TESS

TESS simulates reconstructed phylogenetic trees and estimates time-dependent birth–death diversification parameters (speciation and extinction) using maximum likelihood and Bayesian inference.

Key Features:

• Flexible Diversification Models: Implements global, time-dependent birth–death processes with constant, continuously varying, or episodically changing speciation and extinction rates and can accommodate mass-extinction events at specified times.
• Simulation Capabilities: Simulates reconstructed phylogenetic trees conditioned on the number of species, the duration of the process, or both.
• Statistical Inference and Parameter Estimation: Provides numerical methods for estimating parameters from molecular phylogenies, supporting Maximum Likelihood (ML) and Bayesian inference and accounting for incomplete species sampling.
• Model Comparison: Includes methods to compare the relative and absolute fit of competing branching-process diversification models to a given tree.
• Efficient Simulation: Optimized for efficient simulation under various model specifications to enable large-scale evolutionary scenario exploration.

Scientific Applications:

• Lineage Diversification Dynamics: Infers temporal patterns of speciation and extinction rates from phylogenetic trees to study diversification dynamics over time.
• Hypothesis Testing of Evolutionary Processes: Tests hypotheses about the impact of environmental changes and mass-extinction events on diversification patterns.
• Paleobiological and Incomplete-Sampling Analyses: Analyzes molecular phylogenies and paleontological datasets where species sampling is incomplete to estimate diversification parameters.

Methodology:

Uses branching-process theory to simulate reconstructed trees under time-dependent birth–death models, applies numerical methods for parameter estimation via Maximum Likelihood and Bayesian inference, supports continuous and episodic rate changes, and conditions simulations on species count and/or process duration while accounting for incomplete sampling.