Skip to main content

Sharing the slope: depth partitioning of agariciid corals and associated Symbiodiniumacross shallow and mesophotic habitats (2-60 m) on a Caribbean reef



Scleractinian corals and their algal endosymbionts (genus Symbiodinium) exhibit distinct bathymetric distributions on coral reefs. Yet, few studies have assessed the evolutionary context of these ecological distributions by exploring the genetic diversity of closely related coral species and their associated Symbiodinium over large depth ranges. Here we assess the distribution and genetic diversity of five agariciid coral species (Agaricia humilis, A. agaricites, A. lamarcki, A. grahamae, and Helioseris cucullata) and their algal endosymbionts (Symbiodinium) across a large depth gradient (2-60 m) covering shallow to mesophotic depths on a Caribbean reef.


The five agariciid species exhibited distinct depth distributions, and dominant Symbiodinium associations were found to be species-specific, with each of the agariciid species harbouring a distinct ITS2-DGGE profile (except for a shared profile between A. lamarcki and A. grahamae). Only A. lamarcki harboured different Symbiodinium types across its depth distribution (i.e. exhibited symbiont zonation). Phylogenetic analysis (atp6) of the coral hosts demonstrated a division of the Agaricia genus into two major lineages that correspond to their bathymetric distribution (“shallow”: A. humilis / A. agaricites and “deep”: A. lamarcki / A. grahamae), highlighting the role of depth-related factors in the diversification of these congeneric agariciid species. The divergence between “shallow” and “deep” host species was reflected in the relatedness of the associated Symbiodinium (with A. lamarcki and A. grahamae sharing an identical Symbiodinium profile, and A. humilis and A. agaricites harbouring a related ITS2 sequence in their Symbiodinium profiles), corroborating the notion that brooding corals and their Symbiodinium are engaged in coevolutionary processes.


Our findings support the hypothesis that the depth-related environmental gradient on reefs has played an important role in the diversification of the genus Agaricia and their associated Symbiodinium, resulting in a genetic segregation between coral host-symbiont communities at shallow and mesophotic depths.


Historically, coral species were thought to be extremely ecologically and morphologically plastic, because of the broad variation observed “within species” [1]. Advances in coral taxonomy and ecology have demonstrated that this variation often reflects sibling species occupying distinct ecological niches [2]. The recent advent of molecular approaches has exposed a further wealth of cryptic diversity in scleractinian corals [35] often in relation to particular environments, highlighting the role of niche partitioning [69] in addition to ecophenotypic plasticity [10, 11]. Likewise, the algal endosymbionts that associate with reef-building corals and allow them to exploit light as an energy source in oligotrophic conditions, were originally thought to consist of a single algal symbiont, Symbiodinium microadriaticum[12]. By now, we know that Symbiodinium diversity in tropical scleractinian corals consists of several different phylogenetic clades [1315], species [16, 17] and hundreds of different subclades based on the ITS2 region of the ribosomal DNA [14, 16]. These different Symbiodinium genotypes often represent physiologically distinct entities that can be strongly partitioned across host species, geographic regions and particular reef environments [1823]. Although ecological niche partitioning across environmental gradients (e.g. light, temperature, turbidity) appears fundamental to maintaining the diversity of both scleractinian corals and their endosymbiotic dinoflagellates, the evolutionary context of this host-symbiont niche partitioning remains poorly understood.

Despite the great diversity of Symbiodinium types found in reef invertebrates, many coral host species appear to associate with a specific genetic lineage (or group) of Symbiodinium[16]. Particularly in brooding corals, where the onset of symbiosis occurs through the vertical transmission of Symbiodinium from the maternal colony to the larvae, high levels of host-symbiont specificity have been observed [8, 2427]. Molecular studies targeting both symbiotic partners have identified tightly coupled host-symbiont associations in brooding corals at the family [20], genus [9] and species level [8, 9, 26]. As such, natural selection may be acting on the level of the coral holobiont (i.e., host and symbiont combined) in species with a vertical symbiont acquisition mode, resulting in coevolution of both symbiotic partners. Incongruence between the phylogenies of corals and their associated Symbiodinium indicates that recombination of host-symbiont associations does occur over the course of evolution [13, 16, 28, 29], however the occurrences of such events may be less likely over ecological timescales. It is therefore important to study the evolutionary origin and implications of such host-symbiont specificity, particularly in light of the environmental change predicted over the next decades [30].

The evolutionary context of coral host-symbiont niche partitioning is also important in the context of reef connectivity between distinct environments and more specifically the ability of reef habitats that offer some kind of protection against certain disturbances, such as deep reefs, to act as a “protected” local source of propagules [31, 32]. Although the association of a coral species with different Symbiodinium types may facilitate its distribution across distinct reef environments [20, 3335], larval connectivity between these alternative environments may be hampered if symbiotic associations are constrained through vertical symbiont transmission and recruits are not able to adopt symbiont types better-suited to their “new” environment [26]. Along those same lines, host populations may be locally adapted to opposing environments and distinct symbiont populations may in fact reflect genetic differentiation of both symbiotic partners [31]. Such genetic partitioning of host and symbiont populations has been observed across shallow and deep populations of the pocilloporid coral species Madracis pharensis in the Caribbean [9] and Seriatopora hystrix on the Great Barrier Reef [8, 26, 32]. To gain a better understanding of the ability of mesophotic reefs to act as refugia (for species that occur over large depth ranges) and a subsequent source of reproduction for degraded shallow reefs it is important to determine the overlap in genetic diversity of host and symbiont communities in shallow and deep reef environments. Given the prevalence of a brooding reproductive mode (>65%) and therefore vertical symbiont transmission on Caribbean reefs [31, 36], there is a potential for strong genetic differentiation between host-symbiont associations in shallow and mesophotic communities in this region [27]. However, this hypothesis remains largely untested, primarily as molecular data from mesophotic coral communities are limited.

Mesophotic reef communities in the Caribbean are commonly dominated by members of the Agariciidae [3739], and in particular by the species Agaricia lamarcki and Agaricia grahamae[31, 40]. The plating growth forms, such as those of Agariciidae, are thought to be particularly well suited to maximize light capture in these low-light environments [41]. Nonetheless, species of the genus Agaricia can be abundant throughout the entire depth range of Caribbean reefs and A. humilis, for example, occurs only in very shallow sections of reefs [42]. Species of Agaricia can exhibit high linear growth rates [43] and these brooding species are major contributors to the pool of coral recruits on Caribbean reefs [38, 42, 44, 45]. Data on the phylogenetic affiliation of Symbiodinium associated with Western-Atlantic agariciids is limited, however records so far demonstrate association with Symbiodinium from clade C and occasionally clade D [16, 4650]. It remains unclear whether the brooding reproductive mode of Western-Atlantic agariciids has resulted in host-symbiont specificity and to what extent the associated Symbiodinium diversity allows this genus to be abundant across large depth gradients.

Here, we assessed Symbiodinium genetic diversity for the five most common agariciid corals in Curaçao over a large depth range (2-60 m) encompassing both shallow and mesophotic depths. We addressed the level of specificity between the different coral species and their dominant Symbiodinium (i.e. the algal type(s) that are most abundantly present in the coral tissue), and evaluated whether these host-symbiont associations are partitioned over depth. Additionally, sequencing of a host mitochondrial region disclosed agariciid evolutionary patterns, and allowed evaluation of further genetic structuring of the coral host in relation to symbiont and depth. Results are discussed in light of extensive previous work on the brooding species of the coral genus Madracis[9, 21, 34, 51] to address common patterns of genetic diversity over depth, and explore potential processes of codiversification in brooding Caribbean corals and their algal symbionts. Overall, the potential role of depth-related processes in the evolution of brooding corals and their associated Symbiodinium is discussed, as are the implications with regards to larval connectivity between shallow and deep coral reef habitats.


Study site and environmental conditions

Collections were performed between 2008 and 2009 at the well-studied site Buoy Zero/One (Bak 1977; Bak et al. 2005; Vermeij et al. 2007; Frade et al. 2008a) in Curaçao, southern Caribbean (12°07’31” N, 68°58’27”W) (Figure 1a). Information obtained from additional samples of previous collections at the same study site in 2004 and 2007 were added to the dataset. The study site is, as are many leeward sites on Curaçao, characterized by a shallow terrace (50-100 m wide) that slopes down to 8-12 m, followed by a steep drop-off with a slope extending down to a deep terrace at 50-60 m depth [52]. Environmental conditions, including seawater temperature and light attenuation were characterized during the beginning of the sampling period and described in Frade et al. [9]. Downwelling light availability (or PAR irradiance) decreases exponentially with a Kds of 0.07 m-1[9], leading to ~87% of surface irradiance at 2 m, 70% at 5 m, 50% at 10 m, 17% at 25 m, 6% at 40 m, 3% at 50 m, and 1.5% at 60 m. Temperature at the study site shows seasonal variation, with mean seawater temperatures decreasing over depth (0.02°C per metre) [9]. The deeper reef slope (40-60 m) experiences cold-water influxes due to thermocline movements, which can cause a sudden decrease in temperature of several degrees [9, 39].

