Diversity of Entacmaea quadricolor in Japan

We combine fine- and broad-scale biogeographic sampling with multiple genomic datasets to test for cryptic species-level diversity within the bubble tip sea anemone, Entacmaea quadricolor, a clownfish-hosting species with an extensive range throughout the Indo-West Pacific. This species harbors extensive phenotypic variation and serves as host to the greatest variety of clownfish species, making it an ideal species to study how symbiosis and competing evolutionary processes can generate marine biodiversity. Using fine-scale sampling and Restriction site Associated DNA sequencing (RADseq) across the Japanese Archipelago, we delimited three distinct lineages: two of which co-occur throughout Mainland Japan, and one in the isolated Ogasawara Archipelago ~1000KM away. Interestingly, the two co-occurring lineages can be differentiated by the fish symbiont they host: one lineage hosts Amphiprion clarkii while the other hosts Amphiprion frenatus. To determine whether these lineages have diversified allopatrically or sympatrically within Japan, we expanded our biogeographic sampling to include populations from the Maldives, Australia, and Singapore. We used bait-capture sequencing targeting ultra-conserved elements and exon loci and multiple phylogenomic analyses to show that that the differentiation between co-occurring lineages in Mainland Japan did not occur within the Japanese Archipelago, but instead is representative of a secondary contact event.