Coral Reefs

, Volume 34, Issue 4, pp 1075–1086 | Cite as

Geographic structure and host specificity shape the community composition of symbiotic dinoflagellates in corals from the Northwestern Hawaiian Islands

  • Michael Stat
  • Denise M. Yost
  • Ruth D. Gates


How host–symbiont assemblages vary over space and time is fundamental to understanding the evolution and persistence of mutualistic symbioses. In this study, the diversity and geographic structure of coral–algal partnerships across the remote Northwestern Hawaiian Islands archipelago was investigated. The diversity of symbionts in the dinoflagellate genus Symbiodinium was characterised using the ribosomal internal transcribed spacer 2 (ITS2) gene in corals sampled at ten reef locations across the Northwestern Hawaiian Islands. Symbiodinium diversity was reported using operational taxonomic units and the distribution of Symbiodinium across the island archipelago investigated for evidence of geographic structure using permutational MANOVA. A 97 % sequence similarity of the ITS2 gene for characterising Symbiodinium diversity was supported by phylogenetic and ecological data. Four of the nine Symbiodinium evolutionary lineages (clades A, C, D, and G) were identified from 16 coral species at French Frigate Shoals, and host specificity was a dominant feature in the symbiotic assemblages at this location. Significant structure in the diversity of Symbiodinium was also found across the archipelago in the three coral species investigated. The latitudinal gradient and subsequent variation in abiotic conditions (particularly sea surface temperature dynamics) across the Northwestern Hawaiian Islands encompasses an environmental range that decouples the stability of host–symbiont assemblages across the archipelago. This suggests that local adaptation to prevailing environmental conditions by at least one partner in coral–algal mutualism occurs prior to the selection pressures associated with the maintenance of a symbiotic state.


Adaptation Biogeography Coral Hawaii ITS2 Symbiodinium 


The geographic formation and isolation of the Hawaiian archipelago creates an informative setting for understanding speciation and evolution in both the terrestrial and marine environments (Wagner and Funk 1995; Bowen et al. 2013). Research into the phylogeography and connectivity of marine organisms along the island chain is enhancing our capacity to interpret how pelagic larval dispersal, ocean currents, cryptic physical barriers, and other ecological processes combine to contribute to the partitioning of biological diversity (Bird et al. 2011; Toonen et al. 2011; Selkoe et al. 2014). How partner assemblages in mutualistic symbioses and their interactions vary over spatial scales, referred to as the geographic mosaic of coevolution, presents yet another avenue towards understanding how biotic and abiotic factors coupled with dependence for another organism, interact to shape patterns of marine biodiversity (Thompson and Cunningham 2002).

The mutualistic association between corals and endosymbiotic algae (Symbiodinium sp.) is essential to the formation of coral reefs and provides habitat for the high diversity of organisms found living in reef ecosystems (Goreau and Goreau 1959; Reaka-Kudla 1997). The coral reefs of the Northwestern Hawaiian Islands (NWHI) stretch over 2000 km and are a relatively pristine bioregion with one of the highest levels of marine environmental protection. While the diversity of corals found in the NWHI is low (57 species) compared to the Coral Triangle in the Indo Pacific (600 species), high endemism (30 % of species) accounts for 37–53 % of coral cover (Maragos et al. 2004). Interestingly, the ecologically dominant coral genera in the archipelago, Montipora, Porites, and Pocillopora, all employ vertical symbiont transmission as a life history trait (Fenner 2005; Baird et al. 2009). Symbionts are passed directly from the parent to their offspring in vertical symbiont transmission, as opposed to acquiring them from the surrounding environment, as occurs with horizontal transmission. It has been suggested that vertical symbiont transmission is a pathway to partner specialisation, which is supported by observations in coral–algal symbiosis (Douglas 1998; Stat et al. 2008; Fabina et al. 2012). Indeed, on the island of Oahu in Hawaii, relatively higher symbiont diversity and host specificity in coral–algal partnerships compared to other regions of the world is attributed to the coral community being dominated by hosts with vertical symbiont transmission (LaJeunesse et al. 2004a). Therefore, the unique features of the Hawaiian archipelago and specifically the NWHI, including the isolation and arrangement of the islands, their pristine condition, and the dominance of hosts with vertical symbiont transmission, presents an ideal scenario to further investigate how partner specialisation varies over broad spatial scales.

The genetic diversity of Symbiodinium is currently divided into nine phylogenetic lineages that are called ‘clades’ A-I (Pochon and Gates 2010). Each clade can be resolved into discrete haplotypes, species, or genetic groups depending on the molecular marker and methodology applied (Stat et al. 2012, 2013; LaJeunesse et al. 2014). The most commonly used marker in assessing Symbiodinium diversity is the internal transcribed sequence 2 (ITS2) region of the rDNA, with either sequence clustering approaches used to infer diversity or fingerprint patterns from DGGE as representative of distinct symbiont types (Stat et al. 2009, 2013; LaJeunesse et al. 2010). The conclusions about symbiont diversity using either approach are consistent in that both methods identify coral species, colony depth, symbiont acquisition strategy, and locality as major factors that influence patterns in symbiont distribution. Bacterial cloning, and more recently next-generation sequencing approaches, generate multiple sequences that can be grouped into clusters or operational taxonomic units (OTUs) prior to analysis and interpretations of diversity (Stoeck et al. 2006; Blaalid et al. 2012). For Symbiodinium, a 97 % similarity cutoff of the ITS2 gene has been used to generate OTUs from sequences recovered using cloning and 454 pyrosequencing (Padilla-Gamino et al. 2012; Stat et al. 2013; Thomas et al. 2014), with a 97 % threshold gaining recent support from deep sequencing of clonal cultures (Arif et al. 2014). While this sequence cutoff is the most commonly used across taxa and is below the average level of intragenomic variation in Symbiodinium (Sampayo et al. 2009), further support for its application would help justify its use over other sequence cut-off thresholds.

