Magic bullets and golden rules: data sampling in molecular phylogenetics

Data collection for molecular phylogenetic studies is based on samples of both genes and taxa. In an ideal world, with no limitations to resources, as many genes could be sampled as deemed necessary to address phylogenetic problems. Given limited resources in the real world, inadequate (in terms of choice of genes or number of genes) sequences or restricted taxon sampling can adversely affect the reliability or information gained in phylogenetics. Recent empirical and simulation-based studies of data sampling in molecular phylogenetics have reached differing conclusions on how to deal with these problems. Some advocated sampling more genes, others more taxa. There is certainly no ‘magic bullet’ that will fit all phylogenetic problems, and no specific ‘golden rules’ have been deduced, other than that single genes may not always contain sufficient phylogenetic information. However, several general conclusions and suggestions can be made. One suggestion is that the determination of a multiple, but moderate number (e.g., 6–10) of gene sequences might take precedence over sequencing a larger set of genes and thereby permit the sampling of more taxa for a phylogenetic study.     

Variance estimation for systematic designs in spatial surveys

Summary In spatial surveys for estimating the density of objects in a survey region, systematic designs will generally yield lower variance than random designs. However, estimating the systematic variance is well known to be a difficult problem. Existing methods tend to overestimate the variance, so although the variance is genuinely reduced, it is over‐reported, and the gain from the more efficient design is lost. The current approaches to estimating a systematic variance for spatial surveys are to approximate the systematic design by a random design, or approximate it by a stratified design. Previous work has shown that approximation by a random design can perform very poorly, while approximation by a stratified design is an improvement but can still be severely biased in some situations. We develop a new estimator based on modeling the encounter process over space. The new “striplet” estimator has negligible bias and excellent precision in a wide range of simulation scenarios, including strip‐sampling, distance‐sampling, and quadrat‐sampling surveys, and including populations that are highly trended or have strong aggregation of objects. We apply the new estimator to survey data for the spotted hyena (Crocuta crocuta) in the Serengeti National Park, Tanzania, and find that the reported coefficient of variation for estimated density is 20% using approximation by a random design, 17% using approximation by a stratified design, and 11% using the new striplet estimator. This large reduction in reported variance is verified by simulation.     

Evaluation of different observational sampling regimes for use in zoological parks

Observational sampling methods provide clearly-defined guidelines for collection and analysis of behavioral data. In some situations, use of formal sampling regimes may be impractical or impossible. A case in point is data collection conducted by animal care staff at zoological parks and aquaria. Often, time is sufficiently limited that data collection is perceived as a task that cannot be accomplished given the normal constraints of the day. Here, we explore the efficacy and validity of using more variable and abridged sampling regimes in an effort to identify the appropriateness of such observation schemes for systematic monitoring of behavior. We describe the results of studies on three species (two polar bears, an Atlantic bottlenose dolphin calf, and two brown bears), conducted over a period of several years at the Brookfield Zoo, Brookfield, Illinois, USA. Data collection schemes varied both within and across groups in order to provide a basis of comparison. In all cases, there were significant differences based on sampling regime for rare behaviors (those that individually comprised <15% of the activity budget), but not for common behaviors. Subsampling from larger data sets indicated that data reliability increases with increasing observation number. We discuss the strengths and weaknesses of such sporadic sampling methods, and suggest that, in many instances such limited data collection may yet yield an accurate picture of animal activity and should not be overlooked as a viable management tool.     

