Lifestyle Evolution Analysis by Binary-State Speciation and Extinction (BiSSE) Model.

Area of Science:

• Evolutionary biology
• Microbial genomics
• Phylogenetics

Background:

• Phylogenetic comparative methods (PCMs) integrate evolutionary models and statistics to study trait evolution and diversification.
• PCMs are widely used for macroorganisms but less so for microbes, despite abundant microbial genomic data.
• Microbial evolution research can benefit from PCMs to uncover fundamental evolutionary principles.

Purpose of the Study:

• Introduce the Binary-State Speciation and Extinction (BiSSE) model for microbial trait evolution analysis.
• Provide theoretical background and practical R commands for implementing the BiSSE model.
• Demonstrate the application of BiSSE in a case study on microbial lifestyle evolution.

Main Methods:

• Explanation of the theoretical underpinnings of the BiSSE model.
• Presentation of R code for executing the BiSSE model.
• Application of the BiSSE model in a microbial case study.

Main Results:

• The BiSSE model is presented as a powerful tool for analyzing trait evolution in microbes.
• R commands facilitate the practical application of the BiSSE model.
• A case study successfully utilized BiSSE to explore microbial lifestyle evolution.

Conclusions:

• PCMs, specifically the BiSSE model, are valuable for advancing our understanding of microbial evolution.
• The availability of R commands and case studies lowers the barrier for microbial researchers to adopt PCMs.
• Future applications of PCMs can yield significant insights into microbial diversification and adaptation.