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