Molecular Systematics and Evolution: Theory and Practice

1. Evolutionary analysis at different levels. - to part 1. - Cladistics, populations and species in geographical space: the case of Heliconius butterflies. - Species to genera: phylogenetic inference in the Hawaiian Drosophilidae. - Higher-level systematic analysis of birds: current problems and possible solutions. - Relative quality of different systematic datasets for cetartiodactyl mammals: assessments within a combined analysis framework. - Phylogeny of the holometabolous insect orders based on 18S ribosomal DNA: when bad things happen to good data. - Relationships among metazoan phyla as inferred from 18S rRNA sequence data: a methodological approach. - 2. Current problems in molecular systematics. - to part 2. - DNA multiple sequence alignments. - Theory and practice of parallel direct optimization. - Some statistical aspects of the maximum parsimony method. - `Pluralism and the aims of phylogenetic research. - Molecular systematics and the origin of species: new syntheses or methodological introgressions? . - Is morphology still relevant? . - Development, homology and systematics. - 3. New approaches to molecular evolution. - to part 3. - Gene family phylogenetics: tracing protein evolution on trees. - Evolution of spider silk proteins: insight from phylogenetic analyses. - Comparative methods and evolution. - The use of physiological data to corroborate cospeciation events in symbiosis. - Reexamining microbial evolution through the lens of horizontal transfer. - References.