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Phylogenetically nested comparisons for testing correlates of species richness: a simulation study of continuous
Nick J B Isaac1, Paul-Michael Agapow, Paul H Harvey
1Department of Biological Sciences, Imperial College, Silwood Park, Ascot, Berks SL5 7PY, United Kingdom.
Evolution; International Journal of Organic Evolution
|March 20, 2003
Summary
Understanding species diversity requires robust phylogenetic methods. This study reveals that only two species richness indices are reliable for analyzing trait-based diversity patterns, offering guidelines for evolutionary biologists.
Area of Science:
- Evolutionary Biology
- Phylogenetics
- Biodiversity Science
Background:
- Explaining uneven species distribution across evolutionary lineages is a fundamental question in biology.
- Phylogenetic sister-clade comparisons are commonly used to link biological traits with species diversity.
- Previous studies show inconsistencies due to varying analytical methods.
Purpose of the Study:
- To compare the performance of different species richness indices and statistical tests in phylogenetic nested comparisons.
- To evaluate the impact of branch length choices on the accuracy of trait-based diversity analyses.
- To provide guidelines for improving the reliability of phylogenetically nested comparisons.
Main Methods:
- Simulations were used to test four species richness indices, two branch length estimation methods, and two statistical tests.
- Models of clade growth and character evolution were varied to assess robustness.
- Performance was evaluated based on Type I error rates and statistical power.
Main Results:
- All tested indices showed appropriate Type I error rates when assumptions were met and branch lengths were time-proportional.
- Only two species richness indices demonstrated robustness across different evolutionary models and analytical choices.
- Regression through the origin was more powerful than the t-test, and branch length choice significantly impacted results.
Conclusions:
- Two specific species richness indices are recommended for reliable analysis of trait-mediated species diversity.
- Careful consideration of branch lengths and statistical tests is crucial for valid phylogenetic comparative studies.
- The findings offer practical guidance for researchers investigating correlates of species richness.
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