DaTeR

DaTeR integrates absolute and relative time constraints to improve dating of microbial species phylogenies, yielding chronograms consistent with fossil-derived calibrations and horizontal gene transfer-derived relative constraints.

Key Features:

• Integration of Constraints: Combines absolute time constraints (e.g., dated fossils) with relative time constraints inferred from horizontal gene transfer events to produce consistent chronograms.
• Bayesian Framework: Samples posterior chronograms under existing Bayesian molecular dating methodologies that satisfy specified absolute time constraints.
• Error-Correction Mechanism: Applies a constrained optimization framework to minimally adjust sampled chronograms so they also satisfy all relative time constraints.
• Scalability and Effectiveness: Demonstrated on a dataset of 170 Cyanobacterial taxa with 24 transfer-based relative constraints across six molecular dating models to improve estimated chronograms.

Scientific Applications:

• Microbial Phylogenetics: Dates microbial species phylogenies to improve inference of evolutionary timelines and relationships among microorganisms.
• Evolutionary Biology Research: Supports timing analyses of evolutionary events across lineages using integrated absolute and relative constraints.
• Genomic Studies: Enables analysis of the temporal impact of horizontal gene transfer events on microbial evolution.

Methodology:

DaTeR first samples chronograms that satisfy absolute time constraints using Bayesian approaches, then applies a constrained optimization framework to minimally adjust these chronograms to satisfy relative time constraints, and aggregates the error-corrected chronograms to produce refined dated phylogenies.