Drew C. Wham

HOST‐SPECIALIST LINEAGES DOMINATE THE ADAPTIVE RADIATION OF REEF CORAL ENDOSYMBIONTS

Bursts in species diversification are well documented among animals and plants, yet few studies have assessed recent adaptive radiations of eukaryotic microbes. Consequently, we examined the radiation of the most ecologically dominant group of endosymbiotic dinoflagellates found in reef‐building corals, Symbiodinium Clade C, using nuclear ribosomal (ITS2), chloroplast (psbAncr), and multilocus microsatellite genotyping. Through a hierarchical analysis of high‐resolution genetic data, we assessed whether ecologically distinct Symbiodinium, differentiated by seemingly equivocal rDNA sequence differences, are independent species lineages. We also considered the role of host specificity in Symbiodinium speciation and the correspondence between endosymbiont diversification and Caribbean paleo‐history. According to phylogenetic, biological, and ecological species concepts, Symbiodinium Clade C comprises many distinct species. Although regional factors contributed to population‐genetic structuring of these lineages, Symbiodinium diversification was mainly driven by host specialization. By combining patterns of the endosymbionts host specificity, water depth distribution, and phylogeography with paleo‐historical signals of climate change, we inferred that present‐day species diversity on Atlantic coral reefs stemmed mostly from a post‐Miocene adaptive radiation. Host‐generalist progenitors spread, specialized, and diversified during the ensuing epochs of prolonged global cooling and change in reef‐faunal assemblages. Our evolutionary reconstruction thus suggests that Symbiodinium undergoes “boom and bust” phases in diversification and extinction during major climate shifts.

Ecologically differentiated stress-tolerant endosymbionts in the dinoflagellate genus Symbiodinium (Dinophyceae) Clade D are different species

Abstract: We used an integrative genetics approach using sequences of (1) nuclear ribosomal rDNA (internal transcribed spacers and partial large subunit rDNA), (2) single-copy microsatellite nuclear DNA, (3) chloroplast-encoded 23S rDNA, (4) mitochondrial cytochrome b, and (5) repeat variation at eight microsatellite markers, to test the hypothesis that the stress-tolerant, ‘morphologically cryptic’ Clade D Symbiodinium (Dinophyceae) was composed of more than one species. Concordant phylogenetic and population genetic evidence clearly differentiate separately evolving, reproductively isolated lineages. We describe Symbiodinium boreum sp. nov. and S. eurythalpos sp. nov., two symbionts known to occur in colonies of the zebra coral, Oulastrea crispata (Scleractinia), which lives in turbid, marginal habitats extending from equatorial Southeast Asia to the main islands of Japan in the temperate northwest Pacific Ocean. Symbiodinium boreum was associated with O. crispata in temperate latitudes and S. eurythalpos was common to colonies in the tropics. The geographical ranges of both symbiont species overlapped in the subtropics where they sometimes co-occurred in the same host colony. Symbiodinium trenchii sp. nov. is also described. As a host-generalist symbiont, it often occurs in symbiosis with various species of Scleractinia possessing open (horizontal) modes of symbiont acquisition and is common to reef coral communities thriving in warm turbid reef habitats in the western Pacific Ocean, Indian Ocean, Arabian/Persian Gulf, Red Sea and western Atlantic (Caribbean). As is typical for dinoflagellates, S. boreum and S. eurythalpos were haploid, but microsatellite loci from field-collected and cultured S. trenchii often possessed two alleles, implying that a genome-wide duplication occurred during the evolution of this species. The recognition that Clade D Symbiodinium contains species exhibiting marked differences in host specificity and geographical distribution will yield greater scientific clarity about how stress-tolerant symbionts function in the ecological response of coral–dinoflagellate symbioses to global climate change.

