Article

A preliminary survey of zoantharian endosymbionts shows high genetic variation over small geographic scales on Okinawa-jima Island, Japan

Authors:
To read the full-text of this research, you can request a copy directly from the authors.

Abstract

Symbiotic dinoflagellates (genus Symbiodinium) shape the responses of their host reef organisms to environmental variability and climate change. To date, the biogeography of Symbiodinium has been investigated primarily through phylogenetic analyses of the ribosomal internal transcribed spacer 2 (ITS2) region. Although the marker can approximate species-level diversity, recent work has demonstrated that faster-evolving genes can resolve otherwise hidden species and population lineages, and that this diversity is often distributed over much finer geographical and environmental scales than previously recognized. Here, we use the noncoding region of the chloroplast psbA gene (psbAncr) to examine genetic diversity among clade C Symbiodinium associating with the common reef zoantharian Palythoa tuberculosa on Okinawa-jima Island, Japan. We identify four closely related Symbiodinium psbAncr lineages including one common generalist and two potential specialists that appear to be associated with particular microhabitats. The sea surface temperature differences that distinguish these habitats are smaller than those usually investigated, suggesting that future biogeographic surveys of Symbiodinium should incorporate fine scale environmental information as well as fine scale molecular data to accurately determine species diversity and their distributions.

No full-text available

Request Full-text Paper PDF

To read the full-text of this research,
you can request a copy directly from the authors.

... However, many more recent studies have used the faster-evolving non-coding region of the plastid minicircle (psbA ncr ) as this region has the ability to discern between different Symbiodinium lineages (=species) with higher resolution (LaJeunesse and Thornhill 2011). Reexaminations of past Symbiodinium ITS-2 results with psbA ncr have found previously undetected higher levels of diversity, demonstrating the utility of the psbA ncr marker (LaJeunesse and Thornhill 2011; Reimer et al. 2017;Noda et al. 2017). ...
... psbA ncr rarely sequenced in both directions with overlap, as seen in previous works (e.g. Noda et al. 2017), and therefore in this study we constructed alignments and analyzed reverse and forward sequences separately. In order to compare with other Symbiodinium, additional previously reported GenBank sequences were included in ITS-2 and psbA ncr alignments. ...
... In many previous studies, it has been reported that there may be different lineages of Symbiodinium associated with host anthozoan species at different light levels (=depths), different ocean temperatures, or in different geographic regions (Frade et al. 2008, Hume et al. 2013, Kamezaki et al. 2013, Noda et al. 2017. However, in this study, Waminoa specimens all consisted of the same single psbA ncr genotype regardless of sampling depth or their anthozoan host in the phylogenetic tree of psbA ncr reverse. ...
Article
Full-text available
It is known that the genus Waminoa (order Acoela, Family Convolutidae) associates with anthozoans (Scleractinia, Octocorallia, Zoantharia) and feeds on the mucus of their host. Despite the close relationship between Waminoa and its host species, it is known from phylogenetic analyses of sequences of the internal transcribed spacer 2 of ribosomal DNA (ITS-2) that photosymbiotic Symbiodinium isolated from Waminoa are different from the Symbiodinium of their anthozoan hosts. Additionally, Waminoa inherit their Symbiodinium and Amphidinium via vertical transmission. In the current study, we looked for and collected Waminoa from different anthozoan hosts from the Ryukyu Archipelago in southern Japan, and then examined the Symbiodinium of Waminoa as well as hosts’ Symbiodinium, and utilized sequences of the hyper-variable non-coding region of the plastid minicircle (psbAncr) in order to re-examine the diversity of Symbiodinium within Waminoa. In the resulting psbAncr phylogenetic tree, all Symbiodinium within Waminoa comprised a unique group within Clade C, all with the same genotype in the psbAncr phylogenetic tree. Our results reconfirm that most Waminoa host their own lineage of Symbiodinium, and demonstrate that Waminoa are also found on azooxanthellate anthozoan hosts, as we found Waminoa on Siphonogorgia sp., expanding their potential known habitat. Additionally, two Symbiodinium from Waminoa from both shallow (4 m) and mesophotic (32 m) depths were not included in main group of Symbiodinium from Waminoa in the ITS-2 phylogenetic tree, although we could not acquire psbAncr sequences for these specimens. Therefore it is possible that undetected Symbiodinium diversity may yet exist within Waminoa, and future work at shallow to mesophotic depths examining both zooxanthellate and azooxanthellate hosts may find more Waminoa and Symbiodinium diversity.
... Several studies have examined Symbiodiniaceae hosted by the widely distributed zoantharian Palythoa tuberculosa (Anthozoa: Hexacorallia: Zoantharia) (Burnett 2002;Noda et al. 2017;Reimer and Todd 2009;Reimer et al. 2017a). The host Palythoa is common across the Indo-Pacific Ocean (Hibino et al. 2013) and is an ecological generalist, found in a wide variety of environments (acidified reefs, river mouths, and intertidal zones to 50 m depth). ...
... Two DNA marker regions were amplified via polymerase chain reaction (PCR) targeting specific regions: the internal transcribed spacer 2 of ribosomal DNA (ITS-2) of nuclear ribosomal DNA for all specimens, as well as the noncoding region of the plastid minicircle (psbA ncr ) for specimens containing Cladocopium. The ITS-2 sequences were utilized to place symbiont types within the well-established ITS-2 phylogenetic framework (LaJeunesse and Thornhill 2011), while the psbA ncr sequences were utilized to examine differences at a finer phylogenetic resolution (LaJeunesse and Thornhill 2011;Reimer et al. 2017a;Noda et al. 2017). ...
