phylodyn: an R package for phylodynamic simulation and inference.

Area of Science:

• Computational Biology
• Evolutionary Biology
• Population Genetics

Background:

• Phylodynamic analysis infers population processes from genetic data.
• Estimating effective population size (Ne) fluctuations over time is crucial for understanding population dynamics.
• Existing methods may lack flexibility or computational efficiency for complex demographic histories.

Purpose of the Study:

• Introduce phylodyn, an R package for phylodynamic inference.
• Provide tools for Bayesian nonparametric estimation of effective population size (Ne) trajectories.
• Implement and compare various phylodynamic inference methods.

Main Methods:

• Utilizes gene genealogies from coalescent and sequentially Markov coalescent models.
• Incorporates Bayesian nonparametric methods for Ne estimation.
• Implements Markov chain Monte Carlo (MCMC) and integrated nested Laplace approximation (INLA) approaches.
• Supports isochronous, heterochronous, and preferential sampling schemes.

Main Results:

• The phylodyn package offers a flexible framework for phylodynamic analysis.
• Demonstrates the utility of Bayesian nonparametric approaches for inferring Ne.
• Provides simulation functions for method validation and comparison.
• Evaluates the performance and outputs of implemented phylodynamic methods.

Conclusions:

• phylodyn facilitates advanced phylodynamic inference using gene genealogies.
• The package enhances the ability to study effective population size dynamics.
• Offers a valuable resource for researchers in evolutionary and population genetics.