Lect_4_characters - Integrative Biology 200A "PRINCIPLES OF...

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Integrative Biology 200A "PRINCIPLES OF PHYLOGENETICS" Spring 2008 University of California, Berkeley B.D. Mishler Jan. 31, 2008 . Character Analysis A. Introduction to the logic of the data matrix: The process of phylogenetic analysis per se inherently consists of two phases: first a data matrix is assembled, then a phylogenetic tree is inferred from that matrix. There is obviously some feedback between these two phases, yet they remain logically distinct parts of the overall process. One could easily argue that the first phase of phylogenetic analysis is the most important; the tree is basically just a re-representation of the data matrix with no value added. Paradoxically, despite the logical preeminence of data matrix construction in phylogenetic analysis, by far the largest effort in phylogenetic theory has been directed at the second phase of analysis, the question of how to turn a data matrix into a tree. At stake are each of the logical elements of the data matrix: the rows (what are the terminal units or OTUs?), the columns (what are the characters?), and the individual entries (what are the character states?). The elements of a data matrix (note the interlocking definitions): OTU = group of semaphoronts that can’t be subdivided given current character data Character = an apparently homologous feature, independently varying among OTUs Character-state = a discrete condition within a character, potentially a phylogenetic marker B. What is an OTU? These are represented by rows in the data matrix. People are usually cavalier about what their terminal branches represent. One often sees species or other taxon names, or even geographic designations of populations, attached to terminal branches of published trees without explanation. Larger-scale units might indeed be a well-justified OTU, but they need to be justified by preliminary analyses, never assumed a priori. Taxa or populations are never the fundamental things from which phylogenies are actually built. Not even individuals are the OTUs -- so what is the fundamental OTU? As was carefully elaborated by Hennig (1966), the fundamental terminal entity in phylogenetics is the semaphoront , an instantaneous time slice of an individual organism at some point in its ontogeny. A tube of extracted DNA and its associated museum voucher specimen, photos, data, etc. —a semaphoront— should be considered the ultimate unit. An OTU can then be best defined as: an agglomeration of semaphoronts that are not divisible by the characters currently known. Hence, the interrelationship between the concept of OTU and character.
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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 University of California, Berkeley.

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Lect_4_characters - Integrative Biology 200A "PRINCIPLES OF...

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