Appendix to Paper by Wall and Herbeck

A method is described for determining the number of preferred codons in taxa in which G+C levels differ. If the hypothesis of random codon usage is not rejected, there are no preferred codons. If that hypothesis is rejected, then a model with one or two preferred codons is fitted to the data and a likelihood ratio test is used to determine whether there are one or two preferred codons. A C++ program is freely available to perform the calculations.     

TOPD/FMTS: a new software to compare phylogenetic trees

SUMMARY: TOPD/FMTS has been developed to evaluate similarities and differences between phylogenetic trees. The software implements several new algorithms (including the Disagree method that returns the taxa, that disagree between two trees and the Nodal method that compares two trees using nodal information) and several previously described methods (such as the Partition method, Triplets or Quartets) to compare phylogenetic trees. One of the novelties of this software is that the FMTS (From Multiple to Single) program allows the comparison of trees that contain both orthologs and paralogs. Each option is also complemented with a randomization analysis to test the null hypothesis that the similarity between two trees is not better than chance expectation. AVAILABILITY: The Perl source code of TOPD/FMTS is available at http://genomes.urv.es/topd.     

On the power of some binomial modifications of the Bonferroni multiple test

Widely used in testing statistical hypotheses, the Bonferroni multiple test has a rather low power that entails a high risk to accept falsely the overall null hypothesis and therefore to not detect really existing effects. We suggest that when the partial test statistics are statistically independent, it is possible to reduce this risk by using binomial modifications of the Bonferroni test. Instead of rejecting the null hypothesis when at least one of n partial null hypotheses is rejected at a very high level of significance (say, 0.005 in the case of n = 10), as it is prescribed by the Bonferroni test, the binomial tests recommend to reject the null hypothesis when at least k partial null hypotheses (say, k = [n/2]) are rejected at much lower level (up to 30-50%). We show that the power of such binomial tests is essentially higher as compared with the power of the original Bonferroni and some modified Bonferroni tests. In addition, such an approach allows us to combine tests for which the results are known only for a fixed significance level. The paper contains tables and a computer program which allow to determine (retrieve from a table or to compute) the necessary binomial test parameters, i.e. either the partial significance level (when k is fixed) or the value of k (when the partial significance level is fixed).     

大鼠冠状病毒和仙台病毒的双重PCR检测方法的建立与应用

目的建立快速检测实验大鼠冠状病毒和仙台病毒的双重PCR方法。方法根据大鼠冠状病毒N基因、仙台病毒L基因设计特异性引物;经过双重PCR优化,特异性和敏感性的检测,建立双重PCR体系。应用该PCR体系检测人工感染仙台病毒组织DNA样本和实验动物组织样本,并与ELISA方法比对。结果双重PCR扩增出大鼠冠状病毒(168 bp)和仙台病毒(262 bp)目的条带,PCR扩增产物测序结果利用核酸BLAST功能进行同源序列对比,仙台病毒和大鼠冠状病毒同源性分别为100%和99%。仙台病毒和大鼠冠状病毒的检测下限为1.56×10~2 copies/μL。特异性检测对小鼠肝炎病毒扩增,产生片段大小近似大鼠冠状病毒产物。应用建立的双重PCR体系检测人工感染仙台病毒组织DNA样本,30份DNA标本均被检出;检测94份实验动物肺组织样本,结果均阴性。结论建立的双重PCR方法操作简单、快速、特异性强、灵敏度高,能够实现对实验动物仙台病毒和大鼠冠状病毒病原体的快速检测。     

Detecting Heterogeneity of Substitution along DNA and Protein Sequences

Regions of differing constraint, mutation rate or recombination along a sequence of DNA or amino acids lead to a nonuniform distribution of polymorphism within species or fixed differences between species. The power of five tests to reject the null hypothesis of a uniform distribution is studied for four classes of alternate hypothesis. The tests explored are the variance of interval lengths; a modified variance test, which includes covariance between neighboring intervals; the length of the longest interval; the length of the shortest third-order interval; and a composite test. Although there is no uniformly most powerful test over the range of alternate hypotheses tested, the variance and modified variance tests usually have the highest power. Therefore, we recommend that one of these two tests be used to test departure from uniformity in all circumstances. Tables of critical values for the variance and modified variance tests are given. The critical values depend both on the number of events and the number of positions in the sequence. A computer program is available on request that calculates both the critical values for a specified number of events and number of positions as well as the significance level of a given data set.     

