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A Practical Guide to Phylogenetics for Nonexperts
Published on: February 5, 2014
Inferring and testing hypotheses of cladistic character dependence by using character compatibility
1Department of Anatomy, New York College of Osteopathic Medicine, New York Institute of Technology, Old Westbury, New York 11568-8000, USA. rokeefe@iris.nyit.edu
Systematic Biology
|July 16, 2002
Summary
This study introduces tree-free methods to test for correlated evolution between biological characters, crucial for accurate phylogenetic inference. The new approach visualizes character correlations and improves phylogenetic tree resolution by reducing dependent characters.
Area of Science:
- Evolutionary Biology
- Phylogenetics
- Comparative Genomics
Background:
- Theories of biological integration posit that character evolution is often interdependent.
- Character independence is a fundamental assumption in phylogenetic inference, yet dependent characters can distort evolutionary trees.
- Existing methods for testing correlated evolution typically require a pre-existing phylogenetic tree.
Purpose of the Study:
- To develop novel "tree-free" methods for testing the independence of cladistic characters.
- To provide tools for assessing character correlation before or independent of phylogeny reconstruction.
- To identify and visualize suites of correlated characters.
Main Methods:
- Character compatibility analysis to visualize correlated character suites.
- Construction of pairwise shared compatibility and association matrices.
- Eigenvector analysis of association matrices to reveal character correlations.
- Monte Carlo simulations to assess the statistical significance of observed correlations.
Main Results:
- The developed methods successfully identify suites of correlated characters.
- Application to caecilian amphibian morphological data corroborated known instances of dependent evolution and revealed new ones.
- Reducing correlated character suites to single characters improved phylogenetic tree resolution and reduced implied evolutionary change.
Conclusions:
- Tree-free methods offer a robust approach to testing character independence and correlated evolution.
- These methods enhance the accuracy of phylogenetic inference by accounting for character dependency.
- The identification of correlated character suites can lead to more resolved and parsimonious evolutionary trees.
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