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 geographically 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, or genotypes,
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
biogeographic 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 non-synonymous
mutations predicted to alter protein efficiency. Differences in genomic
variation of S. ‘fitti’ from each host taxon may reflect the unique
selection pressures created by the microenvironments associated with each
host. The non-random 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.