A Comparison of Methods for Estimating Relative Abundance of Grapsid Crabs

Grapsid crabs are one of the most common, and potentially important, elements of the mangrove fauna but relatively little information is available on patterns in their distribution and abundance. In part, this may be due to difficulties in estimating the abundance of burrowing species. By not having reliable methods of estimating changes in distribution and abundance of crabs, ecological impacts of crabs may be greatly underestimated. We tested several methods for estimating the apparent abundance of eight species of grapsids in a north Australian mangrove forest. These methods included continuous and instantaneous visual counts at two distances, two types of pitfall traps and photography. We also excavated crabs to test the reliability of the best of these methods. Overall, pitfall traps equipped with funnels proved most useful, although these did preferentially capture larger crabs. An exception was the large crab, Neosarmatium meinerti, which was rarely captured and more reliably estimated by burrow counts. Traps proved to be most useful in this study and may be for long term studies of grapsid species, however, the selection of a method should be made after careful evaluation of the questions and relevant information required for any particular study. Finally, these methods may also prove to be useful in other environments such as salt marshes.     

Finding a Fox: An Evaluation of Survey Methods to Estimate Abundance of a Small Desert Carnivore

The status of many carnivore species is a growing concern for wildlife agencies, conservation organizations, and the general public. Historically, kit foxes (Vulpes macrotis) were classified as abundant and distributed in the desert and semi-arid regions of southwestern North America, but is now considered rare throughout its range. Survey methods have been evaluated for kit foxes, but often in populations where abundance is high and there is little consensus on which technique is best to monitor abundance. We conducted a 2-year study to evaluate four survey methods (scat deposition surveys, scent station surveys, spotlight survey, and trapping) for detecting kit foxes and measuring fox abundance. We determined the probability of detection for each method, and examined the correlation between the relative abundance as estimated by each survey method and the known minimum kit fox abundance as determined by radio-collared animals. All surveys were conducted on 15 5-km transects during the 3 biological seasons of the kit fox. Scat deposition surveys had both the highest detection probabilities (p = 0.88) and were most closely related to minimum known fox abundance (r² = 0.50, P = 0.001). The next best method for kit fox detection was the scent station survey (p = 0.73), which had the second highest correlation to fox abundance (r² = 0.46, P<0.001). For detecting kit foxes in a low density population we suggest using scat deposition transects during the breeding season. Scat deposition surveys have low costs, resilience to weather, low labor requirements, and pose no risk to the study animals. The breeding season was ideal for monitoring kit fox population size, as detections consisted of the resident population and had the highest detection probabilities. Using appropriate monitoring techniques will be critical for future conservation actions for this rare desert carnivore.     

Comparison of Methods for Estimating Bird Abundance and Trends From Historical Count Data

Abstract: The use of bird counts as indices has come under increasing scrutiny because assumptions concerning detection probabilities may not be met, but there also seems to be some resistance to use of model-based approaches to estimating abundance. We used data from the United States Forest Service, Southern Region bird monitoring program to compare several common approaches for estimating annual abundance or indices and population trends from point-count data. We compared indices of abundance estimated as annual means of counts and from a mixed-Poisson model to abundance estimates from a count-removal model with 3 time intervals and a distance model with 3 distance bands. We compared trend estimates calculated from an autoregressive, exponential model fit to annual abundance estimates from the above methods and also by estimating trend directly by treating year as a continuous covariate in the mixed-Poisson model. We produced estimates for 6 forest songbirds based on an average of 621 and 459 points in 2 physiographic areas from 1997 to 2004. There was strong evidence that detection probabilities varied among species and years. Nevertheless, there was good overall agreement across trend estimates from the 5 methods for 9 of 12 comparisons. In 3 of 12 comparisons, however, patterns in detection probabilities potentially confounded interpretation of uncorrected counts. Estimates of detection probabilities differed greatly between removal and distance models, likely because the methods estimated different components of detection probability and the data collection was not optimally designed for either method. Given that detection probabilities often vary among species, years, and observers investigators should address detection probability in their surveys, whether it be by estimation of probability of detection and abundance, estimation of effects of key covariates when modeling count as an index of abundance, or through design-based methods to standardize these effects.     