In this study, the unique geographic attributes of the NWHI were used to address the spatial distribution of coral–dinoflagellate symbioses on an isolated reef ecosystem. First, the diversity and relationship of Symbiodinium associated with a range of coral taxa was characterised through the identification of ecologically and phylogenetically informative OTUs. Second, the spatial structure of Symbiodinium OTUs in three coral species found throughout the NWHI was statistically explored.

Materials and methods

Study sites and coral collections

Tissue biopsies from 203 coral colonies were sampled between 2005 and 2009 from two depth ranges, 0–10 and 10–20 m, across the Northwestern Hawaiian Islands Marine National Monument (NWHI), Papahānaumokuākea (Fig. 1, Electronic Supplementary Material, ESM, 1). Biopsies from 16 coral species (N = 79 colonies) representing eight genera were collected at French Frigate Shoals, and from three coral species (N = 138 colonies) at ten localities across the NWHI archipelago. Sea surface temperatures for the ten sampling sites for years 2000–2009 were obtained from the NOAA/NESDIS 50 km night time SST (°C) database from NOAAs Coral Reef Watch website (NOAA 2000). Coral samples were preserved in DNA extraction buffer [50 % (w/v) guanidinium isothiocyanate; 50 mM Tris pH 7.6; 10 mM EDTA; 4.2 % (w/v) sarkosyl; 2.1 % (v/v) β-mercaptoethanol] and stored at 4 °C until further processing.
Fig. 1

Map of the Hawaiian archipelago located in the central Pacific Ocean. The Northwestern Hawaiian Islands Marine National Monument, Papahānaumokuākea, spans a distance of approximately 2000 km (bordered region) and contains ten islands where corals were sampled in this study. The islands are grouped into three regions: lower (Nihoa, Necker, and French Frigate Shoals), intermediate (Gardner, Maro, Laysan, and Lisianski), and high-latitude islands (Pearl & Hermes, Midway, and Kure)

DNA extraction, PCR amplification, cloning, and sequencing

Total nucleic acid extraction and PCR was performed as in Stat et al. (2009). Tissue samples were incubated at 72 °C for 10 min followed by centrifugation at 16,000×g for 5 min. The supernatant was removed and the DNA precipitated in an equal volume of isopropanol and overnight incubation at −20 °C. The DNA pellet was washed in 70 % ethanol, dried, and dissolved in Tris buffer (0.1 M pH 9).

The ITS2 region of Symbiodinium was amplified in PCR using primers itsD (5′-GTGAATTGCAGAACTCCGTG-3′) and its2rev2 (5′-CCTCCGCTTACTTATATGCTT-3′; Pochon et al. 2001). PCRs contained 0.5 U of Immolase (Bioline), 2.5 µl 10× PCR buffer, 50 nmols MgCl2, 2.5 nmol each dNTP, 5 pmol each primer, and 1 µl DNA template made up to a 25 µl volume with sterile deionized water. PCR was performed in a Bio-Rad thermal cycler with 5 min at 94 °C followed by 35 cycles of 30 s at 95 °C, 30 s at 52 °C, and 1 min at 72 °C, and ended with a final 10 min extension at 72 °C. Amplicons were purified using the QIAquick® PCR purification kit (Qiagen), ligated into pGEM®-T Easy vector (Promega), transformed into α select gold efficiency competent cells (Bioline) and grown overnight on selective LB media (ampicillin 50 µg ml−1, 0.1 mM IPTG, 50 µg ml−1 X-gal). At least ten colonies per sample containing the target insert were used as template for PCR using M13 primers with the number of cycles reduced to 20. Products were sequenced using BigDye Terminators (PerkinElmer) on an ABI-3100 automated sequencer at the University of Hawaii.

Sequence analysis, operational taxonomic units, and phylogenetic inference

Sequence chromatograms were inspected and multiple sequence alignments constructed using the MAFFT algorithm in Geneious® 6.1.6 (Drummond et al. 2011). Potential chimeric sequences were identified using Perseus in Mothur (Schloss et al. 2009) and removed from the dataset as well as singletons. Mothur was used to generate a distance matrix of sequences in an alignment with indels treated as a single mutation, and to group sequences into operational taxonomic units (OTUs) using the furthest neighbour algorithm. OTU assignment was performed for each Symbiodinium clade separately. The Symbiodinium clade and subclade identity of unique sequences was determined by blasting against GenBank, GeoSymbio (Franklin et al. 2012), and in-house databases. Novel sequences representative of an OTU were named following the method in Stat et al. (2009). Bayesian analysis was performed with the MrBayes (Huelsenbeck and Ronquist 2001) plugin in Geneious® 6.1.6. under the HKY85 substitution model, four heated chains with a length of 1,100,000 and a burn-in length of 100,000. Neighbour-joining and a heuristic search under maximum likelihood and maximum parsimony methods with 1000 bootstraps was performed with PAUP* 4.0b10 (Swofford 2000). Modeltest (Posada and Crandall 1998) was executed under the AIC model prior to maximum likelihood and neighbour-joining searches. Unique sequences were used in the construction of phylogenies and are available from GenBank (KF623552-KF623693).

