Bayesian data analysis in population ecology: motivations,methods, and benefits

During the 20th century ecologists largely relied on the frequentist system of inference for the analysis of their data. However, in the past few decades ecologists have become increasingly interested in the use of Bayesian methods of data analysis. In this article I provide guidance to ecologists who would like to decide whether Bayesian methods can be used to improve their conclusions and predictions. I begin by providing a concise summary of Bayesian methods of analysis, including a comparison of differences between Bayesian and frequentist approaches to inference when using hierarchical models. Next I provide a list of problems where Bayesian methods of analysis may arguably be preferred over frequentist methods. These problems are usually encountered in analyses based on hierarchical models of data. I describe the essentials required for applying modern methods of Bayesian computation, and I use real-world examples to illustrate these methods. I conclude by summarizing what I perceive to be the main strengths and weaknesses of using Bayesian methods to solve ecological inference problems.     

Phylogenetic analysis and intraspecific variation: performance of parsimony,likelihood, and distance methods

Intraspecific variation is abundant in all types of systematic characters but is rarely addressed in simulation studies of phylogenetic method performance. We compared the accuracy of 15 phylogenetic methods using simulations to (1) determine the most accurate method(s) for analyzing polymorphic data (under simplified conditions) and (2) test if generalizations about the performance of phylogenetic methods based on previous simulations of fixed (nonpolymorphic) characters are robust to a very different evolutionary model that explicitly includes intraspecific variation. Simulated data sets consisted of allele frequencies that evolved by genetic drift. The phylogenetic methods included eight parsimony coding methods, continuous maximum likelihood, and three distance methods (UPGMA, neighbor joining, and Fitch-Margoliash) applied to two genetic distance measures (Nei's and the modified Cavalli-Sforza and Edwards chord distance). Two sets of simulations were performed. The first examined the effects of different branch lengths, sample sizes (individuals sampled per species), numbers of characters, and numbers of alleles per locus in the eight-taxon case. The second examined more extensively the effects of branch length in the four-taxon, two-allele case. Overall, the most accurate methods were likelihood, the additive distance methods (neighbor joining and Fitch-Margoliash), and the frequency parsimony method. Despite the use of a very different evolutionary model in the present article, many of the results are similar to those from simulations of fixed characters. Similarities include the presence of the "Felsenstein zone," where methods often fail, which suggests that long-branch attraction may occur among closely related species through genetic drift. Differences between the results of fixed and polymorphic data simulations include the following: (1) UPGMA is as accurate or more accurate than nonfrequency parsimony methods across nearly all combinations of branch lengths, and (2) likelihood and the additive distance methods are not positively misled under any combination of branch lengths tested (even when the assumptions of the methods are violated and few characters are sampled). We found that sample size is an important determinant of accuracy and affects the relative success of methods (i.e., distance and likelihood methods outperform parsimony at small sample sizes). Attempts to generalize about the behavior of phylogenetic methods should consider the extreme examples offered by fixed-mutation models of DNA sequence data and genetic-drift models of allele frequencies.     

Neutron crystallography: opportunities, challenges, and limitations

Neutron crystallography has had an important, but relatively small role in structural biology over the years. In this review of recently determined neutron structures, a theme emerges of a field currently expanding beyond its traditional boundaries, to address larger and more complex problems, with smaller samples and shorter data collection times, and employing more sophisticated structure determination and refinement methods. The origin of this transformation can be found in a number of advances including first, the development of neutron image-plates and quasi-Laue methods at nuclear reactor neutron sources and the development of time-of-flight Laue methods and electronic detectors at spallation neutron sources; second, new facilities and methods for sample perdeuteration and crystallization; third, new approaches and computational tools for structure determination.     

Rings, circles, and null-models for point pattern analysis in ecology

A large number of methods for the analysis of point pattern data have been developed in a wide range of scientific fields. First-order statistics describe large-scale variation in the intensity of points in a study region, whereas second-order characteristics are summary statistics of all point-to-point distances in a mapped area and offer the potential for detecting both different types and scales of patterns. Second-order analysis based on Ripley's K-function is increasingly used in ecology to characterize spatial patterns and to develop hypothesis on underlying processes; however, the full range of available methods has seldomly been applied by ecologists. The aim of this paper is to provide guidance to ecologists with limited experience in second-order analysis to help in the choice of appropriate methods and to point to practical difficulties and pitfalls. We review (1) methods for analytical and numerical implementation of two complementary second-order statistics, Ripley's K and the O-ring statistic, (2) methods for edge correction, (3) methods to account for first-order effects (i.e. heterogeneity) of univariate patterns, and (4) a variety of useful standard and non-standard null models for univariate and bivariate patterns. For illustrative purpose, we analyze examples that deal with non-homogeneous univariate point patterns. We demonstrate that large-scale heterogeneity of a point-pattern biases Ripley's K-function at smaller scales. This bias is difficult to detect without explicitly testing for homogeneity, but we show that it can be removed when applying methods that account for first-order effects. We synthesize our review in a number of step-by-step recommendations that guide the reader through the selection of appropriate methods and we provide a software program that implements most of the methods reviewed and developed here.     

