Julius B. Lucks/Meetings and Notes/SMBE2007/eukaryotic prokaryotic genome beginnings

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Doug Erwin : Are bilaterian animals overdesigned? The early origins of the bilaterian developmental toolkit.

Tue Jun 26 09:58:49 EDT 2007

  • Smithsonian - curator of the Burgess Shale - one of 2 keys to the room (director has other)

Words to Look Up

  • Ediacran - period preceeding Cambrian
  • Hox genes


  • Metazoan Diversification: Fossil Record
  • evol in animals prolonged historical event
    • 1st sponge biomarkers 635 mya
  • increase in num taxa - 2 stages
  • book - Wonderful Life (Steven Jay Gould - 1989)
    • diff between taxonomic divers and disparity (morphological diver)
    • major radiation of morpho forms in Cambrian followed by winnowing
  • constrained diversification
    • rapid increases in morpho disparity
      • look quantitatively at the morpho


Peter Gogarten : Gene transfer, symbiosis, and most recent common ancestors

Tue Jun 26 09:59:30 EDT 2007

  • UConn

Words to Look Up

  • plastid


  • tracing characteris through tree/net of life
    • Darwin's coral of life, coalescence, radiation, Adam and Eve
    • coral of life since the core is dead
  • Origin of the Primary Plastids
    • Chlamidya - a third partner?
  • Cenancestor - last universal common ancestor (LUCA)
    • at the point of its existence, many organisms living at same time - long time away from origin of life
  • Coalescence - process of tracing lineages backwards in time to their common ancest. Every 2 extant leniages coalesce to most recent common ances. Even all lineages coalesce to cenancestor
  • Y chromosome Adam - lived 50,000 years ago - Thomson PNAS 2000, 97, 7280
  • Mitochondrial Eve - 166,000-249,000 years ago - Cann, R. L., 1987, Nature, 326, 31
    • adam and eve never met
    • same is true for ancestral rRNAs, EF, SRP, ATPases

Red Algal and Green Plant Genes of Chlamydial Origin


James Lake : Genome beginnings - rooting the tree of life

Tue Jun 26 10:00:02 EDT 2007

  • very good speaker

Words to Look Up

  • mevalonate pathway


  • bioinformatics
    • work in the present - decide differences between groups
    • clustering algorithms, PCA - 4 major groups
  • phylogenomics
    • going from starting 4 groups (present) to topological relationships that get to the past
    • 27 diff sorts of patterns
    • starting point is unrooted trees
      • how can we root these
  • gene transfer
    • imposes limitations or rooting the tree
    • rampant, but not random
    • informational genes
      • DNA to protein genes
      • came to eukaryotes from achaebacterio
    • operational genes
      • household work - AA, lipid biosynthesis, etc.
      • come to eukaryotes from eubacteria
  • M. Embly, W. Martin, Nature - News and Views
    • diff views on tree of life
    • Doolittle - gene transfer so extensive, can't know how groups form
    • another idea - eukaryotes so diff from prokaryotes - group into 2 classes and move on
    • ring of life - fusion of archea and bacteria to form 1st eukaryote
      • genome sequences - now can look at absences and presences
        • many ways that an absence abscence can appear
        • conditioned reconstruction - take a 3rd genome (conditioning) to identify presences - only analyze these
      • parsimony-like analysis that roots the tree
        • if fusion event, must have been present in same space-time point
        • everything after this fusion is later in the tree of life

Prokarytic Evol becomes pop driven sim to Euk evol

  • find groups that minimize gene exchange between groups
  • 4 groups
    • actinobacteria - diverse clade including many pathogens like Mycobacterium TB
    • archea
    • firmicutes (gram positive) - bacillus (anthrax)
    • double membrane prokaryotes
  • directed indels to make these determinations
    • same technique as rooting tree of life with sequences
    • parsimony arguments - see where changes ocurred wrt conditioning group - where changes occurred cannot be part of the group
    • root of TOL not within archaebacteria and eubacteria

Ubiquitous genes not needed for indel rooting

  • top-down rooting analyzes both indel presence and absence and gene p and a
    • can analyze incomplete gene sets
    • root not within double-membrane prokaryotes
  • beta-alpha-8 barrels (Tim Barrels)
    • structural motif characterized by 8 beta sheets in center, 8 alpha helices on outside
    • alpha-6: region between this and beta sheet - indel
    • 'PyrD' - pyrimidine biosynthesis - housekeeping gene


  • what is ecological basis of ring of life?
    • hydrogen hypothesis