PHYLOGENETIC EXTINCTION RATES AND COMPARATIVE METHODOLOGY

Species are not independent points for comparative analyses because cl osely related species share more evolutionary history and are therefor e more similar to each other than distantly related species. The exten t to which independent-contrast analysis reduces type I and type II st atistical error in comparison with cross-species analysis depends on t he relative branch lengths in the phylogenetic tree: as deeper branche s get relatively long, cross-species analyses have more statistical ty pe I and type II error. Phylogenetic trees reconstructed from extant s pecies, under the assumptions of a branching process with speciation ( branching) and extinction rates remaining constant through time, will have relatively longer deep branches as the extinction rate increases relative to the speciation rate. We compare the statistical performanc e of cross-species and independent-contrast analyses with varying rela tive extinction rates, and conclude that cross-species comparisons hav e unacceptable statistical performance, particularly when extinction r ates are relatively high.