An Evaluation of Survey Methods for Estimating Northern Bobwhite Abundance in Southern Texas

Abstract: Distance sampling has been identified as a reliable and well-suited method for estimating northern bobwhite (Colinus virginianus) density. However, distance sampling using walked transects requires intense sampling to obtain precise estimates, thus making the technique impractical for large acreages. Researchers have addressed this limitation by either resorting to the use of indices (e.g., morning covey-call surveys) or incorporating the use of aerial surveys with distance sampling. Both approaches remain relatively untested. Our objectives were to 1) compare density estimates among morning covey-call surveys, helicopter transects, and walked transects; 2) test a critical assumption of distance sampling pertinent to helicopter surveys (i.e., all objects on line are detected); and 3) evaluate the underlying premise of morning covey-call surveys (i.e., that the no. of calling coveys correlates with bobwhite density). Our study was conducted on 3 study sites in Brooks County, Texas, USA, during October to December, 2001 to 2005. Comparisons between walked transects and morning covey-call surveys involved the entire 5-year data set, whereas helicopter transects involved only the latter 2 years. Density estimates obtained from helicopter transects were similar to walked transect estimates for both years. We documented a detection probability on the helicopter transect line of 70 ± 10.2% (% ± SE; n = 20 coveys). Morning covey-call surveys yielded similar density estimates to walked transect estimates during only 2 of 5 years, when walked transect estimates were the least accurate and precise. We detected a positive relationship (R² = 0.51; 95% CI for slope: 29.5–53.1; n = 63 observations) between covey density and number of coveys heard calling. We conclude that helicopter transects appear to be a viable alternative to walked transects for estimating density of bobwhites. Morning covey-call surveys appear to be a poor method to estimate absolute abundance and to depict general population trajectories.     

Determining Methods of Underwater Visual Census for Estimating the Abundance of Coral Reef Fishes

We aimed to determine optimal methods of underwater visual census (UVC) for estimating the abundance of coral reef fishes exploited by fisheries in the tropical Pacific. Two main methods were tested using SCUBA: strip transect and stationary point counts. We assessed their relative accuracy, precision, power and efficiency (cost), and compared different census area dimensions, observer swimming speeds, and number of replicates. Twenty-five comparisons of the two UVC methods were conducted for 73 species from five families of coral reef fishes, on reefs in Australia and Fiji. Species were grouped within families based on their mobility. Few significant differences were found, either among or between strip transects and stationary point counts. The data were characterised by high variability, low precision and low power. A trend for greater accuracy in density estimates of small sedentary species with smaller census area was apparent, which probably reflects searching efficiency. Only one species group, the sedentary Acanthuridae showed differences between transects and point counts. Higher, hence presumably more accurate, density estimates were obtained with 50m×5m transects. Notably, point counts could be deployed in 70% of the time of transects. A bootstrapping procedure demonstrated a consistent improvement in precision of density estimates with increasing number of replicates, but no appreciable change in precision was found beyond 10 to 15 replicates, in all species groups and for both transects and point counts. Consequently, and because of the high variability inherent in fish density estimates, we recommend that at least 10 replicates be used to quantify the species considered here. The power calculations showed that only large differences in density will be detected with the replication levels typical of UVC surveys. Power was greatest for the roving serranids, with a decrease in density of about 50% detectable for this species group. We discuss the importance of carefully defining the behavioural attributes of species prior to selecting a UVC method. A method of temporal stratification in a count is described for censusing a range of species of varying mobilities. We suggest that fish mobility and search efficiency are key factors in optimising UVC methods.     