... The PCR mixes (20 ll) were composed of 1.0 ll of genomic DNA, 10.0 ll of HotStarTaq Plus Master Mix, 1.0 ll of each primer (10 pmol), 1.0 ll MgCl 2 (25 mmol), 0.5 bovine serum albumin (20 mg/ml), and 1.5 ll Coral Load. Thermocycle conditions were modified slightly from Noda et al. (2017); ITS-2: 95.0°C for 5 min; 35 cycles of 94.0°C for 30 s, 51.0°C for 45 s, and 72.0°C for 2 min; with a final extension at 72.0°C for 10 min; and for psbA ncr : 95.0°C for 5 min; 40 cycles of 94.0°C for 10 s, 55.0°C for 30 s, and 72.0°C for 2 min; with a final extension at 72.0°C for 10 min. The products were sent to Fasmac (Kanagawa, Japan) for sequencing in both directions. ...
Article
Full-text available
Sea surface temperatures (SST) and chlorophyll a concentrations (Chl a) in the southern Red Sea have wide variations based on distance from the coast. To understand how these variations can affect the diversity of symbionts hosted by reef-associated organisms, we conducted a study in the central and southern Red Sea to examine the diversity of Symbiodiniaceae hosted by the zooxanthellate zoantharian Palythoa tuberculosa at different distances from the coast: offshore (FBO), midshelf (FBM) and inshore (FBI) of Farasan Banks, and inshore at Thuwal (TI). Genomic DNA was extracted from 198 specimens, followed by amplification of the ribosomal DNA internal transcribed spacer 2 (ITS-2) and noncoding region of the chloroplast plastid minicircle (psbAncr). Durusdinium and six lineages of Cladocopium (Pt-1-a, Pt-1-b, Pt-1-c, Pt-1-d, Pt-3-a, Pt-3-b) were identified based on sequences of the two marker regions. Changes in composition of Symbiodiniaceae lineages were observed from FBI (high SST, high Chl a) to FBO (low SST, low Chl a). Molecular variance analyses showed that distance from coast was the most likely predictor of differences in Cladocopium lineages. Multinomial logistic regression analysis showed a transition among different Cladocopium lineages as SST increased. One Cladocopium lineage, Pt-1-b, demonstrated higher prevalences at high SSTs and increased in prevalences at the same rate as thermotolerant Durusdinium. Additionally, Cladocopium lineage Pt-3-a had a high affinity to low Chl a concentrations. This study demonstrates that environmental variations in SSTs and Chl a concentrations are significant predictors for the diversity of dominant Symbiodiniaceae within individual host P. tuberculosa colonies. We theorize that flexibility with different lineages of Symbiodiniaceae allows generalist P. tuberculosa to live across a wide range of environments in the southern Red Sea.
... On the other hand, compared to Sarcophyton, the abundance of P. tuberculosa was relatively not as reduced near the gas vent (Inoue et al. 2013). Similarly, other reports provide evidence of the high tolerance of P. tuberculosa to a wide variety of environments such as river mouths with possible lowered salinity and intertidal areas exposed to extreme temperatures Reimer et al. 2017;Noda et al. 2017). ...
... Subsequently, other studies have demonstrated variation in Cladocopium types within P. tuberculosa in southern Japan (Reimer et al. 2006), Taiwan , Singapore (Reimer and Todd 2009), and the Red Sea . More recently, with the examination of high-resolution chloroplast psbA noncoding region (psbA ncr ) sequences (LaJeunesse and Thornhill 2011), evidence of 'specialist' lineages of Cladocopium within P. tuberculosa from different marine environments has been reported , including from Okinawa in southern Japan (Noda et al. 2017). In Okinawa, variation in Cladocopium has been observed across both smaller geographical (e.g. ...
... \ 10 km) and environmental scales (e.g. depth, river mouths) than previously have been considered, and these observations have been proposed as potentially important in structuring Cladocopium and Symbiodiniaceae within P. tuberculosa (Noda et al. 2017). ...
Article
Symbiodiniaceae diversity in hosts is known to change with the environment and particularly with temperature and light intensity. However, higher levels of pCO 2 , as could be expected under future ocean acidifica-tion scenarios, have been documented to show little to no effect in influencing the diversity of Symbiodiniaceae in hosts in previous studies. In this study, we examined hypervariable psbA ncr sequences to identify the Clado-copium (former Symbiodinium 'Clade C') diversity within the zooxanthellate zoantharian Palythoa tuberculosa at an acidified reef in southern Japan. Palythoa tuberculosa were collected from a reef at the volcanic island of Iwotorishima in southern Japan; specimens from a high pCO 2 site and from a nearby control (normal pCO 2) site (Inoue et al. in Nat Clim Change 3:683-687, 2013). We observed a statistically significant reduction in Cladocopium diversity at the high pCO 2 site with only one Cladocopium lineage present, compared to at the control site with two lineages present. Our results demonstrate that higher pCO 2 can potentially negatively influence the diversity of host Symbiodiniaceae within anthozoan hosts, an important implication in the face of ongoing ocean acidification and climate change.
... Cladocopium was the dominant Symbiodiniaceae genus found in Dongsha, with only one Durusdinium-hosting P. tuberculosa colony found within the atoll. psbA ncr results showed three Cladocopium lineages previously recorded in Okinawa (lineages 1, 2 and 3 sensu Noda et al., 2017). An experiment was set up outside the atoll to compare temperature fluctuations caused by internal waves, and the host-symbiont relationships found on spurs (n = 27, depth = 5.95 ± 0.23 m) and within grooves (n = 27, depth = 8.11 ± 0.47 m). ...
... In addition, the application of hypervariable non-coding plastid minicircle region sequences of the chloroplast psbA gene (psbA ncr ) as a DNA marker has improved the resolution of delineating lineages to a finer level besides using the more conservative internal transcribed spacer region 2 (ITS2) of nuclear ribosomal DNA (Moore et al., 2003;LaJeunesse & Thornhill, 2011). Many studies have shown that psbA ncr can discern different lineages of Symbiodiniaceae, even when differences were not detected between ITS2 sequences, and in some cases, the physical distance between specimens may be as little as 200 m (Noda et al., 2017;Reimer et al., 2017a;Wee et al., 2019). Hence, ecological studies of the host-Symbiodiniaceae (henceforth known as holobiont) relationship are now possible at finer genetic and geographic scales than previously possible. ...
