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.