The Evolution of Codon Preferences in Drosophila: A Maximum-Likelihood Approach to Parameter Estimation and Hypothesis Testing

Synonymous codon usage in related species may differ as a result of variation in mutation biases, differences in the overall strength and efficiency of selection, and shifts in codon preference—the selective hierarchy of codons within and between amino acids. We have developed a maximum-likelihood method to employ explicit population genetic models to analyze the evolution of parameters determining codon usage. The method is applied to twofold degenerate amino acids in 50 orthologous genes from D. melanogaster and D. virilis. We find that D. virilis has significantly reduced selection on codon usage for all amino acids, but the data are incompatible with a simple model in which there is a single difference in the long-term N _e, or overall strength of selection, between the two species, indicating shifts in codon preference. The strength of selection acting on codon usage in D. melanogaster is estimated to be |N _e s|≈ 0.4 for most CT-ending twofold degenerate amino acids, but 1.7 times greater for cysteine and 1.4 times greater for AG-ending codons. In D. virilis, the strength of selection acting on codon usage for most amino acids is only half that acting in D. melanogaster but is considerably greater than half for cysteine, perhaps indicating the dual selection pressures of translational efficiency and accuracy. Selection coefficients in orthologues are highly correlated (ρ= 0.46), but a number of genes deviate significantly from this relationship. Received: 20 December 1998 / Accepted: 17 February 1999     

An Application of the Logistic Distribution to the Analysis of a Measles Epidemic

The relationship between the development of measles and age at immunization and time since immunization is examined using a trichotomous logistic distribution with maximum likelihood estimation of the parameters. The first and second partial derivatives used in the estimation scheme are presented.     

槭树科植物广义形态学性状分支分析

通过45个广义的形态学性状对槭树科(Aceraceae)尤其是槭属(Acer L.)的主要类群做了分支分析,结果显示：1)槭属内由于各类群分布着较多的同塑性状状态,而难以为属下组间关系的解决提供更多有价值的信息;通过对具体的性状状态分布分析显示,对于象槭属这样在形态上分化较大的类群,由于多数分类性状在不同类群间经历了平行和逆转演化,因而在较低分类阶元水平很难选择合适的性状来通过分支分析构建其系统发育;2)鸡爪槭组(section Palmata)作为整个槭属的基部类群,虽然支持率较低,但与其它类群相比在槭属内维持了较多的原始性状;3)金钱槭属(Dipteronia Oliv.)的两个种作为单系得到了100％的靴带支持,且和槭属作为姐妹群也得到了较好的支持。     

Intraspecies Analysis: Comparison of ITS Sequence Data and Gene Intron Sequence Data with Breeding Data for a Worldwide Collection of Gonium pectorale

The morphologically uniform species Gonium pectorale is a colonial green flagellate of worldwide distribution. The affinities of 25 isolates from 18 sites on five continents were assessed by both DNA sequence comparisons and sexual compatibility. Complete sequences were obtained (i) for the internal transcribed spacer ITS-1 and ITS-2 regions of ribosomal DNA and (ii) for each of three single-copy spliceosomal introns, two in a small G protein and one in the actin gene. ITS sequences appeared to homogenize sufficiently rapidly to behave as a single copy gene. Intron sequence differences between isolates in this species reached nucleotide substitution saturation, while ITS sequences did not. Parsimony and evolutionary distance analysis of the two types of DNA data gave essentially the same tree conformation. By all these criteria, the group of G. pectorale isolates fell into two main clades, A and B. Clade A, with isolates from four continents, was comprised of four subclades of quite closely related isolates, plus one strain of ambiguous affinity. Clade B was comprised of two subclades represented by South African and South American isolates, respectively; thus, only subclades of clade B showed geographical localization. With respect to mating, all isolates except one homothallic strain and one apparently sterile strain fell into either one or the other of two mating types. Pairings in all possible combinations revealed that isolates from the same site formed abundant zygotes, which germinated to produce new, sexually active organisms. Zygotes were also formed in many pairings of other combinations, including crosses of clade A with clade B organisms, but none of the latter produced viable germlings. The ability to mate and produce viable progeny that were themselves capable of sexual reproduction was restricted to members of subclades established on the basis of DNA sequence similarities. Thus, the grades of difference in both nuclear intron sequences and rDNA ITS sequences paralleled those observed in the sexual analysis. Received: 9 March 1998 / Accepted: 1 June 1998     

