Simulating gene trees under the multispecies coalescent and time-dependent migration.

Area of Science:

• Evolutionary biology
• Population genetics
• Phylogenetics

Background:

• The multispecies coalescent model is widely used for inferring species phylogenies from genetic data.
• This model assumes complete isolation post-speciation, which contradicts real-world scenarios of ongoing gene flow.
• Inferring species phylogenies with incomplete lineage sorting and gene flow is challenging.

Purpose of the Study:

• To develop a method and software for simulating gene trees under both the multispecies coalescent and migration models.
• To investigate the impact of migration on species tree inference and migration detection.

Main Methods:

• Developed a simulation approach incorporating population size and migration rate changes over time.
• Specified migration rates in interpretable units (fraction of emigrants per time unit).
• Used simulated data to analyze the effects of inter-lineage migration on phylogenetic inference.

Main Results:

• Species tree topology estimation shows robustness to gene flow.
• Inference and detection of migration events remain problematic, even with complex models.
• The developed software facilitates the study of gene tree properties under various migration scenarios.

Conclusions:

• Gene flow can be accommodated to some extent in species tree inference.
• Accurate inference and detection of migration from genetic data is a significant challenge.
• Further development of methods is needed for robust migration parameter estimation.