A stochastic catch-effort method for estimating animal abundance

A method for estimating the size of a heavily exploited animal population from catch data and relative-harvest-effort data is presented. The method assumes a competing-risk model of adult deaths and captures that is similar to the hazard-regression model of Cox (1972, Journal of the Royal Statistical Society, Series B 34, 187-220). This model avoids making any assumptions about birth rates or juvenile mortality rates, and allows the user to incorporate an arbitrary number of time-dependent covariates into the natural and catch hazard functions. Estimates of the population's size, together with asymptotic error bounds and predictions of subsequent catches, are derived from maximum likelihood estimates of the parameters of the model. A simulation study is presented which indicates that this method is far more accurate than previously available catch-effort techniques. The method is illustrated with some fisheries data. A series of models is fitted to the data with the objective of improving the goodness of fit while maintaining biologic plausibility of the model. In this example a 68% reduction in the mean sum of squares for error is obtained and the accuracy of future catch predictions is greatly improved. This method is particularly appropriate for estimating the sizes of commercially exploited aquatic populations whose sizes are too large to make mark-recapture techniques feasible, and which are not amenable to line-transect techniques.     

A review of estimating animal abundance

During the past 5 years there have been a number of important developments in the estimation of animal abundance and related parameters such as survival rates. Many of the new techniques need to be more widely publicized as they supplant previous methods. The aim of this paper is to review this literature and suggest further avenues for research.     

Assessment of methods for estimating wild rabbit population abundance in agricultural landscapes

Various methods have been used to estimate rabbit abundance, but comparisons of standard methods are still lacking, and thus, results remain roughly comparable across studies. Ideally, a method should be applicable over a wide range of situations, such as differing abundances or habitat types. Comparisons of methods are required to evaluate the benefits of each of them, and survey methods should be validated for the conditions in which they will be used. In this study, we compare the performance of direct methods (kilometric abundance index and distance sampling) in two seasons and at two times of day (dusk and night) for estimating wild rabbit abundances in agricultural landscapes. Estimates based on direct methods were highly correlated and detected similar seasonal population changes. Night counts provided better estimates than did dusk counts and exhibited more precision. Results are discussed within the context of rabbit behaviour and their implications for rabbit population surveys.     

RNA microarray for estimating relative abundance of 16S rRNA in microbial communities

We developed an RNA microarray protocol in which total RNA from a microbial community was attached to a slide glass, and rRNA was detected by fluorescently labeled oligonucleotide probes. The RNA microarray requires only 4 h for hybridization and enables double staining and estimating relative abundance of rRNA.     

Double-observer approach to estimating egg mass abundance of pool-breeding amphibians

Interest in seasonally flooded pools, and the status of associated amphibian populations, has initiated programs in the northeastern United States to document and monitor these habitats. Counting egg masses is an effective way to determine the population size of pool-breeding amphibians, such as wood frogs (Rana sylvatica) and spotted salamanders (Ambystoma maculatum). However, bias is associated with counts if egg masses are missed. Counts unadjusted for the proportion missed (i.e., without adjustment for detection probability) could lead to false assessments of population trends. We used a dependent double-observer method in 2002–2003 to estimate numbers of wood frog and spotted salamander egg masses at seasonal forest pools in 13 National Wildlife Refuges, 1 National Park, 1 National Seashore, and 1 State Park in the northeastern United States. We calculated detection probabilities for egg masses and examined whether detection probabilities varied by species, observers, pools, and in relation to pool characteristics (pool area, pool maximum depth, within-pool vegetation). For the 2 years, model selection indicated that no consistent set of variables explained the variation in data sets from individual Refuges and Parks. Because our results indicated that egg mass detection probabilities vary spatially and temporally, we conclude that it is essential to use estimation procedures, such as double-observer methods with egg mass surveys, to determine population sizes and trends of these species.     

