A comparison of some population density sampling techniques for biodiversity, conservation, and environmental impact studies

Twelve terrestrial and marine studies were conducted at various sites in Malaysia, Brazil, and the United States between April 1999 and February 2004. These data were analyzed using five density estimate techniques for stationary (non-motile) organisms including Stratified Random Sampling, Point-Center Quarter, Third Nearest Object, Weinberg, and Strong. The Strong method gave the most accurate density estimates of stationary animals and plants. Stratified Random Sampling ranked second best and the Third Nearest Object the third best. Belt or strip transects may be preferable but can be restrictive in some situations because of logistics and associated time constraints. Straight line measurements on reefs were 3–27% more accurate than reef slack line and reef contour measurements. Most study areas measured with the standardized Morisita index of dispersion were moderately aggregated. Results from the Third Nearest Object and Point-Center Quarter techniques indicate that the addition of more data to establish a density correction factor does not necessarily give more accurate estimates of density.     

Wild turkey (<Emphasis Type="Italic">Meleagris gallopavo</Emphasis>) detectability from helicopters and ramifications for estimating abundance

Aerial surveys have been used to estimate abundance for several wild bird species but its application for wild turkey (Meleagris gallopavo) populations has been limited. We surveyed Rio Grande wild turkey (M. gallopavo intermedia) populations during March 2006 using an R44 helicopter. We used flocks with radio-tagged birds to estimate flock detectability. We also used simulations to evaluate accuracy and precision and examine power to detect trends in population change. We observed that wild turkey flock detectability was 94.7% (74.0–99.9%; 95% CI). Our simulations suggested helicopter surveys would underestimate abundance by about 5.6% (4.6% CV). Surveying 980 to 1,960 km² (requiring 27 to 55 h of flight time) can provide sufficient power (≥0.80) to detect a 10 to 25% change in abundance over a 4- to 5-year period.     

Accounting for imperfect detection of groups and individuals when estimating abundance

If animals are independently detected during surveys, many methods exist for estimating animal abundance despite detection probabilities <1. Common estimators include double‐observer models, distance sampling models and combined double‐observer and distance sampling models (known as mark‐recapture‐distance‐sampling models; MRDS). When animals reside in groups, however, the assumption of independent detection is violated. In this case, the standard approach is to account for imperfect detection of groups, while assuming that individuals within groups are detected perfectly. However, this assumption is often unsupported. We introduce an abundance estimator for grouped animals when detection of groups is imperfect and group size may be under‐counted, but not over‐counted. The estimator combines an MRDS model with an N‐mixture model to account for imperfect detection of individuals. The new MRDS‐Nmix model requires the same data as an MRDS model (independent detection histories, an estimate of distance to transect, and an estimate of group size), plus a second estimate of group size provided by the second observer. We extend the model to situations in which detection of individuals within groups declines with distance. We simulated 12 data sets and used Bayesian methods to compare the performance of the new MRDS‐Nmix model to an MRDS model. Abundance estimates generated by the MRDS‐Nmix model exhibited minimal bias and nominal coverage levels. In contrast, MRDS abundance estimates were biased low and exhibited poor coverage. Many species of conservation interest reside in groups and could benefit from an estimator that better accounts for imperfect detection. Furthermore, the ability to relax the assumption of perfect detection of individuals within detected groups may allow surveyors to re‐allocate resources toward detection of new groups instead of extensive surveys of known groups. We believe the proposed estimator is feasible because the only additional field data required are a second estimate of group size.     

Atlantic bluefin tuna in the Gulf of Maine,II: precision of sampling designs in estimating seasonal abundance accounting for tuna behaviour

A primary challenge of animal surveys is to understand how to reliably sample populations exhibiting strong spatial heterogeneity. Building upon recent findings from survey, tracking and tagging data, we investigate spatial sampling of a seasonally resident population of Atlantic bluefin tuna in the Gulf of Maine, Northwestern Atlantic Ocean. We incorporate empirical estimates to parameterize a stochastic population model and simulate measurement designs to examine survey efficiency and precision under variation in tuna behaviour. We compare results for random, systematic, stratified, adaptive and spotter-search survey designs, with spotter-search comprising irregular transects that target surfacing schools and known aggregation locations (i.e., areas of expected high population density) based on a priori knowledge. Results obtained show how survey precision is expected to vary on average with sampling effort, in agreement with general sampling theory and provide uncertainty ranges based on simulated variance in tuna behaviour. Simulation results indicate that spotter-search provides the highest level of precision, however, measurable bias in observer-school encounter rate contributes substantial uncertainty. Considering survey bias, precision, efficiency and anticipated operational costs, we propose that an adaptive-stratified sampling alone or a combination of adaptive-stratification and spotter-search (a mixed-layer design whereby a priori information on the location and size of school aggregations is provided by sequential spotter-search sampling) may provide the best approach for reducing uncertainty in seasonal abundance estimates.