Figure 1

Mesophotic habitat, sampling location, and agariciid abundances over depth. (a) Mesophotic Agaricia communities on the leeward shore of Curaçao at 50 m depth, (b) location of Curaçao (indicated by arrow) and study site Buoy Zero/One (indicated by red dot), and (c) distribution of Agaricia spp. and Helioseris cucullata over depth at the Buoy Zero/One study site.

Agariciid species

The five most common agariciid species in Curaçao, Agaricia humilis Verrill, 1901, A. agaricites (Linnaeus, 1758), A. lamarcki Milne Edwards and Haime, 1851, A. grahamae Wells, 1973, and Helioseris cucullata (Ellis and Solander, 1786) were included in this study. Of the other three Caribbean agariciid species, A. undata (Ellis and Solander, 1786) is rare, and A. fragilis Dana, 1848 and A. tenuifola Dana, 1848 are absent on the reefs of Curaçao. Coral species were identified following the taxonomic features specified by Wells [53], Veron and Stafford-Smith [54] and Humann & Deloach [55] (Table 1). Fragments of colonies that were collected but that did not clearly conform to these species descriptions were labeled as “Agaricia sp.”.

Table 1 Morphological characteristics of the five studied Agariciid species

Species abundances and sampling approach

Species abundances of the different agariciid species were determined in 2009 by counting all individuals in 30-50 quadrats (1 × 1 m) laid out randomly (i.e. using a list of randomly generated numbers) along a 100 m long transect parallel to the shore at each sample-depth (2, 5, 10, 25, 40, 50, and 60 m). A total of 335 agariciid coral colonies were sampled over a depth range from 2 to 60 m from a single reef location (Buoy Zero/One), by removing a small fragment from the colony (~3 cm2). Fragments were collected at depth intervals that reflect the bathymetric distributions of each species: A. humilis at 2, 5 and 10 m (n = 71); A. agaricites at 5, 10, 15, 25, 30, 40 and 50 m (n = 113); A. lamarcki at 10, 25, 40 and 50 m (n = 105); A. grahamae at 50 and 60 m (n = 20); and H. cucullata at 25 and 40 m (n = 16). Tissue from collected coral samples was separated from the skeleton using a modified airgun attached to a SCUBA cylinder or with a sterilized scalpel, and was subsequently stored in 20% DMSO/EDTA preservation buffer or 95% ethanol at -20°C until further processing. DNA was extracted from the tissue using a Qiagen Plant Mini Kit, MoBio Ultra Clean Soil DNA Kit (following the manufacturer’s instructions), or a slightly modified method used for black tiger shrimp [32, 56].

SymbiodiniumITS2 analyses

The internal transcribed spacer (ITS2) region of Symbiodinium rDNA was amplified for all specimens (n = 335) using Symbiodinium-specific primers [46] as described in Bongaerts et al. [8]. The amplified ITS2 fragments were separated using denaturing gradient gel electrophoresis (DGGE) on a CBScientific System following conditions outlined in Sampayo et al. [20], to identify the dominant Symbiodinium types in each sample (ITS2-DGGE fails to detect symbionts present in low abundances [57, 58]). On each DGGE gel, we ran representative samples to allow for profile cross-comparison and identification. Representative, dominant bands of each characteristic profile were excised (from several replicate profiles), eluted overnight in dH2O, re-amplified and purified (using ExoSAP-IT) prior to sequencing. The re-amplified PCR products were sequenced in both the forward and reverse directions (ABI BigDye Terminator chemistry, Australian Genome Research Facility). All chromatograms were analyzed using Codoncode Aligner, with sequences being aligned with MUSCLE and blasted on GenBank ( Phylogenetic analyses of sequences were performed using maximum parsimony and maximum likelihood in MEGA 4 [59] under the delayed transition setting and calculation of bootstrap support values based on 1000 replicates.

Host atp6sequence analyses

The mitochondrial atp6 gene (and parts of the flanking nad6 and nad4) was amplified for a subset of samples (n = 93: ~5 samples were randomly picked per species per depth) using the newly designed primers Aga-atp6-F1: GGCTTTATTTGGGGCTGAA and Aga-atp6-R1: CCCACAAAACCAAAGCACTTA. Primers were designed from the mitogenomes of A. humilis (NC008160) and Pavona clavus (NC008160) [60]. PCR amplifications were performed with 1.0 μl of DNA, 2.0 μl 10× PCR buffer (Invitrogen), 1.0 μl 50 mM MgCl2, 0.7 μl 10 mM dNTPs, 0.7 μl 10 mM Aga-atp6-F1, 0.7 μl 10 mM Aga-atp6-R1, 0.15 μl of Platinum Taq DNA Polymerase (Invitrogen) and dH2O water to a total volume of 20 ml per reaction. The cycling protocol was: 1 × 95°C (5 min); 30 × [95°C (30 s), 58°C (60 s), 70°C (90 s)]; 1 × 70°C (10 min). PCR products were purified, sequenced, aligned and analysed as specified for the Symbiodinium ITS2 sequences. Additional sequences were retrieved from GenBank to compare the atp6-based phylogenies with those based on the mitochondrial cytochrome oxidase 1 (COI) and the nuclear 28S region [6063].

Phylogenetic analyses of sequences were constructed using maximum likelihood (ML), maximum parsimony (MP) and Bayesian (BAY) methods through the programs MEGA5 (Tamura et al. 2011) and MrBayes (Huelsenbeck and Ronquist 2001) respectively. The best-fit model of molecular evolution was selected by hierarchical Akaike information criterion (AIC) using jModeltest [64] with a GTR model with invariant sites best describing the atp6 data under a log likelihood optimality criterion. For the COI and 28S sequences retrieved from GenBank, a GTR model with gamma-shaped variation and invariant sites best described the data of both these regions. Maximum likelihood analyses were performed using 1000 non-parametric bootstrap replicates. Bayesian analyses were performed with the Markov Chain Monte Carlo search run with 4 chains for 106 generations, with a sample frequency of 100 generations and a “burn-in” of 2500 trees.


The contributions of taxonomic species, depth and Symbiodinium type on host genotypic variability (atp6) were assessed for positively identified Agaricia specimens under the AMOVA framework using GenALEx V5 [65], with either depth or Symbiodinium type nested within taxonomic species. In host species for which multiple Symbiodinium profiles were observed, an (nested) analysis of similarity (ANOSIM) was carried out using Bray-Curtis Distance in the software package Primer v6 to test for differences between sampling years (Two-way ANOSIM with depth nested within year) and depths (One-Way ANOSIM comparing individual depth groups).


Species abundances over depth

The species abundances at Buoy Zero/One differed among depths and revealed different distribution ranges for the five agariciid species (Figure 1c). At the shallowest depths (2-5 m), A. humilis is the most dominant species, with A. agaricites starting to occur at 5 m. At 10-15 m, A. agaricites becomes the most dominant species, with colonies of A. humilis and A. lamarcki being present in lower abundances. At 25 m depth A. agaricites and A. lamarcki occur in roughly equal abundances, but A. lamarcki takes over as the dominant species beyond this depth. From 40 m onwards, A. grahamae starts occurring, although in low numbers. H. cucullata was observed from 10-60 m, but always in relatively lower abundances.

Symbiont diversity across host species and depth

Across the five different host species, a total of six distinct ITS2-DGGE profiles were distinguished (Figure 2; see Additional file 1 for DGGE profiles). A distinct profile was observed for A. humilis (P1, n = 71), A. agaricites (P2, n = 113), and H. cucullata (P5, n = 16). Three different profiles (P3, n = 34; P4, n = 69; P4*, n = 2) were observed for A. lamarcki, of which one (P4) was shared with the species A. grahamae (n = 20) (Figure 2). Given that five of the six profiles contained at least three co-dominant ITS2 sequences, we decided to assign a number to the DGGE profiles (P1, P2, P3, P4, P4* and P5) rather than referring to individual Symbiodinium types. Although these co-dominant sequences likely represent intra-genomic variants within the rDNA of a single symbiont lineage (little variation in relative band intensity was observed) [66], it cannot be excluded that some of the profiles may represent a mix of distinct Symbiodinium types. Additionally, other Symbiodium types may be present at background levels that cannot be detected due to the limitations of ITS2-DGGE [57, 58].

Figure 2

Distribution of Symbiodinium ITS2 profiles across the five agariciid host species and depths. Each pie chart represents the sampled population of a host species at a certain depth. Asterisk (*) indicates a P4 profile that had an additional C1 band. Figure legend text.