An assessment of some improved techniques for estimating the abundance (frequency) of sedentary organisms

The traditional sampling method for estimating frequency (the number of sub-quadrats containing a basal part of the organisms) is compared, using both computer simulations and direct comparison in the field, to two new methods that use a compound series of variable-sized concentric sub-quadrats. Both the new frequency-score and the new importance-score methods are closer approximations of density than is the standard frequency method, and the estimates produced by both of the new methods are less affected by the choice of sub-quadrat size and the spatial distribution (dispersion) of the organisms (i.e. clumping and regularity). Thus, the two nested-quadrat methods appear to ameliorate the usual frequency limitations associated with sub-quadrat size and organism dispersion, by the use of a range of different sub-quadrat sizes. This is important in community studies, where the component species may show a wide range of densities and dispersions. Both of the new methods are easily employed in the field. The importance-score method involves no more sampling effort than does standard qualitative (presence-absence) sampling, and it can therefore be used to sample a larger quadrat area than would normally be used for frequency sampling. This makes the method much more cost-effective as a means of estimating abundance, and it allows a greater number of the rarer species to be included in the sampling. The frequency-score method is more time-consuming, but it is capable of detecting more subtle community patterns. This means that it is particularly useful for the study of species-poor communities or where small variations in composition need to be detected.     

Limitations of the N natural abundance method for estimating biological nitrogen fixation in Amazonian forest legumes

This study evaluates the ¹⁵N natural abundance method for estimating biological nitrogen fixation (BNF) in 12 secondary and five primary forest sites in central Amazonia. Investigations were based on spatially systematic sampling of 20 potentially N₂-fixing legume tree and liana species, and of a range of differing references representing the ‘soil-derived nitrogen’.The absence of systematic differences in the δ¹⁵N-signals of potential N₂-fixers and reference plants resulted in many invalid % Ndfa-estimates (i.e., the proportion of foliar N derived from BNF).Whereas the % Ndfa-estimates based on non-legumes were randomly distributed around zero, the use of non-N₂-fixing legumes resulted in largely positive % Ndfa-estimates. Grouping of reference species into species types was a valid strategy to reduce the risk of atypical values. Leaf litter was an inadequate measure of soil-derived nitrogen. The impact of the B-value was low or moderate at best, the percentage of negative % Ndfa-estimates remained unaltered. The manner of individually pairing putative N₂-fixers with reference plants only marginally affected the % Ndfa-estimates, the assumption of an overall site mean reference δ¹⁵N-signal was sufficient.Since legumes were aggregated in clusters, BNF locally affected the surrounding soil nitrogen in secondary regrowth. Negative correlations between the vegetation shares of potential N₂-fixers and leaf litter δ¹⁵N-signals indicate ¹⁵N-dilution from the input side. Interpolated reference plant δ¹⁵N-signals appear low in the surroundings of legume clusters in some of the older regrowth sites, confirming such ¹⁵N-dilution.We conclude that, with our current state of knowledge, the ¹⁵N natural abundance method fails to quantitatively estimate BNF in heterogeneous forests. Future research should focus on the search for a more direct measure of the plant-available δ¹⁵N-signal of the soil, as well as on plant–soil interactions and the resulting small-scale isotopic heterogeneity.

