On probability limits in snowball sampling

The limits on probabilities under which usual sampling model is to be preferred over binomial sampling model have been worked out.     

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.     

Plant-parasitic Nematode Distributions in an Alfalfa Field

A 7-ha alfalfa field (Medicago saliva L. cv Mesa Sirsa) was sampled systematically on a 6 x 6-m grid by removing individual cores (2.54 cm diam) to a depth of 45 cm from each of the 1,936 grid intersections. The soil was mainly coarse-textured with a fine-textured streak running centrally, north to south. Nematodes were extracted by a semiautomatic elutriator and sugar flotation-sieving technique. Five plant-parasitic species were consistently present: Meloidogyne arenaria, Pratylenchus minyus, Merlinius brevidens, Helicotylenchus digonicus, and Paratrichodorus minor. All species had a highly skewed nonnormal frequency distribution that departed significantly from randontness. Goodness-of-fit tests on the distribution of five populations in the entire field showed that three (Meloidogyne, Merlinius, and Helicotylenchus) were described by a negative binomial. When the samples were categorized by soil texture (coarse vs. fine-textured), all populations in the fine-textured areas, and three populations (Meloidogyne, Pratylenchus, and Merlinius) in the coarse areas, fitted a negative binomial distribution. Nearly all populations titted a negative binomial when the frequency distributions from randomly located one-meter-square areas were examined for each species.     

Using data from an encounter sampler to model fish dispersal

A method to estimate speed of free-ranging fishes using a passive sampling device is described and illustrated with data from the Everglades, U.S.A. Catch per unit effort (CPUE) from minnow traps embedded in drift fences was treated as an encounter rate and used to estimate speed, when combined with an independent estimate of density obtained by use of throw traps that enclose 1 m(2) of marsh habitat. Underwater video was used to evaluate capture efficiency and species-specific bias of minnow traps and two sampling studies were used to estimate trap saturation and diel-movement patterns; these results were used to optimize sampling and derive correction factors to adjust species-specific encounter rates for bias and capture efficiency. Sailfin mollies Poecilia latipinna displayed a high frequency of escape from traps, whereas eastern mosquitofish Gambusia holbrooki were most likely to avoid a trap once they encountered it; dollar sunfish Lepomis marginatus were least likely to avoid the trap once they encountered it or to escape once they were captured. Length of sampling and time of day affected CPUE; fishes generally had a very low retention rate over a 24 h sample time and only the Everglades pygmy sunfish Elassoma evergladei were commonly captured at night. Dispersal speed of fishes in the Florida Everglades, U.S.A., was shown to vary seasonally and among species, ranging from 0· 05 to 0· 15 m s(-1) for small poeciliids and fundulids to 0· 1 to 1· 8 m s(-1) for L. marginatus. Speed was generally highest late in the wet season and lowest in the dry season, possibly tied to dispersal behaviours linked to finding and remaining in dry-season refuges. These speed estimates can be used to estimate the diffusive movement rate, which is commonly employed in spatial ecological models.     

害虫防治决策的复序贯分析方法及抽样技术研究

复序贯抽样决策技术实际应用的受限 ,原因在于截止限序贯抽样模型的缺乏。本文在检验昆虫种群空间格局回归模型的基础上 ,推导出了目前国内常用检验回归模型的截止限序贯抽样模型 ,并将其运用于复序贯分析决策过程中。实例分析表明 ,对于同一种生物种群 ,在一定的精度 (D)和置信水平(tα)要求下 ,复序贯抽样决策技术可以大幅度地节约抽样成本     

