Data Analysis in Molecular Biology and Evolution

Since its first release in as mainly a software package for phylogenetic analysis, data analysis for molecular biology and evolution.
Table of contents

There are four nested models. The general model for nucleotide sequences does not constrain either the transition or transversion rates between the two ingroup lineages, the most restrictive model constrain both, and the two intermediate models with one constraining the transition rate and the other constraining the transversion rate. The analysis for the codon sequences is the same except that transition and transversion rates are replaced by synonymous and nonsynonymous substitution rates.

The strength in the codon-based method implemented in DAMBE is that all 18 known genetic codes are implemented. For tree-based tests of the molecular clock hypothesis, DAMBE implements both the ML method a likelihood ratio test between the clock-constrained model and the unconstrained model and the LS method Xia It performs both regular dating with internal node calibration, with single or multiple soft or hard calibration points, and tip dating frequently used for viruses sampled at different times fig.

The confidence intervals of the estimated dates are obtained by resampling. There are two sources of the variation in the estimated dates, one from the uncertainty in the calibration points e. The resampling method only assesses the variation from the sequences. The only logical way of reducing uncertainty associated with the fossil dates is to have more fossils and more calibration points. The function for assessing substitution saturation Xia, Xie, Salemi, et al. Other functions include detecting viral recombination by Simplot, Bootscan, and compatibility methods reviewed in Xia DAMBE features a versatile tree-displaying panel and a tree-drawing panel supplementary fig.

S3d , Supplementary Material online for exporting high-quality trees for publication and for tree drawing by dragging nodes to each other, and it can print large trees to multiple pages. S4 , Supplementary Material online. Detecting functional associations or correlations among the genetic G , phenotypic P , and environmental E variables are typically done by phylogeny-based comparative methods Harvey and Pagel ; Xia , , Chapter 2.

The continuous variables are analyzed by independent contrasts Felsenstein , , p. The method has been used successfully in the test of genome size and ambient temperature in salamanders Xia and in the discovery that rRNA genes in thermophilic bacteria have longer stems in their stem-loop structure as well as more GC-rich in their stems than mesophilic bacteria Wang et al.

The discrete variables e. DAMBE implements phylogeny-based comparative methods for both continuous and discrete variables. DAMBE5 is a comprehensive and user-friendly software workbench for data analysis in molecular biology and evolution.

It features a variety of analytical functions for descriptive and comparative sequence analysis, as well as functions for allele frequencies and microsatellite data. DAMBE is enhanced by a variety of graphic functions, which makes it ideal for teaching bioinformatics and molecular evolution.

DAMBE7: New and Improved Tools for Data Analysis in Molecular Biology and Evolution.

DAMBE are available free of charge from http: The author thanks his students and many colleagues who have used DAMBE and given feedback for improvement, and two anonymous reviewers for their constructive comments. Oxford University Press is a department of the University of Oxford. It furthers the University's objective of excellence in research, scholarship, and education by publishing worldwide. Sign In or Create an Account. Close mobile search navigation Article navigation. Sequence Retrieval, Manipulation, and Format Conversion. Motif Characterization and Discovery.

Introduction

Local and Global Sequence Alignment. Abstract Since its first release in as mainly a software package for phylogenetic analysis, data analysis for molecular biology and evolution DAMBE has gained many new functions that may be classified into six categories: View large Download slide. Predicting functional gene links from phylogenetic-statistical analyses of whole genomes. An evolutionary and functional analysis of FoxL2 in rainbow trout gonad differentiation.

Imputing Missing Distance and Phylogeny Simultaneously

Multiple lines of evidence for demographic and range expansion of a temperate species Hyla sarda during the last glaciation. A geographic mosaic of evolutionary lineages within the insular endemic newt Euproctus montanus. One species, three Pleistocene evolutionary histories: An extensive study of mutation and selection on the wobble nucleotide in tRNA anticodons in fungal mitochondrial genomes.


  1. A GOOD ALIBI - Peter Sharp Legal Mystery #11 (Peter Sharp Legal Mysteries)?
  2. Supplemental Content;
  3. Surprise Motherhood: A Guide to Unexpected Adult Pregnancy.
  4. Result Filters!
  5. Entrepreneurial Strategies: New Technologies in Emerging Markets (Strategic Management Society)!
  6. .

