Cladistics

Part 1 Cladistic theory: form - homology and analogy; special similarity; conflicting similarities and parsimony; the relations between similarities; homoplasty and the interpretation of character conflict; monophyletic, paraphyletic and polyphyletic groups; sister groups and ancestor-descendant relationships; the transformation of cladistics; phenetics; eclectic of evolutionary taxonomy. Part 2 Character coding: character types; binary characteristics; multistate characters; transformation between character states; unordered and ordered characters; additive binary coding; branched character state trees; other user-defined models of transformation; character popularity; cladograms and roots. Part 3 The determination of character polarity: outgroup comparison - the indirect method; ontogeny - the direct method; inadequate criteria; ingroup commonality; a priori models - Robertsonian changes, allelic dominance hierarchy, functional morphology, underlying synapomorphy. Part 4 Tree building techniques: parsimony criteria - Wagner, Fitch, Dollo, Camin-Sokal, polymorphism, generalized; delayed and accelerated transformations; optimization of "missing" values; x-coding; searching for the most parsimonious trees; - exact algorithms, heuristic methods. Part 5 Tree statistics, trees and "confidence", concensus trees, alternatives to parsimony, character weighting, character conflict and its resolution: tree statistics - tree length, measures of fit between trees and data; trees and confidence - bootstrap and jackknife, randomization, data decisiveness; consensus trees - strict consensus, combinable components consensus, Nelson consensus, Adams consensus; alternatives to parsimony - cliques, maximum likelihood, three-taxon statements; phenetics; character weighting; character conflict and its resolution - re-evaluation of characters, consensus trees. Part 6 DNA analysis - theory: homology, homology testing - similarity, conjunction, congruence, results of testing for homology, orthology, paralogy, xenology, paraxenology, plerology; nucleotide sequence data - the characters - substitutions, gaps, insertions and deletions (indels); tree construction - preliminaries; note on rooting trees. Part 7 DNA analysis - methods: matrix methods - definitions, distance measures, metrics, tree reconstruction - phenetic methods, distance methods, problems; parsimony methods - weighing, a priori weighting, a posteriori weighting, problems, invariants. Part 8 Fossils and cladistic analysis: fossils and ancestors; age and rank; stem groups and crown groups; influence of fossils on classification of recent organisms - missing data, basal taxa, fossils and stratigraphy. Part 9 Cladistics and biogeography: life and earth together; cladistics and biogeography - the progression rule, vacariance biogeography. (part contents)