Genomic differentiation in an endemic Philippine genus (Aves: Sarcophanops) due to geographic isolation on recently disassociated islands

Phylogeographic studies of Philippine vertebrates have demonstrated that genetic variation is broadly partitioned by Pleistocene island aggregation. Contemporary island discontinuity is expected to influence genetic differentiation, but remains relatively undocumented perhaps because the current episode of island isolation started relatively recently. We investigated inter- and intra-island population structure in a Philippine endemic bird genus (Sarcophanops) to determine if genetic differentiation has evolved during the recent period of isolation. We sequenced thousands of genome-wide RAD markers from throughout the Mindanao group to assess fine-scale genetic structure across islands. Specifically, we investigated patterns of gene flow and connectivity within and between taxonomic and geographic bounds. A previous assessment of mitochondrial DNA detected deep structure between Sarcophanops samarensis and sister species, S. steerii, but was insufficient to detect differentiation within either species. Analysis of RAD markers, however, revealed structure within S. samarensis between the islands of Samar/Leyte and Bohol. This genetic differentiation likely demonstrates an effect of recent geographic isolation (post-LGM) on the genetic structure of Philippine avifauna. We suggest that the general lack of evidence for differentiation between recently isolated islands is a failure to detect subtle population structure due to past genetic sampling constraints, rather than the absence of such structure.