Sequential stopping rules for species accumulation

Identifying and counting the total number of biological species observed to date, and plotting versusa measure of the effort used to record them, gives rise to a species accumulation curve. Interest typically is concerned with estimating the total number of species in the area of study, having observed only the accumulation curve, having no information on species frequencies. This article considers the problem of optimally stopping the sampling process. We use a sequential procedure with a fixed maximum horizon for accumulation. A utility function based on the number of new species to be observed and the effort saved from the maximum horizon is adopted, and a workable algorithm based on backward induction is obtained. An example in accumulation of bat species is also presented.     

Statistical analysis of interactive cytotoxicity in human epidermal keratinocytes following exposure to a mixture of four metals

Exposure to mixtures of chemicals is an important and relevant environmental issue. Of particular interest is the detection and characterization of departure of biological effects from additivity. Methodology based on the assumption of additivity is used in fitting single-chemicaldata. Interactionsare determined and characterized by making comparisons between the observed and predicted responses at mixtures along a fixed ratio ray of the component substances. Two simultaneous tests are developed for testing for any departure from additivity. Multiple comparisons procedures are used to compare observed responses to that predicted under additivity. A simultaneous confidence band on the predicted responses along the mixture ray is also developed. The methods are illustrated with cytotoxicity data that arise when human epidermal keratinocytes are exposed to a mixture of arsenic, chromium, cadmium, and lead. Synergistic, antagonistic, and additive cytotoxicities were observed at different dose levels of the four-metal mixture.     

Inference and model comparison for species accumulation functions using approximating pure birth processes

Soberon and Llorente proposed using the mean S(t; ϕ) of a pure birth process as a model for species accumulation functions and obtained ordinary least squares point estimates for the vector of parameters ϕ. They provided useful biological interpretations for S(t; ϕ) as well as for the birth rates of the process; they also expressed the strong need for an objective tool to compare different models for a given species accumulation data set. We show that the functions S(t; ϕ) proposed by Soberon and Llorente are generally not means of pure birth processes but that they can be well approximated by the mean of a suitable nonhomogeneous pure birth process B(t). We suggest using S(t; ϕ) and an upper bound for the (unknown) variance of the approximating pure birth process to make statistical inferences about ϕ. A nonlinear regression model with mean S(t; ϕ) and normal errors, possibly correlated, is proposed using a likelihood approach. This model can be compared with other relevant models under consideration by means of their corresponding likelihood ratio, providing a useful, objective, and quantitative tool for comparing different models in the light of the observed data. The suggested approach is exemplified with two species accumulation data sets.     

Quantifying conservation concern - Bayesian statistics, birds and the red lists

For species that are still widespread, obtaining accurate and precise measures of population change inevitably means gathering representative sample data rather than undertaking a complete census. In the UK, a system of raising ‘alerts’ utilises stochastic models for such data to identify species in rapid (>50%) or moderate (25-50%) decline across various temporal and spatial scales. Considerable improvements in interpretation can be made by explaining annual fluctuations in terms of explicit population models (rather than trends of an arbitrary mathematical form); through the simultaneous modelling of data from a complete or partial census with those providing information on the demographic rates employed in these models; and through adopting a Bayesian rather than a frequentist statistical approach. A Bayesian approach is natural for quantifying, in the form of a probability, the support provided by the data for assigning a species to each of the categories. Based on territory mapping and ringing data for the lapwing Vanellus vanellus, we describe such an approach. Trends are estimated more precisely than those under models previously employed in the alerts context. Some smoothing is induced, but realistic responses to years of severe weather are retained, and these are expressed also via model-averaged trends in key demographic parameters. We discuss the conservation implications for this declining species, and the wider potential arising from the ability to quantify confidence that population change has exceeded a threshold either generating conservation concern or justifying a subsequent programme of action for recovery.     