Fixation and imaging of biological elements: heavy metals, diffusible substances, ions, peptides, and lipids

We tested various fixation and analysis methods to demonstrate by electron microscopy elemental imaging in tissues and cells, i.e., soluble substances such as many kinds of ionic elements, water soluble low molecular peptides, and even organic solvent soluble substances such as lipids. For the ionic elements, we tested frozen dried or freeze-substituted methods and organic or inorganic special chemical precipitation methods combined with microwaved fixation methods. The data were analyzed with electron beam X-ray microanalysis, electron energy filtered imaging analysis, and electron microscope autoradiography. The data were demonstrated as elemental distribution images and were calculated quantitatively. For the soluble low molecular peptides, we developed a tannic acid and aldehyde method combined with microwaved fixation. We discuss the theoretical background of the tannic acid fixation and microwaved fixation methods. For the organic solvent soluble substances, i.e., lipids including steroids, we successfully tested the use of a mixed fixative of aldehyde and osmium, digitonization, and osmification with the use of p-phenylendiamine or imidazole. We also proposed some new ideal biotracers for electron beam X-ray microanalysis and electron energy filtered imaging analysis.     

光合细菌的分离、保存及其同化磷能力试验研究

为了研究光合细菌的保藏方法及其同化磷能力,采用液体种室内自然放置、液体种蜡封和穿刺物蜡封等方法对光合细菌进行保藏方法研究,结果表明,液体种蜡封和穿刺物蜡封可作为该菌种的长期保存方法;对两株菌的磷同化能力进行了比较,降解率分别为22%和15%。本研究为获得光合细菌的长期保存方法及其在污水净化中的应用提供参考。     

Fold prediction by a hierarchy of sequence, threading, and modeling methods.

Several fold recognition algorithms are compared to each other in terms of prediction accuracy and significance. It is shown that on standard benchmarks, hybrid methods, which combine scoring based on sequence-sequence and sequence-structure matching, surpass both sequence and threading methods in the number of accurate predictions. However, the sequence similarity contributes most to the prediction accuracy. This strongly argues that most examples of apparently nonhomologous proteins with similar folds are actually related by evolution. While disappointing from the perspective of the fundamental understanding of protein folding, this adds a new significance to fold recognition methods as a possible first step in function prediction. Despite hybrid methods being more accurate at fold prediction than either the sequence or threading methods, each of the methods is correct in some cases where others have failed. This partly reflects a different perspective on sequence/structure relationship embedded in various methods. To combine predictions from different methods, estimates of significance of predictions are made for all methods. With the help of such estimates, it is possible to develop a "jury" method, which has accuracy higher than any of the single methods. Finally, building full three-dimensional models for all top predictions helps to eliminate possible false positives where alignments, which are optimal in the one-dimensional sequences, lead to unsolvable sterical conflicts for the full three-dimensional models.     

Count data, detection probabilities, and the demography, dynamics, distribution, and decline of amphibians

The evidence for amphibian population declines is based on count data that were not adjusted for detection probabilities. Such data are not reliable even when collected using standard methods. The formula C = Np (where C is a count, N the true parameter value, and p is a detection probability) relates count data to demography, population size, or distributions. With unadjusted count data, one assumes a linear relationship between C and N and that p is constant. These assumptions are unlikely to be met in studies of amphibian populations. Amphibian population data should be based on methods that account for detection probabilities.     

Rejoinder: whole-culture synchronization cannot, and does not, synchronize cells

There have been numerous proposals suggesting that whole-culture methods - in which all cells in a growing culture are treated identically - can synchronize cells. An explicit defense of these methods has been presented (Spellman and Sherlock, this issue, pp. 270-273, ). Here, this defense of whole-culture 'synchronization' is subjected to a critical evaluation leading to the conclusion that whole-culture synchronization cannot synchronize cells - at all. Whole-culture methods cannot produce a set of cells that reflects the size and genome composition of cells of any particular cell-cycle age during the normal cell cycle. Thus, in addition to the well-recognized problem of artifacts, it is proposed that experiments using whole-culture treatments (usually starvation or inhibition methods) are not suitable for cell-cycle analysis because these methods do not produce a synchronized culture.     

