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29 Cards in this Set
- Front
- Back
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What are the 4 major approaches to molecular phylogenetics?
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Maximum parsimony, distance methods, maximum likelihood, Bayesian posterior probability methods
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Cladistics
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phylogenies based on analysis of evolutionary patterns of particular characters, only shared derived states count
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PAUP
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program used in maximum parsimony
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Problems with maximum parsimony/PAUP
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DNA seqs have only 4 characters states and can flip back and forth, homoplasy, long branches attract artifact
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Maximum parsimony
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minimizes total number of evolutionary steps required to explain a given set of data for smaller tree
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long branches attract artifact
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more rapidly divergent the sequences, the more (by chance) they are to come together and look alike
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homoplasy
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accidentally shared/comvergent//analogous characters tthat don't reflect true evo relationships
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Distance methods
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Makes overall estimate of similarity/differences of all sequences in dataset, uses these as criterior for building tree by neighbor-joining
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neighbor-joining method
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two closest sequences joined together, then more distantly related ones added, etc
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advantages of distance methods
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good speed for large datasets, distances can be corrected to account for multi changes in distant past so better for highly divergent proteins
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drawbacks of distance methods
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ignores individual characters, throws away much detail of data
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Maximum likelihhood
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Model of how sequences are evolving used as standard to compare various possible trees to see if they best reflect the pattern
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Idea behind maximum likelihood
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DNA/protein seqs evolve in somewhat unique way in every dataset, derive model from actual data, use model as standard to compare to
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Use of own dataset vs standard model
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Large/robust dataset = can use, usually use standard model though
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PAM
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point acccepted mutation: aa exchange frequency matrix for ML trees of protein seqs
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BLOSUM62 matrix shows what?
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aa's most likely to remain same or change to chemically similar ones, higher the number = higher frequency of conversions
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Advantages of Bayesian posterior probability methods
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Sometimes provide support for branches/clusters/clades that other methods don't find/support
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Disadvantages of Bayesian posterior probability methods
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How reliable are the relationships? Takes long time to compute so hard to apply to large datasets
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Types of data for molecular phylogenetics
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allozymes, chromosome banding patterns, immunological, complete genome DNA/DNA hybridizations, DNA/protein sequences, using gene order as characters
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Determining Species level molecular phylogenetics
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use non-coding nucleotides (quickly evolving), design PCR primers to conserved flanking regions and amplify/sequence inbetween variable regions
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Determining genus level molecular phylogenetics
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Use rapidly evolving genes (ADH), 3rd codon positions in otherwises conserved genes, mito sequences
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What have the mitochondrial sequences of pocket gophers and chewing lice suggested?
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They co-speciated
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Determining family level molecular phylogenetics
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more conserved genes like rRNA genes
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Determining order level mollecular phylogenetics
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18S/28S rRNA plus morphology
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Problem with Wheeler's results
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Hymenoptera actually basal within Holometabola, Strepsitera more closely related to Coleoptera than Diptera
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Determining class level phylogenetics
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rRNA, multiple protein-coding genes
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Alternative approach to original class level phylogenetics approach
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phylogenomics: generate large EST sets from each species, extract overlapping set for each from them
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Phylum level molecular phylogenetics
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rRNA was original, now rRNA and EST analyses
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Findings of phylum level molecular phylogenetics
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Nematodes = closest relatives of arthropods, protostomes broken up into Lophotrochozoans and Ecdysozoans
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