All the ITS2-DGGE fingerprint profiles for Agaricia spp. contained the Symbiodinium C3 sequence, in combination with 2-3 sequences that were all closely related to C3 (Figure 3). All of these sequences were novel (GenBank Accession Numbers KF551185-KF551192), except for C3b in A. humilis, C3d in A. lamarcki, and C11 in A. lamarcki/grahamae. Novel sequences are identified (in this manuscript) by a nomenclature that specifies the sequence to which they are most related, followed by a capital N (indicating novel sequence) and an arbitrary number in italics (e.g. C3bN1). Except for the shared C3 sequence, all profiles contained distinct Symbiodinium sequences (i.e. no overlap between profiles) indicating that each of these profiles contain (a) different Symbiodinium type(s). However, one Symbiodinium ITS2 profile (P4*) was observed in only 2 colonies of A. lamarcki (at 25 m) and was identical to the P4 profile but with an extra band that corresponded with the C1 sequence. The several Agaricia morphs that could not be unambiguously identified (Agaricia sp.) all contained the P4 profile (n = 10). For H. cucullata we could only obtain a single recoverable ITS2 sequence (CN8), which represented a more distant, novel Symbiodinium type (GenBank Accession Number KF551192) (Figure 3).

Figure 3

Sequence network of Symbiodinium ITS2 types observed for each DGGE profile obtained from agariciid species. Ancestral Symbiodinium types C1 and C3 are represented by squares. Circle size is not representative of frequency. Dashed lines indicate sequence gaps (with gap size in number of base pairs). Colours group the different ITS2 sequences observed in each DGGE profile. The C3 type (indicated by black square) is found in all DGGE profiles except for P5.

A. humilis, A. agaricites, A. grahamae and H. cucullata all harboured a single symbiont profile across the entire depth range across which they were sampled. A. lamarcki, the only species observed to harbour multiple symbiont profiles, showed a marked zonation, with colonies at 10 and 25 m depth harbouring either P3 (n = 34) or P4 (n = 36), whereas colonies (>40 m) exclusively harboured P4 (n = 33). Colonies hosting a mix of P3 and P4 profiles were not observed. There were no significant differences (Two-Way ANOSIM; depth nested within sampling year) between sampling years. The pairwise comparisons between the different depths confirmed that the symbiont community associated with A. lamarcki at 40 m was significantly different from 10 and 25 m (One-Way ANOSIM; not taking into account sampling year; respectively R = 0.15; p < 0.01 and R = 0.082; p < 0.05).

Host genetic structure across taxonomic species and depth

Seven different mtDNA haplotypes were identified across the 93 specimens for which the atp6 region (1260 bp including indels) was sequenced (Figure 4; GenBank Accession Numbers KF551193-KF551199). A single haplotype was observed for H. cucullata (n = 10), and indels were only observed when Agaricia sequences were aligned with those of H. cucullata. The remaining haplotypes were observed for Agaricia specimens and the number of substitutions between these sequences ranged from 0 to 16. The Agaricia haplotype network consists of two clades and four main haplotypes (i.e. subclades), with the majority of A. lamarcki and all A. grahamae specimens belonging to clade 2 (respectively 90 and 100%), most A. agaricites belonging to subclade 1a (86%), and A. humilis belonging to subclades 1b and 1c (69%). The Agaricia sp. specimens that were sequenced (n = 9 of 10) were found across the two main clades. Under the AMOVA framework (including only identified Agaricia specimens), 60% of molecular variance (ΦSPP-TOT = 0.599; P < 0.001) was explained by morphotaxonomic species designation. No significant contributions of Symbiodinium type (2%; ΦSYM-SPP = 0.058; P = 0.232) and depth (0%; ΦDEP-SPP = -0.059; P = 0.668) could be detected, when nested within taxonomic species.

Figure 4

Unrooted network of host atp6 mitochondrial haplotypes. Circle size indicates the relative frequency of each haplotype. Pie chart indicates for which agariciid species the haplotype was observed (Ahum = A. humilis (n = 16), Aaga = A. agaricites (n = 22), Alam = A. lamarcki (n = 27), Agra = A. grahamaei (n = 9), Asp. = Unidentified Agaricia species (n = 9), Hcuc = H. cucullata (n = 10)), and colour indicates the Symbiodinium profile that was hosted.

Phylogenetic analyses (ML, MP and BAY) of the atp6 region of the Agaricia specimens (Figure 5), using H. cucullata and Pavona clavus as outgroups, supported the monophyly of the genus Agaricia and subdivision of the genus into two main lineages (with bootstrap values across phylogenetic methods higher than 97), with sequences of the two lineages largely corresponding with A. lamarcki / A. grahamae and A. humilis / A. agaricites specimens respectively. The latter lineage is further subdivided into two lineages largely corresponding with A. humilis and A. agaricites (ML/MP/BAY: 94/69/93). Despite the mostly invariant host sequences among conspecifics, a small number of specimens belonging to different species were observed within each lineage. However, in all these cases the symbiont type hosted by these specimens confirmed the taxonomic identity (see Figure 4). Specimens that could not be identified (Agaricia sp.) were found to belong to the three different groups, although all hosting Symbiodinium profile P4, with 5 specimens from 25-40 m in the A. lamarcki/grahamae group, 2 specimens from 50 m in the A. agaricites group, and 2 specimens from 60 m in the A. humilis group.

Figure 5

Phylogenetic trees of Agaricia spp. based on mitochondrial and nuclear markers. Phylogenetic trees (maximum parsimony) of Agaricia spp. based on (a) mitochondrial atp6 (this study), and (b) nuclear 28S and (c) mitochondrial COI (previous studies: Medina et al. 2006; Fukami et al. 2008; Shearer and Coffroth 2008; Barbeitos et al 2010). Pavona spp., Helioseris cucullata and Leptoseris sp. are used as outgroups. Bootstrap values are based on Bayesian (BAY), maximum parsimony (MP) and maximum likelihood (ML) respectively, with only probabilities over 50% shown. Depth range and number of specimens are mentioned for each species, coloured boxes indicates the Symbiodinium profile that was hosted. Sequences retrieved from GenBank are indicated by their Accession Number.

Analyses of COI and 28S sequences for the same Agaricia spp. [6063], using Pavona spp. and respectively Leptoseris sp. and H. cucullata as outgroups, corroborate the phylogenetic pattern revealed through the atp6 region (Figure 5b, c). However, where COI shows no differentiation between A. humilis and A. agaricites, the 28S region differentiates between A. lamarcki and A. grahamae specimens. As such, the 28S region supports the subdivision of the Agaricia genus into two main lineages, corresponding to shallow (A. humilis and A. agaricites) and deeper species (A. lamarcki and A. grahamae).

Despite this cladal division into shallow and deep Agaricia species, no clear genetic subdivision was observed within species over depth (Figure 5), or in the case of A. lamarcki in relation to symbiont type (Figure 4). Nonetheless, several shallow specimens of A. lamarcki were found within the A. humilis (n = 3; 10 m) and A. agaricites groups (n = 1; 25 m). Additionally, several specimens of A. agaricites from 25 (n = 1) and 50 m (n = 2) depth were observed in the A. lamarcki/grahamae lineage.


This study assessed the depth distribution and genetic variation of five agariciid coral species and their associated Symbiodinium across a large depth gradient (2-60 m) on a single reef. Overall, we found a tight coupling between coral species and their dominant Symbiodinium at the study location, and strong evidence for depth-related niche partitioning of these associations. Depth-related parameters appear to have played a major role in the diversification of the coral genus Agaricia and its dominant algal endosymbionts, resulting in a clear genetic partitioning between coral host-symbiont communities across shallow and mesophotic depths.

Symbiodiniumdiversity and host-symbiont specificity

Associations between the coral host and its dominant algal endosymbionts (Symbiodinium) at the study location were found to be specific in that each of the five agariciid species harboured a distinct Symbiodinium profile (except for A. lamarcki and A. grahamae that had one profile in common) (Figure 2). The four Symbiodinium profiles found in association with the four Agaricia species all shared the C3 sequence as an intragenomic variant and contained closely related Symbiodinium sequences (Figure 3). This corroborates observations in other parts of the Caribbean (Bahamas, Barbados, Belize, Florida, Mexico, US Virgin Islands), where Agaricia species have been found in association with C3-related Symbiodinium types [16, 4650].

Nonetheless, except for the C3b-related Symbiodinium type in A. humilis (profile P1), the agariciids studied here hosted distinct Symbiodinium types compared to those previously reported (e.g. B1, C3, C3a, C3q, D1a) [16, 4650]. A. lamarcki associated with two profiles (P3 and P4) containing respectively a C3d and C11 sequence, which indicate Symbiodinium types related to those found in respectively Montastraea (C3d) and mussid and faviid genera such as Scolymia, Mussa and Mycetophyllia (C11) [16, 35, 46]. H. cucullata hosted a Symbiodinium type (CN8/profile P5) that is very distinct from the C3 type previously reported in association with this species in other parts of the Caribbean [46, 48, 50], and does not contain the C3 sequence as an intragenomic variant. Some of these differences in Symbiodinium associated with Agaricia spp. (other studies) can be contributed to geographic separation of populations from the Western and Eastern Caribbean [50], however it also demonstrates that differences in symbiont associations exist even at smaller geographic scales, such as within the Eastern Caribbean (i.e., between Curaçao and Barbados). These observations corroborate the notion that the level of host-symbiont specificity can vary across geographic locations [22, 29, 32], and therefore has to be assessed locally in terms of the ecological implications.