A Simulation Study of Acoustic-Assisted Tracking of Whales for Mark-Recapture Surveys

Collecting enough data to obtain reasonable abundance estimates of whales is often difficult, particularly when studying rare species. Passive acoustics can be used to detect whale sounds and are increasingly used to estimate whale abundance. Much of the existing effort centres on the use of acoustics to estimate abundance directly, e.g. analysing detections in a distance sampling framework. Here, we focus on acoustics as a tool incorporated within mark-recapture surveys. In this context, acoustic tools are used to detect and track whales, which are then photographed or biopsied to provide data for mark-recapture analyses. The purpose of incorporating acoustics is to increase the encounter rate beyond using visual searching only. While this general approach is not new, its utility is rarely quantified. This paper predicts the “acoustically-assisted” encounter rate using a discrete-time individual-based simulation of whales and survey vessel. We validate the simulation framework using existing data from studies of sperm whales. We then use the framework to predict potential encounter rates in a study of Antarctic blue whales. We also investigate the effects of a number of the key parameters on encounter rate. Mean encounter rates from the simulation of sperm whales matched well with empirical data. Variance of encounter rate, however, was underestimated. The simulation of Antarctic blue whales found that passive acoustics should provide a 1.7–3.0 fold increase in encounter rate over visual-only methods. Encounter rate was most sensitive to acoustic detection range, followed by vocalisation rate. During survey planning and design, some indication of the relationship between expected sample size and effort is paramount; this simulation framework can be used to predict encounter rates and establish this relationship. For a case in point, the simulation framework indicates unequivocally that real-time acoustic tracking should be considered for quantifying the abundance of Antarctic blue whales via mark-recapture methods.     

Estimating Water Quality Guidelines for Environmental Contaminants Using Multimodal Species Sensitivity Distributions: A Case Study with Atrazine

Species sensitivity distributions (SSDs) are used globally to generate water quality guidelines (WQGs). In Canada, a suite of models has been endorsed for describing SSDs. However, these models may not be suitable for substances with multiple modes of toxic action such as pesticides. Pesticides can produce multimodal SSDs where sensitive target organisms comprise one mode of the SSD and non-target organisms comprise the remaining mode(s). Guidelines from this type of SSD might be estimated using only the most sensitive taxa or using a multimodal distribution. The multimodal method presented here uses all data meeting data quality criteria and is thus in keeping with the concept that data comprising an SSD are a random sample from the population of interest rather than a subset thereof. The bimodal method can simultaneously emphasize the more sensitive portion of the dataset by allowing estimation of WQGs using a statistical subset of the data. In the case of the atrazine dataset example, this allowed estimating a WQG emphasizing more sensitive taxa whereas no parametric models fit only the more sensitive data and the small sample size (5) precluded the use of nonparametric methods.     

Can Abundance of Protists Be Inferred from Sequence Data: A Case Study of Foraminifera

Protists are key players in microbial communities, yet our understanding of their role in ecosystem functioning is seriously impeded by difficulties in identification of protistan species and their quantification. Current microscopy-based methods used for determining the abundance of protists are tedious and often show a low taxonomic resolution. Recent development of next-generation sequencing technologies offered a very powerful tool for studying the richness of protistan communities. Still, the relationship between abundance of species and number of sequences remains subjected to various technical and biological biases. Here, we test the impact of some of these biological biases on sequence abundance of SSU rRNA gene in foraminifera. First, we quantified the rDNA copy number and rRNA expression level of three species of foraminifera by qPCR. Then, we prepared five mock communities with these species, two in equal proportions and three with one species ten times more abundant. The libraries of rDNA and cDNA of the mock communities were constructed, Sanger sequenced and the sequence abundance was calculated. The initial species proportions were compared to the raw sequence proportions as well as to the sequence abundance normalized by rDNA copy number and rRNA expression level per species. Our results showed that without normalization, all sequence data differed significantly from the initial proportions. After normalization, the congruence between the number of sequences and number of specimens was much better. We conclude that without normalization, species abundance determination based on sequence data was not possible because of the effect of biological biases. Nevertheless, by taking into account the variation of rDNA copy number and rRNA expression level we were able to infer species abundance, suggesting that our approach can be successful in controlled conditions.     

