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A Concoction Pipeline for Generating Molecular Operational Taxonomic Units (MOTUs) Among Riparian and Aquatic Beetles

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ANOTHER MONOPHYLY INDEX: REVISITING THE JACKKNIFE.

Mark E Siddall¹

¹School of Marine Science, Virginia Institute of Marine Science, P.O. Box 1346, Gloucester Point, Virginia 23062, U.S.A.

Cladistics : the International Journal of the Willi Hennig Society

|December 18, 2021

Summary

The jackknife resampling technique can significantly alter phylogenetic analyses, impacting tree stability. A new Jackknife Monophyly Index (JMI) quantifies clade stability, offering a robust alternative to bootstrapping.

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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.