Counting by weighing and its effect on seed testing procedures

Counting by weighing is an approximate procedure for obtaining a given number of items based on an estimate of how much the items will weigh. The procedure can be considerably faster than exact counting. We show how the effects of counting by weighing can be assessed, using a particular problem in seed testing for illustration. We find that using counting by weighing in place of exact counting has little effect on the outcome of the seed test provided that the coefficient of variation of the individual seed weights is not too large, and provided a sufficiently large initial sample is used to estimate mean seed weight.     

Sampling procedures and species estimation: testing the effectiveness of herbarium data against vegetation sampling in an oceanic island

Questions: What is the relationship between species assemblages in herbarium collections and species abundances in the field, and how trustworthy are herbarium data in vegetation science? Location: Guadalupe Island, Baja California, Mexico. Methods: We compared species‐abundance distribution and evenness in 110 vegetation plots in Guadalupe Island against data from four herbaria. We tested whether the relative frequencies derived from herbarium specimens differed significantly from species frequencies in the field. We compared the rarefaction curves for both field and herbarium data sets, and tested whether taxonomic collectors accumulated new species at a higher rate than that observed in ecological plot sampling. Results: At any given sampling effort, the total number of observed species was higher in herbarium data. The relative abundance of common species in the field was higher, and the evenness of the distribution was lower, than in herbarium data. There was no significant correlation between species abundances in the field and in the herbaria. By selectively targeting rare species, collectors accumulate previously unseen species much faster than through ecological sampling. Conclusions: Because collectors aim for the rarer species and avoid the more common ones, the relative abundance of species in herbarium collections cannot be interpreted as a predictor of their true abundance in the field. Any statistical procedure that requires the sample to be representative of the true abundance distribution is likely to show errors when applied to herbarium data. However, because collectors actively search for rare species their rate of species accumulation is higher and their floristic lists are more complete than those obtained through ecological field sampling.     

浮游甲壳类定量采样计数方法评价

１引言浮游生物是养殖鱼类特别是滤食性鱼类的主要饵料,同时又是评价水生态系统质量优劣的重要指标．在大水面增养殖研究中,常常通过水体中浮游生物的采样分析,计算水体生物生产力．而在池塘生态系统中则又常常借助于浮游生物的采样分析来判定养鱼水质,决定增施饵肥料...     

Hypothesis testing approaches to the exon prediction problem

MOTIVATION: Many gene identification methods assign scores to gene elements prior to their assembly into predicted genes. The scoring system is often based on log-likelihood ratios. These methods usually perform well but it is difficult to interpret how significant a score is. RESULTS: We have developed several tests of significance for the scores: (1) a sum-of-scores test (SST), (2) an intersection-union test (IUT), based on a multiple hypothesis testing interpretation of an exon's score and (3) a meta-analytical approach (MA), which combines several P-values, corresponding to the exon's parts, to yield a global P-value. We performed simulation studies, which show that the MA has better sensitivity and specificity than other methods and is easier to interpret by non-expert users. This is an improvement over other methods and is especially relevant for users who would like to predict incomplete gene sequences.     

二化螟种群密度的克力格估值及其模拟抽样

为设计可靠合理的二化螟幼虫种群密度抽样方案,从二化螟幼虫空间分布原始总体出发,另构建了一个随机总体和一个顺序总体,采用无放回随机抽样、间隔变程以上无放回随机抽样和基于克力格估值且初始点随机的顺序抽样对3总体进行了模拟抽样比较．结果表明,间隔变程以上随机抽样对原始总体平均数的估计优于随机抽样,且随总体聚集程度增加,间隔变程以上随机抽样愈优;正确识别种群空间格局极为重要,对聚集分布总体采用随机抽样和对随机分布总体采用间隔变程以上随机抽样均将降低抽样估计精度．针对随机抽样在应用上的局限性,提出了一种基于地统计学克力格估值、初始点随机的顺序抽样方案：它以初始点随机保证随机性,以顺序抽样保证可操作性,以二化螟种群空间分布的区域变量属性保证克力格样本较调查样本对局域样本和总体的平均数估计为优;且聚集范围一定时,总体聚集强度愈大,克力格样本局域估计和全局估计愈优于调查样本;取样间隔(以变程为标准)极为重要,样方的空间布局要平衡考虑相互独立的样方对数和变程范围内的样方对数。     

Ensuring seed quality in ecological restoration: native seed cleaning and testing