... Furthermore, P. tuberculosa is one of the easiest zoantharians to identify in the field (Reimer, 2010) and they host symbiotic dinoflagellate algae of the family Symbiodiniaceae (Dinophyceae: Suessiales) (Burnett, 2002;Ono et al., 2008). The high resilience and wide distribution of P. tuberculosa have encouraged many studies on Symbiodiniaceae diversity in various environments and geographical areas (Burnett, 2002;Reimer et al., 2013;Noda et al., 2017;Reimer et al., 2017a;Wee et al., 2019). Hence, they are often utilized as a model to study the physiology and ecology of this relatively understudied zoantharian group (Shiroma & Reimer, 2010;Polak et al., 2011;Ong et al., 2012;Noda et al., 2017). ...
... Studies on marine benthic communities near river systems in Okinawa in subtropical southern Japan have noted the common presence of a zoantharian, Palythoa tuberculosa (Anthozoa: Hexacorallia: Zoantharia) (West & van Woesik 2001, Yang et al. 2013, Noda et al. 2017. P. tuberculosa is a ubiquitous generalist in the Indo-Pacific Ocean, and is found from the intertidal zone down to the depth of 50 m (Reimer 1971, Hibino et al. 2014, Wee et al. 2015, Risi & Macdonald 2016, Reimer et al. 2017a. ...
... Many studies have utilized sequences of the internal transcribed spacer 2 region of ribosomal DNA (ITS2) (LaJeunesse 2001, Stat et al. 2011, Franklin et al. 2012, Smith et al. 2017, Tan et al. 2020. Additionally, more recently developed DNA marker regions can delineate Symbiodiniaceae at very high resolution, such as the non-coding region of the psbA plastid minicircle (psbA ncr ) (Moore et al. 2003, LaJeunesse & Thornhill 2011, and this marker has recently been utilized to examine the symbionts of P. tuberculosa in the Indo-Pacific (Noda et al. 2017, Reimer et al. 2017b, Wee et al. 2019. Notably, a recent study used psbA ncr sequences to examine the diversity of Symbiodiniaceae in P. tuberculosa on reefs of Okinawa Main Island (Noda et al. 2017). ...
... Additionally, more recently developed DNA marker regions can delineate Symbiodiniaceae at very high resolution, such as the non-coding region of the psbA plastid minicircle (psbA ncr ) (Moore et al. 2003, LaJeunesse & Thornhill 2011, and this marker has recently been utilized to examine the symbionts of P. tuberculosa in the Indo-Pacific (Noda et al. 2017, Reimer et al. 2017b, Wee et al. 2019. Notably, a recent study used psbA ncr sequences to examine the diversity of Symbiodiniaceae in P. tuberculosa on reefs of Okinawa Main Island (Noda et al. 2017). Noda et al. (2017) recorded 4 Symbiodiniaceae Cla do copium lineages hosted by P. tuberculosa in Oki na wa based on psbA ncr sequences. ...
Article
The diversity of symbiotic dinoflagellate Symbiodiniaceae hosted by anthozoans is known to be driven by the environment where the hosts are found. This study examined how environmental variations (<1 to 100s m) can influence the diversity of Symbiodiniaceae within the zoantharian Palythoa tuberculosa . We monitored the dominant Symbiodiniaceae lineages within tagged P. tuberculosa colonies near the Hija River mouth and adjacent coastal reefs at Mizugama, Okinawa, Japan, between July 2016 and April 2018. Seven sites were chosen based on depth and distance from the river mouth, with 5 tagged colonies at each site. Water parameters of tidal pools (TPs) at the river mouth, especially temperature, were significantly different from other sites. Surprisingly, P. tuberculosa colonies at TPs were more resilient to bleaching during summers compared to colonies at other shallow sites. We observed different Cladocopium psbA ncr lineages hosted by the tagged P. tuberculosa , with TPs colonies usually hosting one Cladocopium lineage (designated as lineage 4). Colonies from the deep sites and other shallow sites hosted mostly Cladocopium lineages 1 (generalist) and 2 (riverine specialist). Throughout the study period, the shallow colonies (included TPs) recorded higher rates of switching dominant Cladocopium lineages (mostly to lineage 1), whereas most deep colonies did not switch their dominant Cladocopium lineages. Our results show that Cladocopium lineage 1, previously reported as a generalist lineage in terms of environmental parameters, could also be an opportunist lineage during periods of host stress. Our study confirms that Cladocopium lineage flexibility likely helps the resilience of P. tuberculosa in such variable environments.
... We have previously examined Symbiodiniaceae biogeography and bleaching patterns among zoantharians (Parkinson et al., 2016;Noda et al., 2017;Reimer et al., 2017a), but to our knowledge, no studies have attempted to track zoantharian symbiont community dynamics throughout a stress event. ...
... Consistent with previous studies (Kamezaki et al., 2013;Noda et al., 2017), we confirmed that zoantharians in Okinawa can host several distinct symbiont species over small spatial scales (Figure 4). In the case of Zoanthus sansibaricus, not only were symbionts structured along a depth gradient representing distinct light and temperature regimes (Figure 2), we also detected spatial variation in symbiont distribution within individual intertidal colonies (Figure 6). ...
Article
Full-text available
Coral reefs are complex ecosystems composed of many interacting species. One ecologically important group consists of zoantharians, which are closely related to reef-building corals. Like corals, zoantharians form mutualistic symbioses with dinoflagellate micro-algae (family Symbiodiniaceae), but their associations remain underexplored. To examine the degree to which zoantharians exhibit altered symbiont dynamics under changing environmental conditions, we reciprocally transplanted colonies of Zoanthus sansibaricus between intertidal (2 m) and subtidal (26 m) depths within a reef in Okinawa, Japan. At this location, Z. sansibaricus can associate with three Symbiodiniaceae species from two genera distributed along a light and depth gradient. We developed species-specific molecular assays and sampled colonies pre‐ and post-transplantation to analyze symbiont community diversity. Despite large environmental differences across depths, we detected few symbiont compositional changes resulting from transplantation stress. Colonies sourced from the intertidal zone associated with mixtures of a “shallow” Symbiodinium sp. and a “shallow” Cladocopium sp. independent of whether they were transplanted to shallow or deep waters. Colonies sourced from the subtidal zone were dominated by a “deep” Cladocopium sp. regardless of transplant depth. Subtidal colonies brought to shallow depths did not transition to the presumably high-light adapted shallow symbionts present in the new environment, but rather bleached and died. These patterns mirror observations of highly stable coral-algal associations subjected to depth transplantation. Our results indicate that Zoanthus-Symbiodiniaceae symbioses remain stable despite stress, suggesting these important reef community members have relatively low capacity to shuffle to more stress-tolerant micro-algae in response to ongoing climate change.