The maternal transmission of endosymbionts leads to relative isolation of host-specific Symbiodinium populations, and is likely to be responsible for the local host specificity and the geographic variation in host-symbiont associations, as Symbiodinium types coevolve locally with their coral partners [22]. Similar host-symbiont specificity has been observed in other coral genera with a vertical symbiont acquisition mode, such as in various pocilliporid genera (e.g. Seriatopora, Pocillopora, Stylophora, Madracis) and the genera Montipora and Porites[20, 2225, 29]. Although the incongruence between host and symbiont phylogenies points towards the importance of occasional host-symbiont recombination [13, 16, 28, 29], such recombination through “symbiont replacement” is unlikely to occur over ecological timescales [67]. Therefore, despite the variation in host-symbiont associations observed for Agariciids across the broader Caribbean, it remains questionable whether the agariciid species at the study location can respond to rapid environmental change due to the lack of standing variation (i.e. diversity) in Symbiodinium associations.

The host-symbiont specificity observed here relates to the dominant Symbiodium types that are hosted by each species, and high-resolution approaches to the detection of Symbiodinium (e.g. using quantitative PCR or next-generation sequencing) may demonstrate that these agariciid species also host non-specific background Symbiodinium[57, 58]. In addition, we observed the generalist Symbiodinium type C1 in 2 out of 105 sampled specimens of A. lamarcki (in addition to profile P4), indicating that non-specific associations occasionally do occur [29]. Although the potential of “symbiont shuffling” (i.e. shift in dominant Symbiodinium within a coral colony over its lifespan) as a response to environmental change remains debated [67], unusual associations (such as the C1 hosted in A. lamarcki) may become more abundant if these exhibit higher levels of holobiont fitness under the predicted changing environmental conditions.

Depth-partitioning of agariciid host species and associated Symbiodinium

The five agariciid coral species exhibited a clear partitioning across the depth-mediated environmental gradient, progressing from respectively A. humilis, A. agaricites and A. lamarcki as most abundant species from shallow to deep (Figure 1c). A. humilis is a clear “shallow-water specialist” largely restricted to the shallow reef terrace (2-10 m), whereas A. grahamae is a “deep-water specialist” that exclusively occurs in the mesophotic zone (40-60 m). In contrast, both A. agaricites and A. lamarcki are more generalistic in terms of their depth distribution, albeit that A. agaricites predominates at shallower depths (5-25 m) and A. lamarcki at greater depths (25-60 m), with 25 m representing a transitory depth between both species (Figure 1c). These depth-distributions are from a single study location, and may vary across locations with different environmental conditions (e.g. water clarity) [68]. However, similar zonation of Agaricia species has been reported across the Caribbean [37, 38, 6972], with A. humilis and A. agaricites most abundant on the shallow end of the depth spectrum, and A. lamarcki and A. grahamae predominating at greater depths. H. cucullata was found across a large depth range (10-60 m), however only in very low abundances, reflecting the remarkable decline of this species on the reefs in Curaçao compared to ~30 years ago [44, 45].

Four of the agariciid species hosted a single Symbiodinium type over their entire depth range. In contrast, the depth-generalist species A. lamarcki exhibited symbiont depth zonation, changing from hosting P3 (i.e. C3/C3d -related) or P4 (i.e. C3/C11-related) in the shallow to exclusively P4 at mesophotic depths. The “deep-water specialist” A. grahamae harboured this same P4 symbiont profile, indicating that this Symbiodinium type may be particularly well-adapted to deeper water conditions. Similar putative “deep-specialist” Symbiodinium types have been identified in the genera Madracis and Montastraea[21, 34, 35]. Conversely, the ability of A. lamarcki to associate with another Symbiodinium lineage (represented by the P3 profile) may facilitate its broader depth distribution (i.e., extending into the shallow) compared to A. grahamae (although the P4 profile was found at shallow depths in A. lamarcki as well). Symbiont zonation appears to be a common feature of depth-generalist coral species in the Caribbean [31], however the occurrence of a single Symbiodinium profile in A. agaricites from 5-50 m depth indicates that such zonation, however, is not a prerequisite for broad distribution patterns [27, 73].

When considering both the average densities of host species and dominant symbiont associations across depths, it is obvious that host-Symbiodinium assemblages exhibit a clear niche partitioning over depth, for all assemblages apart from H. cucullata / P5 (conceptual diagram shown in Figure 6). Although both A. humilis/P1 and A. agaricites/P2 predominate in the shallow reef environment, A. humilis/P1 thrives in the shallowest of depths (2-10 m) whereas A. agaricites/P2 is most abundant at intermediate depths (10-25 m). As such, A. humilis/P1 is restricted to depths with high-irradiance conditions (87-50% of surface irradiance) and A. agaricites/P2 occurs in all but the brightest light conditions (1.5-70%). At greater depths (≥ 25 m), however, A. lamarcki/P4 becomes the most dominant host-symbiont assemblage. Given that all sampled colonies of A. lamarcki at 10 m depth (n = 40) were growing in cryptic locations on the reef (Bongaerts and Frade pers. obs.), the shallow end of A. lamarcki’s depth distribution is clearly determined by a maximum tolerable irradiance. Additionally, the A. lamarcki/P3 host-symbiont association, which only occurs at 25 m and cryptically at 10 m, occupies a niche that encompasses a very narrow light range. Instead, A. grahamae that shares symbiont profile P4 (C3/C11-related) with A. lamarcki, starts to appear at slightly greater depths than the A. lamarcki/P4 combination, indicating the potential (acclimatization) importance of the host component in mediating the distribution of this host-symbiont partnership [34]. Although A. lamarcki was found to be most abundant at the deeper end of the sampled depth spectrum (60 m), anecdotal observations at greater depths (65-85 m) indicate that A. grahamae may in fact become the more dominant species (Figure 7; Vermeij and Bongaerts, pers. obs.).

Figure 6

Conceptual diagram depicting niche partitioning of agariciid host-symbiont assemblages over depth. Relative abundances are extrapolated from average densities of host species and relative symbiont abundances across depths.

Figure 7

Photo of Agaricia community beyond the depth range of this study. Paper-thin Agaricia grahamae communities at 86 m depth on the leeward shore of Curaçao.

Although incident irradiance is likely an important factor to explain the observed depth partitioning of host-symbiont associations, other environmental variables, such as light spectral composition [74], temperature [75] and nutrient/plankton availability [26] may be important as well. For example, the depth range between 25 and 40 m appears to be a transition zone of strong genetic change, which corresponds to the depth range where influxes of deep oceanic water become noticeable in the temperature regime [21, 39]. Given the various abiotic factors that vary over depth it remains impossible to evaluate the individual contributions of these factors in the observed partitioning, however light and temperature are likely to play important roles given their dramatic changes over depth at the study site [21, 76]. While representing a massive undertaking, repeating similar symbiont genotyping efforts across a range of different locations would provide us with further insight into the role of different environmental conditions in the depth partitioning of host-symbiont associations.

Host and symbiont (co) evolution

The mtDNA-based phylogenetic analysis showed that none of the Agaricia species studied is monophyletic, however, the presently accepted species designation can explain the majority of the observed molecular variance (~60%). Two major lineages were observed for the Agaricia specimens based on the atp6 region, basically dividing the genus into a shallow (A. humilis/A. agaricites – Clade 1) and a deep (A. lamarcki/A. grahamae – Clade 2) species group. The atp6 phylogeny is consistent with the phylogeny of the ribosomal 28S region (outgroup H. cucullata not included) produced with GenBank sequences, although the 28S region appears more variable (Figure 5). Although the atp6 region does not separate A. lamarcki and A. grahamae, the phylogeny of the 28S region demonstrates that these are unlikely to represent synonyms. The H. cucullata clade is genetically very distinct and even shows (across markers) a closer relation to the Indo-Pacific genus Pavona than the Atlantic Agaricia genus (Figure 5). The phylogeny of Agaricia, forming two major clusters representing shallow and deep species, indicates that depth-related factors have played a major role in the original divergence within this genus. Given that also within each of these clusters, each species again exhibit distinct depth distributions on respectively the shallow and deep reef (Figure 1c), highlights the potential role of depth-related factors in the diversification within this genus throughout its evolutionary history.