Assessment of Root System Dynamics of Species Grown in Mixtures under Field Conditions using Herbicide Injection and 15N Natural Abundance Methods: A Case Study with Pea, Barley and Mustard

Two methods were developed and used to study the root system dynamics of two species grown together or separately under field conditions. The first method, based on herbicide injection at different soil depths, was used to determine the rooting depth penetration rate of each species in pea–barley and pea–mustard mixtures. The roots absorbed the herbicide when they reached the treated zone leading to visible symptoms on the leaves which could be readily monitored. The second method used differences in ¹⁵N natural abundance and N concentration between legume and non-legume species to quantify the contribution of each species to root biomass of a pea–barley mixture. Each contribution was calculated using ¹⁵N abundance and N concentration of root mixtures and of subsamples of roots of individual species within mixtures. Both methods can indeed be used to distinguish roots of species in mixtures and thus to study belowground competition between associated species. The use of these methods demonstrated species differences in root system dynamics between species but also significant effects of interactions between species in mixtures. The rooting depth penetration rate was mainly species specific whereas root biomass was dependant on plant growth, allocation of dry matter between shoot and root components and growth factors such as N fertilization. Root biomass of each species may vary therefore with the level of competition between species.     

Estimating the Material Stock of Roads: The Vietnamese Case Study

This study is a pioneering effort to quantify the materials stocked in the road network of a developing country, Vietnam, and analyze its relationships to the country's recent economic development. National road networks function as capital and infrastructure investments that are necessary catalysts for countries’ development, while requiring the extraction of vast amounts of construction materials for expansion and maintenance causing environmental impacts. However, there has so far been little research on the subject, especially in developing countries. We compile material stock and flow accounts for Vietnam's roads from 2003 to 2013 on the national and provincial levels, finding that approximately 40% of the domestic consumption of construction materials is for expanding and maintaining the road network, and the materials stocked in the road network doubled from 1,321 million metric tons in 2003 to 2,660 million metric tons in 2012. Material stock growth rates closely resembled those of gross domestic product (GDP) in this period, suggesting a codependency of physical infrastructure development and economic development. On the provincial level, our results show local disparities in the stock and its capacity to support the transportation of passengers and freight, especially considering the surging growth of vehicles in urban centers. By showcasing the challenges of conducting a material flow and stock analysis in a developing country, this study not only sheds light on Vietnam's transportation material stock and its policy implications, but also serves as a case study for further work in similar countries.     

Estimating Invasion Probabilities: A Case Study of fire Blight Disease and the Importation of Apple Fruits

A statistical method is proposed for the estimation of the probability of invasion of fire blight disease via the importation of apple fruits, by considering that the proportion of infected fruits varies depending on the production area and the year. The following three assumptions, which might be applicable to biological invasions of several diseases of plants and animals, are used: (1) A beta distribution approximately describes the probability distribution of the proportion of infected fruits in the production area of a given consignment, (2) every consignment contains fruits that were drawn at random from the infinite population of the production area, and (3) each infected fruit causes infection of fire blight in the importing country by an independent constant probability. The estimate of the expected time required for invasion is 1707 years if we ignore the variability of infection, whereas the estimate is 334 years if we consider the variability. Thus, it is suggested that the estimation of the risk of invasion might be quite biased if we ignore the variability of infection.     

作物区域试验点区辨力估算方法的比较研究

对三种估算作物区域试验点区辨力方法（变异系数指标法、回归系数指标法和ＡＭＭＩ模型Ｄｊ值法）进行了比较研究,研究表明,三种方法的结论总体上相近,但ＡＭＭＩ模型Ｄｊ值法相对较科学准确。     

Estimating Energy Expenditure from Heart Rate in Older Adults: A Case for Calibration

Background

Accurate measurement of free-living energy expenditure is vital to understanding changes in energy metabolism with aging. The efficacy of heart rate as a surrogate for energy expenditure is rooted in the assumption of a linear function between heart rate and energy expenditure, but its validity and reliability in older adults remains unclear.

