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SUMMARY:Phylogenies from DArTs: A stochastic Dollo proces with censored da
 ta - Holland\, BR (Massey)
DTSTART:20110621T130000Z
DTEND:20110621T140000Z
UID:TALK31802@talks.cam.ac.uk
CONTACT:Mustapha Amrani
DESCRIPTION:Diversity Array Technologies (DArT) are a relatively new kind 
 of DNA marker system that seem like they could be usefully applied to phyl
 ogenetics (a few papers have already explored this). Like marker systems s
 uch AFLP and RFLP\, the method produces presence absence data\, but unlike
  these methods it is very unlikely for shared presences to occur by chance
 . \n\nThe basic idea is as follows. One or a small number of genomes are s
 elected to form the genomic representation. Two enzymes are used to cut th
 e DNA from these genomes at certain recognition sites (a rare 6bp recognit
 ion site and a more frequent 4bp recognition site). Fragments of DNA whose
  ends have been cut by two rare recognition sites are amplified. These fra
 gments\, which are said to form the genomic representation\, are arranged 
 on a microchip. Other genomes can then been checked to see which fragments
  within the genomic representation they have copies of in their own sequen
 ce. For each other genome that is compared to the genomic representation t
 his results in a binary sequence that indicates presence (1) or absence (0
 ) of each of the fragments. \n\nThe first obvious advantage of this approa
 ch is that it creates a representation of the whole genome rather than jus
 t a few genes. This alleviates the problem of picking a small set of genes
  that may not be representative of the evolutionary history of the species
 . The second advantage is that in comparison to an individual site\, long 
 fragments of DNA are very unlikely to be similar due to chance. So if two 
 species share a fragment it is vastly more likely that they share it due t
 o common ancestry rather than due to a chance similarity. \n\nTo use these
  data for phylogenetics it would be useful to develop a likelihood equival
 ent of Dollo parsimony (in which characters can be lost multiple times but
  gained only once)\, such models have already been explored in the context
  of language evolution and gene content evolution. However\, another compl
 icating issue is the censoring effect created by only being able to see th
 ose fragments that were in the original genomic representation\, i.e. frag
 ments that are shared by a group of species but that are not present in th
 e original species used to make the genomic representation are missing fro
 m the data.\n
LOCATION:Seminar Room 1\, Newton Institute
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