Synthesis and properties of N-, O-, and S-phospho derivatives of amino acids, peptides, and proteins

The literature on chemical (i.e., nonenzymic) phosphorylation of amino acids, peptides, and proteins is reviewed through 1982. The review covers synthetic methods, chemical reactions, and physical properties, with emphasis on the techniques used for separation and characterization of the products. Synthetic methods are classified by reagent rather than product, and are illustrated by experimental procedures for the most important methods. Chemical reactions are classified into four groups depending on whether the reaction site is the phospho group, the amino group, the carboxyl group, or in the case of serine the hydroxyl group. Physical data are given for all of the known N-, O-, and S-phospho derivatives of the amino acids, peptides, and proteins, within certain limitations, and are discussed in detail in the section on physical properties. Emphasis is given to the techniques used for separation of the products, such as chromatography and electrophoresis, and for characterization of the products, particularly spectroscopy. Medical and other uses of the products are mentioned.     

Error,Power, and Blind Sentinels: The Statistics of Seagrass Monitoring

We derive statistical properties of standard methods for monitoring of habitat cover worldwide, and criticize them in the context of mandated seagrass monitoring programs, as exemplified by Posidonia oceanica in the Mediterranean Sea. We report the novel result that cartographic methods with non-trivial classification errors are generally incapable of reliably detecting habitat cover losses less than about 30 to 50%, and the field labor required to increase their precision can be orders of magnitude higher than that required to estimate habitat loss directly in a field campaign. We derive a universal utility threshold of classification error in habitat maps that represents the minimum habitat map accuracy above which direct methods are superior. Widespread government reliance on blind-sentinel methods for monitoring seafloor can obscure the gradual and currently ongoing losses of benthic resources until the time has long passed for meaningful management intervention. We find two classes of methods with very high statistical power for detecting small habitat cover losses: 1) fixed-plot direct methods, which are over 100 times as efficient as direct random-plot methods in a variable habitat mosaic; and 2) remote methods with very low classification error such as geospatial underwater videography, which is an emerging, low-cost, non-destructive method for documenting small changes at millimeter visual resolution. General adoption of these methods and their further development will require a fundamental cultural change in conservation and management bodies towards the recognition and promotion of requirements of minimal statistical power and precision in the development of international goals for monitoring these valuable resources and the ecological services they provide.     

Regression models for linkage: issues of traits,covariates, heterogeneity,and interaction

Regression methods offer a common framework to analyze linkage for quantitative trait loci as well as linkage for affection status using affected sib-pairs. Although numerous papers on regression methods for linkage have been published, some common themes and important caveats tend to be scattered across the literature. For example, the typical approach is to regress a function of traits on identical-by-descent (IBD) information, but the reversal (regression of IBD on a function of traits) offers important insights. A second example is the use of regression equations to assess linkage heterogeneity or gene-environment interaction, and why these two different etiologies are difficult to distinguish with affected sib-pair data. A third example has to do with the differences, and similarities, between linear regression and non-linear regression methods for affected sib-pair data. The purposes of this paper are to review some recent developments in the linkage regression framework, to emphasize strengths and weaknesses of various proposed methods, and to highlight some important assumptions and caveats.     

Experimental and theoretical studies on the molecular properties of ciprofloxacin,norfloxacin, pefloxacin,sparfloxacin, and gatifloxacin in determining bioavailability

The aim of this investigation is to identify, by in silico and in vitro methods, the molecular determinants, e.g., solubility in an aqueous medium and lipophilic properties, which have an effect on the bioavailability of five selected fluoroquinolones. These properties were estimated by analysis of the electrostatic potential pattern and values of free energy of solvation as well as the partition coefficients of the studied compounds. The study is based on theoretical quantum-chemical methods and a simple experimental shake-flask technique with two immiscible phases, n-octanol and phosphate buffer. The solvation free energy values of compounds in both environments appeared to be negative. The wide range of electrostatic potential from negative to positive demonstrates the presence of dipole–dipole intermolecular interactions, while the high electron density at various sites indicates the possibility of hydrogen bond formation with solvent molecules. High partition coefficient values, obtained by summing the atomic contributions, did not take various correction factors into account and therefore were not accurate. Theoretical partition coefficient values based on more accurate algorithms, which included these correction factors (fragmental methods), yielded more accurate values. Theoretical methods are useful tools for predicting the bioavailability of fluoroquinolones.     