Statistical analyses

All statistical analyses were performed using the software PRIMER v.6 (Clarke and Gorley 2006). A similarity matrix using Euclidean distance of SST metrics for each site (Table 1) was used to generate a UPGMA dendrogram using group-average clustering. A Bray–Curtis similarity matrix of Symbiodinium OTUs following standardisation (relative frequency) and transformation (square root) was used to investigate the relationship of Symbiodinium in host taxa and the distribution of Symbiodinium in the NWHI. To test for host specificity, Symbiodinium OTUs in each coral colony from French Frigate Shoals were used in a one-way ANOSIM with host species as a factor, and a SIMPER analysis performed to identify the OTUs driving the relationship among coral species. A UPGMA dendrogram using group-average clustering was also performed on Symbiodinium ITS2 OTUs in each coral species for hosts sampled at French Frigate Shoals, and the SIMPROF test conducted to establish the significance of the dendrogram nodes. To test for the partitioning of Symbiodinium across the NWHI archipelago, Symbiodinium ITS2 OTUs in each coral colony were used in a permutational multivariate analysis of variance (PERMANOVA) with factors host species, latitude, and depth (Anderson 2005). Factor host species included colonies of Montipora capitata, Porites lobata, and Pocillopora meandrina, which were the only three coral species sampled across the ten localities. Corals from Nihoa, Necker, and French Frigate Shoals were grouped as low-latitude islands (23°N), Gardner, Maro, Laysan, and Lisianski were grouped as intermediate latitude islands (25°N), and Pearl and Hermes, Midway, and Kure were grouped as high-latitude islands (27–28°N). Depth was scored as either 0–10 or 10–20 m.
Table 1

Descriptive statistics for sea surface temperatures (°C) at the ten sampling localities in the Northwestern Hawaiian Islands


Low latitude

Intermediate latitude

High latitude
























































































Std deviation











FFS French Frigate Shoals, P&H Pearl & Hermes


Sea surface temperature dynamics

Sea surface temperature dynamics for the ten sampling localities are shown in Fig. 2 and the accompanying descriptive statistics in Table 1. The localities are displayed in three graphs to match the clustering of sites to the latitude groupings depicted in Fig. 1. As expected, there is a general trend in site ocean temperature that corresponds to its latitudinal position. The low-latitude sites at 23°N (Nihoa, Necker, and French Frigate Shoals) have the highest recorded mean SSTs (25.2–25.4 °C), and the lowest temperature range (5.3–5.8 °C) and variance (1.8–2.1 °C; Table 1). In contrast, the high-latitude sites at 27–28°N (Pearl & Hermes, Midway, and Kure) have the lowest recorded mean SSTs (23.3–23.9 °C), and the highest temperature range (9.5–10.7 °C) and variance (6.1–7.0 °C). The intermediate sites at 25°N (Gardner, Maro, Laysan, and Lisianski) display sea surface temperature statistics that fall between ocean data for the low- and high-latitude groups; mean SSTs (24.9–25.0 °C), temperature range (6.6–7.0 °C), and variance (3.2–3.5 °C). The UPGMA dendrogram using SST metrics of each site grouped the localities into three clusters that correspond to the latitude groupings in Fig. 1 (ESM 2). These temperature results support our island clustering into three latitude groups across the NWHI archipelago for statistical analyses (see below).
Fig. 2

Coral Reef Watch 50-km SST time series data for the ten sampling localities NOAA (2000). Sites were grouped according to latitude with Nihoa, Necker, and French Frigate Shoals (FFS) as low-latitude islands (a), Gardner, Maro, Laysan and Lisianski as intermediate latitude islands (b), and Pearl & Hermes (P&H), Midway and Kure as high-latitude islands (c)

Symbiodinium OTUs and diversity in corals at French Frigate Shoals

A total of 803 Symbiodinium ITS2 sequences were recovered from 79 coral colonies at French Frigate Shoals and identified as belonging to clades A, C, D, and G. Clade C was the dominant phylogenetic group recovered representing 86.9 % of sequences, while clades A, D, and G were represented by 6.7, 6.2 and 0.2 % of sequences, respectively.

