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Species sampling has a major impact on phylogenetic inference
G Lecointre1, H Philippe, H L Vân Lê
1Laboratoire d'Ichtyologie générale et appliquée (GDR 1005), Muséum National d'Histoire Naturelle, Paris, France.
Molecular Phylogenetics and Evolution
|September 1, 1993
Summary
Species sampling significantly impacts phylogenetic tree accuracy. Even small subsets of species can lead to results incongruent with analyses of larger datasets, highlighting the need for careful species selection in evolutionary studies.
Area of Science:
- Phylogenetics
- Molecular Evolution
- Computational Biology
Background:
- Phylogenetic trees are crucial for understanding evolutionary relationships among species.
- The accuracy of phylogenetic inference can be influenced by various factors, including the selection of species for analysis.
Purpose of the Study:
- To investigate the impact of species sampling on the reliability of phylogenetic trees inferred from 28S rRNA data.
- To quantify the effect of individual species on bootstrap proportions (BPs) within phylogenetic analyses.
Main Methods:
- Analysis of bootstrap proportions (BPs) in parsimonious trees derived from a 28S rRNA database.
- Utilized original programs for comparing BPs across trees generated with varying species subsets (4 to 24 species) from a total of 31 species.
- Exhaustive sampling of species combinations to determine the impact of each species on node BPs.
Main Results:
- Phylogenetic trees derived from small species subsets (4-24 species) were found to be highly sensitive to sampling and not congruent with analyses of the full 31-species dataset.
- The impact of sampling individual species on BPs was localized to adjacent nodes (two to three neighboring nodes).
- Species impact on BPs varied depending on the sampling context.
Conclusions:
- Emphasizes the critical importance of sampling multiple species within each presumed monophyletic group to ensure robust phylogenetic inference.
- Recommends sampling several successive outgroups for improved phylogenetic accuracy.
- Suggests that the effect of species sampling on BPs is more substantial than previously recognized and should be considered before extensive sequencing.