mol. phy

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wvuong
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182097
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mol. phy
Updated:
2012-11-06 15:33:59
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mol ecology
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midterm II F12
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  1. What is phylogeny?
    evolutionary history of a group of organisms
  2. what is a phylogenetic tree?
    shows ancestor-descendant relationships among populations or species 
  3. what is monophyletic group? called anything else? 
    • called clade/lineage
    • -means an ancestor and all of its descendants forms this 
  4. Nodes of phylgenetic tree is?
    branches? 
    topology?
    • nodes: branching points 
    • branches: lines 
    • topology: branching pattern
  5. what is sister taxa?
    two taxa that are more closely related to each other than either is to a 3rd taxon
  6. Monophyletic groups are? 
    clades that contain all of the descendants and their coommon ancestor 
  7. paraphyletic groups are? 
    do not include all of descendants of an ancestor 
  8. what are polyphyletic groups?
    contain descendents of more than a single ancestor
  9. what is hard polytomy?
    simultaneous divergence
  10. soft polytomy?
    lack of resolution
  11. rooted tree means?
    unique path from root
  12. unrooted tree means?
    degree of kinship, no evolutionary path
  13. Cladogram?
    depicts relative recency of common ancestry among taxa 
  14. additive tree?
    depicts amount of change between taxa along tree branches (# of substitutions)
  15. ultrametric tree?
    depicts time of divergence of taxa 
  16. Newick (shorthand) format
    text based representation of relationships
  17. What is the differ between true and inferred trees? 
    true tree: actual phylogenetic history of a group, which can only be known in case of simulation studies 

    inferred tree: phylogenetic hypothesis generated from data from living or fossil organisms 
  18. what is the differ between quantitative and qualitative data?
    quantitative: continuous data (ie. height/length)

    • qualitative: discrete (2 or more values)
    • if binary; 2 values
    • if multistate, more htan 2 values
  19. what are most molecular data?
    • most molecular data are qualitative
    • binary: presen/ absence of band, or gap in sequence
    • multi state: nucleotide data (A, T, G, C, -)
  20. nucleotide character data. 
    characters: position in nucleotide sequence 

    character states: nucleotide at position in nucleotide sequence, or gap
  21. name the steps in phylogenetic analysis 
    • 1. produce data se- sequence or download sequences 
    • 2. multiple sequence alighment 
    • 3. build trees -choose method, run programs 
    • 4. assess the trees - bootstrapping 
  22. what is the most critical step in phylogenetic analysis? 
    Alignment 
  23. what are the methods of tree reconstruction? 
    • max. parsimony
    • distance method
    • max likelihood
    • bayesian inference 
  24. what is max. parsimony?
    gen. scientific criterion for choosing among competing hypotheses that states that we should accept hypothesis that explains the data most simply and efficiently 

    most likely tree (best hypothesis) - the one with fewest number of change sto explain the data 
  25. cladistics?
    • uses synapomorphies aone to estab. recent common ancestry
    • relies solely on synapomorphies to define monophyletic clades (natural groups) 
  26. synapomorphy:
    shared derived character; shared by more than one species or group
  27. autapomorphy.
    derived character that is unique to single species or group (unique derived character)
  28. homoplasy.
    • non-homologous similarity
    • resemblance not due to common ancestry
    • evolved independently
  29. what are the strengths and weaknesses of the tree.
    • strength: simple, efficient alogrithms, good for morphological data 
    • weakness: cant correctfor multiple substitutions, long branch attraction
  30. distance methods. 
    evolutionary distances (# of substitutions) are computed for all pairs of taxa 
  31. neighbor joining method, what are the strenghts and weaknesses?
    • strengths: fast
    • weak: performs poorly with divergent sequences 
  32. describe max. likelihood method. 
    • finds tree that max. prob. of observing the data 
    • under a given tree and specified model of character state changes 
    • aim: to find tree (among all possible trees) wtih highest L value
  33. Learn how to calculate likelihood - slide 43.  look at book.  
  34. strenghts and weakness for likelihood?
    • strengths: explicit model of sequence evolution
    • weak: computationally damanding 
  35. bayes's theorem.  look at book
    slide 48
  36. strength and weakness for bayes's theorem
    • strength: consistent, efficient, less computationally damanding than ML 
    • weak: philosophical 
  37. consensus methods. 
    trees derived from set of trees and summariez phylogenetic info of several treesi n a single tree 
  38. what is the most commonly used consensus tree?
    strict consensus
  39. what is strict consensus?
    all ocnflucting branching patterns are collapsed 
  40. Bootstrap method.  look at book.  
    slide 53 

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