Subtree power analysis and species selection for comparative genomics.
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.
McAuliffe
Jon D
JD
Department of Statistics and Mathematics, University of California, Berkeley, CA 94720, USA.
Jordan
Michael I
MI
Pachter
Lior
L
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*