Comparative phylogeographic inference with genome-wide data from aggregated population pairs

Area of Science:

• Population genomics
• Comparative phylogeography
• Evolutionary biology

Background:

• Phylogeography traditionally compares population divergences using qualitative methods and organelle DNA.
• Advances in next-generation sequencing and coalescent modeling have improved analyses.
• A unified framework for aggregated genomic-scale data is needed for comparative phylogeography.

Purpose of the Study:

• Introduce and validate the aggregate joint site frequency spectrum (ajSFS) for co-demographic inference.
• Apply the ajSFS to analyze co-divergence and co-migration histories in empirical datasets.
• Demonstrate the utility of ajSFS for complex comparative population genomic studies.

Main Methods:

• Developed the aggregate joint site frequency spectrum (ajSFS).
• Validated ajSFS within a hierarchical Bayesian framework using in silico experiments.
• Applied ajSFS to restriction site-associated DNA (RAD) marker data from lamprey and bird populations.

Main Results:

• Lamprey population pairs showed synchronous co-divergence and secondary contact, with variable migration intensities.
• Bird population pairs exhibited asynchronous co-divergence histories.
• The ajSFS successfully inferred complex co-demographic histories.

Conclusions:

• The ajSFS provides a flexible and powerful tool for comparative phylogeography.
• The method enables unified analysis of aggregated genomic-scale data.
• ajSFS opens new avenues for understanding population divergence and migration.