebate rates. There is little evidence that export taxes are motivated by environmental concerns.