Mar18_Reconstruction - Integrative Biology 200A"PRINCIPLES...

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± Integrative Biology 200A "PRINCIPLES OF PHYLOGENETICS" Spring 2008 University of California, Berkeley B.D. Mishler March 18, 2008 . Phylogenetic Trees I: Reconstruction; Models, Algorithms & Assumptions A. Trees -- what are they, really, and what can go wrong? Here are some important initial questions for discussion: What are phylogenetic trees, really? What do you see when you look closely at a branch? -- the fractal nature of phylogeny (is there a smallest level?) What is the relationship between characters and trees? Characters and OTUs? Characters and levels? The tree of life is inherently fractal, which complicates the search for answers to these questions. Look closely at one lineage of a phylogeny and it dissolves into many separate lineages, and so on down to a very fine scale. Thus the nature of both OTU's ("operational taxonomic units," the "twigs" of the tree in any particular analysis) and characters (hypotheses of homology, markers that serve as evidence for the past existence of a lineage) change as one goes up and down this fractal scale. Furthermore, there is a tight interrelationship between OTUs and character states, since they are reciprocally recognized during the character analysis process. B. Two approaches to tree-building What is the basic goal of tree building? How good is the fit between "reality" and a phylogenetic model designed to represent reality? These questions have many different answers depending on the background of the investigator, but there are two major schools of thought: 1. The "reconstruction" school of thought. The Hennigian phylogenetic systematics tradition, derived from comparative anatomy and morphology, focuses on the implications of individual homologies. This tradition tends to conceive of the inference process as one of reconstructing history following deductive-analytic procedures. The goal is seen as coming up with the best supported hypothesis to explain a unique past event. -- the data matrix as itself a refined result of character analysis -- each character is an independent hypothesis of taxic and transformation homology
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± -- test these independent hypotheses against each other, look for the best-fitting joint hypothesis -- straight parsimony as a "solution" to the data matrix -- only the fewest and least controversial assumptions should be used: characters are heritable and independent, and that changes in state are relatively slow as compared to branching events in a lineage -- when these hold, reconstructions for a character showing one change on one branch will be more likely than reconstructions showing two or more changes in that character on different branches. 2. The "estimation" school of thought
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Mar18_Reconstruction - Integrative Biology 200A"PRINCIPLES...

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