geiger v2.0: an expanded suite of methods for fitting macroevolutionary models to phylogenetic trees

Area of Science:

• Evolutionary Biology
• Computational Biology
• Bioinformatics

Background:

• Phylogenetic comparative methods are vital for testing evolutionary hypotheses using interspecific data.
• The increasing scale and scope of available data present computational challenges for existing methods.
• Many current approaches are computationally infeasible or unsuitable for large datasets.

Purpose of the Study:

• To present geiger v2.0, a significantly updated version of the popular R package for phylogenetic comparative analysis.
• To provide more efficient algorithms for existing phylogenetic methods.
• To introduce novel approaches for handling heterogeneous models and data types in evolutionary analyses.

Main Methods:

• Reimplementation of existing phylogenetic comparative methods using optimized algorithms.
• Development of new computational approaches to accommodate large-scale interspecific datasets.
• Integration with the 'ape' R package for enhanced functionality.

Main Results:

• geiger v2.0 offers computationally feasible solutions for large phylogenetic datasets.
• The package provides enhanced capabilities for analyzing evolutionary hypotheses.
• New methods are introduced for accommodating diverse and complex evolutionary models and data.

Conclusions:

• geiger v2.0 is an essential tool for modern phylogenetic comparative analyses.
• The package addresses the limitations of previous methods when dealing with large datasets.
• It facilitates robust evolutionary research by providing efficient and flexible analytical tools.