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Detection of convergent and parallel evolution at the amino acid sequence level
1Institute of Molecular Evolutionary Genetics, Pennsylvania State University, University Park 16802, USA. zhang@imeg.bio.psu.edu
Molecular Biology and Evolution
|May 1, 1997
Summary
Detecting molecular adaptive evolution requires robust methods for identifying convergent and parallel amino acid changes. This study evaluates ancestral sequence inference techniques, recommending the Bayesian method for its superior performance in detecting parallel evolution and providing conservative estimates for convergent evolution.
Area of Science:
- Evolutionary biology
- Molecular evolution
- Bioinformatics
Background:
- Adaptive evolution at the molecular level is often studied by detecting convergent and parallel evolution in amino acid sequences.
- Inferring ancestral amino acids at phylogenetic tree nodes allows identification of changes along evolutionary lineages.
- Current methods for ancestral sequence inference lack validated efficiency in identifying convergent/parallel changes and assessing statistical significance.
Purpose of the Study:
- To assess the efficiency of parsimony and Bayesian methods for ancestral sequence inference in identifying convergent and parallel amino acid changes.
- To develop statistical tests for determining if observed convergent and parallel changes are statistically significant.
- To re-evaluate evidence for convergent and parallel evolution in stomach lysozyme sequences of foregut fermenters.
Main Methods:
- Computer simulations were used to compare parsimony and Bayesian ancestral sequence inference methods.
- Efficiency was evaluated based on the accurate identification of convergent and parallel amino acid substitution sites.
- Statistical tests were developed and applied to assess the significance of observed evolutionary changes.
Main Results:
- The Bayesian method demonstrated superior performance over the parsimony method in identifying parallel amino acid changes.
- Both methods showed inefficiency in identifying convergent amino acid changes.
- The Bayesian method provides a conservative estimate for the number of convergent-change sites.
- Statistical analysis revealed significant parallel evolution in stomach lysozyme sequences, but not significant convergent evolution.
Conclusions:
- The Bayesian method is recommended for inferring ancestral sequences to study parallel evolution due to its higher efficiency.
- While the Bayesian method offers conservative estimates for convergent evolution, its efficiency remains limited.
- Statistical tests are crucial for validating claims of convergent and parallel evolution at the amino acid sequence level.
- Reanalysis of stomach lysozyme data supports significant parallel evolution but not convergent evolution in foregut fermenters.
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