Exact Maximum Likelihood Estimates of Cox's Regression Parameters Based on Categorized Factorial Data

This paper describes how Cox's Proportional Hazards model may be used to analyze dichotomized factorial data obtained from a right-censored epidemiological study where time to response is of interest. Exact maximum likelihood estimates of the relative mortality rates are obtained for any number of prognostic factors, as well as their joint asymptotic sampling distribution. These rates represent excess mortality due to the various levels of the prognostic factors. The results are used to discuss the effect of the factors on the survival probability distribution of a cohort of industrial workers who have been exposed to a carcinogen. Kaplan-Meier estimates of the survival function of the internal control population are used to determine the expected number of deaths in the study population. This method differs from the usual lite-table procedure. Asymptotic tests are proposed for some simultaneous and conditional statistical hypotheses.     

天麻ITS序列分析及变异类型鉴定

目的:选取天麻3种变型有代表性的样品进行ITS序列(DNA基因的内转录间隔区宇列)测序分析,从分子水平对天麻不同变异类型亲缘关系作出鉴定.方法:采用改进CTAB法提取天麻DNA,利用合成的特异引物对其DNA中ITS区进行扩增、克隆,对目的片段测序分析.结果:黄天麻和绿天麻首先构成两个姊妹群,它们的遗传距离约为25,乌天麻与它们的遗传距离约为50,而且它们之间的遗传距离都达到了100%的置信度.其中ITS1的209个碱基中仅仅有15个位点的差异,相同碱基数目达到92.8%,这15个变异位点可作为天麻变型间的特异性鉴定.结论:表明ITS区序列分析可作为鉴定天麻不同变异类型的一种新方法.     

Phylogenetic Position of Mammoth and Steller's Sea Cow Within Tethytheria Demonstrated by Mitochondrial DNA Sequences

Here we report DNA sequences from mitochondrial cytochrome b gene segments (1,005 base pairs per species) for the extinct woolly mammoth (Mammuthus primigenius) and Steller's sea cow (Hydrodamalis gigas) and the extant Asian elephant (Elephas maximus), the Western Indian manatee (Trichechus manatus), and the hyrax (Procavia capensis). These molecular data have allowed us to construct the phylogeny for the Tethytheria. Our molecular data resolve the trichotomy between the two species of living elephants and the mammoth and confirm that the mammoth was more closely related to the Asian elephant than to the African elephant. Our data also suggest that the sea cow–dugong divergence was likely as ancient as the dugong–manatee split, and it appears to have been much earlier (22 million years ago) than had been previously estimated (4–8 million years ago) by immunological comparison. Received: 8 August 1996 / Accepted: 30 September 1996     

Dynamic Evolution of Oryza Genomes Is Revealed by Comparative Genomic Analysis of a Genus-Wide Vertical Data Set

Oryza (23 species; 10 genome types) contains the world's most important food crop — rice. Although the rice genome serves as an essential tool for biological research, little is known about the evolution of the other Oryza genome types. They contain a historical record of genomic changes that led to diversification of this genus around the world as well as an untapped reservoir of agriculturally important traits. To investigate the evolution of the collective Oryza genome, we sequenced and compared nine orthologous genomic regions encompassing the Adh1-Adh2 genes (from six diploid genome types) with the rice reference sequence. Our analysis revealed the architectural complexities and dynamic evolution of this region that have occurred over the past ~15 million years. Of the 46 intact genes and four pseudogenes in the japonica genome, 38 (76%) fell into eight multigene families. Analysis of the evolutionary history of each family revealed independent and lineage-specific gain and loss of gene family members as frequent causes of synteny disruption. Transposable elements were shown to mediate massive replacement of intergenic space (>95%), gene disruption, and gene/gene fragment movement. Three cases of long-range structural variation (inversions/deletions) spanning several hundred kilobases were identified that contributed significantly to genome diversification.     

