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

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

Talk

• 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

Talk

• 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

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

Talk

• 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

Questions

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