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Updated: Jul 16, 2026
04:52
Following the Dynamics of Structural Variants in Experimentally Evolved Populations
Published on: February 3, 2023
Adaptive evolution in humans revealed by the negative correlation between the polymorphism and fixation phases of
Jun Gojobori1, Hua Tang, Joshua M Akey
1Department of Biological Sciences, Graduate School of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
Summary
Molecular evolution involves distinct selective forces during polymorphism and fixation phases. Analyzing 75 elementary amino acid changes reveals that adaptive evolution primarily occurs when changes have low polymorphic indices, suggesting around 10-13% of human-chimpanzee substitutions are adaptive.
Area of Science:
- Evolutionary Biology
- Molecular Evolution
- Population Genetics
Background:
- Selective pressures on amino acid substitutions differ between molecular evolution's polymorphism and fixation phases.
- Negative selection and genetic drift dominate polymorphism, while positive selection is more significant during fixation.
- Traditional synonymous vs. nonsynonymous analysis lacks resolution for studying these distinct evolutionary phases.
Purpose of the Study:
- To investigate the dynamics of amino acid changes across polymorphism and fixation phases.
- To differentiate the roles of negative and positive selection on specific amino acid substitutions.
- To quantify the proportion of adaptive amino acid substitutions between humans and chimpanzees.
Main Methods:
- Categorized amino acid changes into 75 elementary types based on single-base pair substitutions.
- Calculated the polymorphic index (PI) for each change type relative to synonymous changes.
- Calculated the fixation index (FI) conditional on common polymorphisms, using human polymorphism data (Perlegen, HapMap) and chimpanzee outgroup sequences.
Main Results:
- A significant negative correlation (L-shaped) was observed between fixation index (FI) and polymorphic index (PI) (P < 0.001).
- Amino acid changes with high FI values (indicating adaptive evolution) predominantly exhibited low PI values.
- Approximately 10-13% of amino acid substitutions between humans and chimpanzees appear to be adaptive.
Conclusions:
- Negative and positive selection effectively act on the same set of amino acid changes.
- The study provides a refined method for analyzing evolutionary dynamics beyond the synonymous/nonsynonymous dichotomy.
- A substantial fraction of human-chimpanzee amino acid differences are likely driven by positive selection.
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