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A Practical Guide to Phylogenetics for Nonexperts
Published on: February 5, 2014
Sensitivity of phylogeny estimation to taxonomic sampling.
1Department of Zoology, Texas Memorial Museum, University of Texas, Austin, Texas 78712-1064, USA. stevepoe@mail.utexas.edu
Systematic Biology
|June 18, 2002
Summary
Taxon sampling can impact phylogenetic estimates. However, this study found that for up to 20 taxa, the impact of removing taxa (subsampling) on phylogenetic tree accuracy is generally small.
Area of Science:
- Phylogenetics
- Computational Biology
- Evolutionary Biology
Background:
- Estimating evolutionary relationships (phylogeny) is crucial in biology.
- Previous research indicates that altering the set of species (taxa) included in an analysis can influence phylogenetic outcomes.
- Understanding the impact of taxon sampling is vital for robust phylogenetic inference.
Purpose of the Study:
- To investigate how the number of taxa included in a dataset affects the accuracy of phylogenetic tree estimation.
- To identify factors that influence the sensitivity of phylogenetic analyses to changes in taxon sampling.
Main Methods:
- Analyzed 29 published datasets to assess within-dataset variation in phylogenetic estimation.
- Employed multiple regression to evaluate the influence of dataset characteristics (e.g., number of taxa, characters, homoplasy) on sensitivity to taxon sampling.
- Quantified sensitivity by comparing tree lengths derived from full versus subsampled datasets.
Main Results:
- The number of taxa was a significant predictor of sensitivity to taxon sampling.
- Other factors like the number of characters, homoplasy, support strength, and tree symmetry were not significant predictors.
- A predictive equation was developed to estimate sensitivity based on the fraction of taxa sampled and the total number of taxa.
Conclusions:
- Subsampling taxa generally has a minor impact on phylogenetic tree length, with average differences of 0-2.9 steps.
- For phylogenetic analyses including up to 20 taxa, subsampling is likely not a significant issue.
- The number of taxa is a key factor influencing the reliability of phylogenetic estimates when sampling is altered.
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