STEPPING OUT OF THE SHADOWS: GENOMIC AND EXPERIMENTAL ILLUMINATION OF DIVERSITY WITHIN THE CORAL FAMILY AGARICIIDAE

Abstract

Confidently delimiting species and resolving their evolutionary histories relies on accurate taxonomy and well-supported phylogenies; two things which have been historically challenging in corals. The coral family Agariciidae is composed of species with exceptionally large ranges, and therefore likely contains numerous cryptic species. The aims of this dissertation are to study the phenotypic variation, phylogenomic and geographic diversity of species from the family Agariciidae. To assess the phylogenetics and phylogeography of this family I applied two approaches. First, I used a traditional mitochondrial DNA barcoding approach that focused effort on a taxonomically and geographically broad sampling scheme. I combined 208 new sequences with 191 previously published sequences, representing 31 species. Relationships based on the mtDNA intron revealed considerable discordance between the current taxonomy and recovered clades; just seven species were recovered as monophyletic. Second, I generated RAD libraries for a subset of individuals, which produced far more data from across the genome, albeit from fewer samples (120), which represented twenty nominal taxa. From these libraries I assembled complete mitochondrial genomes, 18 of which are the first recorded for that taxon. I estimated phylogenies from SNPs generated from three different assembly approaches. Both the mitogenome and SNP phylogenies recovered well-supported trees, but they were not fully concordant with one another. I found no evidence of introgression within the SNP datasets, indicating hybridization may not be as prevalent in this family as in some other corals. The SNP trees recovered three well-supported clades, none of which corresponded to a monophyletic Pavona or Leptoseris. Each phylogenetic data set recovered multiple putative cryptic species associated with the nominal taxa P. varians and L. mycetoseroides. Both species form similar encrusting, ridged colonies, indicating this morphology may be the ancestral state of this family or may have evolved independently multiple times. Given the evolutionary and ecological success of the ridged morphology, combined with the high variability both within and between species, I examined the extent of light-associated phenotypic plasticity for P. varians. A common garden experiment revealed light had a strong effect on both the growth rates and morphology of colonies. This is likely an adaptive response which allows this depth generalist species to tolerate a wide variety of light environments. Overall this work suggests whole genome studies and further experiments are necessary to fully resolve the species boundaries and evolutionary processes driving speciation in this family.