Within the genus Agaricia all of the four major host atp6 haplotypes are, in fact, shared by more than one Agaricia taxon. This shared genetic polymorphism and repetitive non-monophyly has been shown in the past for many other coral taxa [9, 7781]. Such incongruence between morphospecies and genetically delimited phylogenies have been explained by several authors as being the result of phenomena such as morphological convergence (homoplasy), phenotypic plasticity, recent speciation with incomplete lineage sorting, morphological stasis, and/or interspecific introgressive hybridization [80]. Although introgressive hybridisation has been suggested in other brooding coral species [9, 80, 82], the fact that we only used a single mitochondrial marker prevents inference of such processes in the current study. The “misplaced specimens” in the phylogeny all hosted the Symbiodinium profile specific to that species (Figure 2), confirming that these are unlikely to represent taxonomic misidentifications. However, the observation that several shallower specimens of A. lamarcki (n = 4) grouped with the “shallow” species group (Clade 1a-c), and several deeper specimens of A. agaricites (n = 3) grouped with the “deep” species group (Clade 2) (Figure 5), could potentially be indicative of hybridization due to low densities of conspecific sperm.

The evolutionary divergence between “shallow” and “deep” Agaricia host species and genetic relatedness among them is reflected in the symbiont associations, with A. lamarcki and A. grahamae sharing an identical Symbiodinium profile (P4), and A. humilis and A. agaricites harbouring a related ITS2 sequence in their Symbiodinium profiles (C3b in P1 and C3N2 in P2) (Figure 3). This highlights, despite potential hybridisation within the Agaricia genus (which could result in the crossing over of Symbiodinium types), the diversification of both host and symbiont through reciprocal evolutionary changes (at least at a microevolutionary scale). These observations corroborate the growing body of evidence suggesting that corals with a vertical symbiont acquisition (i.e., usually brooding corals) and their associated, dominant Symbiodinium are involved in coevolutionary processes [8, 9, 26, 29, 83].

A common pattern for Caribbean brooding corals?

The depth niche partitioning, host phylogenetic structure and local host-symbiont specificity observed for the genus Agaricia has strong similarities to that of the model genus Madracis, which has been extensively studied at the exact same study site [9, 21, 34, 51, 76, 8387]. The Caribbean genus Madracis comprises six common taxonomic species whose distributions are partitioned over the reef slope, including shallow (M. mirabilis and M. decactis) and deep (M. carmabi and M. formosa) specialists and two depth-generalist species (M. pharensis and M. senaria). However, similar to A. lamarcki, the distribution of M. pharensis and M. senaria is restricted to cryptic locations at depths of 10 m and shallower [51]. As such, the genus Madracis can be roughly divided into “shallow” species (M. mirabilis and M. decactis) and “deep” (M. pharensis, M. senaria, M. carmabi and M. formosa) species. This subdivision corresponds to the two main clades observed in the Madracis phylogeny based on the mitochondrial nad5 region [9], similar to the genetic divergence observed between “shallow” and “deep” species in the genus Agaricia.

With regards to the associated Symbiodinium, the genus Madracis harbours three physiologically distinct but phylogenetically closely related symbiont types (B7, B13, B15), which are also partitioned over depth and to a certain extent specific to certain host species [21, 34]. The shift in symbionts observed for M. pharensis corresponds to distinct physiological capacities of the symbionts involved [34], but also corresponds with a genetic divergence between shallow and deep populations of the host species M. pharensis[9]. Such intra-specific genetic divergence was not observed for A. lamarcki (the only Agaricia species that exhibited symbiont zonation), however it does corroborate the general pattern of strong host-symbiont coupling in Agaricia (this study).

Overall, the observed niche partitioning and evolutionary split between shallow and deep host lineages observed for the genera Agaricia and Madracis, highlight the role of the depth-related environmental gradient (i.e. differences in light, temperature, etc.) as a driving factor in the evolution of the congeneric species associated with these genera. The molecular phylogenies of both genera are relatively incongruent relative to the taxonomic classification based on morphological traits [9, 84], highlighting the potential additional importance of introgressive hybridization. However, the role of introgressive hybridization in Agaricia is hard to infer given the use of a single, maternally-inherited marker region in this study. Nonetheless, the fact that species in both genera remain recognizable and have distinct ecological distributions does point towards the importance of divergent/disruptive selection across a depth gradient in the diversification of these genera. Given the prevalence of a brooding reproductive strategy [36] and vertical symbiont acquisition mode in the Caribbean, ecological adaptation to different ends of the depth spectrum may have played a major role in the diversification of many Caribbean corals.

Implications for vertical connectivity

In recent years, there has been a growing interest in the role of deep reef areas as local refugia and a source of propagules [31], particularly given the observed relative stablity of some mesophotic reef environments [39] and accumulating evidence of localized recruitment on coral reefs [8890]. The extent of genetic specialization within the genus Agaricia to both shallow and deep reef environments (Figure 6) indicates that, although the mesophotic Agaricia communities have remained relatively stable in the geographic location of our study [39], these communities are unlikely to provide significant amounts of propagules to ensure rapid shallow-reef recovery post-disturbance. The unrelated genus Madracis, shows a similar genetic segregation between its host-symbiont communities at mesophotic (dominated by M. pharensis / B15 and M. formosa / B15) and shallow depths [9, 21], confirming that this pattern may extent across a broad range of coral genera. Nonetheless, the limited overlap between shallow and deep communities indicates that deep reef may still play an important role in ensuring local protection of certain genotypes (e.g. the small number of A. agaricites colonies that occur in the deep) when adjacent shallow-reefs get affected by a major disturbance.


The findings in this study highlight that depth-related parameters have played a major role in the diversification of brooding corals and their associated Symbiodinium, and corroborate the notion that brooding corals and their Symbiodinium are engaged in processes of coevolution. Further studies should investigate whether any adaptive differentiation of these species has occurred at the population level, and whether the high levels of specificity observed here are also prevalent in other brooding coral genera. Overall, we need a better understanding of the actual mechanisms through which the depth-related environmental gradients have led to population/species divergence on coral reefs and how this evolutionary history affects the current day and future interconnectedness of shallow and deep reef systems.


  1. 1.

    Connell JH: Diversity in tropical rain forests and coral reefs. Science. 1978, 199: 1302-1310. 10.1126/science.199.4335.1302.

    CAS  PubMed  Article  Google Scholar 

  2. 2.

    Knowlton N, Jackson JBC: New taxonomy and niche partitioning on coral reefs: jack of all trades or master of some?. Trends Ecol Evol. 1994, 1: 7-9.

    Article  Google Scholar 

  3. 3.

    Souter P: Hidden genetic diversity in a key model species of coral. Mar Biol. 2010, 157: 875-885. 10.1007/s00227-009-1370-3.

    Article  Google Scholar 

  4. 4.

    Stefani F, Benzoni F, Yang S-Y, Pichon M, Galli P, Chen CA: Comparison of morphological and genetic analyses reveal cryptic divergence and morphological plasticity in Stylophora (Cnidaria, Scleractinia). Coral Reefs. 2011, 30: 1033-1049. 10.1007/s00338-011-0797-4.

    Article  Google Scholar 

  5. 5.

    Flot J-F, Blanchot J, Charpy L, Cruaud C, Licuanan WY, Nakano Y, Payri C, Tillier S: Incongruence between morphotypes and genetically delimited species in the coral genus Stylophora: phenotypic plasticity, morphological convergence, morphological stasis or interspecific hybridization?. BMC Ecol. 2011, 11: 22-10.1186/1472-6785-11-22.

    PubMed Central  PubMed  Article  Google Scholar 

  6. 6.

    Carlon DB, Budd AF: Incipient speciation across a depth gradient in a scleractinian coral?. Evolution. 2002, 56: 2227-2242.

    PubMed  Article  Google Scholar 

  7. 7.

    Vermeij MJA, Sandin SA, Samhouri JF: Local habitat composition determines the relative frequency and interbreeding potential for two Caribbean coral morphospecies. Evol Ecol. 2007, 21: 27-47. 10.1007/s10682-006-9122-z.

    Article  Google Scholar 

  8. 8.

    Bongaerts P, Riginos C, Ridgway T, Sampayo EM, Van Oppen MJH, Englebert N, Vermeulen F, Hoegh-Guldberg O: Genetic divergence across habitats in the widespread coral Seriatopora hystrix and its associated Symbiodinium. PLoS One. 2010, 5: e10871-10.1371/journal.pone.0010871.

    PubMed Central  PubMed  Article  Google Scholar 

  9. 9.

    Frade PR, Reyes-Nivia MC, Faria J, Kaandorp JA, Luttikhuizen PC, Bak RPM: Semi-permeable species boundaries in the coral genus Madracis: introgression in a brooding coral system. Mol Phylogen Evol. 2010, 57 (3): 1072-1090. 10.1016/j.ympev.2010.09.010.

    CAS  Article  Google Scholar 

  10. 10.

    Todd PA: Morphological plasticity in scleractinian corals. Biol Rev. 2008, 83: 315-337.

    PubMed  Article  Google Scholar 

  11. 11.