Seeds are a critical and limited resource for restoring biodiversity and ecological function to degraded and fragmented ecosystems. Cleaning and quality testing are two key steps in the native seed supply chain. Optimizing the practices used in these steps can ensure seed quality. Post‐collection handling of seeds can have a profound impact on their viability, longevity in storage, and establishment potential. The first section of this article describes seed cleaning, outlines key considerations, and details traditional and novel approaches. Despite the growth of the native seed industry and the need for seed quality standards, existing equipment and standards largely target agricultural, horticultural, and commercial forestry species. Native plant species typically have complex seed traits, making it difficult to directly transfer existing cleaning and quality standards to these species. Furthermore, in ecological restoration projects, where diversity is valued over uniformity crop standards can be unsuitable. We provide an overview and recommendations for seed quality testing (sampling, purity, viability, germinability, vigor), identity reporting, and seed transfer as well as highlight the need to implement internationally recognized standards for certification for native seeds. Novel and improved cleaning and testing methods are needed for native species from a range of ecosystems to meet the challenges and goals of the United Nations Decade on Ecosystem Restoration. The guidelines outlined in this article along with others in the Special Issue of Restoration Ecology “Standards for Native Seeds in Ecological Restoration” can serve as a foundation for this critical work.     

Addendum to the Morphology of Steinernema scapterisci

This paper provides additional information on the morphology of Steinernema scapterisci. For females, the amphids are shown for the first time, and clearer scanning electron microscope (SEM) photographs of the six labial and four cephalic papillae are presented. For males, six labial and four cephalic papillae, one or two pairs of additional genital papillae, and the death shape are shown. For infective juveniles, six labial and four cephalic papillae and an elevated oral disc are shown.     

A rapid double-staining technique to improve seed viability testing in terrestrial orchids

Abstract

The need to optimize seed banking efforts has stimulated research for rapid methods to estimate quality in seed-lots. For terrestrial orchids, viability testing using tetrazolium (TTC) staining requires chemical scarification, as seeds have an impermeable testa. Different seed-coat permeability may affect TTC staining, thus affecting the results. The aim of this study was to perform a permeability test to assess the effectiveness of the used scarification method and its usefulness to correct TTC viability results. Mature seeds of Anacamptis laxiflora were subjected to eight scarification treatments with sodium hypochlorite solutions with different concentration and duration. Viability tests were performed using the basic TTC methodology, followed by a permeability test performed by means of trypan blue dye. The different scarification methods resulted in estimated TTC viability ranging from 0% and 94% for the same seed lot of A. laxiflora seeds. Our results proved that the used scarification protocol significantly affects both seed coat permeability and subsequent TTC staining (two-way ANOVA, p?< 0.0001). We describe a new rapid protocol that can be used to test terrestrial orchid seed viability. This double-staining method, providing rapid information on seed coat permeability, can be useful to avoid under-estimation of TTC results.     

Methods of estimating seed banks with reference to long-term seed burial

We compared two standard seed-bank estimation techniques using buried seed populations that had been covered to depths of >1 m by volcanic deposits for 20 years. Some seeds were germinated in a greenhouse (germination method [GM]), and other seeds were extracted by flotation using 50% K₂CO₃ solution (floatation method [FM]). In total, FM could detect more species and seeds in the soils than GM. However, many species that were extracted by FM did not germinate by GM and smaller seeds were extracted to a lesser extent by FM. FM and GM have distinct advantages and disadvantages. We concluded that the application of a single method should be avoided in estimating seed banks, in particular for long-lived seed banks, because the seeds cannot be readily germinated and are structurally weak.     

A Bayesian approach to the multiplicity problem for significance testing with binomial data

Statistical analyses of simple tumor rates from an animal experiment with one control and one treated group typically consist of hypothesis testing of many 2 X 2 tables, one for each tumor type or site. The multiplicity of significance tests may cause excessive overall false-positive rates. This paper presents a Bayesian approach to the problem of multiple significance testing. We develop a normal logistic model that accommodates the incidences of all tumor types or sites observed in the current experiment simultaneously as well as their historical control incidences. Exchangeable normal priors are assumed for certain linear terms in the model. Posterior means, standard deviations, and Bayesian P-values are computed for an average treatment effect as well as for the effects on individual tumor types or sites. Model assumptions are checked using probability plots and the sensitivity of the parameter estimates to alternative priors is studied. The method is illustrated using tumor data from a chronic animal experiment.