Rapid thermal adaptation in coral photosymbionts draws on standing variation and recombination

Bleaching tolerance in corals depends in part on the thermal tolerance of their microalgal symbionts. Laboratory evolution has increased the thermal tolerance of the symbiont Cladocopium proliferum in ~120 generations, but the genetic basis of that response was unknown. We compared single nucleotide polymorphisms in transcriptomes of three heat-evolved C. proliferum strains and one wild-type (unselected) strain from the same progenitor. We found 15,640 polymorphic loci, but no variant was both private to a strain and consistent across its replicates, which indicates that new mutations contributed little to the response in expressed sequences. Instead, allele frequencies at 350 loci differed significantly between strains, and linkage patterns indicated recombination had occurred within scaffolds both before and after the strains were separated. Selection and recombination of variation already present in the progenitor therefore underpinned the rapid thermal adaptation. Experimental evolution for reef restoration should start from genetically diverse cultures rather than single cell isolates.