mstree

mstree estimates ancestral population sizes and species divergence times during speciation with gene flow using a model-flexible multispecies coalescent approach.

Key Features:

• Model Flexibility: Does not assume a predefined relationship between isolation and migration, avoiding reliance on isolation-with-migration model constraints.
• Mathematical Framework: Uses mathematical inequalities among species divergence time, ancestral population size, and the number of gene trees to derive parameter estimates.
• Robustness Across Gene Flow Models: Validated by simulations and provides estimates for data generated under isolation-with-initial-migration, secondary contact, and isolation-with-migration models.

Scientific Applications:

• Estimate Ancestral Population Sizes: Infers ancestral population sizes from genetic data within a multispecies coalescent framework.
• Determine Divergence Times: Estimates species divergence times to reconstruct temporal aspects of speciation with gene flow.
• Test Speciation Theories: Enables testing of speciation scenarios involving different modes of gene flow without model-specific assumptions.

Methodology:

Implements a multispecies coalescent framework and leverages mathematical inequalities among divergence time, ancestral population size, and number of gene trees, with validation via simulation under isolation-with-initial-migration, secondary contact, and isolation-with-migration models.