Maximum likelihood implementation of an isolation-with-migration model with three species for testing speciation with...

Area of Science:

• Population Genetics
• Genomics
• Evolutionary Biology

Background:

• Understanding species divergence requires accurate models of evolutionary processes.
• Gene flow and incomplete lineage sorting can complicate species tree inference.

Purpose of the Study:

• To implement and evaluate a novel isolation-with-migration model for phylogenetic analysis.
• To develop a likelihood ratio test (LRT) for detecting gene flow during speciation.

Main Methods:

• Utilized a multilocus genomic sequence alignment framework.
• Employed a Markov chain to characterize coalescent and migration processes.
• Integrated gene tree topologies and branch lengths analytically and numerically.
• Constructed a likelihood ratio test (LRT) for speciation with gene flow.

Main Results:

• The developed LRT is generally conservative with a low false positive rate.
• Hundreds of loci are required for substantial statistical power.
• Analysis of human-chimpanzee-gorilla data suggests gene flow during their speciation.

Conclusions:

• The isolation-with-migration model provides a robust framework for studying speciation.
• Evidence suggests past gene flow between human and chimpanzee lineages.
• The LRT is a valuable tool for detecting gene flow in population genomic studies.