Microbial invasion of the Caribbean by an Indo-Pacific coral zooxanthella

Significance This research documents the spread of an opportunistic coral endosymbiont, Symbiodinium trenchii, from the Indo-Pacific into the Greater Caribbean, a region afflicted by human-related impacts including climate warming and environmental degradation. As a symbiont, it increases the resilience of photosynthetic corals to environmental perturbation but may diminish the animal’s capacity to calcify and build reefs. This work exposes a critical need to better understand the consequences of microbial introductions (even mutualistic species) on ecosystem stability and function and raises questions about the long-term impact of new, but maladapted, symbioses on the productivity of reef coral communities in the Atlantic Ocean. Human-induced environmental changes have ushered in the rapid decline of coral reef ecosystems, particularly by disrupting the symbioses between reef-building corals and their photosymbionts. However, escalating stressful conditions enable some symbionts to thrive as opportunists. We present evidence that a stress-tolerant “zooxanthella” from the Indo-Pacific Ocean, Symbiodinium trenchii, has rapidly spread to coral communities across the Greater Caribbean. In marked contrast to populations from the Indo-Pacific, Atlantic populations of S. trenchii contained exceptionally low genetic diversity, including several widespread and genetically similar clones. Colonies with this symbiont tolerate temperatures 1–2 °C higher than other host–symbiont combinations; however, calcification by hosts harboring S. trenchii is reduced by nearly half, compared with those harboring natives, and suggests that these new symbioses are maladapted. Unforeseen opportunism and geographical expansion by invasive mutualistic microbes could profoundly influence the response of reef coral symbioses to major environmental perturbations but may ultimately compromise ecosystem stability and function.

Microsatellite loci for the host-generalist “zooxanthella” Symbiodinium trenchi and other Clade D Symbiodinium

Nine new polymorphic microsatellites were developed for Symbiodinium trenchi (sensu type D1a). These loci were tested on populations of S. trenchi from corals in Palau and 3–19 alleles were observed at each haploid locus with an average of 7 alleles. Many of the primer sets successfully amplified loci within other members of Symbiodinium clade D, demonstrating their utility across the group. Clade D Symbiodinium spp. are generally regarded as thermally tolerant and are common in coral reef habitats with warm, turbid, and/or variable environmental conditions. These population genetic markers are therefore useful for investigating how stress-tolerant symbionts may respond to climate warming through range expansion and/or by developing new associations with various host cnidarians. Additionally, the cross-lineage utility of these markers should help delineate the evolutionary relationships among members of this clade.

Population genetics of reef coral endosymbionts (Symbiodinium, Dinophyceae)

Symbiodinium is a diverse genus of unicellular dinoflagellate symbionts associating with various marine protists and invertebrates. Although the broadscale diversity and phylogenetics of the Symbiodinium complex is well established, there have been surprisingly few data on fine‐scale population structure and biogeography of these dinoflagellates. Yet population‐level processes contribute strongly to the biology of Symbiodinium, including how anthropogenic‐driven global climate change impacts these symbionts and their host associations. Here, we present a synthesis of population‐level characteristics for Symbiodinium, with an emphasis on how phylogenetic affinities, dynamics within and among host individuals, and a propensity towards clonality shape patterns on and across reefs. Major inferences include the following: (i) Symbiodinium populations within individual hosts are comprised mainly of cells belonging to a single or few genetic clones. (ii) Symbiont populations exhibit a mixed mode of reproduction, wherein at least one sexual recombination event occurs in the genealogy between most genotypes, but clonal propagation predominates overall. (iii) Mutualistic Symbiodinium do not perpetually persist outside their hosts, instead undergoing turnover and replacement via the continuous shedding of viable clonal cells from host individuals. (iv) Symbiont populations living in the same host, but on different reefs, are often genetically subdivided, suggesting low connectivity, adaptation to local conditions, or prolific asexual reproduction and low effective population sizes leading to disproportionate success within and among hosts. Overall, this synthesis forms a basis for future investigations of coral symbiosis ecology and evolution as well as delimitation of species boundaries in Symbiodinium and other eukaryotic microorganisms.

Symbiodinium population genetics: testing for species boundaries and analysing samples with mixed genotypes

Population genetic markers are increasingly being used to study the diversity, ecology and evolution of Symbiodinium, a group of eukaryotic microbes that are often mutualistic with reef‐building corals. Population genetic markers can resolve individual clones, or strains, from samples of host tissue; however, samples may comprise different species that may confound interpretations of gene flow and genetic structure. Here, we propose a method for resolving species from population genetic data using tests for genetic recombination. Assigning individuals to genetically recombining populations prior to further analyses avoids critical errors in the interpretation of gene flow and dispersal. To demonstrate the effectiveness of the approach, we first apply this method to a simulated data set. We then use the method to resolve two species of host generalist Symbiodinium that commonly co‐occur in reef‐building corals collected from Indo‐West Pacific reefs. We demonstrate that the method is robust even when some hosts contain genotypes from two distinct species. Finally, we examine population genetic data sets from two recently published papers in Molecular Ecology. We show that each strongly supports a two species interpretation, which significantly changes the original conclusions presented in these studies. When combined with available phylogenetic and ecological evidence, the use of population genetic data offers a robust method for unambiguously delimiting morphologically cryptic species.

