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. Annotation. 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 analysisof 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 numericalexamples using the computer program MEGA2 that is provided Numerical Examples. 1. Molecular Basis of Evolution. 2. Evolutionary Change of Amino Acid Sequences. 3. Evolutionary Change in 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. References. Index From the time of Charles Darwin, it has been a dream for many biologists to reconstruct the evolutionary history of all organisms on Earth and express it in the form of a phylogenetic tree (Haeckel 1866). Masatoshi Nei, Sudhir Kumar. Includes Bibliographical References (p. 301-328) And Index.
