Population genomics of a bioluminescent symbiosis sheds light on symbiont transmission and specificity

All organisms depend on symbiotic associations with bacteria for their success, yet the processes by which specific symbioses are established and persist remain largely undescribed. To examine the ecological mechanisms involved in maintaining symbiont specificity over host generations, we examined the population genomics of a binary symbiosis involving the coral reef cardinalfish Siphamia tubifer and the luminous bacterium Photobacterium mandapamensis. Using restriction site-associated sequencing (RAD-Seq) methods we demonstrate that the facultative symbiont of S. tubifer exhibits genetic structure at spatial scales of tens of kilometers in Okinawa, Japan in the absence of physical dispersal barriers and in contrast to the host fish. These results suggest the hosts behavioral ecology help structure symbiont populations at a reef site by symbiont enrichment, consequently fostering symbiont specificity. This approach also revealed several symbiont genes that were divergent between host populations including genes known to play a role in other host-bacteria associations.