北京山区典型人工林的耗水规律

在我国的北方地区植被与水资源之间的关系是森林植被构建的关键性问题.如何依据水分条件的承载力,构建水分稳定的森林植被是一项重要研究.以北京妙峰山侧柏、油松为研究对象,应用大型可称量式蒸渗仪测定林木个体耗水规律,并在此基础上进行尺度扩展,分析2种林分群体耗水特征.研究发现：在晴天条件下,侧柏和油松蒸腾强度的日变化趋势均为单峰曲线;在典型阴天和雨天条件下,2树种间蒸腾速率差异明显,受云量动态变化影响,蒸腾强度的日变化趋势为多峰曲线.通过相关分析发现,在选定的环境因子中太阳辐射通量、大气水汽压饱和差、空气温度、土壤含水率和土壤水势均与林木蒸腾速率呈正相关,而空气相对湿度与林木蒸腾速率呈负相关.另外,利用边材面积作为尺度转换因子实现由单木到林分的尺度扩展,根据测定的样木蒸腾量,推算得出侧柏林6-9月总蒸腾量为321.43 mm,油松林的总蒸腾量为192.83 mm.     

含砷鸡粪施肥后对青菜和番茄植株中砷富集的影响

利用给鸡饲喂50mg·kg-1和80mg·kg-1洛克沙生得到的鸡粪进行盆栽试验,研究两种含砷鸡粪对青菜和番茄中砷含量、砷富集因子的影响。结果表明,含砷鸡粪施肥后青菜和番茄植株中砷含量均明显提高;青菜砷含量、砷富集因子高于番茄植株,青菜有明显的砷富集作用;番茄植株中砷含量与其生物量呈负相关、未表现出对砷的富集作用。不同种属蔬菜在含砷鸡粪施肥后对砷有不同的摄入,青菜对砷有明显的富集现象,提示青菜在含砷鸡粪施肥后砷水平有较大影响,存在着砷超标风险。     

东南烟稻轮作区烤烟临界氮浓度稀释曲线的建立与验证

  【目的】  建立东南烟稻轮作区烤烟临界氮稀释曲线,探讨氮素营养指数用于诊断和评价烤烟氮营养状况的可能性,为实现烤烟合理施用氮肥提供理论依据。  【方法】  两年两地共3个田间氮肥用量试验,每个试验共设6个氮水平 (N 0、45、90、135、180 和300 kg/hm2),分析不同施氮量对移栽后不同天数烤烟地上部和叶片干物质积累量的影响。利用不同时期植株氮浓度和干物质积累量,建立地上部和叶片的临界氮浓度稀释曲线方程和干物质积累方程。结合基于无人机可见光谱平台的烤烟氮浓度无损测定方法,计算氮营养指数,判断烤烟氮营养丰缺情况。  【结果】  施用氮肥明显增加了烤烟地上部和叶片干物质积累量,不同氮肥处理间差异明显,烤烟地上部和叶片氮浓度随烤烟生长进程而降低;东南烟稻轮作区烤烟地上部及叶片的临界氮素浓度和干物质积累量符合幂指数的关系;模型进行独立验证时,氮限制组的数据均在临界氮素稀释曲线以下,而不受氮限制组的数据均在临界氮素稀释曲线附近。模型拟合的临界氮浓度和植株实际临界氮浓度呈线性相关,地上部和叶片的RMSE值分别为0.55和0.44,标准化均方根误差n-RMSE分别为25%和17%,模型具有较好的稳定性;烤烟氮素营养状况的判定可以通过应用临界氮浓度稀释曲线计算氮营养指数(NNI)实现。随着施氮水平的提高,叶片氮营养指数逐步升高,在氮施用量达到135 kg/hm2,叶片氮营养指数可在1以上,处于氮盈余状态。  【结论】  东南烟稻轮作区烤烟叶片临界氮素稀释曲线模型(N_c = 3.2339 × DM_leaves–0.475)和叶片氮营养指数能够诊断评价该区域烤烟氮营养状况,从而为优化烤烟的氮素管理提供指导。     

U1 and U2 small nuclear RNA genetic linkage: a novel molecular tool for identification of six sole species (Soleidae, Pleuronectiformes)

We evaluated the usefulness of a genetic linkage between the U1 and U2 small nuclear RNAs for species identification. Six soles belonging to the genera Solea, Dicologlossa, and Microchirus were studied. A simple methodology based on two single PCRs is described. Reproducible band profiles were generated for all samples. This rapid and discriminatory molecular method is highly promising for determining the authenticity of sole fillets in the food industry.     