At a sequence similarity of 97 % for Symbiodinium ITS2 OTUs, there is phylogenetic support for clade C sequences within the same OTU that associate with Acropora (C27) and Montipora (C31; Fig. 3). All symbiont sequences associated with Porites, and 10 % of symbiont sequences from Pavona, also clustered into a highly supported group (C15). Symbiodinium sequences that clustered into an OTU specific to Pocillopora (C1a.1, C1p.1, C34, and C42) and Leptastrea (C1c.1) are also obtained at a 97 % sequence similarity threshold. Sequences that clustered into the remaining clade C OTUs at 97 % (C1 and C3) are polyphyletic within the unrooted phylogeny and associate with multiple host genera. In contrast, at 99 % similarity, there is no phylogenetic support for Symbiodinium ITS2 sequences that group into an OTU (ESM 3). At a 98 % sequence similarity threshold, evidence supporting the phylogenetic grouping of sequences within an OTU and sequences specific to a host genus begin to emerge, although the level of polyphyly for sequences within an OTU or specific to a host is greater than at 97 % similarity (ESM 3). At 96 % similarity, there is a loss of host-specific Symbiodinium OTUs (ESM 3). These data support a 97 % sequence similarity threshold as the most informative for grouping Symbiodinium ITS2 sequences. At a 97 % similarity threshold, the most distantly related sequences within an OTU are at most nine bp and/or indels different.
Fig. 3

Unrooted Bayesian phylogeny of Symbiodinium ITS2 sequences. Numerals at nodes represent Bayesian posterior probabilities/and bootstrap support from 1000 replicates for neighbour-joining/maximum likelihood/and maximum parsimony tree building algorithms. The HKY + G model for nucleotide substitution was selected by Modeltest for both neighbour-joining and maximum likelihood searches. Coloured bubble plots delimit sequences that are grouped into the same OTU at a 97 % sequence similarity threshold, and the coral genera associated with an OTU (in >5 % abundance) are listed beside each coloured bubble plot. Sequences representing an OTU or that have been previously named are labelled on the tree, while accession numbers indicate all other unique sequences used in the construction of the phylogeny

Using a 97 % sequence similarity threshold, a total of 13 Symbiodinium OTUs associate with corals from French Frigate Shoals; ten clade C, and one each from clades A, D, and G (Fig. 4). The majority of corals contained only clade C (65 colonies, 82 %), while for the remaining corals, four Acropora colonies harboured clade A, five Acropora colonies harboured clades A and C, all five Montipora patula colonies harboured clade D, and a single Porites lichen colony harboured clades C and G. C1 was the most abundant OTU (28 %) and was found associated with all coral genera except Porites. Symbiodinium OTUs associated with a coral species were found to be significant in the global ANOSIM test (R = 0.699, P = 0.01), and 105 of the 120 pairwise comparisons between coral species were also significant (ESM 4), indicating host specificity. There was no significant difference in Symbiodinium diversity among species within Acropora, Pavona, or Porites. In contrast, Symbiodinium diversity in species of Montipora was significantly different and driven by the association of D1a with M. patula and C31 with M. capitata (SIMPER analysis, ESM 5). Similarly, Symbiodinium diversity in Pocillopora damicornis was significantly different from both P. meandrina and Pocillopora eydouxi and was mostly driven by the association of C1a.1 with P. damicornis. The relationship of Symbiodinium diversity among the coral species at French Frigate Shoals is represented in the UPGMA dendrogram (Fig. 5). The main difference between the significant nodes on the dendrogram compared to the ANOSIM pairwise comparisons is the node separating P. meandrina from all other corals, and the large significant grouping of seven coral species. This difference is predominantly driven by the shared association of C1 in relatively large abundance in the seven coral species, which results in them clustering together on the UPGMA dendrogram.
Fig. 4

Symbiodinium OTU diversity in coral genera sampled at French Frigate Shoals in the Northwestern Hawaiian Islands (ah). The ITS2 gene and a 97 % sequence similarity threshold were used as criteria in generating Symbiodinium OTUs

Fig. 5

UPGMA dendrogram from group-average linking of Bray–Curtis similarities of Symbiodinium diversity in coral species sampled at French Frigate Shoals inferred using ITS2 OTUs at a 97 % sequence similarity threshold. Dashed lines identify significant groupings of Symbiodinium diversity in coral species (P < 0.05) calculated using the SIMPROF test

Distribution of Symbiodinium across the NWHI archipelago

A total of 1320 Symbiodinium ITS2 sequences were recovered from 138 coral colonies (M. capitata N = 40, P. lobata N = 49, P. meandrina N = 49) across ten islands in the NWHI. At a 97 % sequence similarity threshold, 17 Symbiodinium OTUs (14 clade C, 1 clade A, 1 clade D, and 1 clade G) associate with M. capitata, P. lobata, and P. meandrina across the NWHI archipelago (Fig. 6). The assemblage of Symbiodinium in the corals sampled is highly structured, with significant differences (P < 0.05) in Symbiodinium OTUs by host species, depth, latitude, and their interaction (Table 2). For the interaction of species × latitude × depth, all species had significant differences in Symbiodinium OTUs for pairwise comparisons of factor latitude for colonies sampled at 10–20 m, except M. capitata between the low and intermediate islands (Table 3). A limited number of colonies sampled between 0 and 10 m restricted the pairwise comparisons that could be performed, and only the Symbiodinium OTUs in P. meandrina between latitudinal groups 2 and 3 were significant at this depth.
Fig. 6

