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

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

Talk

• 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