Genomic variation of an endosymbiotic dinoflagellate (<i>Symbiodinium ‘fitti’</i>) among closely related coral hosts
Hannah Reich, Sheila A. Kitchen, Kathryn H. Stankiewicz, Meghann K Devlin-Durante, Nicole D. Fogarty, Iliana B. Baums
Abstract
Abstract Mutualisms where hosts are coupled metabolically to their symbionts often exhibit high partner fidelity. Most reef‐building coral species form obligate symbioses with a specific species of photosymbionts, dinoflagellates in the family Symbiodiniaceae, despite needing to acquire symbionts early in their development from environmental sources. Three Caribbean acroporids ( Acropora palmata , A. cervicornis and their F 1 hybrid) are sympatric across much of their range, but often occupy different depth and light habitats. Throughout this range, both species and their hybrid associate with the endosymbiotic dinoflagellate Symbiodinium ‘ fitti ’. Because light (and therefore depth) influences the physiology of dinoflagellates, we investigated whether S . ‘ fitti ’ populations from each host taxon were differentiated genetically. Single nucleotide polymorphisms (SNPs) among S . ‘ fitti ’ strains were identified by aligning shallow metagenomic sequences of acroporid colonies sampled from across the Caribbean to a ~600‐Mb draft assembly of the S . ‘ fitti ’ genome (from the CFL14120 A. cervicornis metagenome). Phylogenomic and multivariate analyses revealed that genomic variation among S . ‘ fitti ’ strains partitioned to each host taxon rather than by biogeographical origin. This is particularly noteworthy because the hybrid has a sparse fossil record and may be of relatively recent origin. A subset (37.6%) of the SNPs putatively under selection were nonsynonymous mutations predicted to alter protein efficiency. Differences in genomic variation of S . ‘ fitti ’ strains from each host taxon may reflect the unique selection pressures created by the microenvironments associated with each host. The nonrandom sorting among S . ‘ fitti ’ strains to different hosts could be the basis for lineage diversification via disruptive selection, leading to ecological specialization and ultimately speciation.