Data from: Nemo knows: Clownfishes differentiate cryptic host species across fine and broad geographic scales and reveal a potential adaptive radiation in the clownfish-hosting sea anemones

The symbiosis between clownfish (or anemonefishes) and their host sea
anemones ranks among the most recognizable animal interactions on the
planet. Found on coral reef habitats across the Indian and Pacific Oceans,
28 recognized species of clownfishes adaptively radiated from a common
ancestor to live obligately with only 10 nominal species of host sea
anemones. Are the host sea anemones truly less diverse than clownfish? Did
the symbiosis with clownfish trigger a reciprocal adaptive radiation in
sea anemones, or minimally, a co-evolutionary response to the mutualism?
To address these questions, we combined fine- and broad-scale
biogeographic sampling with multiple independent genomic datasets for the
bubble-tip sea anemone, Entacmaea quadricolor—the most common clownfish
host anemone throughout the Indo-West Pacific. Fine-scale sampling and
restriction site-associated DNA sequencing (RADseq) throughout the
Japanese Archipelago revealed three highly divergent cryptic species: two
of which co-occur throughout the Ryukyu Islands and can be differentiated
by the clownfish species they host. Remarkably, broader biogeographic
sampling and bait-capture sequencing reveal that this pattern is not
simply the result of local ecological processes unique to Japan, but part
of a deeper evolutionary signal where some species of E. quadricolor serve
as host to the generalist clownfish species Amphiprion clarkii and others
serve as host to the specialist clownfish A. frenatus. In total, we
delimit at least five cryptic species in E. quadricolor that have
diversified within the last five million years. The rapid diversification
of E. quadricolor, combined with functional ecological and phenotypic
differentiation, supports the hypothesis that this may represent an
adaptive radiation in response to mutualism with clownfishes. Our data
indicate that clownfishes are not merely settling in locally available
hosts but recruiting to specialized host lineages with which they have
co-evolved. These findings have important implications for understanding
how the clownfish-sea anemone symbiosis has evolved and will shape future
research agendas on this iconic model system.