PHRAPL: Phylogeographic Inference Using Approximate Likelihoods.

Area of Science:

• Population Genetics
• Evolutionary Biology
• Computational Biology

Background:

• Species' demographic histories are shaped by complex evolutionary processes influencing genetic diversity.
• Current phylogeographic models often oversimplify demography, requiring researchers to rely on intuition for model selection.
• Existing methods struggle to incorporate all possible evolutionary scenarios, limiting accurate inference.

Purpose of the Study:

• To introduce PHRAPL, an approximate likelihood method that reduces reliance on intuition for phylogeographic model selection.
• To enable the calculation of probabilities for complex demographic histories using gene trees.
• To facilitate accurate parameter estimation for population genetics models.

Main Methods:

• Developed an approximate likelihood approach (PHRAPL) for phylogeographic inference.
• Utilized gene trees to calculate probabilities of various complex demographic histories.
• Tested PHRAPL's performance in model selection and parameter estimation using simulated data.
• Compared approximate likelihood results with standard analytical likelihood methods.

Main Results:

• PHRAPL accurately identifies the most likely demographic model across diverse scenarios, especially with sufficient loci and deep divergence.
• The method provides generally accurate parameter estimates for population size, gene flow, and coalescence times.
• PHRAPL demonstrates strong performance in model selection, often identifying the true model in simulations.
• Approximate likelihood results align well with standard analytical likelihood methods.

Conclusions:

• PHRAPL is a valuable tool for phylogeographic model selection, enabling more extensive exploration of demographic model space.
• The method facilitates parameter estimation for complex evolutionary models not easily handled by current approaches.
• Accurate demographic modeling with PHRAPL enhances understanding of evolutionary processes shaping phylogeographic patterns.