title: Subtree power analysis and species selection for comparative genomics.
abstract: Sequence comparison across multiple organisms aids in the detection of regions under selection. However, resource limitations require a prioritization of genomes to be sequenced. This prioritization should be grounded in two considerations: the lineal scope encompassing the biological phenomena of interest, and the optimal species within that scope for detecting functional elements. We introduce a statistical framework for optimal species subset selection, based on maximizing power to detect conserved sites. Analysis of a phylogenetic star topology shows theoretically that the optimal species subset is not in general the most evolutionarily diverged subset. We then demonstrate this finding empirically in a study of vertebrate species. Our results suggest that marsupials are prime sequencing candidates.
authors.affiliation: Department of Statistics and Mathematics, University of California, Berkeley, CA 94720, USA.
authors.forename: Jon D
authors.initials: JD
authors.lastname: McAuliffe
authors.forename: Michael I
authors.initials: MI
authors.lastname: Jordan
authors.forename: Lior
authors.initials: L
authors.lastname: Pachter
mesh_terms: D000818:Animals; D017124:Conserved Sequence / Q000235:genetics; D003627:Data Interpretation, Statistical; D019143:Evolution, Molecular; D023281:Genomics / Q000379:methods*; D016013:Likelihood Functions; D010802:Phylogeny; D013045:Species Specificity; D014714:Vertebrates / Q000235:genetics*