Molecular Evolution and Phylogenetics

During the last ten years, remarkable progress has occurred in the study of molecular evolution. Among the most important factors that are responsible for this progress are the development of new statistical methods and advances in computational technology. In particular, phylogenetic analysis
of DNA or protein sequences has become a powerful tool for studying molecular evolution. Along with this developing technology, the application of the new statistical and computational methods has become more complicated and there is no comprehensive volume that treats these methods in depth.
Molecular Evolution and Phylogenetics fills this gap and present various statistical methods that are easily accessible to general biologists as well as biochemists, bioinformatists and graduate students. The text covers measurement of sequence divergence, construction of phylogenetic trees,
statistical tests for detection of positive Darwinian selection, inference of ancestral amino acid sequences, construction of linearized trees, and analysis of allele frequency data. Emphasis is given to practical methods of data analysis, and methods can be learned by working through numerical
examples using the computer program MEGA2 that is provided.

This book presents the statistical methods that are useful in the study of molecular evolution and illustrates how to use them in actual data analysis. Molecular evolution has been developing at a great pace over the past decade or so, driven by the huge increase in genetic sequence data from many organisms, the improvement of high-speed microcomputers, and the development of several new methods for phylogenetic analysis. This book for graduate students and researchers, assuming a basic knowledge of evolution, molecular biology, and elementary statistics, should make it possible for many investigators to incorporate refined statistical analysis of large-scale data in their own work. Nei is one of the leading workers in this area. He and Kumar have developed a computer program called MEGA, which has been sold for about $20 to over 1900 users. For the book, the authors are thoroughly revising MEGA and will make it available via FTP. The book also included analysis using the other most popular programs for phylogenetic studies, including PAUP, PHYLIP, MOLPHY, and PAML.

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