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Unformatted text preview: 1 Integrative Biology 200A “PRINCIPLES OF PHYLOGENETICS” Spring 2008 University of California, Berkeley Kipling Will 12 Feb. More on Characters and Character Coding To Reiterate and expand some ideas- Why are characters as or more important than the method of analysis ? Given a chosen algorithm and a set of coded characters with their assumed homology the set of trees is given. Different tree generating methods often result in the same or similar relationships. However, changing characters and character coding usually changes the actual meaning and interpretation of the evolution of the group (think about transformation series, hypothetical ancestors and branch lengths). - Hennig’s Auxiliary Principle- Assume homology in the absence of contrary evidence. - Conjectural homology assessment (similarity, etc.) prior to cladistic analysis and corroborated homology assessment (homology [underlying process] = synapomorphy [pattern]) and homoplasy [pattern not due to a common process] after cladistic analysis. - Characters = Transformation series= columns in matrix - Character states= cell entries in matrix - Characters states are the alternative forms of characters observed in the semaphorant. - Character states are sub-grouping of characters, and characters are in turn states at a higher-level or dependent on states at a higher level. - When the analysis results in corroboration of our initial hypotheses all superordinate characters remain unchallenged. -When the analysis results in a pattern of homoplasy, i.e., our initial assumption of homology was wrong , the error could be at any level. We may decide that re-coding is appropriate. - At some level no characters are absolutely independent. The level of non- independence varies along a gradient from negligible to covariance. - Coding is an abstraction of observations. -Coding is a state-ordering process. -Methods require discrete states. Universe of all features Variable U s e f u l f o r i d e n t i f i c a t i o n Describable No historical information Historically informative A perfect matrix would contain only characters from this upper right portion. In reality a matrix is composed of a mix of describable and variable characters, some mislead us and some show a pattern of homoplasy. Universe of all features Variable U s e f u l f o r i d e n t i f i c a t i o n Describable No historical information Historically informative A perfect matrix would contain only characters from this upper right portion....
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This note was uploaded on 08/01/2008 for the course IB 200 taught by Professor Lindberg,mishler,will during the Spring '08 term at Berkeley.
- Spring '08