So far this is similar to http://ff.im/4x4Vg of the BioPathways SIG yesterday - Ruchira S. Datta

this lets us study sympatric speciation in the ocean - Ruchira S. Datta

inspired by Mandel, ..., Ruby, "A single regulatory gene is sufficient to alter bacterial host range": what is the genetic basis for adaptation to the niches we found (zooplankton-associated vs small-particle associated)? - Ruchira S. Datta

want to do ecologically-driven population genomics - Ruchira S. Datta

wanted to sequence all genomes in each of the subtrees - Ruchira S. Datta

asked for 20 genomes in grant application, was met with "?!" - Ruchira S. Datta

sat next to Eric Lander at a dinner, who said "20 genomes? why not 100?", so got funding from Broad Institute - Ruchira S. Datta

want to model changes within a population of genomes; gene flow and recombination within the population - Ruchira S. Datta

wanted to find recombination breakpoints - Ruchira S. Datta

dimorphic sites, with one nucleotide changing: supports splits, leading to tree with single mutation - Ruchira S. Datta

however, in one site find a dimorphic site which is *not* consistent with the gene tree(s) consistent with the previous splits, so this must be a double muttation or recombination breakpoints - Ruchira S. Datta

STARRIinIGHTS uses dynamic programming to find the regions that are consistent with the same phylogenetic tree; what's left is due to either recombination or double mutation - Ruchira S. Datta

unfortunately, to determine which (recombination or double mutation) would make the algorithm NP-complete. use single mutations to estimate the rate of double mutations and expected number of trimorphic sites - Ruchira S. Datta

infer recombination breakpoints between self-consistent chunks - Ruchira S. Datta

different regions support different groupings - Ruchira S. Datta

e.g., for the particular ecological split, most of the support for the split is on an 18kb region - Ruchira S. Datta

this turns out to be an operon responsible for chitin catabolism, which makes sense since zooplankton are covered in chitin - Ruchira S. Datta

Shapiro, ...., Alm Trends in microbiology paper suggests usual selection tests may not be applicable to prokaryotes - Ruchira S. Datta

STARRInIGHTS is not up on the web, but will be happy to send it to people to run from the command line - Ruchira S. Datta