Symbiodinium ITS2 OTU diversity calculated with a 97 % similarity threshold in M. capitata (column a), P. meandrina (column b) and P. lobata (column c) across the Northwestern Hawaiian Islands grouped by latitude

Table 2

Permutational MANOVA of Symbiodinium ITS2 OTUs across the Northwestern Hawaiian Islands




P value













Host × latitude




Host × depth




Latitude × depth




Host × latitude × depth




Factor host groups coral colonies into M. capitata, P. lobata, or P. meandrina; factor latitude groups colonies into low (Nihoa, Necker, and French Frigate Shoals), intermediate (Gardner, Maro, Laysan, and Lisianski) or high (Pearl & Hermes, Midway, and Kure) islands; and factor depth groups colonies into 0–10 or 10–20 m. Significant values are in bold with an asterisk

Table 3

Pairwise comparisons of Symbiodinium ITS2 OTUs in coral colonies sampled across the NWHI archipelago for factor latitude



Depth 0–10 m

Depth 10–20 m


P value


P value

Montipora capitata

1 and 2





1 and 3





2 and 3





Porites lobata

1 and 2





1 and 3





2 and 3





Pocillopora meandrina

1 and 2






1 and 3






2 and 3





Colonies sampled at Nihoa, Necker, and French Frigate Shoals represent the low latitude group (1), colonies from Gardner, Maro, Laysan, and Lisianski represent the intermediate latitude group (2), and colonies from Pearl & Hermes, Midway, and Kure represent the high-latitude group (3). Significant values are in bold with an asterisk


Geographic structure and host specificity in coral–algal symbiosis

Coral–algal partnerships show geographic structure in the NWHI archipelago that partition across a latitudinal gradient. Spatial structure of the Symbiodinium community in three host species is consistent with a geographic mosaic of coevolution (Thompson 1999). Similar outcomes have been observed for coral–algal partnerships in other regions of the world. A transition from Symbiodinium clade B in temperate locations along eastern Australia to clade C Symbiodinium in tropical locations further north was found in the coral Plesiastrea versipora (Rodriguez-Lanetty et al. 2001). Similarly, the dominant generalist symbiont associated with a variety of coral species was found to differ between the central and southern Great Barrier Reef (LaJeunesse et al. 2004b). Adaptation to the local environment and random genetic drift of at least one partner in a mutualistic symbiosis is expected to occur over large geographic scales (i.e., 100–1000 km) prior to selection pressures arising from mutualism (Parker 1999). Therefore, it is unlikely that the same partner genotypes will be found across broad spatial scales. The differences in temperature dynamics across the archipelago, predominantly the increase in temperature ranges at higher latitudes, likely plays a role in local adaptation. In corals, fixed genetic traits that correlate with ocean temperature profiles have been identified, and a similar mechanism, whereby the environment selects tolerant genotypes, likely occurs across the NWHI (Palumbi et al. 2014). It is unclear, however, whether host adaptation to the environment precludes changes in the symbiont partner and adaptation to the host environment, or if co-adaptation is the mechanism driving the observed pattern (Parker 1999).

The coral–algal partnerships investigated across the NWHI archipelago involved three host species with a vertical symbiont transmission strategy. The distribution of algal symbionts will therefore partly be determined by their host connectivity. There is a high level of connectivity and dispersal of marine larvae throughout the NWHI archipelago, but a common genetic break occurs around Pearl & Hermes that partitions ten of 18 species including fishes, gastropods, crustaceans, echinoderms, and corals (Toonen et al. 2011). Further, the coral P. lobata in the NWHI conforms to the isolation by distance model, with additional support for population differentiation between the high-latitude islands (Kure, Midway, and Pearl & Hermes) and the remaining islands in the NWHI archipelago (Polato et al. 2010). The results in this study on Symbiodinium diversity support the common genetic break at Pearl & Hermes and correlate with the population structure of P. lobata, whereby the Symbiodinium community harboured by P. lobata, M. capitata, and P. meandrina at the high-latitude islands is significantly different to the remaining NWHI archipelago. These results are consistent with a geographic mosaic of coevolution whereby differentiated populations give rise to different interspecific interactions in the community leading to different interacting traits across spatial scales that shape partner assemblages seen in symbioses (Thompson 1999). Further characterisation of traits involved in local adaptation, coupled with selection pressures to remain in a cooperative state, will help elucidate the evolutionary ecology of coral–algal symbiosis.

While there was geographic structure in the distribution of Symbiodinium in the NWHI, host specificity was maintained in all three coral species across the archipelago. Similar host-specific associations were evident at French Frigate Shoals in a higher diversity of hosts. Host transmission strategy influences the symbiont partner associated with coral hosts, with vertical strategists mostly harbouring their own unique symbionts (Stat et al. 2008; Fabina et al. 2012). In symbioses that have vertical transmission of symbionts as a life history trait, this mechanism would allow symbiont speciation to occur over evolutionary timescales, in a similar process as allopatric speciation in the environment. Consistent with previous observations of coral–algal partnerships on reefs, a dominant Symbiodinium generalist (C1) is present at French Frigate Shoals that interacts with multiple hosts, most of which have a horizontal symbiont transmission strategy (LaJeunesse et al. 2003, 2010; LaJeunesse 2005; Stat et al. 2008, 2009). The presence of a dominant symbiont generalist in a host population is evidence of evolutionary stasis in the symbiosis (Law 1985). Evolutionary stasis occurs via hosts favouring a partnership with a dominant, locally adapted symbiont and the concomitant reduction in host fitness if associating with rare symbionts that evolve. This suggests that the dominant generalist found at French Frigate Shoals (C1), and elsewhere, is well adapted to the local ocean environment that it encounters during its free-living life stage prior to host infection, and is nutritionally beneficial to a variety of hosts when in symbiosis. In addition to the C1 OTU though, there were significant differences in the symbiont population among some horizontal transmitters (e.g., Cyphastrea ocellina and Leptastrea sp.). This suggests that host-specialist lineages may be more prevalent than previously thought, a recent finding that was highlighted using the psbA gene for Symbiodnium genotyping by Thornhill et al. (2014).