Symbiodinium glynnii sp. nov., a species of stress-tolerant symbiotic dinoflagellates from pocilloporid and montiporid corals in the Pacific Ocean

Abstract: A formal Symbiodinium species taxonomy enhances understanding of the physiology and ecology of coral–dinoflagellate symbioses. Here we formally define a new species of stress tolerant Symbiodinium in Clade D, Symbiodinium glynnii sp. nov. This species exhibits high host specificity for members of the stony coral genus Pocillopora in the Pacific Ocean and can also be found in symbiosis with the coral genera Seriatopora and Montipora. Symbiodinium glynnii is especially common in the Eastern Tropical and subtropical Pacific, where Pocillopora is abundant and ecologically important. While S. glynnii is evolutionarily closely related to Symbiodinium trenchii, a combination of multilocus genetic data including rDNA, chloroplast (psbA), and single copy nuclear microsatellites, as well as differences in ecology (host associations), morphology (cell size), and ultrastructure (chromosome size), identify S. glynnii as distinct from S. trenchii and other Clade D species. Finally we use these data to parameterize a provisional classification and regression model to show how closely related species are recognized by integrating multiple sources of evidence.

Eight polymorphic microsatellite loci for the Indo-Pacific-wide zoanthid, Zoanthus sansibaricus

Next generation sequencing allows rapid development of genetic markers for investigating the ecology and evolution of non-model organisms. In the present study we employed 454 sequencing and high through-put screening to ultimately generate eight highly polymorphic microsatellites for Zoanthus sansibaricus, a common colonial anemone in the order Zoantharia that is widely distributed throughout the Indo-Pacific. Each locus was screened against cultured Symbiodinium as well as on individuals harboring distantly related symbiont species to discount contamination by DNA from their obligate dinoflagellate symbionts. The range of Z. sansibaricus extends across the tropical and subtropical Indian and Pacific oceans. Therefore, these population genetic markers will allow examination of dispersal and gene flow in this species across large tropical and subtropical oceanic ranges.

An Indo-West Pacific ‘zooxanthella’ invasive to the western Atlantic finds its way to the Eastern Pacific via an introduced Caribbean coral

Phylogenetic evidence indicates that Siderastrea glynni, a species of coral thought to be endemic to the Eastern Pacific, is actually more likely to be Si. siderea introduced from the Atlantic. Our analyses of the endosymbionts of Si. glynni (Symbiodinium) substantiate this as an introduced species; attempts to conserve and list Si. glynni as an endangered species are probably unwarranted. The specimens we examined harbored Symbiodinium trenchii and some also contained Sy. goreaui, symbionts that occur with Si. siderea in the Atlantic. Moreover, the genotype of Sy. trenchii (a single strain defined by ten diallelic microsatellite loci) was genetically distinct from genotypes of Sy. ‘glynni,’ also in Clade D, found abundantly in colonies of Pocillopora throughout the region. Furthermore, the strain of Sy. trenchii grouped with genotypes from the Greater Caribbean, an inbred population that was recently introduced from the Indo-West Pacific. This secondary introduction suggests that strains of Caribbean Sy. trenchii are capable of dispersal into new reef coral communities where this symbiont does not presently exist.

Ecological factors rather than physical barriers shape genetic structure of algal symbionts in Micronesian corals

Many reef-building corals acquire their algal symbionts (Symbiodinium sp.) from the local environment upon recruitment. This horizontal transmission strategy where hosts pair with locally available symbionts could serve to increase coral fitness across diverse environments, as long as hosts maintain high promiscuity and symbionts adapt locally. Here, we tested this hypothesis in two coral species by comparing host and symbiont genetic structures across different spatial scales in Micronesia. Each host species associated with two genetically distinct Symbiodinium lineages, confirming high promiscuity in broadly dispersing hosts. However, contrary to our initial expectation, symbiont genetic structure was independent of physical barriers to dispersal between islands, unlike genetic structure of their hosts that was nearly perfectly explained by ocean currents. Instead, Symbiodinium consistently demonstrated genetic divergence among local reefs and between the two host species at each island, although not necessarily between distant islands. These observations indicate that Symbiodinium lineages disperse much more broadly than previously thought and continuously adapt to specific hosts and reef environments across their range, following the classical Baas Becking’s hypothesis: “Everything is everywhere, but the environment selects”. Overall, our findings confirm that horizontal transmission could be a mechanism for broadly dispersing coral species to enhance their local fitness by associating with locally adapted symbionts. Dramatic differences in factors driving the genetic structures of horizontally-transmitting corals and their Symbiodinium imply that viewing their combined genomes as a single entity (‘hologenome’) would not be useful in the context of their evolution and adaptation.