User:R. Eric Collins/MBL/Edwards

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  • most common gene tree can not match the species tree (laura k mentioned this 'anomaly zone')
  • likelihood methods based on coalescence can correct for this given many loci
  • in this case concatenation guarantees wrong tree given lots of data

using full set of good trees rather than just best

  • treeviz: tree set visualization projecting tree set into MDS space
  • concaterpillar: measure of conflict in dataset
  • incomplete lineage sorting methods
    • BEST, STAR, BUCKy, concatenation
  • concatenation gives higher 'confidence' but how confident are you in the confidence?
  • eigensoft: hetero/homozygous matrix of alleles
  • royal ontario museum
    • museums are natural places for genome sequencing
  • bayestraits: analyse morphological characteristics with sequence data
  • small genomes may have first arisen in early bird ancestors, much before origin of flight
  • large populations --> small genomes
  • allow natural selection to work unimpeded by genetic drift
    • small deletions generally kept whereas in small populations they could get fixed easier
    • but what about protists with giant genomes? e.g. diatoms
  • base frequency patterns
    • e.g. 5-letter words ending in CG depauperate since CG easily mutates to something else
    • even after correcting for GC content
    • word frequency --> "Bayesian Surprise" (Yogesh)
  • Mycoplasma gallisepticum 1Mb
    • 2% of genetic diversity from M. gal. population made it into House Finch strain (using MIGRATE)
  • expanding populations can have long tips and short internal branches during expansion
    • 17 sequenced strains of Mgal showed variations in population size and evolutionary rate
  • CRISPRs as Lamarckian evolution...
    • time-sampled strains show rapid evolution of CRISPR loci

Questions

  • can you use microbial flora/parasites/pathogens to delineate species?
    • baross did this with bacteria/phage