Objective

To assess the validity and reliability of the linear function between heart rate and energy expenditure in older adults using different levels of calibration.

Design

Heart rate and energy expenditure were assessed across five levels of exertion in 290 adults participating in the Baltimore Longitudinal Study of Aging. Correlation and random effects regression analyses assessed the linearity of the relationship between heart rate and energy expenditure and cross-validation models assessed predictive performance.

Results

Heart rate and energy expenditure were highly correlated (r = 0.98) and linear regardless of age or sex. Intra-person variability was low but inter-person variability was high, with substantial heterogeneity of the random intercept (s.d. = 0.372) despite similar slopes. Cross-validation models indicated individual calibration data substantially improves accuracy predictions of energy expenditure from heart rate, reducing the potential for considerable measurement bias. Although using five calibration measures provided the greatest reduction in the standard deviation of prediction errors (1.08 kcals/min), substantial improvement was also noted with two (0.75 kcals/min).

Conclusion

These findings indicate standard regression equations may be used to make population-level inferences when estimating energy expenditure from heart rate in older adults but caution should be exercised when making inferences at the individual level without proper calibration.     

A Comparison of Computer-Based Methods for Estimating the Age of Animals

Russian Journal of Marine Biology - The advantages and disadvantages of statistical methods for estimating the age of animals that lack recording structures are discussed in the article. The...     

A Comparison of Methods for Estimating Northern Bobwhite Covey Detection Probabilities

Abstract: We compared the time-of-detection and logistic regression methods of estimating probability of detection for northern bobwhite (Colinus virginianus) coveys. Both methods are unusual in that they allow estimation of the total probability of detection (i.e., the product of the probability that a covey is available for detection [i.e., that a covey vocalizes] and detection given availability). The logistic regression method produced an average detection probability of 0.596 (SE = 0.020) and the time-of-detection method produced a detection probability estimate of 0.540 (SE = 0.086), and the 2 estimates were not significantly different. This is the first evaluation of the time-of-detection method with empirical field data. Although the time-of-detection and logistic regression method each have advantages, both can be used under appropriate conditions to improve estimates of bobwhite abundance by allowing for the estimation of detection probabilities. Improved estimates of bobwhite abundance will allow land managers to make more informed management decisions.     

Nitrogen Transfer Between Plants: A 15N Natural Abundance Study with Crop and Weed Species

An increasing amount of evidence indicates that N can be transferred between plants. Nonetheless, a number of fundamental questions remain. A series of experiments was initiated in the field to examine N transfer between N₂-fixing soybean (Glycine max [L.] Merr.) varieties and a non-nodulating soybean, and between N₂-fixing peanut (Arachis hypogaea L.) or soybean and neighboring weed species. The experiments were conducted in soils with low N fertilities and used differences in N accumulation and/or ¹⁵N natural abundance to estimate N transfer. Mixtures of N₂-fixing and non-nod soybean indicated that substantial inter-plant N transfer occurred. Amounts were variable, ranging from negligible levels to 48% of the N found in the non-nod at maturity. Transfer did not appear to strongly penalize the N₂-fixing donor plants. But, in cases where high amounts of N were transferred, N content of donors was noticeably lowered. Differences were evident in the amount of N transferred from different N₂-fixing donor genotypes. Results of experiments with N₂-fixing crops and the weed species prickly sida (Sida spinosa L.) and sicklepod (Senna obtusifolia [L.] Irwin & Barneby) also indicated substantial N transfer occurred over a 60-day period, with amounts accounting for 30–80% of the N present in the weeds. Transfer of N, however, was generally very low in weed species that are known to be non-hosts for arbuscular mycorrhizae (yellow nutsedge, Cyperus esculentus L. and Palmer amaranth, Amaranthus palmeri [S.] Watson). The results are consistent with the view that N transfer occurs primarily through mycorrhizal hyphal networks, and they reveal that N transfer may be a contributing factor to weed problems in N₂-fixing crops in low N fertility conditions.