Identification of Horizontal Gene Transfer from Phylogenetic Gene Trees

We suggest a new procedure to search for the genes with horizontal transfer events in their evolutionary history. The search is based on analysis of topology difference between the phylogenetic trees of gene (protein) groups and the corresponding phylogenetic species trees. Numeric values are introduced to measure the discrepancy between the trees. This approach was applied to analyze 40 prokaryotic genomes classified into 132 classes of orthologs. This resulted in a list of the candidate genes for which the hypothesis of horizontal transfer in evolution looks true.     

Numerical responses by populations of red fox and mountain hare during an outbreak of sarcoptic mange

Summary During a severe outbreak of sarcoptic mange (Sarcoptes scabiei vulpes) starting among red foxes (Vulpes vulpes) in Sweden in the 1970s, we studied: 1) the establishment and spread of the disease in northernmost Sweden (by inquiries), and 2) the 1970–84 bag records for foxes and mountain hares (Lepus timidus) (an alternative prey to the fox's main prey, voles). Since the first case of sarcoptic mange in 1975 the disease spread rapidly, with >50% of the hunting organizations having reported the disease in 1981 and >75% in 1983. Also the disease became more abundant within the areas affected. In areas with a low mange infection rate (index) the number of foxes killed in the 1980s did not deviate markedly from the average level in the 1970s. However, there was a slight tendency towards a decline in areas with a medium index and numbers declined markedly where the index was high. Hare harvests initially were low (after a tularemia epidemic) in the 1970s. In that decade harvests increased dramatically and stabilized, increased gradually or changed little, respectively, where mange infection rates were low, medium or high in the early 1980s. In areas with a low mange index hare harvests remained cyclical and at the same level in the 1980s as in most of the 1970s. However, in areas with a medium index harvests increased and seemed to begin to lose their cyclicity, and where the index was high the low and relatively stable hare harvests increased annually. A predator-prey hypothesis, assuming predators to synchronize alternative prey declines to those of the cyclic main prey, predicts that a predator reduction would cause a gradual disappearance of the cyclicity and increasing numbers among alternative prey. Our hare data are partially consistent with this prediction.     

A practical validation approach for virus titer testing of avian infectious bursal disease live vaccine according to current regulatory guidelines

The method for virus titer determination of avian infectious bursal disease (IBD) live vaccine, developed long before regulatory validation guidelines is a cell culture based biological assay intended for use in vaccine release testing.The aim of our study was to perform a validation, based on fit-for-purpose principle, of an old 50% tissue culture infectious dose (TCID₅₀) method according to Guidelines of the International Cooperation on Harmonization of Technical Requirements for Registration of Veterinary Medicinal Products (VICH).This paper addresses challenges and discusses some key aspects that should be considered when validating biological methods. A different statistical approach and non-parametric statistics was introduced in validation protocol in order to derive useful information from experimental data. This approach is applicable for a wide range of methods.In conclusion, the previous virus titration method had showed to be precise, accurate, linear, robust and in accordance with current regulatory standards, which indicates that there is no need for additional re-development or upgrades of the method for its suitability for intended use.     

Rapid Evaluation of Least-Squares and Minimum-Evolution Criteria on Phylogenetic Trees

We present fast new algorithms for evaluating trees with respectto least squares and minimum evolution (ME), the most commonlyused criteria for inferring phylogenetic trees from distancedata. The new algorithms include an optimal O(N2) time algorithmfor calculating the edge (branch or internode) lengths on atree according to ordinary or unweighted least squares (OLS);an O(N3) time algorithm for edge lengths under weighted leastsquares (WLS) including the Fitch-Margoliash method; and anoptimal O(N4) time algorithm for generalized least-squares (GLS)edge lengths (where N is the number of taxa in the tree). TheME criterion is based on the sum of edge lengths. Consequently,the edge lengths algorithms presented here lead directly toO(N2), O(N3), and O(N4) time algorithms for ME under OLS, WLS,and GLS, respectively. All of these algorithms are as fast asor faster than any of those previously published, and the algorithmsfor OLS and GLS are the fastest possible (with respect to orderof computational complexity). A major advantage of our new methodsis that they are as well adapted to multifurcating trees asthey are to binary trees. An optimal algorithm for determiningpath lengths from a tree with given edge lengths is also developed.This leads to an optimal O(N2) algorithm for OLS sums of squaresevaluation and corresponding O(N3) and O(N4) time algorithmsfor WLS and GLS sums of squares, respectively. The GLS algorithmis time-optimal if the covariance matrix is already inverted.The speed of each algorithm is assessed analytically—thespeed increases we calculate are confirmed by the dramatic speedincreases resulting from their implementation in PAUP* 4.0.The new algorithms enable far more extensive tree searches andstatistical evaluations (e.g., bootstrap, parametric bootstrap,or jackknife) in the same amount of time. Hopefully, the fastalgorithms for WLS and GLS will encourage the use of these criteriafor evaluating trees and their edge lengths (e.g., for approximatedivergence time estimates), since they should be more statisticallyefficient than OLS.     

Observations on the Staining of Corynebacterium Diphtheriae

Albert's method, of staining diphtheria cultures consists of staining a fixed smear for one minute (some laboratories stain for five minutes) with a solution containing toluidine blue and malachite (or methyl) green, washing with water, and applying Albert's iodine for one minute. This procedure is discussed and criticized, and in addition the mechanism of the stain is elucidated. Also, the procedure which involves staining a fixed smear for one minute with Loeffler's alkaline methylene blue solution is discussed and criticized.