    Ow XY, Todd PA: Light-induced morphological plasticity in the scleractinian coral Goniastrea pectinata and its functional significance. Coral Reefs. 2010, 29: 797-808. 10.1007/s00338-010-0631-4.

    Article  Google Scholar 

  12. 12.

    Freudenthal HD: Symbiodinium gen. nov. and Symbiodinium microadriaticum sp. nov, a zooxanthella: taxonomy, life cycle and morphology. J Protozool. 1962, 9: 45-53. 10.1111/j.1550-7408.1962.tb02579.x.

    Article  Google Scholar 

  13. 13.

    Rowan R, Powers DA: A molecular genetic classification of zooxanthellae and the evolution of animal-algal symbiosis. Science. 1991, 251: 1348-1351. 10.1126/science.251.4999.1348.

    CAS  PubMed  Article  Google Scholar 

  14. 14.

    LaJeunesse TC: Investigating the biodiversity, ecology, and phylogeny of endosymbiotic dinoflagellates in the genus Symbiodinium using the ITS region: in search of a ‘species’ level marker. J Phycol. 2001, 37 (5): 866-880. 10.1046/j.1529-8817.2001.01031.x.

    CAS  Article  Google Scholar 

  15. 15.

    Takabayashi M, Santos SR, Cook CB: Mitochondrial DNA phylogeny of the symbiotic dinoflagellates (Symbiodinium, Dinophyta). J Phycol. 2004, 40 (1): 160-164. 10.1111/j.0022-3646.2003.03-097.x.

    CAS  Article  Google Scholar 

  16. 16.

    LaJeunesse TC: "Species" radiations of symbiotic dinoflagellates in the Atlantic and Indo-Pacific since the Miocene-Pliocene transition. Mol Biol Evol. 2005, 22: 570-581.

    CAS  PubMed  Article  Google Scholar 

  17. 17.

    LaJeunesse TC, Parkinson JE, Reimer JD: A genetics-based description of Symbiodinium minutum sp. nov. and S. psygmophilum sp. nov. (dinophyceae), two dinoflagellates symbiotic with cnidaria. J Phycol. 2012, 48: 1380-1391. 10.1111/j.1529-8817.2012.01217.x.

    Article  Google Scholar 

  18. 18.

    Ulstrup KE, Van Oppen MJ: Geographic and habitat partitioning of genetically distinct zooxanthellae (Symbiodinium) in Acropora corals on the Great Barrier Reef. Mol Ecol. 2003, 12: 3477-3484. 10.1046/j.1365-294X.2003.01988.x.

    CAS  PubMed  Article  Google Scholar 

  19. 19.

    Iglesias-Prieto R, Beltran VH, LaJeunesse TC, Reyes-Bonilla H, Thome PE: Different algal symbionts explain the vertical distribution of dominant reef corals in the eastern Pacific. Proc R Soc B. 2004, 271: 1757-1763. 10.1098/rspb.2004.2757.

    CAS  PubMed Central  PubMed  Article  Google Scholar 

  20. 20.

    Sampayo EM, Franceschinis L, Hoegh-Guldberg O, Dove S: Niche partitioning of closely related symbiotic dinoflagellates. Mol Ecol. 2007, 16: 3721-3733. 10.1111/j.1365-294X.2007.03403.x.

    CAS  PubMed  Article  Google Scholar 

  21. 21.

    Frade PR, De Jongh F, Vermeulen F, Van Bleijswijk J, Bak RPM: Variation in symbiont distribution between closely related coral species over large depth ranges. Mol Ecol. 2008, 17: 691-703.

    CAS  PubMed  Article  Google Scholar 

  22. 22.

    LaJeunesse TC, Pettay DT, Sampayo EM, Phongsuwan N, Brown B, Obura DO, Hoegh-Guldberg O, Fitt WK: 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. 2010, 37: 785-800. 10.1111/j.1365-2699.2010.02273.x.

    Article  Google Scholar 

  23. 23.

    LaJeunesse TC, Thornhill DJ, Cox EF, Stanton FG, Fitt WK, Schmidt GW: High diversity and host specificity observed among symbiotic dinoflagellates in reef coral communities from Hawaii. Coral Reefs. 2004, 23: 596-603.

    Google Scholar 

  24. 24.

    Loh WKW, Loi T, Carter D, Hoegh-Guldberg O: Genetic variability of the symbiotic dinoflagellates from the wide ranging coral species Seriatopora hystrix and Acropora longicyathus in the Indo-West Pacific. Mar Ecol Prog Ser. 2001, 222: 97-107.

    Article  Google Scholar 

  25. 25.

    Stat M, Hoegh-Guldberg O, Fitt WK, Carter D: Host symbiont acquisition strategy drives Symbiodinium diversity in the southern Great Barrier Reef. Coral Reefs. 2008, 27: 763-772. 10.1007/s00338-008-0412-5.

    Article  Google Scholar 

  26. 26.

    Bongaerts P, Riginos C, Hay K, Van Oppen MJH, Hoegh-Guldberg O, Dove S: Adaptive divergence in a scleractinian coral: physiological adaptation of Seriatopora hystrix to shallow and deep reef habitats. BMC Evol Biol. 2011, 11: 303-10.1186/1471-2148-11-303.

    CAS  PubMed Central  PubMed  Article  Google Scholar 

  27. 27.

    Bongaerts P, Sampayo EM, Bridge TLC, Ridgway T, Vermeulen F, Englebert N, Webster JM, Hoegh-Guldberg O: Symbiodinium diversity of mesophotic coral communities on the GBR: a first assessment. Mar Ecol Prog Ser. 2011, 439: 117-126.

    Article  Google Scholar 

  28. 28.

    LaJeunesse TC, Smith RT, Finney J, Oxenford H: Outbreak and persistence of opportunistic symbiotic dinoflagellates during the 2005 Caribbean mass coral ‘bleaching’ event. Proc R Soc B. 2009, 276: 4139-4148. 10.1098/rspb.2009.1405.

    PubMed Central  PubMed  Article  Google Scholar 

  29. 29.

    Van Oppen MJH: Mode of zooxanthella transmission does not affect zooxanthella diversity in acroporid corals. Mar Biol. 2004, 144: 1-7. 10.1007/s00227-003-1187-4.

    Article  Google Scholar 

  30. 30.

    Hoegh-Guldberg O, Mumby PJ, Hooten AJ, Steneck RS, Greenfield P, Gomez E, Harvell CD, Sale PF, Edwards AJ, Caldeira K, Knowlton N, CEakin M, Iglesias-Prieto R, Muthiga N, Bradbury RH, Dubi A, Hatziolos ME: Coral reefs under rapid climate change and ocean acidification. Science. 2007, 318: 1737-1742. 10.1126/science.1152509.

    CAS  PubMed  Article  Google Scholar 

  31. 31.

    Bongaerts P, Ridgway T, Sampayo EM, Hoegh-Guldberg O: Assessing the ‘deep reef refugia’ hypothesis: focus on Caribbean reefs. Coral Reefs. 2010, 29 (2): 309-327. 10.1007/s00338-009-0581-x.

    Article  Google Scholar 

  32. 32.

    Van Oppen MJH, Bongaerts P, Underwood J, Peplow L, Cooper T: The role of deep reefs in shallow reef recovery: an assessment of vertical connectivity in a brooding coral from west and east Australia. Mol Ecol. 2011, 20: 1647-1660. 10.1111/j.1365-294X.2011.05050.x.

    PubMed  Article  Google Scholar 

  33. 33.

    Rowan R, Knowlton N: Intraspecific diversity and ecological zonation in coral-algal symbiosis. Proc Natl Acad Sci USA. 1995, 92: 2850-2853. 10.1073/pnas.92.7.2850.

    CAS  PubMed Central  PubMed  Article  Google Scholar 

  34. 34.

    Frade PR, Bongaerts P, Winkelhagen AJS, Tonk L, Bak RPM: In situ photobiology of corals over large depth ranges: a multivariate analysis on the roles of environment, host, and algal symbiont. Limnol Oceanogr. 2008, 53: 2711-2723. 10.4319/lo.2008.53.6.2711.

    Article  Google Scholar 

  35. 35.

    Lesser MP, Slattery M, Stat M, Ojimi M, Gates RD, Grottoli A: Photoacclimatization by the coral Montastraea cavernosa in the mesophotic zone: light, food, and genetics. Ecology. 2010, 91: 990-1003. 10.1890/09-0313.1.

    PubMed  Article  Google Scholar 

  36. 36.

    Richmond RH, Hunter CL: Reproduction and recruitment of corals: Comparisons among the Caribbean, the Tropical Pacific, and the Red Sea. Mar Ecol Prog Ser. 1990, 60: 185-203.

    Article  Google Scholar 

  37. 37.

    Goreau TF, Goreau NI: The ecology of Jamaican coral reefs. II. Geomorphology, zonation, and sedimentary phases. Bull Mar Sci. 1973, 23: 399-464.

    Google Scholar 

  38. 38.

