How to estimate gene flow time

[jiangzy26]

Dear Dr. Gronau,
G-PhoCS could estimate the divergence time, but how about the migration time, like secondary contact time. Do you have any suggestions to estimate it?

[igronau]

Most of the information on the time of migration should come from the length distribution of the tracks from different ancestry in admixed populations. Unfortunately, the data that G-PhoCS uses consists of short unlinked sequence alignments. This data does not provide much information about track lengths. That said, if you have enough populations in your model, then you may be able to determine the branch in the population phylogeny that served as the target of gene flow. The time frame of this branch does provide some information about the possible time of migration.