Insights into X chromosome inactivation from studies of species variation, DNA methylation and replication, and vice versa

I am indebted to Mary Lyon as her X-inactivation hypothesis stimulated my mentor, Barton Childs, and in turn, myself, to think about the consequences of X-inactivation in heterozygous females. I often reread her original papers setting forth the single active X hypothesis, and still marvel at the concise and compelling exposition of the hypothesis and the logical predictions which seemed prophetic at my first reading, and have survived the test of time. My contribution to this Festschrift reviews evidence derived from studies of DNA methylation, species variation and DNA replication that reveals an important role for methylated CpG islands and suggests a role for late DNA replication in propagating X inactivation from one cell to its progeny. These studies also show that X inactivation is a powerful research tool for identifying the factors which program and maintain developmental processes.     

Unconditional inferences on the difference of two proportions in cross-sectional studies

In order to analyse a 2 x 2 table it is usual to perform inferences (hypothesis test or interval of confidence) on the difference d = p2 - p1 between two independent proportions. To this end it has been customary to adopt the Fisher conditional method, but nowadays the unconditional method of Barnard is increasingly adopted. However, all the present unconditional inferences are based on a double-binomial model. This article performs these inferences - exact and asymptotic - under a multinomial model, which is the appropriate one when the data proceed from a cross-sectional survey. At http://www.ugr.es/-bioest/SG_ASO.EXE there is a program for performing the said unconditional tests that may be copied.     

Computer software for performing likelihood tests of pedigree relationship using genetic markers

Molecular techniques are making ever more genetic markers available for use in parentage assignment, and measures of relatedness. We present a program, Kinship, designed to use likelihood techniques to test for any non-inbred pedigree relationship between pairs of individuals, using single-locus codominant genetic markers. Kinship calculates the likelihood that each pair of individuals in a data set are related by a given pedigree hypothesis, and likelihood ratios for any pair of hypotheses. The program also uses a simulation routine to attach statistical significance to its results.     

A FORTRAN program for testing trend and homogeneity in proportions

A FORTRAN program is provided for testing linear trend and homogeneity in proportions. Trend is evaluated by the Cochran-Armitage method and homogeneity is tested by an overall X2 test as well by multiple pairwise comparisons by the Fisher-Irwin exact method. The program should be easy to implement on any size of computer with a FORTRAN compiler.     

The Null Distributions of Test Statistics in Genomewide Association Studies

Genomewide association (GWA) studies assay hundreds of thousands of single nucleotide polymorphisms (SNPs) simultaneously across the entire genome and associate them with diseases, other biological or clinical traits. The association analysis usually tests each SNP as an independent entity and ignores the biological information such as linkage disequilibrium. Although the Bonferroni correction and other approaches have been proposed to address the issue of multiple comparisons as a result of testing many SNPs, there is a lack of understanding of the distribution of an association test statistic when an entire genome is considered together. In other words, there are extensive efforts in hypothesis testing, and almost no attempt in estimating the density under the null hypothesis. By estimating the true null distribution, we can apply the result directly to hypothesis testing; better assess the existing approaches of multiple comparisons; and evaluate the impact of linkage disequilibrium on the GWA studies. To this end, we estimate the empirical null distribution of an association test statistic in GWA studies using simulated population data. We further propose a convenient and accurate method based on adaptive spline to estimate the empirical value in GWA studies and validate our findings using a real data set. Our method enables us to fully characterize the null distribution of an association test that not only can be used to test the null hypothesis of no association, but also provides important information about the impact of density of the genetic markers on the significance of the tests. Our method does not require users to perform computationally intensive permutations, and hence provides a timely solution to an important and difficult problem in GWA studies.     

EDISON-WMW: Exact Dynamic Programing Solution of the Wilcoxon–Mann–Whitney Test

In many research disciplines, hypothesis tests are applied to evaluate whether findings are statistically significant or could be explained by chance. The Wilcoxon–Mann–Whitney(WMW) test is among the most popular hypothesis tests in medicine and life science to analyze if two groups of samples are equally distributed. This nonparametric statistical homogeneity test is commonly applied in molecular diagnosis. Generally, the solution of the WMW test takes a high combinatorial effort for large sample cohorts containing a significant number of ties. Hence, P value is frequently approximated by a normal distribution. We developed EDISON-WMW, a new approach to calculate the exact permutation of the two-tailed unpaired WMW test without any corrections required and allowing for ties. The method relies on dynamic programing to solve the combinatorial problem of the WMW test efficiently. Beyond a straightforward implementation of the algorithm, we presented different optimization strategies and developed a parallel solution. Using our program,the exact P value for large cohorts containing more than 1000 samples with ties can be calculated within minutes. We demonstrate the performance of this novel approach on randomly-generated data, benchmark it against 13 other commonly-applied approaches and moreover evaluate molecular biomarkers for lung carcinoma and chronic obstructive pulmonary disease(COPD). We foundthat approximated P values were generally higher than the exact solution provided by EDISONWMW. Importantly, the algorithm can also be applied to high-throughput omics datasets, where hundreds or thousands of features are included. To provide easy access to the multi-threaded version of EDISON-WMW, a web-based solution of our algorithm is freely available at http://www.ccb.uni-saarland.de/software/wtest/.     