Strain,biochemistry, and cultivation-dependent measurement variability of algal biomass composition

Accurate compositional analysis in biofuel feedstocks is imperative; the yields of individual components can define the economics of an entire process. In the nascent industry of algal biofuels and bioproducts, analytical methods that have been deemed acceptable for decades are suddenly critical for commercialization. We tackled the question of how the strain and biochemical makeup of algal cells affect chemical measurements. We selected a set of six procedures (two each for lipids, protein, and carbohydrates): three rapid fingerprinting methods and three advanced chromatography-based methods. All methods were used to measure the composition of 100 samples from three strains: Scenedesmus sp., Chlorella sp., and Nannochloropsis sp. The data presented point not only to species-specific discrepancies but also to cell biochemistry-related discrepancies. There are cases where two respective methods agree but the differences are often significant with over- or underestimation of up to 90%, likely due to chemical interferences with the rapid spectrophotometric measurements. We provide background on the chemistry of interfering reactions for the fingerprinting methods and conclude that for accurate compositional analysis of algae and process and mass balance closure, emphasis should be placed on unambiguous characterization using methods where individual components are measured independently.     

The determination of isoniazid and its metabolites acetylisoniazid, monoacetylhydrazine, diacetylhydrazine, isonicotinic acid and isonicotinylglycine in serum and urine

1. A solvent system was devised for the extraction of isoniazid and its metabolites acetylisoniazid, monoacetylhydrazine, diacetylhydrazine, isonicotinic acid and isonicotinylglycine from serum and urine. 2. Specific chemical and fluorimetric methods were developed for the determination of the extracted isoniazid and acetylisoniazid, and chemical methods for the determination of monoacetylhydrazine, diacetylhydrazine, isonicotinic acid and isonicotinylglycine. 3. When applied to serum, these methods were capable of measuring concentrations of down to about 0.005mug of isoniazid/ml, 0.05mug of acetylisoniazid/ml, 0.2mug of monoacetylhydrazine/ml, 0.2mug of diacetylhydrazine/ml, 0.02mug of isonicotinic acid/ml and 0.1mug of isonicotinylglycine/ml. 4. In urine, these methods were capable of measuring concentrations of down to about 0.05mug of isoniazid/ml, 0.2mug of acetylisoniazid/ml, 1mug of diacetylhydrazine/ml, 0.1mug of isonicotinic acid/ml and 0.2mug of isonicotinylglycine/ml. 5. The stability of these compounds was studied in serum and urine and a method devised to decrease their decomposition in serum.     

A comparison between SNaPshot, pyrosequencing, and biplex invader SNP genotyping methods: accuracy, cost, and throughput

Three methods of Single Nucleotide Polymorphism (SNP) detection: SNaPshot, Pyrosequencing and Biplex Invader, with two different chemistries were investigated to compare, (1) accuracy, (2) ease of use, (3) throughput capability, and (4) cost. We genotyped 192 human DNA samples across 24 SNPs (minor allele frequencies above 30%), of which seven SNPs were genotyped with all three methods. We show that the Biplex Invader genotyping method was found to be the most accurate and easiest to use with lowest cost, although Pyrosequencing provided similar results at a low cost. With little optimization, the accuracy of the SNaPshot method was also comparable to these two methods with a higher cost, if only singleplex reactions are used.     

植物花蜜提取、保存与检测分析方法及比较

花蜜富含多种有机物和微量元素,不同植物花蜜的分泌量以及化学物质构成存在很大差异,不同花蜜采集和保存方法都会影响其成分分析结果。本研究参考相关文献,总结了常用的6种野外花蜜收集方式(注射器法、毛细管法、滤纸法、溶液稀释法、离心法和抽吸法),6种花蜜保存方式(4℃冷藏保存、-20℃冷冻保存、-80℃超低温保存、-196℃液氮保存、添加防腐剂保存和滤纸保存)以及3类花蜜化学特征检测方式(手持折光仪、比色法和色谱分析)。深入比较了各种方法的优缺点及其潜在的适用对象,在条件允许的情况下,毛细管法、-80℃超低温保存及色谱分析是花蜜收集、保存及分析最常使用的方法。     

Molecular Illustration in Research and Education: Past,Present, and Future

Two-dimensional illustration is used extensively to study and disseminate the results of structural molecular biology. Molecular graphics methods have been and continue to be developed to address the growing needs of the structural biology community, and there are currently many effective, turn-key methods for displaying and exploring molecular structure. Building on decades of experience in design, best-practice resources are available to guide creation of illustrations that are effective for research and education communities.     

Determination of each constituent in mixtures of catechol and protocatechuic acid,quinol and gentisic acid,phenol and p-hydroxybenzoic acid,and pyrogallol and gallic acid

Simple, rapid spectrophotofluorometric methods were developed for determining each constitutent in the mixtures of catechol and protocatechuic acid and in mixtures of quinol and gentisic acid. A colorimetric method involving the use of 4-aminoantipyrine and extraction with chloroform was proposed for determining each constituent in mixtures of phenol and p-hydroxybenzoic acid. Two simple and rapid colorimetric methods were used in conjunction to determine each constituent in mixtures of pyrogallol and gallic acid. The accuracy of all methods was within ±5%.