Stochastic approach to determine spatial patterns of lizard community on a desert island

One of the principal sources of error in identifying spatial arrangements is autocorrelation, since nearby points in space tend to have more similar values than would be expected by random change. When a Markovian approach is used, spatial arrangements can be measured as a transition probability between occupied and empty spaces in samples that are spatially dependent. We applied a model that incorporates first-order Markov chains to analyse spatial arrangement of numerical dominance, richness, and abundance on a lizard community at different spatial and temporal scales. We hypothesized that if a spatial dependence on abundance and richness exists in a diurnal desert community, then the Markov chains can predict the spatial arrangement. We found that each pair of values was dependent only on its immediate predecessor segment. In this sense, we found intergeneric differences at temporal and spatial scales of recurrence estimates. Also, in desert scrub, species show higher spatial aggregation and had lower species richness than at the island level; the inverse pattern occurred on rocky hillsides. At the species level, Uta stansburiana is the most abundant species in desert scrub, while Sauromalus slevini is the most abundant species on rocky hillsides. This report attempts to understand, using Markovian spatial models, the effect of nearby samples on local abundance and richness on different scales and over several seasons.     

Patchy recruitment patterns in marine invertebrates: a spatial test of the density-dependent hypothesis in the bivalve Spisula ovalis

Density-dependent and density-independent processes have been shown to influence the population dynamics of marine invertebrates, especially recruitment. However, their relative importance has not been evaluated in natural populations. High adult densities have been suggested to inhibit recruitment, especially in suspension-feeders which may ingest incoming larvae. Age structure and juvenile abundance were investigated in the bivalve Spisula ovalis in order to evaluate the importance of density dependence in generating spatial patterns. Age structure is readily established in this species owing to annual shell lines. An extensive sample (from about 100 sites a few hundred meters apart over 4 consecutive years) was analyzed in the statistical framework of spatial analyses, avoiding spurious correlations due to non-independence between neighboring sites. The area studied supports about ten annual cohorts, though only a few occur at each site. The overall picture is a mosaic of kilometer-scale patches of contrasted age structures, as revealed by highly significant spatial autocorrelations. To our knowledge, such large-scale spatial patterns in age structure have not previously been described in benthic invertebrates. Strong patterns are detected even for juveniles, and are independent of the adult biomass present before settlement. Therefore, patchy patterns of age structure mainly reflect density-independent effects, such as spatial variations in larval supply, passive transport of juveniles, or predation on recruits. In the absence of detailed spatial analyses, such patterns have been misinterpreted previously as negative effects of adult density on settlement success. Received: 21 November 1996 / Accepted: 20 February 1997     

Spatio-temporal distribution of Ricania shantungensis (Hemiptera: Ricaniidae) in chestnut fields: Implications for site-specific management

Chestnut is one of most important forest products in Korea. However, Ricania shantungensis, an invasive species, has been increasingly causing economic damage to chestnut. To increase management efficiency of R. shantungensis in chestnut fields, its spatio-temporal distributions were analyzed using spatial analysis by distance indices (SADIE) and semivariogram. Experiments were conducted by observing selected, marked, and geo-referenced trees in two commercial chestnut fields for each developmental stage (i.e., spring egg, nymph, adult, and fall egg) of R. shantungensis from 2017 to 2019. Spatial distributions of R. shantungensis were statistically (P < 0.05) aggregated except for its nymphal stage. Spatial associations of its distributions also showed the statistically (P < 0.05) positive associations regardless of years or developmental stages except for the spatial relationship between egg and nymphal stages. These results indicated that site-specific management for R. shantungensis would be applicable. In application of site-specific management for R. shantungensis, the distance of spatial dependence for nymphs, 60 m, should be considered to minimize reoccurrence possibility and additional samplings. Incorporating site-specific management into pest control program of R. shantungensis could increase its control efficiency in chestnut fields.     

Tests for density dependence

Several statistical tests for density dependence have been proposed in the literature, and so in any practical case the question poses itself which one of these tests to choose. This paper offers a few remarks additional to those made by Fox and Ridsill-Smith (1995) and others. Parametric statistical tested are based on a fully specified mathematical model. Examples of such tests are Bulmer's (1975) first test, and the test of Dennis and Taper (1994). Distribution-free tests are based on far less stringent assumptions. An example of such a test is the one proposed by Pollard et al. (1987). The choice between parametric tests can best be made by considering which one of the underlying mathematical models ist most plausible. If all models are almost equally plausible, considerations of computational requirement and ease of application may be important. Strong doubts concerning the plausibility of mathematical models may lead one to prefer a distribution-free test. An important feature of any test is its power, i.e. the probability of its rejecting the null hypothesis when this hypothesis is not true. Other things being equal, tests are preferable when they have superior powers. But power of a test depends on the true state of nature, and the only way to study power quantitatively is by assuming some mathematical model as approximately representing this true state. As any mathematical model can at best only be an approximation to the situation in nature, a mathematical model and the statistical tests based on it should be robust against small deviations from model assumptions. Solow (1990) showed that Bulmer's test is not robust with respect to the assumption that the residuals in the underlying autoregression model be stochastically independent. Contrary to what was suggested by Fox and Ridsill-Smith (1995), who misinterpreted some statements in Reddingius (1990), the present author thinks this is a serious shortcoming of this test since an ecologist cannot assume a priori that important density-independent ecological factors are not somehow serially correlated. Moreover, he is rather sceptical about the usefulness of statistical tests for density dependence. They have contributed more to misunderstandings than to a significant increase in ecological insight. In any case, statistical tests are designed to test hypotheses that are stated before data are collected, and the question which test to use also has to be answered before the data have been collected. Designing and using statistical tests a posteriori to detect things in data mainly leads to confusion and controversy.     

