ChromEvol v.3: modeling rate heterogeneity in chromosome number evolution

Area of Science:

• Evolutionary Biology
• Genetics
• Bioinformatics

Background:

• Chromosome number changes are fundamental to plant evolution, influencing diversification, stress adaptation, and phenotypic traits.
• The ChromEvol software is a key tool for analyzing chromosome number evolution along phylogenetic trees.
• Existing methods may not fully capture the complex variations in chromosome transition rates.

Purpose of the Study:

• To introduce ChromEvol v.3, a significantly upgraded version of the ChromEvol software.
• To implement novel methodological advancements for analyzing variable chromosome transition rates.
• To provide researchers with a more flexible and accurate tool for studying chromosome number evolution.

Main Methods:

• Development of ChromEvol v.3 with new models to capture rate variations.
• Incorporation of analyses for dysploidy and polyploidy rates influenced by genome size, discrete traits, or subclades.
• Application of the updated models to the Solanaceae (nightshade family) phylogeny.

Main Results:

• Identification of four distinct chromosome-number transition regimes within Solanaceae clades.
• Demonstration of an association between self-compatibility and altered chromosome number evolution dynamics.
• Validation of ChromEvol v.3's enhanced capabilities in analyzing complex evolutionary patterns.

Conclusions:

• ChromEvol v.3 offers a more comprehensive and accurate approach to studying chromosome number evolution.
• The findings highlight clade-specific evolutionary dynamics and trait-associated rate variations in Solanaceae.
• This tool will advance research into the processes driving plant diversification and adaptation through chromosomal changes.