Mutualistic microalgae co-diversify with reef corals that acquire symbionts during egg development

Abstract

The application of molecular genetics has reinvigorated and improved how species are defined and investigated scientifically, especially for morphologically cryptic micro-organisms. Here we show how species recognition improves understanding of the ecology and evolution of mutualisms between reef-building corals and their mutualistic dinoflagellates (i.e. Symbiodiniaceae). A combination of genetic, ecological, and morphological evidence defines two sibling species of Cladocopium (formerly Symbiodinium Clade C), specific only to host corals in the common genus Pocillopora, which transmit their obligate symbionts during oogenesis. Cladocopium latusorum sp. nov. is symbiotic with P. grandis/meandrina while the smaller-celled C. pacificum sp. nov. associates with P. verrucosa. Both symbiont species form mutualisms with Pocillopora that brood their young. Populations of each species, like their hosts, are genetically well connected across the tropical and subtropical Pacific Ocean, indicating a capacity for long-range dispersal. A molecular clock approximates their speciation during the late Pliocene or early Pleistocene as Earth underwent cycles of precipitous cooling and warming; and corresponds to when their hosts were also diversifying. The long temporal and spatial maintenance of high host fidelity, as well as genetic connectivity across thousands of kilometers, indicates that distinct ecological attributes and close evolutionary histories will restrain the adaptive responses of corals and their specialized symbionts to rapid climate warming.

Fig. 1. Collection locations, light micrographs, and cell sizes of symbiotic dinoflagellates from corals in the genus Pocillopora.

A Indo-Pacific collection locations of Pocillopora corals. Arrows correspond to major ocean currents that influence dispersal and connectivity. B Light micrographs of cells representative of Cladocopium latusorum sp. nov. and C cells representative of Cladocopium pacificum sp. nov. Scale bar = 20 µm. D Size differences between C. latusorum (white circles) and C. pacificum (gray triangles). Each symbol corresponds to mean cell dimensions from independent samples. Error bars represent 95% confidence intervals.

Fig. 2. Phylogenetic and population genetic data resolving two species of Cladocopium.

A Unrooted phylogenic reconstruction inferred from aligned concatenated DNA including rRNA genes (ITS2 and LSU), partial chloroplast cp23, mitochondrial cob, and cox 1 genes, showing the relationship of Cladocopium latusorum and C. pacificum with other described species of Cladocopium. B Two-dimensional representation of Principle Components calculated for the multi-locus genotypes using t-SNE [77]. C STRUCTURE plot (K = 2) showing reproductive isolation between Cladocopium latusorum and C. pacificum in the Pacific Ocean. Vertical bars represent the probability of assignment of one individual to a distinct population. D Bubble plots show differences in allele frequencies between species for each of 8 microsatellite loci. Analyses were conducted using scripts available at https://github.com/KiraTurnham/ISME.Turnham.et.al.2021.

Fig. 3. High-resolution phylogenetic analysis of Cladocopium latusorum and C. pacificum.

A Maximum Parsimony phylogeny of the psbA^ncr (Bootstrap support values based on 1000 replicates). B Pocillopora grandis typical host species mutualistic with C. latusorum. C Approximate geographic distribution of C. latusorum. D Pocillopora verrucosa typical host species mutualistic with C. pacificum. E Approximate geographic distribution of C. pacificum. Symbols correspond to samples sourced from geographic locations presented in Fig. 1A; squares denote samples from the Indian Ocean, triangles from the western Pacific, circles from the central Pacific and hexagons from the eastern Pacific.

Fig. 4. Age estimates for the co-diversification of Cladocopium with their pocilloporid hosts.

A Differences in specificity (gray shading) of Cladocopium latusorum and C. pacificum to different lineages of broadcast spawning Pocillopora (circles), whereas both associate with brooding species (squares). Unrooted host phylogeny based on the mitochondrial open reading frame (number designations as described in 49). B Time of divergence between Cladocopium latusorum and C. pacificum in correspondence with the adaptive radiation of Pocillopora [42]. Reduced time-calibrated psbA phylogeny estimated from BEAST 2.3.5 with bars representing the 95% highest posterior density interval and mean divergence times (ages) listed at each node. The Cladocopium associated with sibling species Porites panamensis (Eastern Pacific) and Porites porites var. colonensi (Western Atlantic) were used to calibrate the molecular clock based on the geological separation of the Atlantic and Pacific Oceans by the Isthmus of Panama (4.5–3.0 mya).