A dispersal-limited sampling theory for species and alleles

The importance of dispersal for biodiversity has long been recognized. However, it was never advertised as vigorously as Stephen Hubbell did in the context of his neutral community theory. After his book appeared in 2001, several scientists have sought and found analytical expressions for the effect of dispersal limitation on community composition, still in the neutral context. This has been done along two relatively independent lines of research that have a different mathematical approach and focus on different, yet related, types of results. Here, we study both types in a new framework that makes use of the sampling nature of the theory. We present sampling distributions that contain binomial or hypergeometric sampling on the one hand, and dispersal limitation on the other, and thus views dispersal limitation as ubiquitous as sampling effects. Further, we express the results of one line of research in terms of the other and vice versa, using the concept of subsamples. A consequence of our findings is that metacommunity size does not independently affect the outcome of neutral models in contrast to a previous assertion (Ecol. Lett., 7, 2004, p. 904) based on an incorrect formula (Phys. Rev. E, 68, 2003, p. 061902, eqns 11-14). Our framework provides the basis for development of a dispersal-limited non-neutral community theory and applies in population genetics as well, where alleles and mutation play the roles of species and speciation respectively.     

油松毛虫(Dendrolimus labulaeformis)幼虫抽样技术的研究

本文在测定油松毛虫幼虫静态格局和动态格局的条件下,全面而系统地进行了株抽样、轮抽样和“枝”抽样的研究。根据幼虫在各轮垂直分布的特征和喜食二年生针叶的特性,建立回归模型,从轮抽样发展到“枝”抽样,通过检验,预报精度在91—98％之间。轮抽样比株抽样平均提高效率6倍,“枝”抽样比轮抽样又平均提高1.5倍。如费用以每株0.20元计,轮抽样比株抽样每株平均减少0.16元,“枝”抽样每株又减少0.032元。     

Ranked set sampling for replicated sampling designs

In practical ecological sampling studies, a certain design (such as plot sampling or line-intercept sampling) is usually replicated more than once. For each replication, the Horvitz-Thompson estimation of the objective parameter is considered. Finally, an overall estimator is achieved by averaging the single Horvitz-Thompson estimators. Because the design replications are drawn independently and under the same conditions, the overall estimator is simply the sample mean of the Horvitz-Thompson estimators under simple random sampling. This procedure may be wisely improved by using ranked set sampling. Hence, we propose the replicated protocol under ranked set sampling, which gives rise to a more accurate estimation than the replicated protocol under simple random sampling.     

A comparison of pump sampling systems for live zooplankton collection

Simultaneous and sequential tests of pump sampling equipment showed that sampling mortality of Lake Michigan zooplankton collected from the cooling water intake of a nuclear power plant was dependent on the sampling method used. Two sampling devices and two pump types were tested to determine which combination resulted in the lowest sampling mortality. An in-line filter trap located on the suction side of the pump provided the lowest sampling mortality. Higher sampling rates were achieved with a centrifugal pump without increasing sampling mortality.     

A floatable,benthic corer for use with scuba

A diver-operated corer to sample benthic macroinvertebrates is described. Removable drive-handles allow the 9-cm (ID) barrel to be driven into substrates too firm to be sampled by line-held or conventional diver-operated corers. The sampler is emptied underwater using compressed air and its buoyancy can be controlled by filling a rubber inner tube.This study was supported by the Pennsylvania Power and Light Company     

不同采样设计评估鱼类群落效果比较

鱼类群落生态学研究结果的准确性很大程度上依赖于采样设计的合理性和准确性,正确的采样调查设计不仅可以降低调查成本,其结果也对渔业资源的评估或者管理起到相当重要的作用.本文利用计算机模拟定点采样、简单随机采样和分层采样,比较了3种采样设计的采样效果、相对误差及相对偏差.结果表明： 定点采样设计的采样效果 (采样效果平均值为3.37)要弱于简单随机采样和分层随机采样 (采样效果平均值为0.961).3种采样设计中,分层采样设计在鱼类群落丰富度评估时表现最好,其采样效果、相对误差和相对偏差表现最佳.随着采样数的增加,分层采样设计的采样效果有所下降,但其采样精度提高.     

Optimum Design in Multivariate Stratified Sampling

The procedure of determining the optimum sample size in each stratum in stratified sampling for several variables is expressed and solved as a multistage decision process through dynamic programming. Using data published elsewhere, the dynamic programming approach was shown to give results identical to those obtained by some other already suggested approaches. The advantage is that dynamic programming can more easily handle problems involving several strata and/or variables.     

