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lecture07 - 2 Methods of phylogenetic inference a maximum...

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BioEE 278 Fall 2007 Evolutionary Biology Lecture 7 PHYLOGENETICS II MOLECULAR PHYLOGENETICS A. DNA sequence data 1. Characteristics of sequence data that are important for phylogenetic analysis. a. large number of characters with easily recognized character states (A, T, G, C) b. consistent “rules” for character state changes c. distinct “classes” of characters with different rates of change 2. The nature of nucleotide substitutions. a. transitions and transversions b. for protein-coding genes, rates depend on codon position (synonymous and non- synonymous substitutions) c. rates of substitution in different parts of genes and in pseudogenes B. Phylogenetic inference from DNA sequences. 1. Assessing homology a. need to compare same gene or gene region across taxa b. early reliance on mtDNA and cpDNA c. homology assessment is complicated by duplication events d. two types of homology - orthology and parology
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Unformatted text preview: 2. Methods of phylogenetic inference. a. maximum parsimony b. likelihood and Bayesian approaches - depend on having a defined "model" of evolution (e.g., know rules that govern substitutions) 3. Examples of phylogenetic inference from molecular data. a. relationships among primates - humans and chimps as sister species b. the plague locust and relatives c. Hawaiian crickets - data from different genes or gene regions do not always tell the same story C. Molecular clocks. 1. Sequence divergence as a function of time a. calibrating clock rate b dating lineage splitting events from the fossil record 2. Variation in clock rate. a. among different sequences b. among different lineages c. no "universal" molecular clock SECTION ASSIGNMENT: Phylogenetic Inference. Handout will be posted on web today or tomorrow. Please read thehandout BEFORE coming to section next week....
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