Phylogenetic network

Abstract: A new method called the neighbor-joining method is proposed for reconstructing phylogenetic trees from evolutionary distance data. The principle of this method is to find pairs of operational taxonomic units (OTUs [= neighbors]) that minimize the total branch length at each stage of clustering of OTUs starting with a starlike tree. The branch lengths as well as the topology of a parsimonious tree can quickly be obtained by using this method. Using computer simulation, we studied the efficiency of this method in obtaining the correct unrooted tree in comparison with that of five other tree-making methods: the unweighted pair group method of analysis, Farris's method, Sattath and Tversky's method, Li's method, and Tateno et al.'s modified Farris method. The new, neighbor-joining method and Sattath and Tversky's method are shown to be generally better than the other methods.

Abstract: PAML, currently in version 4, is a package of programs for phylogenetic analyses of DNA and protein sequences using maximum likelihood (ML). The programs may be used to compare and test phylogenetic trees, but their main strengths lie in the rich repertoire of evolutionary models implemented, which can be used to estimate parameters in models of sequence evolution and to test interesting biological hypotheses. Uses of the programs include estimation of synonymous and nonsynonymous rates (d(N) and d(S)) between two protein-coding DNA sequences, inference of positive Darwinian selection through phylogenetic comparison of protein-coding genes, reconstruction of ancestral genes and proteins for molecular restoration studies of extinct life forms, combined analysis of heterogeneous data sets from multiple gene loci, and estimation of species divergence times incorporating uncertainties in fossil calibrations. This note discusses some of the major applications of the package, which includes example data sets to demonstrate their use. The package is written in ANSI C, and runs under Windows, Mac OSX, and UNIX systems. It is available at -- (http://abacus.gene.ucl.ac.uk/software/paml.html).

Abstract: The evolutionary history of a set of taxa is usually represented by a phylogenetic tree, and this model has greatly facilitated the discussion and testing of hypotheses. However, it is well known that more complex evolutionary scenarios are poorly described by such models. Further, even when evolution proceeds in a tree-like manner, analysis of the data may not be best served by using methods that enforce a tree structure but rather by a richer visualization of the data to evaluate its properties, at least as an essential first step. Thus, phylogenetic networks should be employed when reticulate events such as hybridization, horizontal gene transfer, recombination, or gene duplication and loss are believed to be involved, and, even in the absence of such events, phylogenetic networks have a useful role to play. This article reviews the terminology used for phylogenetic networks and covers both split networks and reticulate networks, how they are defined, and how they can be interpreted. Additionally, the article outlines the beginnings of a comprehensive statistical framework for applying split network methods. We show how split networks can represent confidence sets of trees and introduce a conservative statistical test for whether the conflicting signal in a network is treelike. Finally, this article describes a new program, SplitsTree4, an interactive and comprehensive tool for inferring different types of phylogenetic networks from sequences, distances, and trees.

Abstract: 1. Molecular basis of evolution 2. Evolutionary changes of amino acid sequences 3. Evolutionary changes of DNA sequences 4. Synonymous and nonsynonymous nucleotide substitutions 5. Phylogenetic trees 6. Phylogenetic inference: Distance methods 7. Phylogenetic inference: Maximum parsimony methods 8. Phylogenetic inference: Maximum likelihood methods 9. Accuracies and statistical tests of phylogenetic trees 10. Molecular clocks and linearized trees 11. Ancestral nucleotide and amino acid sequences 12. Genetic polymorphism and evolution 13. Population trees from genetic markers 14. Perspectives Appendices A. Mathematical sumbols and notations B. Geological timescale C. Geological events in the Cenozoic and Meszoic eras D. Evolution of organisms based on the fossil record

Abstract: DNA-sequence data from the mitochondrial genome are being used with increasing frequency to estimate phylogenetic relationships among animal taxa. The advantage to using DNA-sequence data is that many of the processes governing the evolution and inheritance of DNA are already understood. DNA data, however, do not guarantee the correct phylogenetic tree because of problems associated with shared ancestral polymorphisms and multiple substitutions at single nucleotide sites. Knowledge of evolutionary processes can be used to improve estimates of patterns of relationships and can help to assess the phylogenetic usefulness of individual genes and nucleotides. This article reviews molecular processes, discusses the correction of genetic distances and the weighting of DNA data, and provides an assessment of the phylogenetic usefulness of specific mitochondrial genes. The Appendix presents a compilation of conserved polymerase chain reaction primers that can be used to amplify virtually any gene in the mitochondrial genome. DNA data sets vary tremendously in degree of phylogenetic usefulness. Correction or weighting (or both) of DNA-sequence data based on level of variability can improve results in some cases. Gene choice is of critical importance. For studies of relationships among closely related species, the use of ribosomal genes can be problematic, whereas unconstrained sites in protein coding genes appear to have fewer problems. In addition, information from studies of amino acid substitutions in rapidly evolving genes may help to decipher close relationships. For intermediate levels of divergence where silent sites contain many multiple hits, amino acid changes can be useful for construction phylogenetic relationships. For deep levels of divergence, protein coding genes may be saturated at the amino acid level and highly conserved regions of ribosomal RNA and transfer RNA genes may be useful. Because of the arbitrariness of taxonomic categories, no sweeping generalizations can be made about the taxonomic rank at which particular genes are useful. As more DNA-sequence data accumulate, we will be able to gain an even better understanding of the way in which genes and species evolve.