Genomic variation of an endosymbiotic dinoflagellate (Symbiodinium ‘fitti’) among closely related coral hosts

Hannah G. Reich, Sheila A. Kitchen, Kathryn H. Stankiewicz, Meghann Devlin-Durante, Nicole D. Fogarty, Iliana B. Baums

Research output: Contribution to journalArticlepeer-review

12 Scopus citations


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 F1 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.

Original languageEnglish (US)
Pages (from-to)3500-3514
Number of pages15
JournalMolecular ecology
Issue number14
StatePublished - Jul 2021

All Science Journal Classification (ASJC) codes

  • Ecology, Evolution, Behavior and Systematics
  • Genetics


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