... This species is common and abundant in the intertidal zone and shallow depths, across rock and coral reef crests, lagoons, and tide pools (Shiroma and Reimer 2010;Irei et al. 2011;Kumari et al. 2015;Risi and Macdonald 2016) and has also been observed on reef slopes down to more than 30 m depth (Reimer et al. 2017b). Palythoa tuberculosa is associated with Symbiodiniaceae endosymbionts of the genera Cladocopium and Durusdinium (Burnett 2002;Reimer and Todd 2009;Noda et al. 2017). Due to its extensive distribution, it is likely that this species has evolved generalist feeding modes and symbioses to survive under a wide range of environmental conditions, yet the trophic strategies of this species are unknown. ...
Article
Full-text available
Benthic cnidarians are suspension feeders that ingest items ranging from particulate organic matter to macrozooplankton. Additionally, many species receive photosynthetic products from associated endosymbiotic microalgae (Symbiodiniaceae). Although benthic cnidarians are ubiquitous to reef ecosystems, variation in their nutrition acquisition strategy across distinct environments is poorly understood. In this study, we evaluated the trophic niche and symbiotic interactions of the widespread species Palythoa tuberculosa (Hexacorallia: Zoantharia) inhabiting depths ranging from the intertidal to 35 m across three Indo-Pacific regions, using carbon and nitrogen stable isotope ratios and isotopic niche metrics. Our results revealed that populations in shallow (0-8 m) and deep zones (down to 35 m) had distinct niche placements and overlap with the endosymbionts’ niches across all regions. Associated Symbiodiniaceae were identified as Cladocopium. Contradicting the paradigm of a more productive endosymbiosis in shallower waters, P. tuberculosa had less isotopic niche overlap with its endosymbionts in shallow reefs (0–9%) but a higher niche overlap in deep waters (up to 70%). Among regions, this was most evident in Dongsha Atoll, South China Sea, which has comparatively high influence of internal waves and, thus, high concentrations of plankton. The low niche overlap with endosymbionts in shallow waters indicated that P. tuberculosa may have a high heterotrophic performance, which partially explains the species’ resilience during bleaching events. Regarding the distinct niche placements across depths, lower δ13C in the shallower zone could be due to light-driven effects on fixation by the endosymbionts. Additional non-exclusive explanations include that water flow regimes and nocturnal feeding behavior could enable P. tuberculosa populations to ingest more/distinct prey items, with lower δ13C, in the shallow compared to the deep zone. The nutritional plasticity of P. tuberculosa likely contributes to its widespread distribution and provides an advantage under a warming climate that will affect cnidarian-endosymbiont relationships.
... The purity of DNA was checked with a NanoDrop 1000 (Thermo Thermo Scientific, United States). For the Symbiodiniaceae identification, the internal transcribed spacer ITS2 was amplified using zITSf (5 -CCGGTGAATTATTCGGACTGACGCAGT-3 ) and ITS4 (5 -TCCTCCGCTTATTGATATGC-3 ) as described in Noda et al. (2017). A PCR amplification of 35 cycles was performed (95 • C for 30 s, 51 • C for 45 s, and 72 • C for 2 min). ...
Article
Full-text available
Scrutinizing the traits of octocorals that could affect their physiological performance becomes increasingly important as several of these species are observed to become dominant on reefs pressured by the Anthropocene. In the present study, we compare the organismal traits of two branching octocorals Litophyton sp. and Stereonephthya sp. commonly populating in sympatry the high-latitude coral communities of northern Taiwan. Using 13 traits, we describe and compare performance traits in these two symbiotic species that we discuss in light of the association they maintain with their algal partners. Litophyton sp. and Stereonephthya sp. hosted Durusdinium and Gerakladium, respectively. Both genera represent singular associations, with the latter further establishing the first solid report of Gerakladium in octocorals. Traits distinguished two groups explained by the two partnerships considered. Litophyton sp. associated with Durusdinium had significantly higher organic matter, chlorophyll (chl) a, total lipid and lower chl c/chl a ratio than Stereonephthya sp. associated with Gerakladium. The d15N in the host and algae, as well as d13C in the host were also higher in Litophyton species. Although no significant difference was observed in the d13C of the algae, Litophyton sp. presented a significantly higher variance for this trait and for chl a content than Stereonephthya species. Altogether, the traits examined suggested contrasting performances among the two octocorals. Both octocoral species clearly deviate from an autotrophic diet. Litophyton sp. appears to complement its heterotrophic diet with photosynthetically acquired energy, while Stereonephthya sp. tends to be more specialized and benefits relatively little from its symbiotic relationship. Our study calls for greater consideration of the individual variation in octocoral physiology and in the definition of their ecological strategies.
... Considering ecological, geographic, reproductive, and genetic patterns, Cladocopium may consist of hundreds of species (Thornhill et al., 2014). If so, there are likely distinct Cladocopium species present within toxic species of Palythoa, the identification of which may only be demonstrated with higher phylogenetic resolution markers (LaJeunesse & Thornhill, 2011;Noda et al., 2017;Reimer et al., 2017b). To further describe the relationships between the Cladocopium strains and toxicity variability of their Palythoa hosts, it will be necessary to carry out studies based on alternative markers such as, for example, the plastid mini-circle non-coding region (Mizuyama et al., 2020;Moore et al., 2003;Reimer et al., 2017b;Takishita et al., 2003). ...