黄土旱塬不同氮肥用量下冬小麦干物质累积和氮素吸收利用过程研究

利用旱作长期定位施肥试验研究了不同氮肥用量对冬小麦干物质累积和氮素吸收利用的影响,结果显示,不同处理下干物质累积变化趋势都呈"S"型曲线,且冬小麦各生育期干物质量,随氮肥用量的增加而增大,说明氮肥对促进冬小麦干物质累积作用显著。干物质累积速率均呈现明显的单峰曲线,拔节-灌浆阶段累积速率最大,是干物质累积的重要时期。小麦植株含氮量和氮素累积量都随氮肥用量增加而升高,在冬前-拔节期和开花-灌浆期两个阶段,冬小麦植株氮素累积量较大,累积速率快,是氮素吸收利用的两个关键阶段。     

The impact of exposure to a mixture of eighteen polyhalogenated aromatic hydrocarbons on thyroid function: Estimation of an interaction threshold

When an interaction has been detected among the chemicals in a mixture, it may be of interest to predict the interaction threshold. A method is presented for estimation of an interaction threshold along a mixture ray which allows differences in the shapes of the dose-response curves of the individual components (e.g., mixtures of full and partial agonists with differing response maxima). A point estimate and confidence interval for the interaction threshold may be estimated. The methods are illustrated with data from a study of a mixture of 18 polyhalogenated aromatic hydrocarbons (PHAHs) in rats exposed by oral gavage for four consecutive days. Serum total thyroxine (T4) was the response variable. Previous analysis of these data demonstrated a dose-dependent interaction among the 18 chemicals in the mixture, with additivity suggested in the lower portion of the dose-response curve and synergy (greater than additive response) in the higher portion of the dose-response curve. The present work builds on this analysis by construction of an interaction threshold model along the mixture ray. This interaction threshold model has two components: an implicit additivity region and an explicit region that describes the departure from additivity; the interaction threshold is the boundary between the two regions. Estimation of the interaction threshold within the observed experimental region suggested evidence of additivity in the low dose region. Total doses of the mixture that exceed the upper limit of the confidence interval on the interaction threshold were associated with a greater-than-additive interaction.     

Multiple Comparisons for Multiple Endpoints in Agricultural Experiments

Agricultural experiments often have a completely randomized design, and multiple, correlated variables are measured. This paper addresses an appropriate statistical evaluation. A multivariate t-distribution is used for the calculation of multiplicity-adjusted p-values and simultaneous confidence intervals. The number of the multiple variables as well as their correlations are taken into account this way. We consider ratios of means instead of differences, and comparisons versus the overall mean instead of all-pair comparisons. A data set from a greenhouse experiment with glucosinolates of several cultivars of Chinese cabbage (Brassica rapa subsp. pekinensis) is used as an example. Related code based on the R-package SimComp is presented. This package allows a wide application in many agricultural experiments with a similar design.     

关中平原夏玉米临界磷浓度稀释曲线构建与磷营养诊断

  【目的】  通过分析不同施磷水平下夏玉米地上部生物量与其植株磷浓度的变化关系,构建临界磷浓度稀释曲线模型,为夏玉米磷素优化管理及磷营养诊断提供理论基础。  【方法】  2019—2020年在陕西关中平原,以两个玉米品种郑单958和豫玉22为试验材料进行田间定位试验。共设4个施磷量处理 (P₂O₅):0、60、120、180 kg/hm2。在夏玉米拔节期、抽雄期、灌浆期和成熟期进行地上部取样,分析夏玉米地上部干物质量、全磷含量以及产量。利用2019年试验数据构建夏玉米临界磷浓度稀释曲线模型和磷素营养指数,利用2020年数据对模型进行验证。  【结果】  增施磷肥能显著提高夏玉米产量、地上部生物量和植株磷浓度,两个品种之间没有显著差异。随施磷水平的提高,夏玉米产量表现为先增加后减少,P120处理可获得最高产量,产量效应方程显示两年两个品种夏玉米平均理论最高产量对应的施磷量为110.2 kg/hm2。由产量构成要素看出,施磷对穗数没有显著影响,但能显著提高穗粒数和百粒重,且施磷对玉米穗粒数的影响大于对百粒重的影响。地上部生物量表现为P0c) 变化曲线:P_c = 8.11DM?0.22 (R2 = 0.886)。模型拟合的植株磷浓度和2020年玉米实际磷浓度线性相关,稀释曲线模型的RMSE和n-RMSE分别为1.146和18.23%,说明模型具有较好的稳定性。基于临界磷浓度稀释曲线计算磷营养指数 (PNI),各生育时期PNI值随磷肥用量增加而增大,随生育进程推进呈现先升高后降低趋势。PNI与相对吸磷量 (RP_upt)、相对地上部生物量 (RDW) 和相对产量 (RY) 均呈极显著相关。  【结论】  本研究建立的夏玉米临界磷浓度稀释曲线和磷营养指数 (PNI)模型能够很好地预测植株不同生育时期的磷素盈亏状况,对指导夏玉米生长季磷素营养诊断及最佳磷肥施用量具有可行性。     