Characterisation of Symbiodinium OTUs

The per cent similarity used to group sequences into OTUs at a 97 % sequence similarity threshold had both phylogenetic and ecological support. This sequence threshold for the ITS2 gene of Symbiodinium is consistent with a recent report by Arif et al. (2014) who identified 97 % as the appropriate OTU sequence cut-off based off deep sequencing of Symbiodinium cultures and collectively provide support for its application in future research using the ITS2 gene. However, it should be noted that while OTUs provide a valuable tool for assessing diversity, there is no consistent threshold criteria that can be used to accurately capture all organisms into the same taxonomic level, as has been previously documented for not only Symbiodinium, but more widely across the field of microbial ecology (Koeppel and Wu 2013; Thornhill et al. 2014). As an example, in this study Symbiodinium ITS2 sequences C3 and C21 that differ by a single indel clustered into the same OTU, however, based on ITS2 DGGE analysis from other regions, these sequences have been shown to represent ecologically differentiated symbionts (LaJeunesse et al. 2003). In contrast, C3 and C1, which are commonly referred to as representing two ecologically distinct and globally distributed Symbiodinium types, only differ by 1 bp yet were separated into different OTUs (LaJeunesse 2005). The discrepancies in sorting closely related sequences into the same or different OTUs is likely the result of a large number of ITS2 variants within clade C that differ by only a single mutation, and the polytomic nature of the ITS2 clade C phylogeny (e.g., LaJeunesse et al. 2003). Therefore, as has been previously documented, in some instances the partitioning of sequences into OTUs aligns well with the collective ecology of coral–Symbiodinium assemblages, but not in all cases (Arif et al. 2014). This limitation though should not undermine the utility of an OTU approach in diversity assessments, which provides the platform for further examination into the taxonomic resolution and functional variability that they resolve.



This research was supported by the National Marine Sanctuary Program (memorandum of agreement 2005-008/66882), and a US National Science Foundation (NSF) Grant through Biological Oceanography (OCE-0752604). This is HIMB contribution # 1628 and SOEST contribution # 9438.

