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SUMMARY:Modeling the Evolutionary Dynamics of CRISPR spacers - Kupczok\, A
  (IST Austria)
DTSTART:20110621T151000Z
DTEND:20110621T153000Z
UID:TALK31806@talks.cam.ac.uk
CONTACT:Mustapha Amrani
DESCRIPTION:We present a phylogenetic insertion- and deletion-model for CR
 ISPR spacer turnover.\nCRISPR (Clustered Regularly Interspaced Short Palin
 dromic Repeats) is an adaptive heritable immune system found in Eubacteria
  and Archaea. The system consists of a number of CRISPR associated (CAS) p
 roteins and an array of repeats and spacers - the later represent the vira
 l/plasmid targeting sequences and the system functions in an analogous way
  to the eukaryotic siRNA system. The length and content of the spacer arra
 y varies considerably among individuals within species (suggesting a rapid
  arms race) and it has been suggested that there is a selective cost\, in 
 the absence of parasites\, associated with maintaining these arrays. At on
 e point in time and space spacers can be beneficial\, if a parasite with t
 he corresponding sequence exists in the community\, or they can be useless
  and thus neutral or slightly deleterious.\n\nThe rate at which spacers ar
 e gained and lost from these arrays provides insight into the evolutionary
  dynamics of host-parasite interactions. To this end we model spacer inser
 tion and deletion as a continuous-time two-state Markov process. The model
  parameters are then estimated by maximum likelihood along the phylogeny. 
 We assume different dynamics\, modeled by different two-state Q-matrices\,
  for beneficial and neutral spacers. An underlying switching process allow
 s for changes between these Q-matrices. The information whether a spacer i
 s beneficial or neutral is not known\, thus we use ambiguous states. Using
  known spacer annotation we can also apply a partition model allowing the 
 evolutionary rates to differ between spacers of different sources. We eval
 uate the switching model by simulation and also analyse bacterial data set
 s.\n
LOCATION:Seminar Room 1\, Newton Institute
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