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Molecular systematic methods have been applied in most fields of biology to provide an evolutionary framework whenever comparisons are made among individuals, populations, or higher taxa. The first edition of Molecular Systematics became a standard reference for this vigorous field by describing each aspect of the planning, execution, and analysis of a molecular systematic study. The Second Edition updates and expands this coverage, and includes considerable information on new molecular techniques and methods of analysis. Molecular Systematics includes chapters on sampling design, the collection and storage of tissues, each of the major molecular techniques, and intraspecific and phylogenetic analysis. The sampling chapters describe how to plan a study and how to collect, transport, and store the appropriate tissues for each study. The techniques chapters cover principles, assumptions, applications, limitations, and protocols for isozyme electrophoresis, molecular cytogenetics, DNA hybridization, the polymerase chain reaction, restriction site and fragment analysis, and nucleic acid sequencing and alignment. Advantages and disadvantages of alternative approaches are discussed for each technique, and recent developments (such as new methods of fluorescent in situ hybridization, rapid screening methods for detecting DNA sequence variation, automated sequencing methods, new approaches for PCR, and microsatellite analyses) are detailed. Three additional chapters cover the rationale and methodology of molecular data analysis at both the population and interspecific levels, and provide information on using and obtaining the relevant computer programs (including the many programs available for free across the Internet). The chapter on phylogenetic analysis has been considerably expanded to include the latest developments in maximum likelihood analysis, spectral analysis, methods for reconstructing reticulating networks, corrections for compl