On the Estimation of Relative Risks and Longevities of a Class of Cancer Patients Based on Randomly Censored Data

An attempt has been made to measure the relative risks and longevities of a group of cancer patients using a Weibull model whose parameters are function of covariatcs (viz treatment and condition of the patient). The methodology is Cox's Partial Likelihood and the Maximum Likelihood techniques for randomly censored data. The data consists of the records of 134 patients under a clinical trial in the treatment of Carcinoma of the Oro Pharynx as quoted by Kalbfleisch and Prentice (1980).     

kakusan: a computer program to automate the selection of a nucleotide substitution model and the configuration of a mixed model on multilocus data

The application of different substitution models to each gene (a.k.a. mixed model) should be considered in model‐based phylogenetic analysis of multigene sequences. However, a single molecular evolution model is still usually applied. There are no computer programs able to conduct model selection for multiple loci at the same time, though several recently developed types of software for phylogenetic inference can handle mixed model. Here, I have developed computer software named ‘kakusan’ that enables us to solve the above problems. Major running steps are briefly described, and an analysis of results with kakusan is compared to that obtained with other program.     

Evolution of the Gibbon Subgenera Inferred from CytochromebDNA Sequence Data

DNA sequences for the mitochondrial cytochromebgene from the four extant gibbon subgenera are described. The data confirm that the gibbon subgenera evolved from a common hylobatid ancestor and suggest that they diverged from each other after the divergence of the extant African great ape species. The cytochromebgene does not resolve the evolutionary relationships between the gibbon subgenera themselves.     

利用肠道菌群的分布和16S DNA序列研究鲤科肠道菌系统演化关系

肠道微生物与寄主具有复杂的、多方面的相互依存效应,这种依存效应所产生的共生关系或协同进化关系既可反映寄主间的系统演化关系,也可显示肠道微生物间的系统演化关系,共生关系或协同进化关系是由于寄主与肠道微生物两者之间存在着相互自然选择作用所形成的,在长期的进化历程中逐步发生的共生关系信息很可能被记录在DNA序列中。本文通过检测鱼鲤鱼科8种鱼中9种肠道菌群的分布含量对这9种菌群进行分析,且利用从GenBank调取这9种肠道细菌菌属的43个种或亚种的16S DNA序列的构建NJ树和MP树,将这6个科9个属43个种或亚种分为革兰氏阴性和革兰氏阳性两大类群（一级分枝）。在这两类群中,又以科为单位分为6个亚类群（二级分枝）,而肠杆菌科中则以属为单位分为4个小类群（三级分枝）,此外球状菌与杆状菌也能截然分开。将16S DNA的NJ树隐去所有的种,以属为单位所得到的以分枝形式的无根树在拓扑结构上与菌群分布含量（寄主范围）所构建的无根树相近,但芽孢杆菌在两种无根树的位置中有较大的差异。如果提高检测水平,扩大所检测的寄主对象,这种差异有可能消除。     

Statistical Analysis of the Comet Assay Using a Mixture of Gamma Distributions

Tail moments in the single cell gel electrophoresis (comet) assay usually do not follow a normal distribution, making the statistical analysis complicated. Researchers have used a wide variety of statistical techniques in an attempt to overcome this problem. In many cases, the tail moments follow a bimodal distribution that can be modeled with a mixture of gamma distributions. This bimodality may be due to cells being in two different stages of the cell cycle at the time of treatment. Maximum likelihood, modified to accommodate censored data, can be used to estimate the five parameters of the gamma mixture distribution for each slide. A weighted analysis of variance on the parameter estimates for the gamma mixtures can be performed to determine differences in DNA damage between treatments. These methods were applied to an experiment on the effect of thymidine kinase in DNA damage and repair. Analysis based on the mixture of gamma distributions was found to be more statistically valid, more powerful, and more informative than analysis based on log-transformed tail moments.     

