Biogeography, reproductive biology and phylogenetic divergence within the Fungiidae (mushroom corals).

While the escalating impacts of climate change and other anthropogenic pressures on coral reefs are well documented at the level of the coral community, studies of species-specific trends are less common, owing mostly to the difficulties and uncertainties in delineating coral species. It has also become clear that traditional coral taxonomy that is largely based on skeletal morphology has underestimated the diversity of many coral families. Here we use targeted enrichment methods to sequence 2476 ultraconserved and exonic loci to investigate the relationship between populations of Fungia fungites from Okinawa, Japan, where this species reproduces by brooding (i.e., internal fertilization), and Papua New Guinea and Australia, where it reproduces by broadcast-spawning (i.e., external fertilization). We also analyzed the relationships between populations of additional fungiid species (Herpolitha limax and Ctenactis spp.) that reproduce only by broadcast-spawning. Our phylogenetic and species delimitation analyses reveal strong biogeographic structuring in both Fungia fungites and Herpolitha limax, consistent with cryptic speciation in Okinawa in both species and additionally in the Red Sea for H. limax. Using both ultraconserved elements and exon data, alongside mitochondrial data captured in off-target reads, we demonstrate that Ctenactis, a genus consisting of three nominal morphospecies, is not a natural group. Our results highlight the need for a comprehensive taxonomic and systematic revision of the coral family Fungiidae. The work presented here demonstrates that sequence data generated by the application of targeted capture methods can provide objective criteria by which to test hypotheses based on morphological and/or life history data.