棉田绿盲蝽种群密度的调查方法

本文比较研究了棉田绿盲蝽Apolygus lucorum(Meyer-Dür)种群的调查方法。全株调查法中,目测法调查到的绿盲蝽种群密度最高,显著高于扫网法和盆拍法。局部调查法发现,蕾上的绿盲蝽种群数量显著高于叶片和花上;蕾上种群数量与整株密度之间呈显著正相关关系(y=1.18 x+3.69)。间接调查法表明:在苗期和蕾期,叶片受害等级和绿盲蝽种群密度之间呈显著正相关关系(苗期:y=25.28 x+8.20;蕾期:y=43.99 x+27.58)。     

Challenges and opportunities for estimating abundance of a low-density moose population

Monitoring large herbivores across their core range has been readily accomplished using aerial surveys and traditional distance sampling. But for peripheral populations, where individuals may occur in patchy, low-density populations, precise estimation of population size and trend remains logistically and statistically challenging. For moose (Alces alces) along their southern range margin in northern New York, USA, we sought robust estimates of moose distribution, abundance, and population trend (2016–2019) using a combination of aerial surveys (line transect distance-sampling), repeated surveys in areas where moose were known to occur to boost the number of detections, and density surface modeling (DSM) with spatial covariates. We achieved a precise estimate of density (95% CI = 0.00–0.29 moose/km²) for this small population (656 moose, 95% CI = 501–859), which was patchily distributed across a large and heavily forested region (the 24,280-km² Adirondack Park). Local moose abundance was positively related to active timber management, elevation, and snow cover, and negatively related to large bodies of water. As expected, moose abundance in this peripheral population was low relative to its core range in other northern forest states. Yet, in areas where abundance was greatest, moose densities in New York approached those where epizootics of winter tick (Dermacentor albipictus) have been reported, underscoring the need for effective and efficient monitoring. By incorporating autocorrelation in observations and landscape covariates, DSM provided spatially explicit estimates of moose density with greater precision and no additional field effort over traditional distance sampling. Combined with repeated surveys of areas with known moose occurrence to achieve viable sample sizes, DSM is a useful tool for effectively monitoring low density and patchy populations.     

An upper limit to the abundance of aquatic organisms

Summary The maximum density achievable by aquatic organisms is an inverse linear function of their body size. As a consequence, the maximum achievable biomass is independent of body size, and is 2 orders of magnitude higher than the biomass in natural populations. The minimum interorganismic terorganismic distance, calculated from the maximum density to allow comparison between aquatic and terrestrial organisms, scales as the 1/3 power of body size in both habitats. The similarities in the interorganismic distance of terrestrial and aquatic plant and animal communities suggest a fundamental regularity in the way organisms use the space.     

Role of plant abundance in determining the abundance of herbivorous insects

Summary The proposal (Gaston and Lawton 1988a, b) that small species of insects are more abundant because they have lower per capita resource requirements than large species does not hold for aphids (Dixon 1990a). There are good theoretical grounds, supported by empirical data, for the suggestion that host specific aphids that live on uncommon plants incur great losses in finding their host plants and as a consequence have a lower realized r _m and are rarer than aphids living on common plants. This is also likely to apply to other organisms that are host specific and time-limited dispersers.     

An assessment of the puku (Kobus vardonii Livingstone 1857) population at Lake Rukwa,Tanzania

The population of puku, Kobus vardonii, at Lake Rukwa, one of only two in Tanzania, is poorly known. A multi‐species dry season game count carried out in Rukwa Game Reserve (RGR) in 2004 estimated a population size of 1729, but was associated with a high margin of error [coefficient of variation (CV) 0.88]. To increase the precision for the local puku population estimate, we conducted a zig‐zag line transect survey restricted only to areas occupied by puku in the dry season of 2006. This survey technique produced an estimate of 776 individuals and the CV was considerably reduced to 0.29. Puku herd size was comparable with the studies carried out in the Kilombero valley, Tanzania and in Kasanka National Park, Zambia, thus broadly confirming the herding ecology of this species. We found that pukus were restricted to the central parts of the floodplains, suggesting an avoidance of habitats used by pastoralists at the edge of RGR. Compared with the estimates of the puku population made in the 1980s, the puku population has declined. We recommend regular monitoring and enforcement of the current management plan to conserve the local puku population.     