Automatic whole broth multi-fermentor sampling

Summary An efficient, aseptic method of obtaining whole broth fermentation samples was developed based on a piston-valve, a local sample loop, and an ability to drive the entire sample volume with sterile air through a sample line and into a remote tube. The configuration delivers 10-ml samples 10 m away with about 4 ml of broth wasted in the sampling process. An autosampler was enhanced and programmed to control acquisition into chilled tubes. The autosampler-based system represents a convenient way to provide frequent samples to profile intracellular and extracellular components for yeast and bacterial fermentations. A configuration to provide sampling from six fermentors with a multi-rack autosampler will be presented.     

Nematode Community Structure in Desert Soils: Nematode Recovery

The sugar-flotation-sieving (SFS) and Baermann-funnel (BF) methods were compared for nematode extraction efficiency. The SFS method recovered nematodes from more trophic groups whereas greater total numbers of individuals were recovered by BF. In a test to validate the efficiency of SFS, virtually 100% of the nematodes added to desert soil prior to extraction were recovered by four consecutive SFS washings of each soil sample. Estimations of nematode biomass in desert soils based on numbers of nematodes extracted by the two methods were similar unless there was large reserve of eggs in the soil. The biomass of nematodes from a Colorado desert soil was 0.9 g/m² as determined by both methods, whereas BF gave 0.17 g/m² for nematodes from a Mojave desert soil as compared to 0.9 g/m² with SFS.     

Estimating the encounter rate variance in distance sampling

Summary .  The dominant source of variance in line transect sampling is usually the encounter rate variance. Systematic survey designs are often used to reduce the true variability among different realizations of the design, but estimating the variance is difficult and estimators typically approximate the variance by treating the design as a simple random sample of lines. We explore the properties of different encounter rate variance estimators under random and systematic designs. We show that a design-based variance estimator improves upon the model-based estimator of Buckland et al. (2001, Introduction to Distance Sampling. Oxford: Oxford University Press, p. 79) when transects are positioned at random. However, if populations exhibit strong spatial trends, both estimators can have substantial positive bias under systematic designs. We show that poststratification is effective in reducing this bias.     

Evaluation of rayon swab surface sample collection method for Bacillus spores from nonporous surfaces

AIM: To evaluate US Centers for Disease Control and Prevention recommended swab surface sample collection method for recovery efficiency and limit of detection for powdered Bacillus spores from nonporous surfaces. METHODS AND RESULTS: Stainless steel and painted wallboard surface coupons were seeded with dry aerosolized Bacillus atrophaeus spores and surface concentrations determined. The observed mean rayon swab recovery efficiency from stainless steel was 0.41 with a standard deviation (SD) of +/-0.17 and for painted wallboard was 0.41 with an SD of +/-0.23. Evaluation of a sonication extraction method for the rayon swabs produced a mean extraction efficiency of 0.76 with an SD of +/-0.12. Swab recovery quantitative limits of detection were estimated at 25 colony forming units (CFU) per sample area for both stainless steel and painted wallboard. CONCLUSIONS: The swab sample collection method may be appropriate for small area sampling (10 -25 cm2) with a high agent concentration, but has limited value for large surface areas with a low agent concentration. The results of this study provide information necessary for the interpretation of swab environmental sample collection data, that is, positive swab samples are indicative of high surface concentrations and may imply a potential for exposure, whereas negative swab samples do not assure that organisms are absent from the surfaces sampled and may not assure the absence of the potential for exposure. SIGNIFICANCE AND IMPACT OF THE STUDY: It is critical from a public health perspective that the information obtained is accurate and reproducible. The consequence of an inappropriate public health response founded on information gathered using an ineffective or unreliable sample collection method has the potential for undesired social and economic impact.