Collision probabilities for AFLP bands,with an application to simple measures of genetic similarity

AFLP is a frequently used DNA fingerprinting technique that is popular in the plant sciences. A problem encountered in the interpretation and comparison of individual plant profiles, consisting of band presence-absence patterns, is that multiple DNA fragments of the same length can be generated that eventually show up as single bands on a gel. The phenomenon of two or more fragments coinciding in a band within an individual profile is a type of homoplasy, that we call collision. Homoplasy biases estimates of genetic similarity. In this study, we show how to calculate collision probabilities for bands as a function of band length, given the fragment count, the band count, or band lengths. We also determine probabilities of higher order collisions, and estimate the total number of collisions for a profile. Since short fragments occur more often, short bands are more likely to contain collisions. For a typical plant genome and AFLP procedure, the collision probability for the shortest band is 25 times larger than for the longest. In a profile with 100 bands a quarter of the bands may contain collisions, concentrated at the shorter band lengths. All calculations require a careful estimate of the monotonically decreasing fragment length distribution. Modifications of Dice and Jaccard coefficients are proposed. The principles are illustrated on data from a phylogenetic study in lettuce.     

A New Approach to Modelling the Relationship Between Annual Population Abundance Indices and Weather Data

Weather has often been associated with fluctuations in population sizes of species; however, it can be difficult to estimate the effects satisfactorily because population size is naturally measured by annual abundance indices whilst weather varies on much shorter timescales. We describe a novel method for estimating the effects of a temporal sequence of a weather variable (such as mean temperatures from successive months) on annual species abundance indices. The model we use has a separate regression coefficient for each covariate in the temporal sequence, and over-fitting is avoided by constraining the regression coefficients to lie on a curve defined by a small number of parameters. The constrained curve is the product of a periodic function, reflecting assumptions that associations with weather will vary smoothly throughout the year and tend to be repetitive across years, and an exponentially decaying term, reflecting an assumption that the weather from the most recent year will tend to have the greatest effect on the current population and that the effect of weather in previous years tends to diminish as the time lag increases. We have used this approach to model 501 species abundance indices from Great Britain and present detailed results for two contrasting species alongside an overall impression of the results across all species. We believe this approach provides an important advance to the challenge of robustly modelling relationships between weather and species population size.Supplementary materials accompanying this paper appear online.     

Comparing pivotal and REML-based confidence intervals for heritability

Heritability quantifies the extent to which a physical characteristic is passed from one generation to the next. From a statistical perspective, heritability is the proportion of the phenotypic variance attributable to (additive) genetic effects and is equal to a function of variance components in linear mixed models. Relying on normal distribution assumptions, one can compute exact confidence intervals for heritability using a pivotal quantity procedure. Alternatively, large-sample properties of the restricted maximum likelihood (REML) estimator can be used to construct asymptotic confidence intervals for heritability. Exact and asymptotic intervals are compared loineye muscle area measurements and balanced one-way random effects models having groups of correlated responses. In some cases the two interval methods yield vastly different results and the REML-based confidence interval does not maintain the nomiral coverate value even for seemingly large sample sizes. For finite sample size applications, the validity of the REML-based procedure depends on the correlation structure of the data.     