宝天曼国家级自然保护区落叶阔叶林密度制约效应对树木存活的影响

密度制约对物种共存起着重要作用。随着密度制约效应研究的深入, 亲缘关系较近的物种间表现出的密度制约效应逐渐被人们认识。本研究基于2009和2014年对宝天曼1 ha落叶阔叶林样地的2次调查数据, 利用广义线性混合模型分析了重要值排名前11位的物种不同邻域尺度的密度制约效应对不同径级(小径级(1 cm ≤ DBH < 5 cm)、中径级(5 cm ≤ DBH < 10 cm)、大径级(DBH ≥ 10 cm))目标个体存活的影响。研究表明: (1) 5年间样地中DBH ≥ 1 cm的所有个体的年均死亡率和增员率分别为5.85%和0.27%; (2)有5个物种的个体存活率与同种邻体个体数及同种邻体胸高断面积显著负相关; (3)小径级个体的存活在5 m的邻域范围内受同种密度制约和谱系密度制约的影响都很显著; 中径级个体在3个尺度上受到的密度制约和谱系密度制约的影响都不大; 大径级个体在7.5 m、10 m邻域范围内受谱系密度制约影响显著。结果表明, 同种密度制约和谱系密度制约效应对宝天曼落叶阔叶林不同生长阶段的树木个体影响不同。     

Moment Equations and Dynamics of a Household SIS Epidemiological Model

An SIS epidemiological model of individuals partitioned into households is studied, where infections take place either within or between households, the latter generally happening much less frequently. The model is explored using stochastic spatial simulations, as well as mathematical models which consist of an infinite system of ordinary differential equations for the moments of the distribution describing the proportions of individuals who are infectious among households. Various moment-closure approximations are used to truncate the system of ODEs to finite systems of equations. These approximations can sometimes lead to a system of ill-behaved ODEs which predict moments which become negative or unbounded. A reparametrization of the ODEs is then developed, which forces all moments to satisfy necessary constraints.Changing the proportion of contacts within and between households does not change the endemic equilibrium, but does affect the amount of time it takes to approach the fixed point; increasing the proportion of contacts within households slows the spread of the infection toward endemic equilibrium. The system of moment equations does describe this phenomenon, although less accurately in the limit as the proportion of between-household contacts approaches zero. The results indicate that although controlling the movement of individuals does not affect the long-term frequency of an infection with SIS dynamics, it can have a large effect on the time-scale of the dynamics, which may provide an opportunity for other controls such as immunizations to be applied.     

Density dependence of Anaphes sordidatus (Hymenoptera: Mymaridae) parasitism on eggs of Listronotus oregonensis (Coleoptera: Curculionidae)

Listronotus oregonensis (LeConte) (Coleoptera: Curculionidae) oviposits in carrot leaves and the larvae feed in carrot roots. Its eggs are parasitized by Anaphes sordidatus (Girault) (Hymenoptera: Mymaridae) throughout its oviposition period. This parasitoid is the major biotic mortality factor for L. oregonensis. Parasitism by A. sordidatus was studied for three years in sequentially sown plots of carrots, Daucus carota var. sativa. Over the scason, significantly fewer L. oregonensis eggs were oviposited in later sown carrots than in earlier sown carrots because oviposition started later in late sown plots of carrots. A positive temporal density-dependent relationship was observed each year between parasitism rates and host densities. This positive density dependence occurred in early and mid-summer for earlysown carrots where host density reached 1–2 host eggs per plant but disappeared in late summer when host density decreased while parasitism remained high. Latesown carrots had low host egg density (0.2 host egg per plant) and contributed little to the total number of eggs. In these late sown plots, parasitism increased rapidly to over 80% but no density dependence was observed. Spatially, few statistically significant regressions were found but all indicated a positive spatial density-dependence. Most non-significant regressions occurred because the range of egg density was too small between plots for a given date.     