A model for estimating abundance of cattle grub (Diptera: Oestridae) from the proportion of uninfested cattle as determined by serology*

A model is presented for determining the abundance of cattle grubs in the backs of calves from the proportion of uninfested calves in a herd. The distribution of grubs in calves' backs was compared with the negative binomial, but no relationships were found among the distribution parameters, suggesting that the negative binomial is an inappropriate choice for the basis of a sampling model. The relationship between the mean number of grubs per animal (mean), variance (delta 2), and proportion of uninfested calves (p0) in a herd was determined and used as the basis for the sampling model. The relationship between p0 and p0e [determined using serology (ELISA)] was evaluated. The variance of estimates of mean grubs per animal based on the regression model and uncertainty due to using p0e as an estimate of p0 was examined. A test of the model indicated that p0e could be used to obtain a reliable estimate of mean grubs per animal and that the method would be applicable for monitoring grub populations, assessing chemical control programmes, and determining release rates of sterile insects for control.     

An improved technique for indexing abundance of Himalayan thar

Current monitoring of Himalayan thar (Hemitragus jemlahicus) populations in New Zealand involves a technique based on repeated observations by different, experienced observers. The method gives no measure of error and hence does nor allow for statistical comparison of repeated surveys. We outline a faster and cheaper technique that enables statistical comparison between surveys based on mark-recapture theory. Two counts can be made by the same observer on subsequent evenings, or can be conducted simultaneously by two observers of differing experience provided they do not cue each other to the location of animals. As an example of the use of the technique, we monitored a control operation aimed at reducing thar impact on alpine flora. We recorded a non-significant (P = 0.27) decline in thar abundance from 38 (± 27; 95% C.L.) to 28 (± 19) females (including kids) in the survey area.     

The adequacy of collecting techniques for estimating species richness of grassland invertebrates

1.  There is still considerable debate about the most effective methods of sampling invertebrates in monitoring and assessment programmes.
2.  The above-ground invertebrates of a limestone grassland in north-east England were compared between samples from pitfall traps and from a D-vac suction trap combined with a lightweight swish net (SW/DV).
3.  Over 14 000 individuals were captured, with similar numbers in the pitfall and SW/DV samples. A total of 480 species of Hemiptera, Coleoptera, Diptera and Araneae was identified and placed into 14 taxa for further analysis.
4.  The pitfall sample produced species/specimen curves from which it was possible to estimate species richness for all the Coleoptera and Araneae taxa and the calypterate Schizophora. The SW/DV sample was adequate to estimate the species richness of Hemiptera, most Diptera taxa, herbivorous Coleoptera and Linyphiidae.
5.  The proportion of Coleoptera and Araneae taxa that were method-unique was higher in the pitfall sample than the SW/DV sample and vice versa for the Hemiptera and Diptera taxa. Nevertheless, a relatively high proportion of method-unique species of most taxa was found in both sample types, indicating that they can each contribute to assessing species assemblages in grasslands.
6.  Both pitfall traps and SW/DV samples are needed to estimate species richness in grasslands for all taxa except Heteroptera, Homoptera and Lycosidae. Herbivorous Coleoptera and Linyphiidae were collected in numbers adequate for assessing richness in both sample types, but more specimens were required in one or other sample for the remaining taxa.     

An improved method for estimating inbreeding depression in pedigrees

Fitness is expected to decrease with inbreeding in proportion to the amount of deleterious genetic variation present in a population. The effect of inbreeding on survivorship is usually modeled as a negative exponential relationship, and this model has been widely used to estimate the amount of deleterious genetic variation in populations. Linear regression has traditionally been used to estimate the parameters of the model, including the number of lethal equivalents. This article describes an alternative method for estimating parameters and their confidence limits: the maximum likelihood approach. The accuracy of regression and maximum likelihood estimates of the number of lethal equivalents is compared through simulation. The maximum likelihood approach is found to be both median unbiased and capable of estimating confidence limits with nearly the stated degree of accuracy, while the linear regression approach is found to be median biased. The significance of this on previous estimates of inbreeding depression is discussed. Zoo Biol 17:481–497, 1998. © 1998 Wiley-Liss, Inc.     