Metal Accumulation by Woody Species on Contaminated Sites in the North of France

Metal accumulation was investigated in a range of woody species that were planted on Cd-, Zn- and Pb- polluted sites in North of France. The study is unique in that we directly compare a large number of woody species (25). The highest accumulation of Zn and Cd was found in the Salicaceae family members with up to 950 mg Zn kg^?1 dry weight (DW) and 44 mg Cd kg^?1 DW in leaves of Populus tremula × Populus tremuloides. Zn content was positively correlated with Cd content, both in leaves and stems. Pb concentration was generally low and was species-independent. Oak and birch species accumulated more Mn as compared to other woody species. A seasonal variation in metal accumulation could be found. Although soil compositions and metal bioavailabilities differed amongst the experimental sites chosen in this study, variation of metal concentrations within a given species was small. High bioconcentration factors for poplar and willow suggested the high potential of these species over other woody species for metal accumulation. Taken together, these data suggest that poplar and willow species are good candidates for phytoremediation programmes.     

Using compiled species lists to make biodiversity comparisons among regions: A test case using Oregon butterflies

We explore two methods that correct for differential sampling effort when estimating the true number of species in a region based on samples such as those typically recorded in museum or conservation databases. The two methods are: (1) a phenomenological model that relies on a saturating sampling curve; and (2) a model based on a lognormal distribution of species abundances. We test these methods using a database for the butterflies of Oregon and find that the distribution of high-diversity areas, using the estimated, or “asymptotic”, diversities, is strikingly different from the geographic pattern one would deduce if the raw data were used, without correcting for differential sampling effort. Further, we show that differences in accuracy exist between the two estimation procedures, and that these differences are aggravated at small sample sizes; we argue that estimates based on the lognormal distribution should be preferred because they can offer substantial improvement over analyses based solely on the raw data, generally without risking overestimation. Lastly, using both the database and estimated values of butterfly diversity, we show that the distribution of endangered and numerically rare butterflies rarely coincides with “hotspots” or centers of biodiversity. Thus, protecting regions of Oregon rich in overall butterfly diversity will not normally protect the bulk of rare or endangered butterfly species.     

Large-sample pairwise comparisons among multinomial proportions with an application to analysis of mutant spectra

In studies examining patterns of mutational damage, the primary variables of interest are expressed typically as discrete counts within defined categories of damage. The multinomial distribution is a common model for such data settings. Of interest is statistical comparison of the pattern, or spectrum, of mutation among the various mutant categories. A specific question in such instances is the identification of differences among the spectral categories, identified, e.g., via simultaneous confidence intervals for pairwise differences in or ratios of the multinomial response probabilities. Herein, a selection of possible methods for constructing such intervals is described and compared via computer simulations to determine which are most appropriate for practical use in the evaluation of mutant spectra.     

Analysis of a moisture characteristic curve employing a crystalline lattice of capillary pores

The conventional method used to investigate the pore structure of a core of wet sand is to construct a moisture characteristic curve. The plot summarizes the dimensionless volume obtained from the sample at a given suction pressure. We assume here that pore diameters are selected from an arbitrary normal distribution. The problem of estimating the parameters of this distribution reduces to the solution of a quadratic equation and substitution of the resulting value into a polynomial. There is no necessity to plot the characteristic curve, the only values being needed are the first two moments of the raw distribution.     

Composite sampling enhances the confidence of soil microarthropod abundance and species richness estimates

The quantification of abundance and species richness of soil microarthropods is most often severely hindered by extraordinary data variability, highly skewed frequency distributions, many extreme and zero counts, and small sample sizes. We developed a composite sampling technique to enhance the confidence of abundance and species richness estimates. Many soil cores (n ≥ 100) are sampled, animals extracted, the extracts pooled, mixed, and subsamples (aliquots) taken. Compared to the standard (separate sampling units), no microarthropods were lost or mechanically damaged during the compositing procedure. The confidence of abundance estimates was substantially greater in the composite than in the standard, although not for taxa of low abundance (< ≈ 10³ ind.m⁻²). Moreover, compositing was the superior technique in estimating species richness. The number of sampling units needed to recover a certain number of species with the composite was 70% of the standard method. We conclude that composite sampling is a promising alternative to the standard technique and may help to increase the generally low confidence of microarthropod field data. Finally, potential limitations of composite plans are discussed: a great number of field cores from an unbiased sampling plan have to be composited; comparisons between composites of unequal size should be avoided; all information on the variation among field cores is lost by compositing; parallel measurements of fauna and other variables in the same cores are not possible.