Using the BirdTree.org website to obtain robust phylogenies for avian comparative studies: A primer

Area of Science:

• Evolutionary biology
• Comparative genomics
• Ornithology

Background:

• Comparative studies of trait evolution necessitate accounting for shared evolutionary history.
• Phylogenetic hypotheses are integrated into statistical analyses of species' traits, with birds as model organisms.
• The BirdTree online database provides the most complete molecular phylogeny for extant bird species.

Purpose of the Study:

• To discuss methods for utilizing BirdTree tree sets in comparative studies.
• To compare approaches using a consensus tree versus accounting for phylogenetic uncertainty.
• To investigate the impact of tree set size on parameter estimate variability.

Main Methods:

• Utilizing sets of equally plausible phylogenetic trees from BirdTree.
• Building a consensus tree for standard comparative analyses.
• Employing tree sets to address phylogenetic uncertainty in statistical models.
• Conducting simulations with a real comparative dataset on bird traits.

Main Results:

• Using at least 1,000 trees from BirdTree yields parameter estimates with minimal variation (<0.15% coefficient of variation).
• Methods accounting for phylogenetic uncertainty provide more reliable estimates and confidence intervals.
• BirdTree offers significant advantages over traditional methods for obtaining phylogenetic hypotheses.

Conclusions:

• BirdTree is poised to become the standard reference for avian comparative studies.
• The database simplifies the incorporation of phylogenetic hypotheses into evolutionary analyses.
• Accounting for phylogenetic uncertainty is recommended for robust comparative studies.