Molecular adaptation in Rubisco: Discriminating between convergent evolution and positive selection using mechanistic...

Area of Science:

• Evolutionary Biology
• Molecular Evolution
• Plant Science

Background:

• Rubisco is a crucial enzyme in photosynthesis, vital for energy storage in plants.
• C4 plants exhibit enhanced photosynthetic efficiency due to molecular adaptations in Rubisco.
• Convergent evolution of Rubisco in C4 plants provides a model for studying molecular adaptation.

Purpose of the Study:

• To detect and quantify convergent adaptation patterns in Rubisco within eudicots using a differential-selection model.
• To compare the findings of the differential-selection model with classical codon models based on dN/dS ratios.
• To highlight the conceptual differences between models and the need for diverse approaches in molecular evolutionary studies.

Main Methods:

• Utilized a codon-based differential-selection model to analyze Rubisco evolution.
• Applied classical codon models estimating the ratio of non-synonymous to synonymous substitutions (dN/dS).
• Contrasted the positional selection identified by both model classes.

Main Results:

• The differential-selection model identified distinct sets of amino acid positions under selection compared to classical dN/dS models.
• A notable overlap exists between the positions identified by both model types.
• The study underscores the importance of considering different selective regimes in molecular evolution.

Conclusions:

• Convergent adaptation in Rubisco leaves unique molecular signatures that may be missed by traditional dN/dS analyses.
• Employing a broader range of codon models is essential for accurately discriminating between distinct selective pressures.
• This research advances our understanding of molecular adaptation and convergent evolution in plants.