ANOTHER MONOPHYLY INDEX: REVISITING THE JACKKNIFE

Area of Science:

• Phylogenetic Systematics
• Computational Biology
• Evolutionary Biology

Background:

• Randomization routines are widely used in phylogenetics.
• The jackknife resampling technique, though introduced a decade ago, is rarely applied in cladistics.
• Data resampling is crucial for assessing the robustness of phylogenetic results.

Purpose of the Study:

• To re-investigate the jackknife technique for cladistic analysis.
• To determine the effect of taxon removal on the stability of parsimony analyses.
• To develop and evaluate a novel index for clade stability.

Main Methods:

• Application of the jackknife data resampling technique to phylogenetic datasets.
• Parsimony analyses to infer phylogenetic trees.
• Development of the Jackknife Monophyly Index (JMI) for clade stability assessment.
• Comparison of JMI with bootstrapping using hypothetical and real datasets.

Main Results:

• Removal of single taxa can drastically increase the number of equally parsimonious trees.
• Removal of other taxa can stabilize phylogenetic results.
• The developed Jackknife Monophyly Index (JMI) assigns stability values to clades based on jackknife pseudoreplicates.
• JMI is not influenced by uninformative characters or relative synapomorphy number, unlike the bootstrap.

Conclusions:

• Taxon removal can significantly impact phylogenetic tree stability in parsimony analyses.
• The Jackknife Monophyly Index (JMI) provides a reliable measure of clade stability.
• JMI offers advantages over bootstrapping by avoiding suboptimal hypotheses and insensitivity to uninformative characters.