Symbiotic dinoflagellates in the genus Breviolum (formerly Symbiodinium Clade B) dominate coral communities in shallow waters across the Greater Caribbean. While some formally described species exist, mounting genetic, and ecological evidence indicate that numerous more comprise this genus, many of which are closely related. To test this, colonies of common reef‐building corals were sampled across a large geographical range. Phylogenetic and population genetic markers then used to examine evolutionary divergence and delineate boundaries of genetic recombination. Three new candidate species were distinguished by fixed differences in nucleotide sequences from nuclear and chloroplast DNA. Population connectivity was evident within each lineage over thousands of kilometers, however, substantial genetic structure persisted between lineages co‐occurring within sampling locations, signifying reproductive isolation. While geographically widespread with overlapping distributions, each species is ecologically distinct, exhibiting specific mutualisms with phylogenetically distinct coral hosts. Moreover, significant differences in mean cell sizes provide some morphological evidence substantiating formal species distinctions. In providing evidence that satisfies the biological, phylogenetic, ecological, and morphological species concepts, we classify and formally name Breviolum faviinorum n. sp., primarily associated with Caribbean corals belonging to the Caribbean subfamily Faviinae; B. meandrinium n. sp., associated with corals belonging to the family Meandrinidae; and B. dendrogyrum n. sp., a symbiont harbored exclusively by the threatened coral Dendrogyra cylindrus. These findings support the primary importance of niche diversification (i.e. host habitat) in the speciation of symbiotic dinoflagellates.
Nexus file of the chloroplast large sub-unit RNA gene (cp23S)
This nexus file contains an alignment of partial sequences of the cp23S gene (~ 600 bases) from new species of the endosymbiotic dinoflagellate genus Breviolum (formerly Symbiodinium Clade B) obtained from host colonies in the reef coral families Mussidae (sub-family Faviinae), Meandrinidae, Merulinidae, and Astrocoeniidae. Sequences from Breviolum minutum, B. psygmophilum, and B. 'muscatinei' were included for comparison.
cp23S_Breviolum_species.nex
Cytochrome oxidase 1 (Cox 1) gene for Caribbean reef corals
This nexus file contains cox 1 gene sequences from representative host samples obtained during the genetic analysis of their dinoflagellates endosymbionts. It includes sequences from animals in the families Mussidae (subfamily Faviinae), Meandrinidae, Astrocoeniidae, and Merulinidae (represented by Orbicella, formerly of the Montastraea annularis species complex).
Cox1_Caribbean_Corals.nex
Nexus file for the mitochondrial cob gene
This file contains aligned sequences of the mitochondrial cytochrome b (cob) gene (~ 900 bases) from species in the endosymbiotic dinoflagellate genus Breviolum (formerly Symbiodinium Clade B) obtained from host colonies of the reef coral families Mussidae (sub-family Faviinae), Meandrinidae, Merulinidae, and Astrocoeniidae. Representative sequences for Breviolum minutum, B. psygmophilum, and B. ‘muscatinei’ were included for comparison.
Breviolum_sp_cob.nex
Nexus file of coding and non-coding DNA sequences of the psbA minicircle
This file contains partial DNA sequences for the coding (~300 bases encoding the D1 protein of photosystem II) and non-coding region (~200-300 bases) of the chloroplast psbA minicircle (psbAncr). Two large portions (~150 and 50 bases, respectively) were removed from the Breviolum faviinorum sequences to minimize the alignment’s length. Sequences are from species of endosymbiotic dinoflagellates in the genus Breviolum (formerly Symbiodinium Clade B) obtained from host colonies in the reef coral families Mussidae (sub-family Faviinae), Meandrinidae, Merulinidae, and Astrocoeniidae. Sequences from Breviolum minutum associated with the anemone Exaiptasia were included for comparison.
Breviolum_psbA_ncr_Carib_radiation
Microsatellite locus Sym15 from Breviolum spp.
This nexus file contains sequence alignments of the flanking– and repeat–regions (approximately 200 bases) for the nuclear microsatellite locus Sym15, which is possessed by most species in the dinoflagellate genus Breviolum (family Symbiodiniaceae). Samples were obtained from host colonies of the reef coral families Mussidae (especially the sub-family Faviinae), Meandrinidae, Merulinidae, and Astrocoeniidae. Sequences from Breviolum minutum (common to the sea anemone Exaiptasia) and B. psygmophilum were included for comparison.
Breviolum_Sym15_JEUKMIC_2018.nex
Multi-locus genotypes for population genetic analyses of closely related Breviolum spp.
This excel file contains multilocus genotypes based on 9 independently sorting microsatellite loci from four species of Breviolum obtained from Atlantic reef-building corals in the families Mussidae (subfamily Faviinae), Meandrinidae, Astrocoeniidae and Merulinidae (represented by Orbicella, formerly of the Montastraea annularis species complex).
Multilocus_Data_complete.xlsx