MLtree

MLtree performs maximum likelihood optimization of models of character evolution for DNA sequences and phenotypic traits on predefined phylogenetic trees.

Key Features:

• Maximum Likelihood Optimization: Computes maximum likelihood estimates for models of character evolution.
• Model Flexibility: Supports evolutionary models for DNA sequences and phenotypic (character) traits.
• Phylogenetic Integration: Operates on a known or predefined phylogenetic tree to optimize model parameters along tree branches.

Scientific Applications:

• Evolution of C4 photosynthesis in grasses: Used to test hypotheses linking historical atmospheric CO2 decline to the transition from C3 to C4 photosynthesis by comparing CO2-informed models against null models on a large grass phylogeny.

Methodology:

Maximum likelihood estimation of character-evolution parameters on a predefined phylogenetic tree; construction of a large grass phylogeny and estimation of divergence times using Bayesian molecular dating; comparison of models incorporating atmospheric CO2 levels against null models.