Does the T-PTP Test Tell Us Anything We Want to Know?

John Harshman, Richard Olmstead
2001 Systematic Biology  
Archie (1989) , Faith (1990) , and Faith and Cranston (1991) devised a test for phylogenetic structure in character data sets, which Faith and Cranston called the permutation tail probability (PTP) test. Faith (1991) introduced a re nement intended to test the strength of support for monophyly of individual clades, which he called the topologydependent permutation tail probability (T-PTP) test. Faith presented a priori and a posteriori forms of the test; here, I will discuss the a priori test.
more » ... ll phylogenetic permutation tests involve comparing some property of the original data set with a null distribution constructed by randomly scrambling character states within each character across taxa, generating a large number of replicate data sets. The randomized data sets have some of the properties of the real data set-particularly the number of taxa with a given state for each characterbut they certainly have no phylogenetic information. The test property used by the a priori T-PTP test for monophyly is the Bremer (1994) support or decay index: the length of the most-parsimonious tree lacking the clade of interest minus the length of the most-parsimonious tree having the clade. The Bremer index of a clade for the original data set is compared with the distribution of Bremer indices of that clade over many randomized data sets. The P-value is simply the proportion of randomized data sets for which the clade's Bremer index is as great as or greater than its Bremer index for the original data set.
doi:10.1080/10635150121530 pmid:12116932 fatcat:scvjmzatcrexregf4hxreth2sm