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ANOTHER MONOPHYLY INDEX: REVISITING THE JACKKNIFE
Author(s) -
Siddall Mark E.
Publication year - 1995
Publication title -
cladistics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 2.323
H-Index - 92
eISSN - 1096-0031
pISSN - 0748-3007
DOI - 10.1111/j.1096-0031.1995.tb00003.x
Subject(s) - jackknife resampling , clade , resampling , monophyly , taxon , cladistics , synapomorphy , statistics , data matrix , stability (learning theory) , biology , tree (set theory) , phylogenetic tree , mathematics , computer science , machine learning , ecology , combinatorics , biochemistry , estimator , gene
— Randomization routines have quickly gained wide usage in phylogenetic systematies. Introduced a decade ago, the jackknife has rarely been applied in cladistic methodology. This data resampling technique was re‐investigated here as a means to discover the effect that taxon removal may have on the stability of the results obtained from parsimony analyses. This study shows that the removal of even a single taxon in an analysis can cause a solution of relatively few multiple equally parsimonious trees in an inclusive matrix to result in hundreds of equally parsimonious trees with the single removal of a taxon. On the other hand, removal of other taxa can stabilize the results to fewer trees. An index of clade stability, the Jackknife Monophyly Index (JMI) is developed which, like the bootstrap, applies a value to each clade according to its frequency of occurrence in jackknife pseudoreplicates. Unlike the bootstrap and earlier application of the jackknife, alternative suboptimal hypotheses are not forwarded by this method. Only those clades in the most parsimonious tree(s) are given JMI values. The behaviour of this index is investigated both in relation to a hypothetical and a real data set, as well as how it performs in comparison to the bootstrap. The JMI is found to not be influenced by uninformative characters or relative synapomorphy number, unlike the bootstrap.