chifish: a computer program testing for genetic heterogeneity at multiple loci using chi‐square and Fisher's exact test

chifish is a 32‐bit Windows/DOS program evaluating divergence at multiple gene loci. It tests the hypothesis of no difference at any locus both by means of Pearson's traditional chi‐square and by using Fisher's method of combining P values obtained by Fisher's exact test. Input data are read from a file formatted for genepop . Commonly used population genetics software do not perform chi‐square tests, and the simultaneous application of both techniques aids in situations where poor power of the ‘exact approach’ may prevent detection of true differentiation (e.g. few populations and few alleles per locus).     

The glycolyzer: Automated glycan annotation software for high performance mass spectrometry and its application to ovarian cancer glycan biomarker discovery

Human serum glycomics is a promising method for finding cancer biomarkers but often lacks the tools for streamlined data analysis. The Glycolyzer software incorporates a suite of analytic tools capable of identifying informative glycan peaks out of raw mass spectrometry data. As a demonstration of its utility, the program was used to identify putative biomarkers for epithelial ovarian cancer from a human serum sample set. A randomized, blocked, and blinded experimental design was used on a discovery set consisting of 46 cases and 48 controls. Retrosynthetic glycan libraries were used for data analysis and several significant candidate glycan biomarkers were discovered via hypothesis testing. The significant glycans were attributed to a glycan family based on glycan composition relationships and incorporated into a linear classifier motif test. The motif test was then applied to the discovery set to evaluate the disease state discrimination performance. The test provided strongly predictive results based on receiver operator characteristic curve analysis. The area under the receiver operator characteristic curve was 0.93. Using the Glycolyzer software, we were able to identify a set of glycan biomarkers that highly discriminate between cases and controls, and are ready to be formally validated in subsequent studies.     

Signaling health versus parasites

The Hamilton-Zuk hypothesis, that parasite-host coevolution can maintain heritable variation in fitness, has inspired a very successful research program on sexual selection on signals of health. The immunocompetence handicap hypothesis was developed to provide a handicapping mechanism to stabilize the correlation between signals and health. In earlier articles, I showed that handicap signaling is a special case, not a general law that we can rely on to deduce relative costs across signalers of different quality at equilibrium. The essential requirement for reliable signaling is that higher-quality signalers are more efficient; they get greater marginal fitness returns from an incremental increase in the signal. This does not undermine the Hamilton-Zuk hypothesis or the immunocompetence mechanism, but it does raise doubts about a widespread assumption that is commonly used to test these hypotheses: that sexual selection on signals of health implies the choice of mates with the fewest parasites. Immunity and parasites might play a fundamental role in many biological signaling systems, but viability-indicating traits are not necessarily parasite-load-indicating traits. Theory allows for the possibility that high-quality big signalers have greater health and more parasites than low-quality small signalers (and the data suggest that in many systems they do). This means that we cannot test the Hamilton-Zuk hypothesis or the immunocompetence handicap hypothesis by counting parasites. More generally, we cannot understand sexual selection on signals of health by focusing on the viability costs of signals.     

Better nutritional condition changes the distribution of juvenile dispersal distances: an experiment with Spanish imperial eagles

We investigated the distribution of juvenile dispersal distances of a territorial long‐lived species with deferred maturity, the Spanish imperial eagle Aquila adalberti. Here we used a reintroduction program as an experimental approach to test predictions of different hypotheses about the distribution of juvenile dispersal distances: competition and wandering behavior. We determined maximal juvenile dispersal distances of 59 young eagles; 1) 30 wild non‐manipulated individuals, and 2) 29 tranlocated young under an ad libitum feeding program, released with adults breeding in the area. The competitive displacement hypothesis predicts a leptokurtic distribution of distances in wild non‐manipulated young as well as in released young. Under the ‘wandering’ hypothesis, however, a leptokurtic distribution is expected in wild young but a normal distribution would be expected in young released (with adults in the release area), owing to a general improvement in the nutritional status of released young that have been fed ad libitum, as is usual in reintroduction programs. Additionally, a negative relationship between hatching date and dispersal distances is expected in wild young but no relationship in released young under ad libitum feeding. Mean maximum dispersal distances for all the juvenile eagles was 142.8 km. No differences between sexes were found, nor between populations or between wild and reintroduced young. Wild young distances were not normally distributed, being closer to a Poisson distribution. In contrast, released young with adults (under ad libitum feeding) showed a normal distribution. Wild birds showed a significant negative relationship between dispersal distance and hatching date, with young that hatched late in the season dispersing shorter distances. However, released young under ad libitum feeding showed no significant relationship between hatching date and dispersal distance. These results support the ‘wandering’ hypothesis as the main driver of the distribution of dispersal distances.     