The mitochondrial genome of Sinentomon erythranum Arthropoda: Structure, evolution and expression of the FOXL2 transcription unit. Fast and accurate phylogeny reconstruction algorithms based on the minimum-evolution principle. A multilocus phylogeny of Asian noodlefishes Salangidae Teleostei: Osmeriformes with a revised classification of the family.

Rivaling the world's smallest reptiles: A simple method for estimating the parameter of substitution rate variation among sites. Correlation between the abundance of Escheriachia coli transfer RNAs and the occurrence of the respective codons in its protein genes. Use of ribosomal-RNA secondary structure in phylogenetic studies to identify homologous positions—an example of alignment and data presentation from the frogs.

Adaptive evolution of the matrix extracellular phosphoglycoprotein in mammals. GC skew in protein-coding genes between the leading and lagging strands in bacterial genomes: A likelihood approach for comparing synonymous and nonsynonymous nucleotide substitution rates, with application to the chloroplast genome.

Chromosomal speciation and molecular divergence—accelerated evolution in rearranged chromosomes.

MEGA 5 - Molecular Evolutionary Genetics Analysis

Contributions of speed and accuracy to translational selection in bacteria. Drosophila genes that affect meiosis duration are among the meiosis related genes that are more often found duplicated. The codon Adaptation Index—a measure of directional synonymous codon usage bias, and its potential applications. Prospects for inferring very large phylogenies by using the neighbor-joining method. A retrospective overview of enterovirus infection diagnosis and molecular epidemiology in the public hospitals of Marseille, France How optimized is the translational machinery in Escherichia coli , Salmonella typhimurium and Saccharomyces cerevisiae?

The rate heterogeneity of nonsynonymous substitutions in mammalian mitochondrial genes. Phylogenetic relationship among horseshoe crab species: Mutation and selection on the anticodon of tRNA genes in vertebrate mitochondrial genomes. Topological bias in distance-based phylogenetic methods: Bioinformatics and the cell: The cost of wobble translation in fungal mitochondrial genomes: Information-theoretic indices and an approximate significance test for testing the molecular clock hypothesis with genetic distances.

DNA replication and strand asymmetry in prokaryotic and mitochondrial genomes. Position weight matrix, gibbs sampler, and the associated significance tests in motif characterization and prediction. Conflict between translation initiation and elongation in vertebrate mitochondrial genomes. Genomic adaptation to acidic environment: Protein structure, neighbor effect, and a new index of amino acid dissimilarities.

Effects of GC content and mutational pressure on the lengths of exons and coding sequences. Genomic changes in nucleotide and dinucleotide frequencies in Pasteurella multocida cultured under high temperature. For commercial re-use, please contact journals. Email alerts New issue alert. Receive exclusive offers and updates from Oxford Academic. Related articles in Web of Science Google Scholar. Citing articles via Web of Science Latest Most Read Most Cited High and variable rates of repeat-mediated mitochondrial genome rearrangement in a genus of plants.

Data Analysis in Molecular Biology and Evolution

For example, when a missing distance is for two sister taxa e. The patristic distances D p. DAMBE use the midpoint distance in such cases.

For each pair of sequences, we can obtain a vector S of 10 N ij values number of pairs with nucleotide i in one sequence and j in another. With 10 sequences and 45 pairwise comparisons, there are 45 S vectors from which we can compute the 45 pairwise distances. This function complements the function of phylogenetics with imputed missing distances.

Substitution rate varies over sites and is particularly pronounced in protein-coding genes Xia DAMBE improves this estimation in two ways. First, it uses simultaneous estimation SE. Take the K80 model for example. Applying equations 3 and 4 to data from the three sites fig.

DAMBE: software package for data analysis in molecular biology and evolution.

SE generates no inapplicable cases D SE in fig. Supplementary data are available at Molecular Biology and Evolution online. National Center for Biotechnology Information , U. Published online Apr Xuhua Xia 1, 2. Sudhir Kumar, Associate editor. For commercial re-use, please contact journals. Open in a separate window. An Improved Method for Estimating the Shape Parameter of Gamma Distribution Substitution rate varies over sites and is particularly pronounced in protein-coding genes Xia Supplementary Material Supplementary Data Click here for additional data file.