Article
Anemone-like animals belonging to the order Zoantharia are common anthozoans widely distributed from shallow to deep tropical and subtropical waters. Some species are well-known because of their high toxicity due to the presence of palytoxin (PLTX) in their tissues. PLTX is a large polyhydroxylated compound and one of the most potent toxins known. Currently, the PLTX biosynthetic pathway in zoantharians and the role of the host or the putative symbiotic organism(s) involved in this pathway are entirely unknown. To better understand the presence of PLTX in some Zoantharia, twenty-nine zoantharian colonies were analysed in this study. All zoantharian samples and their endosymbiotic dinoflagellates (Symbiodiniaceae = Zooxanthellae) were identified using DNA barcoding and phylogenetic reconstructions. Quantification of PLTX and its analogues showed that the yields contained in Palythoa heliodiscus, Palythoa aff. clavata and one potentially undescribed species of Palythoa are among the highest ever found (up to > 2 mg/g of wet zoantharian). Mass spectrometry imaging was used for the first time on Palythoa samples and revealed that in situ distribution of PLTX is mainly located in ectodermal tissues such as the epidermis of the body wall and the pharynx. Moreover, high levels of PLTX have been detected in histological regions where few or no Symbiodiniaceae cells could be observed. Finally, issues such as host‐specificity and environmental variables driving biogeographical patterns of hosted Symbiodiniaceae in zoantharian lineages were discussed in light of our phylogenetic results as well as the patterns of PLTX distribution. It was concluded that (1) the variability of Symbiodiniaceae diversity may be related to ecological divergence in Zoantharia, (2) all Palythoa species hosted Cladocopium Symbiodiniaceae (formerly clade C), (3) the sole presence of Cladocopium is not sufficient to explain the presence of high concentrations of PLTX and/or its analogues, and (4) the ability to produce high levels of PLTX and/or its analogues highlighted in some Palythoa species could be a plesiomorphic character inherited from their last common ancestor and subsequently lost in several lineages.
... The cause of the apparent site specificity of this profile is unclear as Sisters' Island is not located at the geographic extremes of our sampling regime and because all sites are within 16 km of each other. Fine-scale differences in Cladocopium genotypes over short distances (tens of kilometres) have been observed in other marginal environments and were linked to local environmental conditions (Noda et al. 2017;Hume et al. 2018a). Deployment of in situ loggers to assess key environmental parameters (temperature, light, salinity) will help elucidate microhabitat differences and the potential environmental drivers for fine-scale differences observed in this study. ...
Article
Full-text available
The coastal waters of Singapore support coral reefs that are biodiverse but characterized by high turbidity and sedimentation. Here, we used internal transcribed spacer two (ITS2) amplicon sequencing to investigate the Symbiodiniaceae communities associated with this marginal reef system, as turbid reefs may serve as potential refugia from future thermal stress. Using the analytical framework SymPortal, we identified a predominance of Cladocopium among the five coral species studied across six reef sites. Durusdinium was present in comparatively lower abundances and was composed of multiple Durus-dinium trenchii strains. In contrast to other marginal environments, the Cladocopium communities exhibited low diversity and lacked the host-specificity of strains reported elsewhere. Nevertheless, we identified a site-specific strain across three species, which was supported by sequencing of the non-coding region of the psbA minicircle (psbA ncr). The overall low diversity of the symbiont communities suggests that, although Singapore's reefs may provide habitat for a diverse coral assemblage, the strong selective pressure exerted by the prevalent turbidity likely limits the diversity of the associated symbiont community.
... The total number of sequences of Symbiodiniaceae from specimens of the four Palythoa species obtained in this study was 98 sequences for the ITS-rDNA region (513-773 bp), 40 sequences for the psbA ncr forward region (330-547 bp), and 41 sequences for the psbA ncr reverse region (352-494 bp). As the primer set for psbA ncr used in this study did not make a congruent contig, obtained sequences of forward regions and reverse regions were aligned separately (Noda et al., 2017). After alignment, a total of 449 sites with 5 parsimony informative (=PI) sites for the ITS-rDNA region, 260 sites with 94 PI sites for the psbA ncr forward region, and 293 sites with 40 PI sites for the psbA ncr reverse region were used for each phylogenetic estimation. ...
Article
In this study we compared genotypes of zoantharian host-associating algal symbionts among Palythoa species, which are among the dominant benthic reef organisms in the Ryukyu Archipelago, Japan, and evaluated Symbiodiniaceae diversities of closely related congeneric Palythoa species. We targeted a species complex of the zoantharian genus Palythoa ( P. tuberculosa , P. sp. yoron, P. mutuki ) living among different microhabitats in a narrow reef area of Tokunoshima Island. For phylogenetic analyses, we used two DNA marker regions; nuclear internal transcribed spacer (ITS) and plastid mini-circle non-coding region (psbA ncr ), both of which have previously been used to determine Symbiodiniaceae genotypes of zoantharian species. Our results showed that all Palythoa species hosted symbionts of the genus Cladocopium , with genotypic compositions of this genus showing some variations among the three different Palythoa species. Additionally, we found that the Cladocopium genotypic composition was statistically different among Palythoa species, and among P. tuberculosa specimens in different microhabitats. Our results suggest that ecological divergence among these three Palythoa species may be related to differing Symbiodiniaceae diversities that may in turn contribute to eco-physiological adaptation into different microhabitats on coral reefs.
... Environmental factors known to greatly influence the biogeography of marine bacteria include both temperature and salinity (Martiny et al., 2006). Fine scale differences in these and other variables between sites around Okinawa Island have previously been suggested to influence the distribution of different lineages of the algal symbiont of the zoantharian Palythoa tuberculosa (Noda et al., 2017) and could also influence the distribution of P. mandapamensis in the environment in this study. However, host organisms can also play a major role in the dispersal and geographic distribution of microbes in the marine environment (Troussellier et al., 2017). ...