Zusammenfassung

Diese Arbeit untersucht die Eignung der ¹⁵N natürlichen Abundanz Methode zur Schätzung der Biologischen Stickstoffixierung (BSF) in 12 Sekundär- und 5 Primärwaldflächen Zentralamazoniens. Die Studie ist räumlich systematisch und umfasst 20 potentiell N₂-fixierende Leguminosen Baum- und Lianenarten, sowie verschiedene Referenzpflanzen die den ,,bodenbürtigen Stickstoff” repräsentieren.Da die δ¹⁵N-Signale der potentiellen N₂-Fixierer sich nicht systematisch von denen der Referenzpflanzen unterschieden, waren viele % Ndfa-Schätzwerte (Anteil des luftbürtigen Stickstoffs im Blatt) ungültig.Während die auf nicht-Leguminosen basierenden % Ndfa-Schätzwerte zufällig um Null verteilt waren, ergaben die nicht N₂-fixierenden Leguminosen überwiegend positive % Ndfa. Unsere Referenzpflanzengruppierung in Art-Typen war erfolgreich. Der Einfluss des B-Wertes war nur gering, der Anteil der ungültigen Schätzwerte blieb unbeeinflusst. Die Art in der potentielle N₂-Fixierer und Referenzpflanzen gepaart wurden, beeinflusste nur unwesentlich die % Ndfa-Schätzwerte; die Annahme eines gemittelten Referenz δ¹⁵N-Signals für jede Fläche war ausreichend.Wegen ihrer geklumpten Verteilung können N₂-fixierende Leguminosen den Bodenstickstoff in ihrer Umgebung beeinflussen. Die negative Korrelation zwischen dem Biomassenanteil potentieller N₂-Fixierer und den δ¹⁵N-Signalen der Blattstreu deutet auf eine ¹⁵N-Verdünnung des N-Eintrages. Visuelle Karteninterpretation bestätigt eine solche ¹⁵N-Verdünnung auf einigen älteren Sekundärwaldflächen.Zusammenfassend folgern wir, dass die ¹⁵N natürliche Abundanz Methode bei gegenwärtigem Wissensstand zur quantitativen BSF-Schätzung in heterogenen Wäldern ungeeignet ist. Zukünftige Forschung sollte sich auf eine schlüssige Methode zur Bestimmung des bodenbürtigen δ¹⁵N-Signals, sowie auf die Interaktionen zwischen Vegetation und Boden und der daraus resultierenden kleinräumigen δ¹⁵N-Variabilität konzentrieren.     

Precision of different methods used for estimating the abundance of the nitrogen-fixing marine cyanobacterium, Trichodesmium Ehrenberg

Variances involved in estimating the abundance of the nitrogen-fixing marine cyanobacterium, Trichodesmium Ehrenberg, were evaluated by repeated sampling using bottle casts and plankton net tows at two stations in the southern East China Sea. The variance among individual samples and the variance arising from subsampling processes were separated by the method of analysis of variance, and the coefficient of variation (C.V.) of an abundance estimate based on a single subsample was calculated. For bottle-collected samples, the major source of variation came from taking subsamples from a water bottle. The C.V. of a single subsample estimate ranged from 57% to 184%. For net-collected samples, variance in abundance estimation was mainly caused by distinctive net tows, and when distributing materials in the receiving bucket into smaller containers. The C.V.s of single subsample estimates were 34% and 40%, respectively. Trichodesmium abundance estimated with bottle- and net-collected samples were further compared using data obtained from 17 stations in the East China Sea. Although a general distribution pattern was supported by both methods, the correlation coefficient between them was 0.461, not significantly different from 0.     

Comparison of visual survey and seining methods for estimating abundance of an endangered,benthic stream fish

We compared visual survey and seining methods for estimating abundance of endangered Okaloosa darters, Etheostoma okaloosae, in 12 replicate stream reaches during August 2001. For each 20-m stream reach, two divers systematically located and marked the position of darters and then a second crew of three to five people came through with a small-mesh seine and exhaustively sampled the same area. Visual surveys required little extra time to complete. Visual counts (24.2 ± 12.0; mean ± one SD) considerably exceeded seine captures (7.4 ± 4.8), and counts from the two methods were uncorrelated. Visual surveys, but not seines, detected the presence of Okaloosa darters at one site with low population densities. In 2003, we performed a depletion removal study in 10 replicate stream reaches to assess the accuracy of the visual survey method. Visual surveys detected 59% of Okaloosa darters present, and visual counts and removal estimates were positively correlated. Taken together, our comparisons indicate that visual surveys more accurately and precisely estimate abundance of Okaloosa darters than seining and more reliably detect presence at low population densities. We recommend evaluation of visual survey methods when designing programs to monitor abundance of benthic fishes in clear streams, especially for threatened and endangered species that may be sensitive to handling and habitat disturbance.     