Probabilistic Analysis Indicates Discordant Gene Trees in Chloroplast Evolution

Abstract Analyses of whole-genome data often reveal that some genes have evolutionary histories that diverge from the majority phylogeny estimated for the entire genome. We present a probabilistic model that deals with heterogeneity among gene trees, implement it via the Gibbs sampler, and apply it to the plastid genome. Plastids and their genomes are transmitted as a single block without recombination, hence homogeneity among gene trees within this genome is expected. Nevertheless, previous work has revealed clear heterogeneity among plastid genes (e.g., Delwiche and Palmer 1996). Other studies, using whole plastid genomes of various algae and land plants, found little additional heterogeneity (Martin et al. 1998; Adachi et al. 2000). We augment the earlier studies by using a data set of 14 taxa: 6 land plants, 2 green algae, a diatom, 2 red algae and a cryptophyte, the cyanelle of the glaucocystophyte Cyanophora, and the blue–green alga Synechocystis as an outgroup. Contrary to the earlier analyses, we cannot find even a single, dominant consensus tree. Therefore, we formulate a probabilistic model that divides the genes into two sets: those that follow the consensus tree and those that have independent gene trees. No particular tree is supported by more than three-fourths of the genes. But the set of genes that follows a certain tree is fairly independent of data processing and the method of analysis. With one possible exception, we find no evidence for collinear or functionally related genes to follow similar trees. The phylogenetic pattern also seems independent of bias in amino acid composition. Among possible explanations for the observed phenomenon, the hypothesis that different genes have different covarion structures is difficult to assess. But gene duplication may be possible through the inverted or direct repeat regions, while horizontal gene transfer seems less likely. In contrast to green algae and land plants, inverted repeat regions in red algae and in Cyanophora show abundant differences among the copies. Thus, genes may get duplicated when they are recruited into the inverted repeat region and one of the two copies may be lost after leaving the inverted repeat region.     

香蕉假茎象甲卵的空间格局研究

应用多种聚集度指标研究了香蕉假茎象甲卵在香蕉园的空间分布格局 ,结果表明该虫卵在所有密度下都是聚集分布 ,聚集程度与密度不相关 ,分布的基本成份是个体群。在空间格局研究基础上提出了理论抽样数公式 ,给出了不同密度下、不同误差要求的最适抽样数。     

A note on the accuracy of PAC-likelihood inference with microsatellite data

Stephens and Donnelly have introduced a simple yet powerful importance sampling scheme for computing the likelihood in population genetic models. Fundamental to the method is an approximation to the conditional probability of the allelic type of an additional gene, given those currently in the sample. As noted by Li and Stephens, the product of these conditional probabilities for a sequence of draws that gives the frequency of allelic types in a sample is an approximation to the likelihood, and can be used directly in inference. The aim of this note is to demonstrate the high level of accuracy of "product of approximate conditionals" (PAC) likelihood when used with microsatellite data. Results obtained on simulated microsatellite data show that this strategy leads to a negligible bias over a wide range of the scaled mutation parameter theta. Furthermore, the sampling variance of likelihood estimates as well as the computation time are lower than that obtained with importance sampling on the whole range of theta. It follows that this approach represents an efficient substitute to IS algorithms in computer intensive (e.g. MCMC) inference methods in population genetics.     

昆虫种群密度的二项抽样估计模型研究进展

昆虫种群密度的二项抽样估计模型主要有两类,一类是根据空间分布型理论演绎而来,另一类是根据样方中有虫样方比例或不大于某一阈值密度T头的样方比例与平均密度的经验关系拟合的．本文综述了这两类模型、模型的变异分析、模型的理论抽样数估计等方面的研究进展．     

稻田青翅蚁形隐翅虫成虫空间分布型和抽样模型的研究

稻田青翅蚊形隐翅虫成虫空间分布型测定结果表明：①频次分布检验为负二项分布;②聚集度指标测定为聚集分布;③m^n-m的线性回归方程为m^n=0．0099 2．4753m,表明属于具有公共K值的负二项分布．根据聚集均数(λ)测定结果,分析了聚集原因．在分布型研究基础上,探讨了资料代换模型、Kuno's种群序贯抽样模型和最适抽样数模型．     

An under-appreciated difficulty: sampling of plant populations for analysis using molecular markers

