Julius B. Lucks/Meetings and Notes/SMBE2007/lateral gene transfer the ring web or network of life

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James McInerny : What does it mean when we make a Tree of life from genomes?

Wed Jun 27 12:36:22 EDT 2007

Words to Look Up

  • Robertson Foulds distance (tree distance method)

Talk

  • early 80s - Carl Woese added archea via 16/18S rRNA trees
  • 1995 - H. Influenzae sequenced - shortly later 2 strains of E. coli
    • 2 strains of E. coli - same species - 25% different genome sizes
  • differences in phylogenetic trees when use 16S rRNA or pseudouridine tRNA
    • lots of lateral transfer of genes
  • Ford Doolittle - Nov 1999 - Science
    • 'most archael and bact genes contain genes from multiple sources'
    • 'if lgt can be limited to special categories of gene, then no heirarchical classification can be taken as natural'
  • Darwin - 'a classification based on any single character, however important that may be, has always failed.'
  • look at all the trees - do they agree or not?
  • supertree approach
    • amalgamate information from disparate data sources (extension of consensus approach)
    • explore congruence across datasets
    • identify datasets w/ unusual features
    • Clann software
      • input trees derived from orthologs - diff sets of leaves
      • candidate supertree
      • tree to tree distance between input tree and supertree
        • prune supertree to have same set of leaves until has same set of leaves as input, then look at distance
      • score (sum distances) supertree (0 if perf compatible with all input trees, > 0 otherwise)
      • search over supertrees
      • do a permutation to create random dataset - permutation test
  • gamma proteobacteria - compatibility of each of input trees better than random
    • can have a meaningful supertree
  • deep-level prokaryotic - compatibility of each of input trees NOT better than random
    • input trees could be very bad
    • bad ortholog detection
    • horizontal transfer so pervasive that phylogenetic relationship completely eroded
  • Choi, PNAS, 104, 4489, 2007 - Global extent of horizontal gene transfer.
  • diff methods for same data give diff trees - method problem
  • see where eukaryote fitted on prokaryote tree - use supertree method
    • eukaryotes went with cyanobacteria
      • cyanobacteria endosymbiosis more recent than mitochondrial
    • removed - went with alpha-proteobacteria (mitochondrial endosymbiosis)
    • removed - went in middle of archaea (thermoplasmatalis)
  • bacteria and archaea not monopdylecit
  • eukaryo are monophyletic, but have 3 parents (cyanobacteria, alpho-proteobacteria, archaea)

Questions

Ford Doolittle : Not much - testing the tree of life hypothesis

Wed Jun 27 13:00:29 EDT 2007

Words to Look Up

Talk

  • 1st slide is a tree stump
  • new title: 'The practice of classification and the theory of evolution, and what the demise of Darwins Tree of Life hypothesis means for both of them'
  • outline
    • classification
    • evolution as a theory
    • TOL specific version of an evol theory - how TOL hypoth untrue
    • implications of this for practices of classification
  • classification
    • natural and useful heman practice
    • 'our job as sytematists is not to discover wahat an organism truly is, but rather to decide what we should call it' - Baptiste and Doolittle
    • inclusive heirarchies
      • arbitrary and negotiable - dewey decimal system
      • taxanomy - we think natural and non-negotiable - not something we decide, but something we discover
        • Why this difference?
          • 2000 years of western philosophy (essentialist - things really are things)
          • species are real things
          • Darwin's TOL hypothesis - spec form of evolution that relates to classification
  • evolution as gen theory
    • 1858 William Paley - watch - intelligent design
    • 2 part theory claiming past explains present
      • (1) adaptation and (2) classification have historical, not theistic or metaphysical purpose
    • Darwin's theory - specific model how past processes affect current
      • 'from the 1st dawn of life all org beings class in groups onto groubs, not arb - something we dont decide, but discover'
      • organisms appear to be related because they are related
    • TOL - classification tree like because process of creation is tree like - one of successive branching
    • TOL - ladder which helped community to adopt larger theory of evolution
    • 1859 - tree-like class gotten credibility by association with TOL hypoth (which got further credibility)
    • Alec Panchen - 'Clossification, Evolution and the Nature of Biology', 1992
      • TOL circular argument
    • Zuckerlandl and Pauling, 1965 - basic theory of molec phylogeny
  • 1987- Woese - Bacteriological Reviews - summary of his work
    • considered lateral gene transfer
  • Claim TOL hypothesis untrue
    • Bergey's Manual (1st ed 1923) of Bacteriology - made some claims obout phylogenetic relationships
    • Welch, 2002 - 3 sequenced E. coli strains sequenced - only 40% genes overlay
      • species - many of these genes used in a species classification
    • Walsh, 2007 - more than 1/2 genes of archeae for metab have best hits in bacterio
      • phenotypes not being det by process not underlined by branching
    • eukaryotes as a whole - more a sister group to bacteria than archaea for more than 1/2 the genes
    • universal core of genes shared by all genomes - something around 30
  • implications of this untruthfulness for classification and evolution
    • many of prokaryote properties not inhereted in branching classification
    • helps to disentangle evolution and classification (used to be completely intertwined)
      • can still do phylogenies, but treat them as classifications - no 'really is' pressure anymore
        • multiple proper places for organimsm in classification scheme
    • general theory - present happened spontaneusly from the past - through general evolution
    • but evolution not a branching process

Questions

Peter Gogarten : Ancient Gene Transfer and Phylogenetic Reconstruction: Friends or Foes

Wed Jun 27 13:00:54 EDT 2007

Words to Look Up

Talk

  • can use hgt events as tool to learn more like evol history
  • alternative hypoth to observations other than hgt
    • genome duplication followed by differential gene loss

Questions

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