To overcome the objections to the above staining methods, a different method is proposed. This consists of staining a fixed smear with an acid solution of toluidine blue, washing with water, applying Albert's iodine for one minute, washing with water, and finally applying a safranin solution for 15-20 seconds. The theoretical basis for this method is presented.     

Priors for the Bayesian star paradox

We show that the Bayesian star paradox, first proved mathematically by Steel and Matsen for a specific class of prior distributions, occurs in a wider context including less regular, possibly discontinuous, prior distributions.     

Estimating population structure from AFLP amplification intensity

In the last decade, amplified fragment length polymorphisms (AFLPs) have become one of the most widely used molecular markers to study the genetic structure of natural populations. Most of the statistical methods available to study the genetic structure of populations using AFLPs consider these markers as dominant and are thus unable to distinguish between individuals being heterozygous or homozygous for the dominant allele. Some attempts have been made to treat AFLPs as codominant markers by using AFLP band intensities to infer the most likely genotype of each individual. These two approaches have some drawbacks, the former discarding potentially valuable information and the latter being sometimes unable to correctly assign genotypes to individuals. In this study, we propose an alternative likelihood‐based approach, which does not attempt at inferring the genotype of each individual, but rather incorporate the uncertainty about genotypes into a Bayesian framework leading to the estimation of population‐specific F_IS and F_ST coefficients. We show with simulations that the accuracy of our method is much higher than one using AFLP as dominant markers and is generally close to what would be obtained by using the same number of Single‐Nucleotide Polymorphism (SNP) markers. The method is applied to a data set of four populations of the common vole (Microtus arvalis) from Grisons in Switzerland, for which we obtained 562 polymorphic AFLP markers. Our approach is very general and has the potential to make AFLP markers as useful as SNP data for nonmodel species.     

Vector field statistical analysis of kinematic and force trajectories

When investigating the dynamics of three-dimensional multi-body biomechanical systems it is often difficult to derive spatiotemporally directed predictions regarding experimentally induced effects. A paradigm of ‘non-directed’ hypothesis testing has emerged in the literature as a result. Non-directed analyses typically consist of ad hoc scalar extraction, an approach which substantially simplifies the original, highly multivariate datasets (many time points, many vector components). This paper describes a commensurately multivariate method as an alternative to scalar extraction. The method, called ‘statistical parametric mapping’ (SPM), uses random field theory to objectively identify field regions which co-vary significantly with the experimental design. We compared SPM to scalar extraction by re-analyzing three publicly available datasets: 3D knee kinematics, a ten-muscle force system, and 3D ground reaction forces. Scalar extraction was found to bias the analyses of all three datasets by failing to consider sufficient portions of the dataset, and/or by failing to consider covariance amongst vector components. SPM overcame both problems by conducting hypothesis testing at the (massively multivariate) vector trajectory level, with random field corrections simultaneously accounting for temporal correlation and vector covariance. While SPM has been widely demonstrated to be effective for analyzing 3D scalar fields, the current results are the first to demonstrate its effectiveness for 1D vector field analysis. It was concluded that SPM offers a generalized, statistically comprehensive solution to scalar extraction's over-simplification of vector trajectories, thereby making it useful for objectively guiding analyses of complex biomechanical systems.     

Temperature influence on cohort parameters and demographic characteristics of the two cowpea coreids Clavigralla tomentosicollis and C. shadabi

Age-specific life tables of two important pests of cowpea, Vigna unguiculata (L.) Walp., the pod sucking bugs Clavigralla tomentosicollis Stål and C. shadabi Dolling (Heteroptera: Coreidae), were obtained from observations carried out at different temperatures. A biophysical model was found satisfactory to describe the temperature-response of developmental and mortality rates of egg and nymphal stages, with a peak developmental rate around 34°C in both species. The variability in development times was small and the experimental data did not permit any conclusion with regard to the Erlang probability density function. Survival of eggs and nymphs remained high between 20° and 30°C for both species. At temperatures above 34°C, C. tomentosicollis survivorship and fecundity was higher than that of C. shadabi, which in turn laid more eggs at temperatures between 20° and 30°C. Maximum fecundity is estimated to be at 29°C for C. tomentosicollis (99 eggs/female) and 26°C for C. shadabi (261 eggs/female). At 30°C, the intrinsic rate of increase reached a maximum in both species, 0.152 per day for C. tomentosicollis and 0.145 per day for C. shadabi, and remained high for C. tomentosicollis until 36°C. C. tomentosicollis performed significantly better on pigeonpea, Cajanus cajan Millsp., than on cowpea at higher temperatures.     

A brief method for analyzing Rotorod® samples for pollen content

Analyzing Rotorod^® pollen samples can be time consuming when one uses the standard method of evaluating an entire collector rod. This present investigation explored an abbreviated analysis method which is indicated by Poisson statistical theory. The authors systematically analyzed 18 Rotorod pollen samples from Spring 1994 which contained 408–7394 pollen grains per rod. The atmospheric pollen concentration (pollen grains/m³) was calculated from the number of pollen grains contained on the entire rod surface (P_total) and a sub-area containing at least 400 grains (P_>400). The estimate of the atmospheric pollen concentration resulting from P_total and P_>400 for each rod did not vary by more than ±9% (mean, 2.0%±3.7). These data indicate that pollen grains populated the sample rods rather uniformly, suggesting a mode of random recovery from the atmosphere. This study's results are consistent with the expectations concerning a Poisson process and support analyzing collector rods until a threshold number of pollen grains is counted.