Results of studies using molecular markers for determining demographic and genetical population parameters especially in plants or sessile animals under field conditions are strongly dependent on the sampling strategy adopted. There are two critical decisions to make when determining this strategy: (i) what is the unit to be sampled?, (ii) how should units to be sampled in the field be selected? For the first decision, there are two conceptually different approaches: sampling ramets of clonal plants as units (to get information about within-genet parameters, such as genet sizes or numbers) and sampling genets of clonal or non-clonal plants as units (to get information of the genetic structure of the population). For the second decision, it is critically important to make the goal of the study explicit. We argue that in this case fully random sampling is needed only when an estimate of the true value of the population parameter is needed; if a comparison between populations is the goal, however, other sampling schemes may be adopted. The efficiency of different types of sampling strategies to recover relative values in a spatially extended population is studied by means of a spatially explicit simulation model. The results show that a regular pattern of sampling is best for obtaining information on genet sizes or inbreeding coefficients; in contrast, random or hierarchical sampling strategies are better for obtaining information on parameters that are based on comparison of pairs of individuals, such as distribution of genet sizes or autocorrelation in genetic structure. A set of recommendations is provided for designing a good sampling strategy.     

The zero-sum assumption in neutral biodiversity theory

The neutral theory of biodiversity as put forward by Hubbell in his 2001 monograph has received much criticism for its unrealistic simplifying assumptions. These are the assumptions of functional equivalence among different species (neutrality), the assumption of point mutation speciation, and the assumption that resources are continuously saturated, such that constant resource availability implies constant community size (zero-sum assumption). Here we focus on the zero-sum assumption. We present a general theory for calculating the probability of observing a particular species-abundance distribution (sampling formula) and show that zero-sum and non-zero-sum formulations of neutral theory have exactly the same sampling formula when the community is in equilibrium. Moreover, for the non-zero-sum community the sampling formula has this same form, even out of equilibrium. Therefore, the term "zero-sum multinomial (ZSM)" to describe species abundance patterns, as coined by Hubbell [2001. The Unified Neutral Theory of Biodiversity and Biogeography, Princeton University Press, Princeton, NJ], is not really appropriate, as it also applies to non-zero-sum communities. Instead we propose the term "dispersal-limited multinomial (DLM)", thus making explicit one of the most important contributions of neutral community theory, the emphasis on dispersal limitation as a dominant factor in determining species abundances.     

A simple lattice model that exhibits a protein-like cooperative all-or-none folding transition

In a recent paper (D. Gront et al., Journal of Chemical Physics, Vol. 115, pp. 1569, 2001) we applied a simple combination of the Replica Exchange Monte Carlo and the Histogram methods in the computational studies of a simplified protein lattice model containing hydrophobic and polar units and sequence-dependent local stiffness. A well-defined, relatively complex Greek-key topology, ground (native) conformations was found; however, the cooperativity of the folding transition was very low. Here we describe a modified minimal model of the same Greek-key motif for which the folding transition is very cooperative and has all the features of the "all-or-none" transition typical of real globular proteins. It is demonstrated that the all-or-none transition arises from the interplay between local stiffness and properly defined tertiary interactions. The tertiary interactions are directional, mimicking the packing preferences seen in proteins. The model properties are compared with other minimal protein-like models, and we argue that the model presented here captures essential physics of protein folding (structurally well-defined protein-like native conformation and cooperative all-or-none folding transition).     

利用分布有/无数据预测物种空间分布的研究方法综述

详细的物种地理分布信息是生态学研究和制定保护策略的基础。相比较于直接估测种群数量,获取物种分布的有/无数据更为实用。因此,利用分布有/无数据并结合环境变量建立模型预测物种空间分布的方法在近年来得到了长足发展,并被广泛应用。利用分布有/无数据预测物种分布,关键的步骤包括：1)构建总体概念模型,2)收集物种分布有/无数据,并准备环境变量图层;3)选择合适的统计模型和算法,以及4)对模型进行评估。概念模型提出研究假设,并确定数据收集及模型方法。收集物种分布数据有系统调查及非系统调查方法。筛选并准备与物种分布相关的环境变量,利用GIS工具处理,使之成为符合模型条件的具有合适的空间尺度的数字化图层。利用环境变量和物种分布有/无的数据,选择合适的方法及软件建立模型,并对模型进行检验和评估。我们总结了用于构建物种分布模型的不同算法和软件。本文将针对以上各个环节,阐述利用物种分布有/无数据进行研究所需要的技术细节,以期望为读者提供借鉴。