Investigating the Different Mechanisms of Genotoxic and Non-Genotoxic Carcinogens by a Gene Set Analysis

Based on the process of carcinogenesis, carcinogens are classified as either genotoxic or non-genotoxic. In contrast to non-genotoxic carcinogens, many genotoxic carcinogens have been reported to cause tumor in carcinogenic bioassays in animals. Thus evaluating the genotoxicity potential of chemicals is important to discriminate genotoxic from non-genotoxic carcinogens for health care and pharmaceutical industry safety. Additionally, investigating the difference between the mechanisms of genotoxic and non-genotoxic carcinogens could provide the foundation for a mechanism-based classification for unknown compounds. In this study, we investigated the gene expression of HepG2 cells treated with genotoxic or non-genotoxic carcinogens and compared their mechanisms of action. To enhance our understanding of the differences in the mechanisms of genotoxic and non-genotoxic carcinogens, we implemented a gene set analysis using 12 compounds for the training set (12, 24, 48 h) and validated significant gene sets using 22 compounds for the test set (24, 48 h). For a direct biological translation, we conducted a gene set analysis using Globaltest and selected significant gene sets. To validate the results, training and test compounds were predicted by the significant gene sets using a prediction analysis for microarrays (PAM). Finally, we obtained 6 gene sets, including sets enriched for genes involved in the adherens junction, bladder cancer, p53 signaling pathway, pathways in cancer, peroxisome and RNA degradation. Among the 6 gene sets, the bladder cancer and p53 signaling pathway sets were significant at 12, 24 and 48 h. We also found that the DDB2, RRM2B and GADD45A, genes related to the repair and damage prevention of DNA, were consistently up-regulated for genotoxic carcinogens. Our results suggest that a gene set analysis could provide a robust tool in the investigation of the different mechanisms of genotoxic and non-genotoxic carcinogens and construct a more detailed understanding of the perturbation of significant pathways.     

Comparison of Bayesian and maximum likelihood bootstrap measures of phylogenetic reliability

Owing to the exponential growth of genome databases, phylogenetic trees are now widely used to test a variety of evolutionary hypotheses. Nevertheless, computation time burden limits the application of methods such as maximum likelihood nonparametric bootstrap to assess reliability of evolutionary trees. As an alternative, the much faster Bayesian inference of phylogeny, which expresses branch support as posterior probabilities, has been introduced. However, marked discrepancies exist between nonparametric bootstrap proportions and Bayesian posterior probabilities, leading to difficulties in the interpretation of sometimes strongly conflicting results. As an attempt to reconcile these two indices of node reliability, we apply the nonparametric bootstrap resampling procedure to the Bayesian approach. The correlation between posterior probabilities, bootstrap maximum likelihood percentages, and bootstrapped posterior probabilities was studied for eight highly diverse empirical data sets and were also investigated using experimental simulation. Our results show that the relation between posterior probabilities and bootstrapped maximum likelihood percentages is highly variable but that very strong correlations always exist when Bayesian node support is estimated on bootstrapped character matrices. Moreover, simulations corroborate empirical observations in suggesting that, being more conservative, the bootstrap approach might be less prone to strongly supporting a false phylogenetic hypothesis. Thus, apparent conflicts in topology recovered by the Bayesian approach were reduced after bootstrapping. Both posterior probabilities and bootstrap supports are of great interest to phylogeny as potential upper and lower bounds of node reliability, but they are surely not interchangeable and cannot be directly compared.     

Comparison of statistical methods for the analysis of limiting dilution assays

Summary This study reports the results of a critical comparison of five statistical methods for estimating the density of viable cells in a limiting dilution assay (LDA). Artificial data were generated using Monte Carlo simulation. The performance of each statistical method was examined with respect to the accuracy of its estimator and, most importantly, the accuracy of its associated estimated standard error (SE). The regression method was found to perform at a level that is unacceptable for scientific research, due primarily to gross underestimation of the SE. The maximum likelihood method exhibited the best overall performance. A corrected version of Taswell's weighted-mean method, which provides the best performance among all noniterative methods examined, is also presented.