Assessment of Transmission in Trachoma Programs over Time Suggests No Short-Term Loss of Immunity

Trachoma programs have dramatically reduced the prevalence of the ocular chlamydia that cause the disease. Some have hypothesized that immunity to the infection may be reduced because of program success in reducing the incidence of infection, and transmission may then increase. Longitudinal studies of multiple communities would be necessary to test this hypothesis. Here, we quantify transmission using an estimated basic reproduction number based on 32 communities during the first, second, and third years of an antibiotic treatment program. We found that there is little to no increase in the basic reproduction number over time. The estimated linear trend in the basic reproduction number, , was found to be −0.025 per year, 95% CI −0.167 to 0.117 per year. We are unable to find evidence supporting any loss of immunity over the course of a 3-year program. This is encouraging, as it allows the possibility that repeated mass antibiotic distributions may eliminate infection from even the most severely affected areas.     

Hypothesis assessment with qualitative reasoning: Modelling the Fontestorbes fountain

This paper demonstrates the utility of the Qualitative Reasoning approach for hypothesis testing in the domain of ecology regarding the functioning of ‘black box’ systems. As a test case, we refer to the study performed by Mangin (1969) with scale models to investigate the hidden mechanism of the Fontestorbes fountain, a spring that exhibits a periodic flow situated in the south of France. In our approach, a Qualitative Reasoning method (and hence a qualitative model) is used to test the ‘siphon-hypothesis’, which traditionally explains the oscillations of the flow rate of a periodic spring by the principle of filling and emptying an underground reservoir through a siphon action. Parts of the simulation results show that the hypothesis is qualitatively accurate; in particular the model produces a cyclic behaviour that matches with the observed one. However, the qualitative model also exhibits a contradictory behaviour (true negative) that challenges the hypothesis consistency. The causal account of this true negative denotes and explains a flaw in the siphon-hypothesis. The paper concludes that, with the Qualitative Reasoning method, models can be constructed for hypothesis testing. Such models should generate the desired behaviour as a first and necessary step to support the viability of the hypothesis. However, the occurrence of unexpected behaviours provides information that challenges the hypothesis, and may lead to having to discard it.     

Sample size determination for confidence intervals on the population mean and on the difference between two population means

Sample size determination is usually based on the premise that a hypothesis test is to be used. A confidence interval can sometimes serve better than a hypothesis test. In this paper a method is presented for sample size determination based on the premise that a confidence interval for a simple mean, or for the difference between two means, with normally distributed data is to be used. For this purpose, a concept of power relevant to confidence intervals is given. Some useful tables giving required sample size using this method are also presented.     

Postural preparation to making a step: is there a 'motor program' for postural preparation?

We tested the hypothesis that a sequence of mechanical events occurs preceding a step that scales in time and magnitude as a whole in a task-specific manner, and is a reflection of a "motor program." Young subjects made a step under three speed instructions and four tasks: stepping straight ahead, down a stair, up a stair, and over an obstacle. Larger center-of-pressure (COP) and force adjustments in the anterior-posterior direction and smaller COP and force adjustments in the mediolateral direction were seen during stepping forward and down a stair, as compared with the tasks of stepping up a stair and over an obstacle. These differences were accentuated during stepping under the simple reaction time instruction. These results speak against the hypothesis of a single motor program that would underlie postural preparation to stepping. They are more compatible with the reference configuration hypothesis of whole-body actions.     

Design and analysis of accelerated degradation tests for the stability of biological standards II. A flexible computer program for data analysis

The accelerated degradation test is commonly used to predict the stability of a biological standard during long-term storage at low temperature. A flexible computer program is described which has been written to analyse degradation test results by the method of maximum likelihood. In addition to predicting the degradation rate at low temperature, the program furnishes estimates of statistical precision and it carried out a test of goodness of fit of the data to the assumed Arrhenius equation model.