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Detection of Pathways Affected by Positive Selection in Primate Lineages Ancestral to Humans
J T Daub1,2, S Moretti2,3, I I Davydov2,3
1CMPG, Institute of Ecology and Evolution, University of Berne, Berne, Switzerland.
Molecular Biology and Evolution
|March 24, 2017
Summary
This study reveals ancient positive selection in primate evolution, identifying key biological pathways like immune response and metabolism that were optimized over time. Different genes drove these adaptations across various evolutionary branches.
Area of Science:
- Evolutionary biology
- Genomics
- Primate evolution
Background:
- Gene set enrichment analysis is effective for detecting recent human polygenic selection.
- Understanding ancient evolutionary adaptations requires different approaches.
Purpose of the Study:
- To detect biological pathways influenced by positive selection in ancient primate evolution.
- To investigate adaptation signals across four key branches leading to modern humans.
Main Methods:
- Applied likelihood-based branch site tests to protein-coding gene trees in the Primate clade.
- Utilized locus-specific test results for gene set enrichment analysis to score entire pathways for selection.
- Focused on pathway-level signals rather than solely on individual significant genes.
Main Results:
- Identified significant signals of positive selection in pathways related to immune response, sensory perception, metabolism, and energy production.
- Pathway-level significance was high, even when individual gene enrichment was not apparent.
- Observed consistent pathway significance across different phylogenetic levels, with distinct genes driving selection in each branch.
Conclusions:
- Ancient positive selection has shaped crucial biological pathways in primate evolution.
- Functional optimization occurred independently through different genetic mechanisms at various evolutionary stages.
- Pathway-level analysis provides a more comprehensive view of evolutionary adaptation than gene-level analysis alone.
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