Julius B. Lucks/Meetings and Notes/SMBE2007/plenary 4

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Michael Lynch : The origins of genome architecture

Thu Jun 28 06:47:29 EDT 2007

  • popularized 'mutational meltdown'
  • 'Genetics analysis of quantitative traits' - Book
  • At Indiana

Words to Look Up

  • KT boundary Extinction Event


  • all nucl on planet earch - 10^25 kilometers of DNA - 10 diameter of known universe
  • big diff between comparative genomics and evolutionary genomics (more explanitory)
    • need deep understanding of cell and mol biol
    • evol is pop genetic process
    • explain genomic diversity (and invoke natural selection) - need null hypothesis (genome evol in absence of selection)
  • pop genetic env - 4 forces of evol
    • recombination
    • mutation
    • random genetic drift
    • selection
  • complexity required for more complex phenotypes?
  • recombination rate scales with organism size
  • bigger genomes - bigger chromosomes (not more, generally)
  • scaling between genome size and mutation rate / generation
    • euk - a lat of mutations in replication
  • mobile elements
    • human genome - almost 50%
    • huge disparity in the number of these in diff genomes
    • what does it take for mobile el pop to survive inside a genome
      • parasitic DNA - accumulates at cost of host
    • avg insertion is deleterious (flies)
      • causes reduction of fitness of around 1%
    • increase host eff pop size - can eliminate del. effects by natural selection
      • avg autonomous el can't produce offspring within host lifetime
      • critical host pop size
    • unicellular species have larger pop sizes - more effective nat selection
      • no mobile elements
    • LTR - new element at time of birth has 100% identical repeats
      • can get age distribution from looking at repeat structure
      • invertebte, plants, fish - negative exp decays
        • long term steady state birth death process
        • don't find many that are old - being eliminated by natural selection
      • exception to this in placental mammals
        • bulge in age distribition
        • change in evol time in birth rate and/or death rate of LTRs
      • prior to KT boundary, looked single decay
        • was age of dinosaurs - after this, mammals eff pop size increased
        • avg placental mammal genome been shrinking after KT boundary
  • 2 episodes make planet unhospitable - snowball earth
    • whole planet frozen - 35 million years each
    • oblique situation for any organism - pop sizes go through bottleneck
    • 1st prior to euk
    • 2nd prior to all animal groups
  • mut makes variation, nat sel operates on it
  • mutation itself can have a weak selective force
  • avg human introns 1000s bp - exons 125 bp on avg
    • this arose prior to multicellularity
  • 5' UTR bad for you
    • euk - scanning mechanism to find 1st AUG codon
    • 5' UTR can cause premature start - leads to effective protein
  • gigantic viruses
    • polygna viresus - endosymbiotic - part of parasitic wasps
    • huge genomes - 80% non-coding DNA - including introns
    • once put in certain pop-gen context, even viral genomes can behave like this
  • point - many of these genome features (introns, 5' UTR's, etc) can arise by random drift processes - not selection
  • how does modular gene-regulatory structure originate?
    • advantage to host (allow more gen variation)?
    • can emerge passively without any selective force
    • increase mod struture, also increase mutational target size
  • network evolution