Article
Full-text available
All organisms depend on symbiotic associations with bacteria for their success, yet how these interspecific interactions influence the population structure, ecology, and evolution of microbial symbionts is not well understood. Additionally, patterns of genetic variation in interacting species can reveal ecological traits that are important to gene flow and co-evolution. In this study, we define patterns of spatial and temporal genetic variation of a coral reef fish, Siphamia tubifer, and its luminous bacterial symbiont, Photobacterium mandapamensis in the Okinawa Islands, Japan. Using restriction site-associated sequencing (RAD-Seq) methods, we show that populations of the facultative light organ symbiont of S. tubifer exhibit genetic structure at fine spatial scales of tens of kilometers despite the absence of physical barriers to dispersal and in contrast to populations of the host fish. These results suggest that the host’s behavioral ecology and environmental interactions between host and symbiont help to structure symbiont populations in the region, consequently fostering the specificity of the association between host generations. Our approach also revealed several symbiont genes that were divergent between host populations, including hfq and a homolog of varS, both of which play a role in host association in Vibrio cholerae. Overall, this study highlights the important role that a host animal can play in structuring the distribution of its bacterial symbiont, particularly in highly connected marine environments, thereby promoting specificity of the symbiosis between host generations.
... In the joint species distribution model, where location had been dropped as a predictor due to co-variation with annual mean SST, mean SST explained the distribution of individual Symbiodiniaceae taxa well (Table 3), confirming the importance of temperature shown in numerous biogeographic field studies (e.g. Noda et al. 2017) and laboratory experiments (Rowan 2004, Sampayo et al. 2008, including in our study taxon (Chen et al. 2005. Unexpectedly, temperature was not significant in the GDM analysis of community composition (Table 2), even when tested for any other temperature metric (min. ...
Article
Full-text available
Coral-algae symbiosis represents the trophic and structural basis of coral reef ecosystems. However, despite global threats to coral reefs and the dependence of coral health and stress resistance upon such mutualisms, little is known about the community ecology of endosymbiotic Symbiodiniaceae. Concepts and methods from metacommunity ecology may be used to help us understand the assembly and stability of symbiont communities and the mutualisms they comprise. In this study, we sampled colonies of the symbiont-generalist coral Galaxea fascicularis in southwestern Japan and assessed the effects of environmental and host factors on Symbiodiniaceae community composition, while simultaneously exploring residual correlations among symbiont types that may reflect non-random assembly processes such as species interactions. We metabarcoded the Symbiodiniaceae ribosomal internal transcribed spacer 2 (ITS2) region and characterized the endosymbiotic community using 2 different OTU identity cut-offs, and analyzed them with generalized dissimilarity modeling and joint species distribution modeling. We found that Symbiodiniaceae form discrete communities characterized by the dominance of ITS2 types C1, C21a, or D1, that are each associated with a different suite of co-occurring background types and tend to exclude each other in an endosymbiotic community. The communities showed modest responses to temperature, water depth, host genotype, polyp size, and bleaching status, and there was local sequence variation within the ITS2 types. After accounting for the effects of those variables, residual correlations remained in community composition, pointing to the possibility that Symbiodiniaceae community assembly in corals may be structured by interspecific competitive or facilitating interactions rather than only exogenous variables.
... Both Zoanthus and Palythoa spp. have been reported to be quite flexible in their associations with different Symbiodiniaceae types (Burnett 2002, Reimer et al. 2006, Noda et al. 2017, have adaptable photobiology (Leal et al. 2016, and are plastic mixotrophs , 2018, Santos et al. 2021). In addition, while data are sparse, it appears Zoanthus and Palythoa spp. ...
... It is expected that host species at shallower depths exhibit a marked shift in symbiont type due to higher light intensities and radiation that could exclude some symbiont types (LaJeunesse 2002;Finney et al. 2010). However, our results are based on ITS sequences, and there it is likely that there are different species present within these specimens, based on results from higher resolution markers (LaJeunesse and Thornhill 2011) in Palythoa in the Pacific Ocean (Noda et al. 2017) and the Red Sea (Reimer et al. 2017b). ...
Article
Zooxanthellate zoantharians (Cnidaria: Anthozoa) are commonly found in tropical and subtropical marine regions around the world. However, due to the low genetic variability of commonly used DNA markers combined with high levels of intraspecific morphological variation, misidentifications and species synonyms are commonly found in the literature. In this study, zoantharians from the suborder Brachycnemina collected in the Macaronesia and Cape Verde ecoregions were studied combining morphological, molecular and ecological data, in order to comprehensively assess the species diversity of the region. Moreover, molecular analyses of endosymbiotic Symbiodiniaceae zooxanthellae were also performed to provide more information on each holobiont. Our integrative results demonstrate that Brachycnemina species diversity increases as seawater temperature rises toward the tropics with a total of nine species recorded: one from waters around northern Madeira, five in the Canary Islands and seven in the southernmost Cape Verde Archipelago. All species were seen to host either Symbiodiniaceae of the genera Symbiodinium (former Symbiodinium ‘Clade A’) or Cladocopium (former Symbiodinium ‘Clade C’). Moreover, this study records for the first time the presence of Palythoa grandis, P. aff. clavata, P. grandiflora, an unknown Zoanthus species and Z. pulchellus in the East Atlantic Ocean. These results show no endemic zooxanthellate zoantharians in the East Atlantic, with all species shared with the West Atlantic.
... Baird et al. 2007;Oliver and Palumbi 2011), indicating that coral-symbiont relationships need to be understood at a local level. Indeed, many coral communities host symbiont consortia distinct to that particular region (Fabina et al. 2012;Stat et al. 2015); this can be due to factors such as specialised symbiont types requiring certain conditions Noda et al. 2017). As such, simple richness studies from different regions are continually finding novel relationships (e.g. ...
