TreeSim

TreeSim simulates phylogenetic trees with a fixed number of extant species using constant-rate birth-death processes to model speciation, extinction, mass-extinction, and rate-shift events occurring at arbitrarily defined times (before the present or after the origin).

Key Features:

• Implementation: Implemented as an R package for simulation and analysis within the R environment.
• Fixed-extant simulations: Simulates trees conditioned on a fixed number of extant species.
• Birth–death models: Uses constant-rate birth–death processes to model speciation and extinction dynamics.
• Event modeling: Incorporates mass-extinction and rate-shift events at arbitrarily defined times, including times before the present or after the origin.
• Fast simulations: Provides fast simulation routines to enable large-scale simulation experiments and inference.
• Inference methods: Supports approximate Bayesian computation for parameter inference and can be used following maximum likelihood parameter estimation.

Scientific Applications:

• Evolutionary hypothesis testing: Tests hypotheses about how speciation, extinction, mass extinctions, and rate shifts shape phylogenetic tree structure.
• Mass extinction vs stasis analysis: Evaluates scenarios where mass-extinction events and periods of stasis may be indistinguishable from extant-only trees and assesses how inclusion of fossil data can distinguish them.
• Rate inference: Facilitates inference of speciation and extinction rates using fast simulations combined with approximate Bayesian computation and maximum likelihood approaches.
• Sensitivity and robustness analyses: Enables sensitivity analyses and assessment of model robustness under varied event timing and rate scenarios.

Methodology:

Simulations use constant-rate birth–death processes with optional mass-extinction and rate-shift events at arbitrarily defined times; downstream analyses employ fast simulation-based inference, approximate Bayesian computation, and can incorporate maximum likelihood parameter estimation.