Toxic effects of resazurin on cell cultures

Resazurin, introduced as a cell viability indicator under the trade name alamarBlue^®, is generally regarded as nontoxic when used according to manufacturer’s suggested shorter-term incubation time specifications. However, problems arise when exposure times are extended to longer-term cultures on the order of days. To assess the effect of resazurin over longer incubation times, MCF7 (HTB-22), MCF10A (CRL-10317), 3T3-L1 (CL-173), and D1 (CRL-12424) cultures were tested with varying amounts of resazurin over 4- and 8-day periods. MCF7, 3T3-L1, and D1 cells cultured for 8 days with 20 % alamarBlue^® had significantly less cell survivability. Specifically, levels of metabolic activity, deoxyribonucleic acid (DNA) concentration, and glucose consumption of the cell lines cultured for 8 days in medium with 20 % alamarBlue^® were significantly lower (p < 0.05) than metabolic activity, DNA concentration, and glucose consumption of MCF7 cells cultured for 8 days in medium with no alamarBlue^®. MCF7, 3T3-L1, and D1 cells used less glucose at concentrations as low as 5 %. Data also suggests the toxic effects are more pronounced in the cancerous cell line as compared to the noncancerous cells.     

Conservation in a cup of water: estimating biodiversity and population abundance from environmental DNA

Three mantras often guide species and ecosystem management: (i) for preventing invasions by harmful species, ‘early detection and rapid response’; (ii) for conserving imperilled native species, ‘protection of biodiversity hotspots’; and (iii) for assessing biosecurity risk, ‘an ounce of prevention equals a pound of cure.’ However, these and other management goals are elusive when traditional sampling tools (e.g. netting, traps, electrofishing, visual surveys) have poor detection limits, are too slow or are not feasible. One visionary solution is to use an organism’s DNA in the environment (eDNA), rather than the organism itself, as the target of detection. In this issue of Molecular Ecology, Thomsen et al. (2012) provide new evidence demonstrating the feasibility of this approach, showing that eDNA is an accurate indicator of the presence of an impressively diverse set of six aquatic or amphibious taxa including invertebrates, amphibians, a fish and a mammal in a wide range of freshwater habitats. They are also the first to demonstrate that the abundance of eDNA, as measured by qPCR, correlates positively with population abundance estimated with traditional tools. Finally, Thomsen et al. (2012) demonstrate that next‐generation sequencing of eDNA can quantify species richness. Overall, Thomsen et al. (2012) provide a revolutionary roadmap for using eDNA for detection of species, estimates of relative abundance and quantification of biodiversity.     

Combining counts and incidence data: an efficient approach for estimating the log-normal species abundance distribution and diversity indices

Obtaining accurate estimates of diversity indices is difficult because the number of species encountered in a sample increases with sampling intensity. We introduce a novel method that requires that the presence of species in a sample to be assessed while the counts of the number of individuals per species are only required for just a small part of the sample. To account for species included as incidence data in the species abundance distribution, we modify the likelihood function of the classical Poisson log-normal distribution. Using simulated community assemblages, we contrast diversity estimates based on a community sample, a subsample randomly extracted from the community sample, and a mixture sample where incidence data are added to a subsample. We show that the mixture sampling approach provides more accurate estimates than the subsample and at little extra cost. Diversity indices estimated from a freshwater zooplankton community sampled using the mixture approach show the same pattern of results as the simulation study. Our method efficiently increases the accuracy of diversity estimates and comprehension of the left tail of the species abundance distribution. We show how to choose the scale of sample size needed for a compromise between information gained, accuracy of the estimates and cost expended when assessing biological diversity. The sample size estimates are obtained from key community characteristics, such as the expected number of species in the community, the expected number of individuals in a sample and the evenness of the community.     

Growth induced curve dynamics for filamentary micro-organisms

The growth of filamentary micro-organisms is described in terms of the geometry of evolving planar curves in which the dynamics is determined by an underlying growth process. Steadily propagating tip shapes in two and three dimensions are found that are consistent with experimentally observed growth sequences.