Article
To persist in oligotrophic waters, reef-building corals rely on nutritional interactions with symbiotic dinoflagellates of the family Symbiodiniaceae, but the true diversity of this family remains poorly characterised. In this paper, we assess Symbiodiniaceae richness at Atauro Island (Timor-Leste) as well as on reefs of the neighbouring Timor mainland, using direct sequencing of three gene regions: cob gene, mitochondrion; ITS2 region, nucleus; and psbAncr region, chloroplast; in addition to a highly multiplexed application of next-generation sequencing. These geographic sites are among the most biodiverse in the world, but have never had their symbiont communities studied. Despite their proximity, our results reveal symbiont richness 1.25 times higher at Atauro Island than the Timor mainland, a result evident in dominant sequences. In contrast, Timor had a significantly richer background sequence diversity. Although sampling was restricted to shallow sites only, symbiont richness at Atauro Island was also higher than comparative reefscapes globally, after standardising for number of taxa sampled. While Atauro and Timor have related symbiont populations, with the same novel types recorded at both sites, there were also clear differences in symbiont composition between the two geographic regions, with Timor displaying a consortium more characteristic of stressed reef environments (proportionally hosting twice as many Durusdinium sequences, formerly clade D, as Atauro). These results reveal a symbiont richness that matches the high biodiversity of these reefs, but also potentially negative effects of proximal human populations on Symbiodiniaceae, even when previous studies have shown corals to be largely unaffected.
... The insignificance of temperature, both WOA-SST and in situ was unexpected, since temperature has long been established as one of the most influential factors for the distribution of Symbiodiniaceae taxa (Baker, 2003). This was found in numerous biogeographic field studies on the clade level regarding clade C versus clade D, as well as on the subclade level (Noda et al., 2017) and in numerous laboratory experiments (Rowan, 2004;Sampayo et al., 2008), and including in our study taxon (Chen et al., 2005;Tong et al., 2017;Zhou et al., 2017). In contrast, we found clade D-dominated communities at almost every site, and therefore seemingly unlinked to mean temperatures of the sampling site. ...
Thesis
Full-text available
The evolution and systematics of corals have been difficult to unravel despite being the fundament of one of the world's most charismatic ecosystems. Coral diversity and diversification processes are not well understood due to morphological plasticity, potential hybridization and generally high rates of dispersal. Both geographically and methodologically extensive studies are needed to improve our understanding of coral ecology and evolution, including spatial biodiversity processes involving hosts and their associated symbionts. This dissertation investigates coral evolution in three complementary studies using the genus Galaxea L. as a model. First, I ask whether endosymbiotic community composition differentiate among morphologically cryptic genetic lineages in G. fascicularis. The Symbiodinium ITS2-sequence was metabarcoded using next generation sequencing (NGS) and community assembly was analyzed with joint distribution models. Symbiodinium communities were found to cluster into three regular community types that cannot be explained by environment or host genotype, potentially indicating species interactions between Symbiodinium types. Second, I assessed how spatial connectivity between geographic populations corresponds to neutral differentiation on the subspecies level using population genomic methods. Coral populations from the Ryukyu archipelago, the Daito islands, and the Ogasawara Islands were characterized by restriction site-associated DNA sequencing (RAD) to investigate whether the Daito Islands could be a stepping stone between Ryukyu and Ogasawara. The Ogasawara population was found to be highly differentiated and to have diverged under little amounts of continuous gene flow since the early Pliocene. No stepping stone role of the Daito Islands was found and the Ogasawara population may receive most migrants from the Ryukyu Islands, which was consistent with the dispersal patterns predicted by a oceanographic dispersal model. Lastly, I investigated the evolutionary history in the genus Galaxea taking a phylogeographic approach. I asked whether the genetically well-differentiated and sympatric lineages within G. fascicularis in Okinawa maintain their separation over geographic space and to what extent their spatial distributions overlap in the genus distribution range. Galaxea field collections were gathered from across the Indo-Pacific, and complemented by museum specimens to increase geographical coverage. At the same time the relationship between genetic lineages and taxonomic species was evaluated based on five out of seven currently accepted species (G. fascicularis, G. astreata, G. cryptoramosa, G. paucisepta, G. horrescens). The genus Galaxea clustered into three highly divergent clades; one Indo-Pacific, one Pacific, and one basal small clade found in Chagos. All morphological species were part of the Pacific clade. Overall this study indicates spatial rather than ecological or symbiosis-related processes to drive diversification and that the current taxonomy does not reflect biological species in this genus.
... However, because the psbA ncr region cannot be amplified across Symbiodiniaceae using a single set of primers, this marker is suboptimal for some types of community-level analyses, such as assessing total community diversity or beta diversity metrics. Nevertheless, it would be appropriate to pair psbA ncr with other markers; i.e., to resolve additional diversity within established ITS2 lineages (Noda et al., 2017;Reimer et al., 2017); and also to use this marker to verify ITS2 sequence variants generated via amplicon sequencing Smith et al., 2020). ...
Preprint
Full-text available
Within microeukaryotes, genetic and functional variation sometimes accumulate more quickly than morphological differences. To understand the evolutionary history and ecology of such lineages, it is key to examine diversity at multiple levels of organization. In the dinoflagellate family Symbiodiniaceae, which can form endosymbioses with cnidarians (e.g., corals, octocorals, sea anemones, jellies), other marine invertebrates (e.g., sponges, molluscs, flatworms), and protists (e.g., foraminifera), molecular data have been used extensively over the past three decades to describe phenotypes and to make evolutionary and ecological inferences. Despite advances in Symbiodiniaceae genomics, a lack of consensus among researchers with respect to interpreting genetic data has slowed progress in the field and acted as a barrier to reconciling observations. Here, we identify key challenges regarding the assessment and interpretation of Symbiodiniaceae genetic diversity across three levels: species, populations, and communities. We summarize areas of agreement and highlight techniques and approaches that are broadly accepted. In areas where debate remains, we identify unresolved issues and discuss technologies and approaches that can help to fill knowledge gaps related to genetic and phenotypic diversity. We also discuss ways to stimulate progress, in particular by fostering a more inclusive and collaborative research community. We hope that this perspective will inspire and accelerate coral reef science by serving as a resource to those designing experiments, publishing research, and applying for funding related to Symbiodiniaceae and their symbiotic partnerships.
