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

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.

This is the peer reviewed version of the following article: [Reich HG, Kitchen SA, Stankiewicz KH, Devlin-Durante M, Fogarty ND, Baums IB (2021) Genomic variation of an endosymbiotic dinoflagellate (Symbiodinium 'fitti') among closely related coral hosts. Mol Ecol 30 (14):3500-3514], which has been published in final form at []. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Use of Self-Archived Versions. This article may not be enhanced, enriched or otherwise transformed into a derivative work, without express permission from Wiley or by statutory rights under applicable legislation. Copyright notices must not be removed, obscured or modified. The article must be linked to Wiley’s version of record on Wiley Online Library and any embedding, framing or otherwise making available the article or pages thereof by third parties from platforms, services and websites other than Wiley Online Library must be prohibited



Work Title Genomic variation of an endosymbiotic dinoflagellate (Symbiodinium ‘fitti’) among closely related coral hosts
Open Access
  1. Hannah G. Reich
  2. Sheila A. Kitchen
  3. Kathryn H. Stankiewicz
  4. Meghann Devlin-Durante
  5. Nicole D. Fogarty
  6. Iliana B. Baums
License In Copyright (Rights Reserved)
Work Type Article
  1. Molecular Ecology
Publication Date July 1, 2021
Publisher Identifier (DOI)
Deposited November 15, 2021




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Work History

Version 1

  • Created
  • Added MEC-20-1216.R2_Proof_hi.pdf
  • Added Creator Hannah G. Reich
  • Added Creator Sheila A. Kitchen
  • Added Creator Kathryn H. Stankiewicz
  • Added Creator Meghann Devlin-Durante
  • Added Creator Nicole D. Fogarty
  • Added Creator Iliana B. Baums
  • Published
  • Updated
  • Updated
  • Updated