挥发性有机化合物(VOCs)采样方法的研究进展

对近年来国内外挥发性有机化合物（VOCs）采集方法的研究进展进行了综合和概括。对VOCs几种主要的采样方法包括顶空收集法、液液萃取法、超临界流体萃取、吸附剂收集法、吹扫捕集法、画相微萃取等技术进行了阐述和比较,提出应根据实验材料的特性选择合适的采样方法,旨在为应用VOCs的采集方法及相关研究提供参考和借鉴。     

Modeling unobserved sources of heterogeneity in animal abundance using a Dirichlet process prior

Summary .   In surveys of natural populations of animals, a sampling protocol is often spatially replicated to collect a representative sample of the population. In these surveys, differences in abundance of animals among sample locations may induce spatial heterogeneity in the counts associated with a particular sampling protocol. For some species, the sources of heterogeneity in abundance may be unknown or unmeasurable, leading one to specify the variation in abundance among sample locations stochastically. However, choosing a parametric model for the distribution of unmeasured heterogeneity is potentially subject to error and can have profound effects on predictions of abundance at unsampled locations. In this article, we develop an alternative approach wherein a Dirichlet process prior is assumed for the distribution of latent abundances. This approach allows for uncertainty in model specification and for natural clustering in the distribution of abundances in a data-adaptive way. We apply this approach in an analysis of counts based on removal samples of an endangered fish species, the Okaloosa darter. Results of our data analysis and simulation studies suggest that our implementation of the Dirichlet process prior has several attractive features not shared by conventional, fully parametric alternatives.     

A statistical approach to quantification of genetically modified organisms (GMO) using frequency distributions

Background

According to Regulation (EU) No 619/2011, trace amounts of non-authorised genetically modified organisms (GMO) in feed are tolerated within the EU if certain prerequisites are met. Tolerable traces must not exceed the so-called ‘minimum required performance limit’ (MRPL), which was defined according to the mentioned regulation to correspond to 0.1% mass fraction per ingredient. Therefore, not yet authorised GMO (and some GMO whose approvals have expired) have to be quantified at very low level following the qualitative detection in genomic DNA extracted from feed samples. As the results of quantitative analysis can imply severe legal and financial consequences for producers or distributors of feed, the quantification results need to be utterly reliable.

Results

We developed a statistical approach to investigate the experimental measurement variability within one 96-well PCR plate. This approach visualises the frequency distribution as zygosity-corrected relative content of genetically modified material resulting from different combinations of transgene and reference gene Cq values. One application of it is the simulation of the consequences of varying parameters on measurement results. Parameters could be for example replicate numbers or baseline and threshold settings, measurement results could be for example median (class) and relative standard deviation (RSD). All calculations can be done using the built-in functions of Excel without any need for programming. The developed Excel spreadsheets are available (see section ‘Availability of supporting data’ for details). In most cases, the combination of four PCR replicates for each of the two DNA isolations already resulted in a relative standard deviation of 15% or less.

Conclusions

The aims of the study are scientifically based suggestions for minimisation of uncertainty of measurement especially in —but not limited to— the field of GMO quantification at low concentration levels. Four PCR replicates for each of the two DNA isolations seem to be a reasonable minimum number to narrow down the possible spread of results.

Electronic supplementary material

The online version of this article (doi:10.1186/s12859-014-0407-x) contains supplementary material, which is available to authorized users.     

Impact of abundance data errors on the uncertainty of an ecological water quality assessment index

Increased awareness about the uncertainty of ecological water quality (EWQ) assessment tools in river management has led to the identification of the underlying uncertainty sources and the quantification of their effect on assessment. More specifically, with respect to macroinvertebrate-based EWQ assessment, use of erroneous abundance data has been identified as a (possible) source of uncertainty. In this paper, the effect of erroneous abundance data on the uncertainty of an EWQ assessment index was investigated. A model simulation based method, the virtual ecologist approach, was used to estimate the impact of abundance data errors on the uncertainty of the Multimetric Macroinvertebrate Index Flanders (MMIF). The results of this study show that the effects of relative small errors on the MMIF and assessment are limited. Additionally, it is observed that uncertainties due to abundance errors increase with decreasing EWQ (i.e. lower MMIF). This is important, since decision-makers typically formulate management actions for rivers with a low EWQ. In short, the innovative virtual ecologist approach proved to be very successful to research the index uncertainty and present a unique insight in the functioning of the assessment index.     

An improved probe for sampling soil atmospheres

A probe for the extraction of soil gases is described. Novel features are the way the probe aperture within the soil can be manipulated from above, and the design of the tip to maximize gas extraction.     

Impact of power plant heated effluent on the abundance of sedentary organisms,off Kalpakkam,East coast of India

The impact of heated effluents from the condenser outfall of the Madras Atomic Power Station (MAPS), on the flora and fauna settled on an iron pile in the discharge area was studied. At temperatures ranging between 27.2 to 31.0 °C, the sedentary community was composed of epiphytic algae, sea anemones, tubeworms, polychaetes, crabs, amphipods, barnacles, periwinkles, mussels and ascidians. During January–February, ambient temperature ranged between 37.0 to 37.6 °C, and almost all the macroepifauna and flora, except for periwinkles and Cthamalid barnacles perished.