In the paper they build individual-based phylogenetic trees using genome-wide SNP data. We could look into this approach for our RAD data sets.

Phylogeography and adaptation genetics of stickleback from the Haida Gwaii archipelago revealed using genome-wide single nucleotide polymorphism genotyping.

Deagle, B. E., Jones, F. C., Absher, D. M., Kingsley, D. M. and Reimchen, T. E. (2013),  Molecular Ecology, 22: 1917–1932. doi: 10.1111/mec.12215