    Hughes TP, Jackson JBC: Population dynamics and life histories of foliaceous corals. Ecol Monogr. 1985, 55: 141-166. 10.2307/1942555.

    Article  Google Scholar 

  39. 39.

    Bak RPM, Nieuwland G, Meesters EH: Coral reef crisis in deep and shallow reefs: 30 years of constancy and change in reefs of Curaçao and Bonaire. Coral Reefs. 2005, 24: 475-479. 10.1007/s00338-005-0009-1.

    Article  Google Scholar 

  40. 40.

    Kahng SE, Garcia R, Spalding HL, Brokovich E, Wagner D, Weil E, Hinderstein L, Toonen RJ: Community ecology of mesophotic coral reef ecosystems. Coral Reefs. 2010, 29: 255-275. 10.1007/s00338-010-0593-6.

    Article  Google Scholar 

  41. 41.

    Titlyanov EA: Structure and morphological differences of colonies of reef-building branched corals from habitats with different light conditions. Mar Biol. 1987, 1: 32-36.

    Google Scholar 

  42. 42.

    Van Moorsel GWNM: Reproductive strategies in two closely related stony corals (Agaricia, Scleractinia). Mar Ecol Prog Ser. 1983, 13: 273-283.

    Article  Google Scholar 

  43. 43.

    Bak RPM: The growth of coral colonies and the importance of crustose coralline algae and burrowing sponges in relation with carbonate accumulation. Neth J Sea Res. 1976, 10: 285-337. 10.1016/0077-7579(76)90009-0.

    Article  Google Scholar 

  44. 44.

    Bak RPM, Engel MS: Distribution, abundance and survival of juvenile hermatypic corals (Scleractinia) and the importance of life history strategies in the parent coral community. Mar Biol. 1979, 54: 341-352. 10.1007/BF00395440.

    Article  Google Scholar 

  45. 45.

    Vermeij MJ, Bakker J, Hal N, Bak RP: Juvenile coral abundance has decreased by more than 50% in only three decades on a small Caribbean island. Diversity. 2011, 3 (3): 296-307.

    Article  Google Scholar 

  46. 46.

    LaJeunesse T: Diversity and community structure of symbiotic dinoflagellates from Caribbean coral reefs. Mar Biol. 2002, 141: 387-400. 10.1007/s00227-002-0829-2.

    Article  Google Scholar 

  47. 47.

    Warner ME, LaJeunesse TC, Robison JD, Thur RM: The ecological distribution and comparative photobiology of symbiotic dinoflagellates from reef corals in Belize: potential implications for coral bleaching. Limnol Oceanogr. 2006, 51: 1887-1897. 10.4319/lo.2006.51.4.1887.

    Article  Google Scholar 

  48. 48.

    Banaszak AT, Santos MGB, LaJeunesse TC, Lesser MP: The distribution of mycosporine-like amino acids (MAAs) and the phylogenetic identity of symbiotic dinoflagellates in cnidarian hosts from the Mexican Caribbean. J Exp Mar Bio Ecol. 2006, 337 (2): 131-146. 10.1016/j.jembe.2006.06.014.

    CAS  Article  Google Scholar 

  49. 49.

    Santos RS, LaJeunesse TC: Searchable database of Symbiodinium diversity-geographic and ecological diversity (SD2-GED). 2006,,

    Google Scholar 

  50. 50.

    Finney JC, Pettay DT, Sampayo EM, Warner ME, Oxenford HA, LaJeunesse TC: The relative significance of host–habitat, depth, and geography on the ecology, endemism, and speciation of coral endosymbionts in the genus symbiodinium. Microb Ecol. 2010, 60: 250-263. 10.1007/s00248-010-9681-y.

    PubMed  Article  Google Scholar 

  51. 51.

    Frade PR, Englebert N, Faria J, Visser PM, Bak RPM: Distribution and photobiology of Symbiodinium types in different light environments for three colour morphs of the coral Madracis pharensis: is there more to it than total irradiance?. Coral Reefs. 2008, 27: 913-925. 10.1007/s00338-008-0406-3.

    Article  Google Scholar 

  52. 52.

    Bak RPM: Coral reefs and their zonation in Netherlands Antilles. Stud Geol. 1977, 4: 3-16.

    Google Scholar 

  53. 53.

    Wells JW: New and old scleractinian corals from Jamaica. Bull Mar Sci. 1973, 23: 16-54.

    Google Scholar 

  54. 54.

    Veron JEN, Stafford-Smith M: Corals of the World. 2000, Townsville: Australian Institute of Marine Science

    Google Scholar 

  55. 55.

    Humann P, DeLoach N: Reef coral identification. 2002, New World, Jacksonville, Florida: Florida Caribbean Bahamas including marine plants

    Google Scholar 

  56. 56.

    Wilson K, Li Y, Whan V, Lehnert S, Byrne K, Moore S, Pongsomboon S, Tassanakajon A, Rosenberg G, Ballment E: Genetic mapping of the black tiger shrimp Penaeus monodon with amplified fragment length polymorphism. Aquaculture. 2002, 204: 297-309. 10.1016/S0044-8486(01)00842-0.

    CAS  Article  Google Scholar 

  57. 57.

    Mieog JC, Van Oppen MJH, Cantin NE, Stam WT, Olsen JL: Real-time PCR reveals a high incidence of Symbiodinium clade D at low levels in four scleractinian corals across the Great Barrier Reef: implications for symbiont shuffling. Coral Reefs. 2007, 26: 449-457. 10.1007/s00338-007-0244-8.

    Article  Google Scholar 

  58. 58.

    Silverstein RN, Correa AMS, Baker AC: Specificity is rarely absolute in coral–algal symbiosis: implications for coral response to climate change. Proc Roy Soc B. 2012, 10.1098/rspb.2012.0055.

    Google Scholar 

  59. 59.

    Tamura K, Dudley J, Nei M, Kumar S: MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol Biol Evol. 2007, 24: 1596-1599. 10.1093/molbev/msm092.

    CAS  PubMed  Article  Google Scholar 

  60. 60.

    Medina M, Collins AG, Takaoka TL, Kuehl JV, Boore JL: Naked corals: skeleton loss in Scleractinia. Proc Natl Acad Sci USA. 2006, 103 (24): 9096-9100. 10.1073/pnas.0602444103.

    CAS  PubMed Central  PubMed  Article  Google Scholar 

  61. 61.

    Shearer TL, Coffroth MA: DNA Barcoding: Barcoding corals: limited by interspecific divergence, not intraspecific variation. Mol Ecol Resour. 2008, 8 (2): 247-255. 10.1111/j.1471-8286.2007.01996.x.

    CAS  PubMed  Article  Google Scholar 

  62. 62.

    Fukami H, Chen CA, Budd AF, Collins A, Wallace C, Chuang YY, Chen C, Dai CF, Iwao K, Sheppard C, Knowlton N: Mitochondrial and nuclear genes suggest that stony corals are monophyletic but most families of stony corals are not (Order Scleractinia, Class Anthozoa, Phylum Cnidaria). PLoS One. 2008, 3: e3222-10.1371/journal.pone.0003222.

    PubMed Central  PubMed  Article  Google Scholar 

  63. 63.

    Barbeitos MS, Romano SL, Lasker HR: Repeated loss of coloniality and symbiosis in scleractinian corals. Proc Natl Acad Sci USA. 2010, 107 (26): 11877-11882. 10.1073/pnas.0914380107.

    CAS  PubMed Central  PubMed  Article  Google Scholar 

  64. 64.

    Posada D: jModelTest: phylogenetic model averaging. Mol Biol Evol. 2008, 25 (7): 1253-1256. 10.1093/molbev/msn083.

    CAS  PubMed  Article  Google Scholar 

  65. 65.

    Peakall R, Smouse PE: GenAlEx V5: Genetic Analysis in Excel. 2001, Population Genetic Software for Teaching and Research: Australian National University

    Google Scholar 

  66. 66.

    Thornhill DJ, LaJeunesse TC, Santos SR: Measuring rDNA diversity in eukaryotic microbial systems: how intragenomic variation, pseudogenes, and PCR artifacts confound biodiversity estimates. Mol Ecol. 2007, 16: 5326-5340. 10.1111/j.1365-294X.2007.03576.x.

    CAS  PubMed  Article  Google Scholar 

  67. 67.

    LaJeunesse TC, Smith R, Walther M, Pinzón J, Pettay DT, McGinley M, Aschaffenburg M, Medina-Rosas P, Cupul-Magaña AL, López Pérez A, Reyes-Bonilla H, Warner ME: Host − symbiont recombination versus natural selection in the response of coral − dinoflagellate symbioses to environmental disturbance. Proc Roy Soc B. 2010, 277: 2925-2934. 10.1098/rspb.2010.0385.

    Article  Google Scholar 

  68. 68.

    Hoeksema BW: Evolutionary trends in onshore-offshore distribution patterns of mushroom coral species (Scleractinia: Fungiidae). Contrib Zool. 2012, 81: 199-221.