Supplementary material

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  1. Anderson MJ (2005) PERMANOVA: a FORTRAN computer program for permutational multivariate analysis of variance. Department of Statistics, University of Auckland, New ZealandGoogle Scholar
  2. Arif C, Daniels C, Bayer T, Banguera-Hinestroza E, Barborrk A, Howe CJ, LaJeunesse TC, Voolstra CR (2014) Assessing Symbiodinium diversity in scleractinian corals via next-generation sequencing-based genotyping of the ITS2 rDNA region. Mol Ecol 23:4418–4433PubMedCentralCrossRefPubMedGoogle Scholar
  3. Baird AH, Guest JR, Willis BL (2009) Systematic and biogeographical patterns in the reproductive biology of scleractinian corals. Annu Rev Ecol Evol S 40:551–571CrossRefGoogle Scholar
  4. Bird CE, Holland BS, Bowen BW, Toonen RJ (2011) Diversification of sympatric broadcast-spawning limpets (Cellana spp.) within the Hawaiian archipelago. Mol Ecol 20:2128–2141CrossRefPubMedGoogle Scholar
  5. Blaalid R, Carlsen T, Kumar S, Halvorsen R, Ugland KI, Fontana G, Kauserud H (2012) Changes in the root-associated fungal communities along a primary succession gradient analysed by 454 pyrosequencing. Mol Ecol 21:1897–1908CrossRefPubMedGoogle Scholar
  6. Bowen BW, Rocha LA, Toonen RJ, Karl SA, Laboratory ToBo (2013) The origins of tropical marine biodiversity. Trends Ecol Evol 28:359–366CrossRefPubMedGoogle Scholar
  7. Clarke KR, Gorley RN (2006) PRIMER v6: user manual/tutorial. PRIMER-E, PlymouthGoogle Scholar
  8. Douglas AE (1998) Host benefit and the evolution of specialization in symbiosis. Heredity 81:599–603CrossRefGoogle Scholar
  9. Drummond AJ, Ashton B, Buxton S, Cheung M, Cooper A, Duran C, Field M, Heled J, Kearse M, Markowitz S, Moir R, Stones-Havas S, Sturrock S, Thierer T, Wilson A (2011) Geneious v6.1.6, Available at:
  10. Fabina NS, Putnam HM, Franklin EC, Stat M, Gates RD (2012) Transmission mode predicts specificity and interaction patterns in coral-Symbiodinium networks. PLoS One 7:e44970PubMedCentralCrossRefPubMedGoogle Scholar
  11. Fenner D (2005) Corals of Hawaii. Mutual Publishing, Honolulu, HIGoogle Scholar
  12. Franklin EC, Stat M, Pochon X, Putnam HM, Gates RD (2012) GeoSymbio: a hybrid, cloud-based web application of global geospatial bioinformatics and ecoinformatics for Symbiodinium-host symbioses. Mol Ecol Resour 12:369–373CrossRefPubMedGoogle Scholar
  13. Goreau TF, Goreau NI (1959) The physiology of skeleton formation in corals. II Calcium deposition by hermatypic corals under various conditions in the reef. Biol Bull 117:239–250CrossRefGoogle Scholar
  14. Huelsenbeck J, Ronquist F (2001) MRBAYES: a program for the Bayesian inference of phylogeny. Bioinformatics 17:754–755CrossRefPubMedGoogle Scholar
  15. Koeppel AF, Wu M (2013) Surprisingly extensive mixed phylogenetic and ecological signals among bacterial operational taxonomic units. Nucleic Acids Res 41:5175–5188PubMedCentralCrossRefPubMedGoogle Scholar
  16. LaJeunesse TC (2005) “Species” radiations of symbiotic dinoflagellates in the Atlantic and Indo-Pacific since the Miocene-Pliocene Transition. Mol Biol Evol 22:570–581CrossRefPubMedGoogle Scholar
  17. LaJeunesse TC, Loh WKW, van Woesik R, Hoegh-Guldberg O, Schmidt GW, Fitt WK (2003) Low symbiont diversity in southern Great Barrier Reef corals, relative to those of the Caribbean. Limnol Oceanogr 48:2046–2054CrossRefGoogle Scholar
  18. LaJeunesse TC, Thornhill DJ, Cox EF, Stanton FG, Fitt WK, Schmidt GW (2004a) High diversity and host specificity observed among symbiotic dinoflagellates in reef coral communities from Hawaii. Coral Reefs 23:596–603Google Scholar
  19. LaJeunesse TC, Wham DC, Pettay DT, Parksinson JE, Keshavmurthy S, Chen CA (2014) Ecologically differentiated stress-tolerant endosymbionts in the dinoflagellate genus Symbiodinium (Dinophyceae) clade D are different species. Phycologia 53:305–319CrossRefGoogle Scholar
  20. LaJeunesse TC, Bhagooli R, Hidaka M, deVantier L, Done T, Schmidt GW, Fitt WK, Hoegh-Guldberg O (2004b) Closely related Symbiodinium spp. differ in relative dominance in coral reef host communities across environmental, latitudinal and biogeographic gradients. Mar Ecol Prog Ser 284:147–161CrossRefGoogle Scholar
  21. LaJeunesse TC, Pettay DT, Sampayo EM, Phongsuwan N, Brown B, Obura DO, Hoegh-Guldberg O, Fitt WK (2010) Long-standing environmental conditions, geographic isolation and host-symbiont specificity influence the relative ecological dominance and genetic diversification of coral endosymbionts in the genus Symbiodinium. J Biogeogr 37:785–800CrossRefGoogle Scholar
  22. Law R (1985) Evolution in a mutualistic environment. In: Boucher DH (ed) The biology of mutualism. Oxford University Press, Oxford, UK, pp 145–191Google Scholar
  23. Maragos JE, Potts DC, Aeby GS, Gulko D, Kenyon JC, Siciliano D, van Ravenswaay D (2004) 2000-2002 rapid ecological assessments of corals (Anthozoa) on shallow reefs of the Northwestern Hawaiian Islands. Part 1: species and distribution. Pac Sci 58:211–230CrossRefGoogle Scholar
  24. NOAA Coral Reef Watch (2000) Coral Reef Watch 50-km satellite time series data. Silver Spring, Maryland, USA.
  25. Padilla-Gamino JL, Hanson KM, Stat M, Gates RD (2012) Phenotypic plasticity of the coral Porites rus: acclimatization responses to a turbid environment. J Exp Mar Bio Ecol 434–435:71–80CrossRefGoogle Scholar
