Summary: The program MODELTEST uses log likelihood scores to establish the model of DNA evolution that best fits the data. Availability: The MODELTEST package, including the source code and some documentation is available at http://bioag.byu.edu/zoology/crandall―lab/modeltest.html. Contact: dp47@email.byu.edu.

/pdf/modeltest-testing-the-model-of-dna-substitution-2dmippvvyz.pdf

MODELTEST: testing the model of DNA substitution.

PhyML is a phylogeny software based on the maximum-likelihood principle. Early PhyML versions used a fast algorithm performing nearest neighbor interchanges to improve a reasonable starting tree topology. Since the original publication (Guindon S., Gascuel O. 2003. A simple, fast and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst. Biol. 52:696-704), PhyML has been widely used (>2500 citations in ISI Web of Science) because of its simplicity and a fair compromise between accuracy and speed. In the meantime, research around PhyML has continued, and this article describes the new algorithms and methods implemented in the program. First, we introduce a new algorithm to search the tree space with user-defined intensity using subtree pruning and regrafting topological moves. The parsimony criterion is used here to filter out the least promising topology modifications with respect to the likelihood function. The analysis of a large collection of real nucleotide and amino acid data sets of various sizes demonstrates the good performance of this method. Second, we describe a new test to assess the support of the data for internal branches of a phylogeny. This approach extends the recently proposed approximate likelihood-ratio test and relies on a nonparametric, Shimodaira-Hasegawa-like procedure. A detailed analysis of real alignments sheds light on the links between this new approach and the more classical nonparametric bootstrap method. Overall, our tests show that the last version (3.0) of PhyML is fast, accurate, stable, and ready to use. A Web server and binary files are available from http://www.atgc-montpellier.fr/phyml/.

https://www.zora.uzh.ch/id/eprint/155669/1/ZORA_NL_155669.pdf

New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0

A set of oligonucleotide primers capable of initiating enzymatic amplification (polymerase chain reaction) on a phylogenetically and taxonomically wide range of bacteria is described along with methods for their use and examples. One pair of primers is capable of amplifying nearly full-length 16S ribosomal DNA (rDNA) from many bacterial genera; the additional primers are useful for various exceptional sequences. Methods for purification of amplified material, direct sequencing, cloning, sequencing, and transcription are outlined. An obligate intracellular parasite of bovine erythrocytes, Anaplasma marginale, is used as an example; its 16S rDNA was amplified, cloned, sequenced, and phylogenetically placed. Anaplasmas are related to the genera Rickettsia and Ehrlichia. In addition, 16S rDNAs from several species were readily amplified from material found in lyophilized ampoules from the American Type Culture Collection. By use of this method, the phylogenetic study of extremely fastidious or highly pathogenic bacterial species can be carried out without the need to culture them. In theory, any gene segment for which polymerase chain reaction primer design is possible can be derived from a readily obtainable lyophilized bacterial culture.

16S ribosomal DNA amplification for phylogenetic study.

jModelTest is a new program for the statistical selection of models of nucleotide substitution based on "Phyml" (Guindon and Gascuel 2003. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol. 52:696-704.). It implements 5 different selection strategies, including "hierarchical and dynamical likelihood ratio tests," the "Akaike information criterion," the "Bayesian information criterion," and a "decision-theoretic performance-based" approach. This program also calculates the relative importance and model-averaged estimates of substitution parameters, including a model-averaged estimate of the phylogeny. jModelTest is written in Java and runs under Mac OSX, Windows, and Unix systems with a Java Runtime Environment installed. The program, including documentation, can be freely downloaded from the software section at http://darwin.uvigo.es.

/pdf/jmodeltest-phylogenetic-model-averaging-4hpp3p5d0f.pdf

jModelTest: Phylogenetic Model Averaging

Model selection is a topic of special relevance in molecular phylogenetics that affects many, if not all, stages of phylogenetic inference. Here we discuss some fundamental concepts and techniques of model selection in the context of phylogenetics. We start by reviewing different aspects of the selection of substitution models in phylogenetics from a theoretical, philosophical and practical point of view, and summarize this comparison in table format. We argue that the most commonly implemented model selection approach, the hierarchical likelihood ratio test, is not the optimal strategy for model selection in phylogenetics, and that approaches like the Akaike Information Criterion (AIC) and Bayesian methods offer important advantages. In particular, the latter two methods are able to simultaneously compare multiple nested or nonnested models, assess model selection uncertainty, and allow for the estimation of phylogenies and model parameters using all available models (model-averaged inference or multimodel inference). We also describe how the relative importance of the different parameters included in substitution models can be depicted. To illustrate some of these points, we have applied AIC-based model averaging to 37 mitochondrial DNA sequences from the subgenus Ohomopterus (genus Carabus) ground beetles described by Sota and Vogler (2001). (AIC; Bayes factors; BIC; likelihood ratio tests; model averaging; model uncertainty; model selection; multimodel inference.) It is clear that models of nucleotide substitution (henceforth models of evolution) play a significant role in molecular phylogenetics, particularly in the context of distance, maximum likelihood (ML), and Bayesian es- timation. We know that the use of one or other model affects many, if not all, stages of phylogenetic inference. For example, estimates of phylogeny, substitution rates, bootstrap values, posterior probabilities, or tests of the molecular clock are clearly influenced by the model of evolution used in the analysis (Buckley, 2002; Buckley

Model Selection and Model Averaging in Phylogenetics: Advantages of Akaike Information Criterion and Bayesian Approaches Over Likelihood Ratio Tests

Mammalian protein metabolism

Publisher Summary Dietary proteins, through digestion in the gastrointestinal tract, furnish amino acids and polypeptides, which are the raw materials needed to build the body proteins of animals. These body proteins essentially form the matrix of the living system; the centers around which the dynamic equilibria of life develop. This chapter focuses on the biological evaluation of these proteins. The biological value of a protein refers to the amount of nitrogen retained in the body of an animal. A new phase of research on the nutritive value of proteins includes mixtures of amino acids replacing proteins. The pattern of essential amino acids varies with the physiological state of the animal and with the species. The retention of nitrogen in the animal is a function of this pattern. The simplest method used to evaluate nitrogen retention in an animal is to determine the difference between nitrogen intake and nitrogen excreted. This difference, called nitrogen balance, shows whether an animal is maintaining, losing, or gaining nitrogen. Correlations between the nutritive value of a protein and the amino acid composition can be excellent, when the composition represents the pattern of amino acids, which are absorbed into the animal. Along with the evaluation through nitrogen balance, evaluation of proteins through growth and tissue regeneration is also presented.

Biological Evaluation of Proteins

The concept and significance of labile and over-all protein reserves of the body

The Relation between Absorbed Nitrogen, Nitrogen Balance and Biological Value of Proteins in Adult Dogs Two Figures

Food protein nitrogen, entering into the dynamic equilibrium of the body, develops a characteristic nitrogen balance, reflecting the retention of nitrogen by the body. Recognizing the fundamental nature of the fraction of nitrogen retained in the body, Mitchell and others (1944) have called i t the “biological value” of the protein. The significance of “biological value” ( B V ) correlated with nitrogen balance ( N B ) and absorbed nitrogen ( A N ) , was illustrated by Allison and Anderson (1945), in the following equation:

James B. Allison

Papers

Mammalian protein metabolism

Biological Evaluation of Proteins

The concept and significance of labile and over-all protein reserves of the body

The Relation between Absorbed Nitrogen, Nitrogen Balance and Biological Value of Proteins in Adult Dogs Two Figures

The determination of the nitrogen balance index in normal and hypoproteinemic dogs