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

Reich, Hannah G. and Kitchen, Sheila A. and Stankiewicz, Kathryn H. and Devlin‐Durante, Meghann and Fogarty, Nicole D. and Baums, Iliana B. (2021) Genomic variation of an endosymbiotic dinoflagellate (Symbiodinium 'fitti') among closely related coral hosts. Molecular Ecology, 30 (14). pp. 3500-3514. ISSN 0962-1083. doi:10.1111/mec.15952.

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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.

Item Type:Article
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URLURL TypeDescription ItemData ItemCode
Reich, Hannah G.0000-0002-8622-8801
Kitchen, Sheila A.0000-0003-4402-8139
Fogarty, Nicole D.0000-0003-3811-3791
Baums, Iliana B.0000-0001-6463-7308
Additional Information:© 2021 John Wiley & Sons Ltd. Issue Online: 23 July 2021; Version of Record online: 28 May 2021; Accepted manuscript online: 08 May 2021; Manuscript accepted: 04 May 2021; Manuscript revised: 01 May 2021; Manuscript received: 07 October 2020. Data Availability Statement: Sequences are available under NCBI SRA PRJNA473816. Code for data analysis and figure generation is available on github ( The draft genome assembly for the reference A. cervicornis–S. ‘fitti’ is available on dryad Research Funding: National Science Foundation. Grant Numbers: 1537959, 1538469, 1929979
Funding AgencyGrant Number
Subject Keywords:Acropora; hybrid; niche diversification; single‐nucleotide polymorphisms; Symbiodiniaceae; symbiosis
Issue or Number:14
Record Number:CaltechAUTHORS:20210510-140117824
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Official Citation:Reich, H.G., Kitchen, S.A., Stankiewicz, K.H., Devlin-Durante, M., Fogarty, N.D. and Baums, I.B. (2021), Genomic variation of an endosymbiotic dinoflagellate (Symbiodinium ‘fitti’) among closely related coral hosts. Mol Ecol, 30: 3500-3514.
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:109039
Deposited By: Tony Diaz
Deposited On:10 May 2021 21:11
Last Modified:11 Aug 2021 16:47

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