  26. Palumbi SR, Barshis DJ, Traylor-Knowles N, Bay RA (2014) Mechanisms of reef coral resistance to future climate change. Science 344:895–898CrossRefPubMedGoogle Scholar
  27. Parker MA (1999) Mutualism in metapopulations of legumes and Rhizobia. Am Nat 153:48–60CrossRefGoogle Scholar
  28. Pochon X, Gates RD (2010) A new Symbiodinium clade (Dinophyceae) from soritid foraminifera in Hawaii. Mol Phylogenet Evol 56:492–497CrossRefPubMedGoogle Scholar
  29. Pochon X, Pawlowski J, Zaninetti L, Rowan R (2001) High genetic diversity and relative specificity among Symbiodinium-like endosymbiotic dinoflagellates in soritid foraminiferans. Mar Biol 139:1069–1078CrossRefGoogle Scholar
  30. Polato NR, Concepcion GT, Toonen RJ, Baums IB (2010) Isolation by distance across the Hawaiian archipelago in the reef-building coral Porites lobata. Mol Ecol 19:4661–4677CrossRefPubMedGoogle Scholar
  31. Posada D, Crandall KA (1998) MODELTEST: testing the model of DNA substitution. Bioinformatics 14:817–818CrossRefPubMedGoogle Scholar
  32. Reaka-Kudla M (1997) The global biodiversity of coral reefs: A comparison with rainforests. In: Reaka-Kudla M, Wilson D, Wilson E (eds) Biodiversity II. Joseph Henry Press, Washington, DC, Understanding and protecting our biological resources, pp 83–108Google Scholar
  33. Rodriguez-Lanetty M, Loh W, Carter D, Hoegh-Guldberg O (2001) Latitudinal variability in symbiont specificity within the widespread scleractinian coral Plesiastrea versipora. Mar Biol 138:1175–1181CrossRefGoogle Scholar
  34. Sampayo EM, Dove S, LaJeunesse TC (2009) Cohesive molecular data delineate species diversity in the dinoflagellate genus Symbiodinium. Mol Ecol 18:500–519CrossRefPubMedGoogle Scholar
  35. Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, Hollister EB, Lesniewski RA, Oakley BB, Parks DH, Robinson CJ, Sahl JW, Stres B, Thallinger GG, van Horn DJ, Weber CF (2009) Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol 75:7537–7541PubMedCentralCrossRefPubMedGoogle Scholar
  36. Selkoe KA, Gaggiotti OE, Laboratory ToBo, Bowen BW, Toonen RJ (2014) Emergent patterns of population genetic structure for a coral reef community. Mol Ecol 23:3064–3079CrossRefPubMedGoogle Scholar
  37. Stat M, Loh WKW, Hoegh-Guldberg O, Carter DA (2008) Symbiont acquisition strategy drives host-symbiont associations in the southern Great Barrier Reef. Coral Reefs 27:763–772CrossRefGoogle Scholar
  38. Stat M, Pochon X, Cowie OM, Gates RD (2009) Specificity in communities of Symbiodinium in corals from Johnston atoll. Mar Ecol Prog Ser 386:83–96CrossRefGoogle Scholar
  39. Stat M, Pochon X, Franklin EC, Bruno JF, Casey KS, Selig ER, Gates RD (2013) The distribution of the thermally tolerant symbiont lineage (Symbiodinium clade D) in corals from Hawaii: correlations with host and the history of ocean thermal stress. Ecol Evol 3:1317–1329PubMedCentralCrossRefPubMedGoogle Scholar
  40. Stat M, Baker AC, Bourne DG, Correa AMS, Forsman Z, Huggett MJ, Pochon X, Skillings D, Toonen RJ, van Oppen MJH, Gates RD (2012) Molecular delineation of species in the coral holobiont. Adv Mar Biol 63:1–65CrossRefPubMedGoogle Scholar
  41. Stoeck T, Hayward B, Taylor GT, Varela R, Epstein SS (2006) A multiple PCR-primer approach to access the microeukaryotic diversity in environmental samples. Protist 157:31–43CrossRefPubMedGoogle Scholar
  42. Swofford D (2000) PAUP*: phylogenetic analysis using parsimony (*and other methods). Version 4.0b10. Sinauer Associates, Sunderland, MA. Available at: http// Scholar
  43. Thomas L, Kendrick GA, Kennington JW, Richards ZT, Stat M (2014) Exploring Symbiodinium diversity and host specificity in Acropora corals from geographical extremes of Western Australia with 454 amplicon pyrosequencing. Mol Ecol 23:3133–3136CrossRefGoogle Scholar
  44. Thompson JN (1999) Specific hypotheses on the geographic mosaic of coevolution. Am Nat 153:1–14CrossRefGoogle Scholar
  45. Thompson JN, Cunningham BM (2002) Geographic structure and dynamics of coevolutionary selection. Nature 417:735–738CrossRefPubMedGoogle Scholar
  46. Thornhill DJ, Lewis AM, Wham DC, LaJeunesse TC (2014) Host-specialist lineages dominate the adaptive radiation of reef coral endosymbionts. Evolution 68:352–367CrossRefPubMedGoogle Scholar
  47. Toonen RJ, Andrews KR, Baums IB, Bird CE, Concepcion GT, Daly-Engel TS, Eble JA, Faucci A, Gaither MR, Iacchei M, Puritz JB, Schultz JK, Skillings DJ, Timmers MA, Bowen BW (2011) Defining boundaries for ecosystem-based management: a multispecies case study of marine connectivity across the Hawaiian archipelago. J Mar Biol 2011:460173PubMedCentralCrossRefPubMedGoogle Scholar
  48. Wagner WL, Funk VA (1995) Hawaiian biogeography: evolution on a hotspot archipelago. Smithsonian Institute Press, Washington, DCGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2015

Authors and Affiliations

  1. 1.Trace and Environmental DNA (TrEnD) Laboratory, Department of Environment and AgricultureCurtin UniversityPerthAustralia
  2. 2.Hawaii Institute of Marine Biology, School of Ocean and Earth Science and TechnologyUniversity of HawaiiKaneoheUSA

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