    Google Scholar 

  69. 69.

    Goldberg WM: The ecology of the coral octocoral communities off the southeast Florida coast: geomorphology, species composition and zonation. Bull Mar Sci. 1973, 23: 465-488.

    Google Scholar 

  70. 70.

    Van den Hoek C, Breeman AM, Bak RPM, Van Buurt G: The distribution of algae, corals, and gorgonians in relation to depth, light attenuation, water movement, and grazing pressure in the fringing coral reef of Curaçao, Netherlands Antilles. Aquat Bot. 1978, 5: 1-46.

    Article  Google Scholar 

  71. 71.

    Bak RPM, Luckhurst BE: Constancy and change in coral reef habitats along depth gradients at Curaçao. Oecologia. 1980, 47: 145-155. 10.1007/BF00346812.

    Article  Google Scholar 

  72. 72.

    Kühlmann D: Composition and ecology of deep-water coral associations. Helgol Mar Res. 1983, 36: 183-204.

    Google Scholar 

  73. 73.

    Chan Y, Pochon X, Fisher MA, Wagner D, Concepcion GT, Kahng SE, Toonen RJ, Gates RD: Generalist dinoflagellate endosymbionts and host genotype diversity detected from mesophotic (67-100 m depths) coral Leptoseris. BMC Ecol. 2009, 9: 21-10.1186/1472-6785-9-21.

    PubMed Central  PubMed  Article  Google Scholar 

  74. 74.

    Mass T, Kline DI, Roopin M, Veal CJ, Cohen S, Iluz D, Levy O: The spectral quality of light is a key driver of photosynthesis and photoadaptation in Stylophora pistillata colonies from different depths in the Red Sea. J Exp Biol. 2010, 213: 4084-4091. 10.1242/jeb.039891.

    CAS  PubMed  Article  Google Scholar 

  75. 75.

    Winters G, Beer S, Zvi BB, Brickner I, Loya Y: Spatial and temporal photoacclimation of Stylophora pistillata: zooxanthella size, pigmentation, location and clade. Mar Ecol Prog Ser. 2009, 384: 107-119.

    Article  Google Scholar 

  76. 76.

    Vermeij MJA, Bak RPM: Species-specific population structure of closely related coral morphospecies along a depth gradient (5–60 m) over a Caribbean reef slope. Bull Mar Sci. 2003, 73: 725-744.

    Google Scholar 

  77. 77.

    Van Oppen MJ, Palstra FP, Piquet AM, Miller DJ: Patterns of coral-dinoflagellate associations in Acropora: significance of local availability and physiology of Symbiodinium strains and host-symbiont selectivity. Proc R Soc B. 2001, 268: 1759-1767. 10.1098/rspb.2001.1733.

    CAS  PubMed Central  PubMed  Article  Google Scholar 

  78. 78.

    Van Oppen MJ, Willis BL, Van Rheede T, Miller DJ: Spawning times, reproductive compatibilities and genetic structuring in the Acropora aspera group: evidence for natural hybridization and semi-permeable species boundaries in corals. Mol Ecol. 2002, 11: 1363-1376. 10.1046/j.1365-294X.2002.01527.x.

    PubMed  Article  Google Scholar 

  79. 79.

    Fukami H, Budd AF, Levitan DR, Jara J, Kersanach R, Knowlton N: Geographic differences in species boundaries among members of the Montastraea annularis complex based on molecular and morphological markers. Evolution. 2004, 58: 324-337.

    CAS  PubMed  Article  Google Scholar 

  80. 80.

    Flot JF, Licuanan WY, Nakano Y, Payri C, Cruaud C, Tillier S: Mitochondrial sequences of Seriatopora corals show little agreement with morphology and reveal the duplication of a tRNA gene near the control region. Coral Reefs. 2008, 27: 789-794. 10.1007/s00338-008-0407-2.

    Article  Google Scholar 

  81. 81.

    Forsman ZH, Barshis DJ, Hunter CL, Toonen RJ: Shape-shifting corals: molecular markers show morphology is evolutionarily plastic in Porites. BMC Evol Biol. 2009, 9: 45-10.1186/1471-2148-9-45.

    PubMed Central  PubMed  Article  Google Scholar 

  82. 82.

    Miller KJ, Ayre DJ: The role of sexual and asexual reproduction in structuring high latitude populations of the reef coral Pocillopora damicornis. Heredity. 2004, 92: 557-568. 10.1038/sj.hdy.6800459.

    CAS  PubMed  Article  Google Scholar 

  83. 83.

    Diekmann O, Olsen J, Stam W, Bak R: Genetic variation within Symbiodinium clade B from the coral genus Madracis in the Caribbean (Netherlands Antilles). Coral Reefs. 2003, 22: 29-33.

    Google Scholar 

  84. 84.

    Diekmann OE, Bak RPM, Stam WT, Olsen JL: Molecular genetic evidence for probable reticulate speciation in the coral genus Madracis from a Caribbean fringing reef slope. Mar Biol. 2001, 139: 221-233. 10.1007/s002270100584.

    CAS  Article  Google Scholar 

  85. 85.

    Vermeij MJA, Bak RPM: How are coral populations structured by light? Marine light regimes and the distribution of Madracis. Mar Ecol Prog Ser. 2002, 233: 105-116.

    Article  Google Scholar 

  86. 86.

    Vermeij MJA, Sampayo E, Bröker K, Bak RPM: Variation in planulae release of closely related coral species. Mar Ecol Prog Ser. 2003, 247: 75-84.

    Article  Google Scholar 

  87. 87.

    Vermeij MJA, Sampayo E, Bröker K, Bak RPM: The reproductive biology of closely related coral species: gametogenesis in Madracis from the southern Caribbean. Coral Reefs. 2004, 23: 206-214.

    Article  Google Scholar 

  88. 88.

    Ayre DJ, Hughes TP: Genotypic diversity and gene flow in brooding and spawning corals along the Great Barrier Reef, Australia. Evolution. 2000, 54: 1590-1605.

    CAS  PubMed  Article  Google Scholar 

  89. 89.

    Baums IB, Miller MW, Hellberg ME: Regionally isolated populations of an imperiled Caribbean coral, Acropora palmata. Mol Ecol. 2005, 14: 1377-1390. 10.1111/j.1365-294X.2005.02489.x.

    CAS  PubMed  Article  Google Scholar 

  90. 90.

    Underwood JN, Smith LD, Van Oppen MJH, Gilmour JP: Multiple scales of genetic connectivity in a brooding coral on isolated reefs following catastrophic bleaching. Mol Ecol. 2007, 16: 771-784.

    CAS  PubMed  Article  Google Scholar 

Download references


The authors thank Floris de Jongh, John Crocker, Dennis Hamro-Drotz, and other students that have helped over the years with the collection of coral specimens. We thank Judith Bakker and Joshua Boldt for their support during deep dives, Carlos “No joh” Winterdaal for tremendous support in the field, Harry Witte and Linda Tonk for their assistance in the lab, and Maria Bongaerts for providing input on manuscript figures. This study was funded by the Australian Research Council (ARC) Centre of Excellence for Coral Reef Studies, Pacific Blue Foundation, Schure-Beijerinck-Popping fund (KNAW), and supported by the CARMABI Research Station.

Author information



Corresponding author

Correspondence to Pim Bongaerts.

Additional information

Competing interests

The authors declare that they have no competing interests.

Authors’ contributions

PB designed and conceived of the study, collected specimens, carried out labwork, performed the genetic analyses, and drafted the manuscript. PRF designed and conceived of the study, collected specimens, carried out labwork, helped with the interpretation of data, and drafted the manuscript. JJO, KBH and NE collected specimens, carried out labwork and helped to draft the manuscript. JvB carried out labwork, and helped to draft the manuscript. MJHV carried out the transects, collected specimens and helped to draft the manuscript. RPMB, PMV, and OHG designed and conceived of the study and helped to draft the manuscript. All authors read and approved the final manuscript.

Electronic supplementary material

Denaturing gradient gel electrophoresis of

Additional file 1: Symbiodinium ITS2 types associated with Agaricia species. Sequences used to characterize each symbiont profile are shown adjacent to bands in the gel image. Types in italics represent novel sequences, with the name specifying the sequence to which they are most related, followed by a capital N (indicating novel sequence) and an arbitrary number (e.g. C3bN1). (JPEG 1 MB)

Authors’ original submitted files for images

Rights and permissions

This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Reprints and Permissions

About this article

Cite this article

Bongaerts, P., Frade, P.R., Ogier, J.J. et al. Sharing the slope: depth partitioning of agariciid corals and associated Symbiodiniumacross shallow and mesophotic habitats (2-60 m) on a Caribbean reef. BMC Evol Biol 13, 205 (2013).

Download citation


  • Niche partitioning
  • Species diversification
  • Mesophotic
  • Deep reef
  • Agariciidae
  • Symbiodinium