TraitRateProp

TraitRateProp detects associations between sequence evolutionary rates and whole-organism phenotypes by jointly modeling sequence and phenotype evolution within a phylogenetic framework.

Key Features:

• Phylogenetic Contextual Analysis: Analyzes sequences and phenotypes of extant species in the context of their evolutionary history to identify sequence sites where evolutionary rate shifts correlate with phenotype changes.
• Joint Likelihood Framework: Employs a joint likelihood framework that combines explicit models of sequence evolution and phenotype evolution to test for associations between the two processes.
• Prediction of Trait-Associated Sites: Predicts specific sequence sites within genes or proteins that are most likely associated with particular phenotypic traits.
• Integration of Structural 3D Information (Optional): Optionally integrates structural 3D information to detect spatially juxtaposed trait-associated sites that may indicate shared functional roles.

Scientific Applications:

• Detecting rate-phenotype associations: Tests for associations between sequence evolutionary rates and whole-organism phenotypes across phylogenies.
• Identifying molecular bases of phenotypic adaptation: Identifies candidate sequence sites that may underlie adaptive phenotypic changes.
• Case study — RPS8 in Orchidaceae: Has been applied to detect shifts in the sequence evolution rate of the RPS8 protein during transitions into heterotrophy in Orchidaceae.

Methodology:

Analyzes sequences and phenotypes within a phylogenetic framework using a joint likelihood framework that combines models of sequence evolution and phenotype evolution, predicts trait-associated sequence sites, and can incorporate structural 3D information.