Interrelations between the efficiency of translation start sites and other sequence features of yeast mRNAs

The translation start site (TSS) plays an important role in the control of the translational efficiency and cytoplasmic stability of eukaryotic mRNAs. The efficiency of TSS recognition is known to be influenced by sequence context, and mRNAs with weak TSSs are relatively abundant. We analyzed a sample of 4113 yeast genes in a search for features that might serve to compensate for the inefficient recognition of weak TSSs by initiating ribosomes. The first feature found to correlate with variations in TSS strength is differences in the stability of secondary structure upstream and downstream of the start AUG codon. The second feature concerns the characteristics of AUG triplets found at the beginning of the coding sequence, i.e., downstream of the predicted TSS. In particular, the proximal downstream AUG lies in frame with the CDS significantly more often if the TSS itself is located in a weak context. The accuracy of TSS annotation, the possibility of polypeptide heterogeneity due to the use of alternative downstream AUGs, and the influence of related features of mRNA sequences are discussed.Communicated by C. P. Hollenberg     

Gene flow in maize fields with different local pollen densities

The development of maize (Zea mays L.) varieties as factories of pharmaceutical and industrial compounds has renewed interest in controlling pollen dispersal. The objective of this study was to compare gene flow into maize fields of different local pollen densities under the same environmental conditions. Two fields of approximately 36 ha were planted with a nontransgenic, white hybrid, in Ankeny, Iowa, USA. In the center of both fields, a 1-ha plot of a yellow-seeded stacked RR/Bt transgenic hybrid was planted as a pollen source. Before flowering, the white receiver maize of one field was detasseled in a 4:1 ratio to reduce the local pollen density (RPD). The percentage of outcross in the field with RPD was 42.2%, 6.3%, and 1.3% at 1, 10, and 35 m from the central plot, respectively. The percentage of outcross in the white maize with normal pollen density (NPD) was 30.1%, 2.7%, and 0.4%, respectively, at these distances. At distances greater than 100 m, the outcross frequency decreased below 0.1 and 0.03% in the field with RPD and NPD, respectively. A statistical model was used to compare pollen dispersal based on observed outcross percentages. The likelihood ratio test confirmed that the models of outcrossing in the two fields were significantly different (P is practically 0). Results indicated that when local pollen is low, the incoming pollen has a competitive advantage and the level of outcross is significantly greater than when the local pollen is abundant. This journal paper of the Iowa Agricultural and Home Economics Experiment Station, Ames, Iowa, Project No. 3638, was supported by Hatch Act, State of Iowa fund and by a USDA-CREES BRA Grant.     

A statistical geometrical description of the human liver for probabilistic occupant models

Realistic numerical assessments of liver injury risk for the entire occupant population require incorporating inter-subject variations into numerical models. Statistical shape models of the abdominal organs have been shown to be useful tools for the investigation of the organ variations and could be applied to the development of statistical computational models. The main objective of this study was to establish a standard procedure to quantify the shape variations of a human liver in a seated posture, and construct three-dimensional (3D) statistical shape boundary models.     

Detecting clinal and balanced selection using spatial autocorrelation analysis under kin-structured migration

Recently spatial autocorrelation has been employed to infer microevolutionary processes from patterns of genetic variation. In theory, different processes should show characteristic signature correlograms; e. g., clinal selection should produce correlograms decreasing from positive to negative autocorrelation, whereas uniform balanced selection should lead to no spatial autocorrelation. The ability of a statistical method such as spatial autocorrelation analysis to distinguish between these selective regimes or even to detect departures from neutrality is dependent on the strength of the evolutionary force and the population structure. Weak selection or migration will not be apparent against the expected background of stochastic noise. Moreover, the population structure may generate sufficient stochastic variation such that even strong evolutionary forces may fail to be detected. This study uses computer simulation to examine the effects of kin-structured migration and three different selective regimes on the shape of spatial correlograms to assess the ability of this technique to detect different microevolutionary processes. Genetic variation among 8 loci is simulated in a linear set of 25 artificial populations. Kin-structured stepping-stone migration among adjacent populations is modeled; directional, balanced, and clinal selection, as well as neutral loci are considered. These experiments show that strong selection produces correlograms of the predicted shape. However, with an anthropologically reasonable population structure, considerable stochastic variation among correlograms for different alleles may still exist. This suggests the need for caution in inferring genetic process from spatial patterns. © 1994 Wiley-Liss, Inc.     

肿瘤表达谱基因芯片数据的混合效应模型分析

目的:研究混合效应模型(Mixed Effects Model)在肿瘤表达谱基因芯片数据分析中的检验效能,并探讨其分析效果。方法:采用混合效应模型分析肿瘤实例基因芯片数据,并以基因集富集分析方法(GSEA)作为参照比较分析结果的有效性和科学性,探讨其检验效果。结果:通过混合效应模型和基因集富集分析(GSEA)两种方法对肿瘤基因芯片数据的分析和比较,两种方法筛选出共同的差异表达通路外,混合效应模型额外地筛选出来GSEA未能检验到的8条差异表达通路,且得到文献支持;混和效应模型筛选出的前10个差异表达通路中有6个已有生物学证明而基因集富集分析方法(GSEA)筛选出的前10个差异表达通路中仅有4个已有生物学证明。结论:混合效应模型作为top-down方法中的典型代表,其优势在于通过构建潜变量达到降维目的,可有效地减少多个复杂的变异来源从而保证了结果的准确性和科学性,其检验效能优于基因集富集分析方法(GSEA),是一种行之有效的筛选肿瘤基因芯片数据的分析方法。