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

= 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

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

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