Article
Full-text available
Zooxanthellate corals are threatened by climate change but may be able to escape increasing temperatures by colonizing higher latitudes. To determine the effect of host range expansion on symbiont genetic diversity, we examined genetic variation among populations of Symbiodinium psygmophilum associated with Oculina patagonica, a range-expanding coral that acquires its symbionts through horizontal transmission. We optimized five microsatellite primer pairs for S. psygmophilum and tested them on Oculina spp. samples from the western North Atlantic and the Mediterranean. We then used them to compare symbiont genotype diversity between an Iberian core and an expansion front population of O. patagonica. Only one multilocus S. psygmophilum genotype was identified at the expansion front, and it was shared with the core population, which harbored seven multilocus genotypes. This pattern suggests that O. patagonica range expansion is accompanied by reduced symbiont genetic diversity, possibly due to limited dis
Article
Full-text available
Understanding genetic connectivity is fundamental for ecosystem-based management of marine resources. Here we investigate the metapopulation structure of the edible sea cucumber Holothuria edulis Lesson, 1830 across Okinawa Island, Japan. This species is of economic and ecological importance and is distributed from the Red Sea to Hawai‘i. We examined sequence variation in fragments of mitochondrial cytochrome oxidase subunit I (COI) and 16S ribosomal RNA (16S), and nuclear histone (H3) at six locations across Okinawa Island. We found higher haplotype diversity for mtDNA (COI: Hd = 0.69 and 16S: Hd = 0.67) and higher heterozygosity of nDNA (H3: H E = 0.39) in populations from the west coast of Okinawa compared to individuals from populations on the east coast (COI: Hd = 0.40; 16S: Hd = 0.21; H3: H E = 0.14). Overall population structure was significant (AMOVA results for COI: Φ ST = 0.49, P < 0.0001; 16S: Φ ST = 0.34, P < 0.0001; H3: Φ ST = 0.12, P < 0.0001). One population in the east, Uruma, showed elevated pairwise Φ ST values in comparisons with all other sites and a marked reduction of genetic diversity (COI: Hd = 0.25 and 16S: Hd = 0.24), possibly as a consequence of a shift to a more dominant asexual reproduction mode. Recent reports have indicated that coastal development in this area influences many marine organisms, and ecosystem degradation in this location could cause the observed decrease of genetic diversity and isolation of H. edulis in Uruma. Our study should provide valuable data to help with the urgently needed management of sea cucumber populations in Okinawa, and indicates particular attention needs to be paid to vulnerable locations.
Article
Full-text available
Following a global coral bleaching event in 1998, Acropora corals surrounding most of Okinawa island (OI) were devastated, although they are now gradually recovering. In contrast, the Kerama Islands (KIs) only 30 km west of OI, have continuously hosted a great variety of healthy corals. Taking advantage of the decoded Acropora digitifera genome and using genome-wide SNP analyses, we clarified Acropora population structure in the southern Ryukyu Archipelago (sRA). Despite small genetic distances, we identified distinct clusters corresponding to specific island groups, suggesting infrequent long-distance dispersal within the sRA. Although the KIs were believed to supply coral larvae to OI, admixture analyses showed that such dispersal is much more limited than previously realized, indicating independent recovery of OI coral populations and the necessity of local conservation efforts for each region. We detected strong historical migration from the Yaeyama Islands (YIs) to OI, and suggest that the YIs are the original source of OI corals. In addition, migration edges to the KIs suggest that they are a historical sink population in the sRA, resulting in high diversity. This population genomics study provides the highest resolution data to date regarding coral population structure and history.
Article
Full-text available
Coral reefs are biodiverse ecosystems structured by abiotic and biotic factors operating across many spatial scales. Regional-scale interactions between climate change, biogeography and fisheries management remain poorly understood. Here, we evaluated large-scale patterns of coral communities in the western Indian Ocean after a major coral bleaching event in 1998. We surveyed 291 coral reef sites in 11 countries and over 30° of latitude between 2004 and 2011 to evaluate variations in coral communities post 1998 across gradients in latitude, mainland-island geography and fisheries management. We used linear mixed-effect hierarchical models to assess total coral cover, the abundance of four major coral families (acroporids, faviids, pocilloporids and poritiids), coral genus richness and diversity, and the bleaching susceptibility of the coral communities. We found strong latitudinal and geographic gradients in coral community structure and composition that supports the presence of a high coral cover and diversity area that harbours temperature-sensitive taxa in the northern Mozambique Channel between Tanzania, northern Mozambique and northern Madagascar. Coral communities in the more northern latitudes of Kenya, Seychelles and the Maldives were generally composed of fewer bleaching-tolerant coral taxa and with reduced richness and diversity. There was also evidence for continued declines in the abundance of temperature-sensitive taxa and community change after 2004. While there are limitations of our regional dataset in terms of spatial and temporal replication, these patterns suggest that large-scale interactions between biogeographic factors and strong temperature anomalies influence coral communities while smaller-scale factors, such as the effect of fisheries closures, were weak. The northern Mozambique Channel, while not immune to temperature disturbances, shows continued signs of resistance to climate disturbances and remains a priority for future regional conservation and management actions.
Article
Full-text available
We announce the release of an advanced version of the Molecular Evolutionary Genetics Analysis (MEGA) software, which currently contains facilities for building sequence alignments, inferring phylogenetic histories, and conducting molecular evolutionary analysis. In version 6.0, MEGA now enables the inference of timetrees, as it implements our RelTime method for estimating divergence times for all branching points in a phylogeny. A new Timetree Wizard in MEGA6 facilitates this timetree inference by providing a graphical user interface (GUI) to specify the phylogeny and calibration constraints step-by-step. This version also contains enhanced algorithms to search for the optimal trees under evolutionary criteria and implements a more advanced memory management that can double the size of sequence data sets to which MEGA can be applied. Both GUI and command-line versions of MEGA6 can be downloaded from www.megasoftware.net free of charge.
Article
Full-text available
The genus Symbiodinium comprises mostly symbiotic dinoflagellates that form a mutual association with a wide variety of marine protists and invertebrates. It is widely believed that the taxa included in it are genetically diverse. In the present study, the messenger RNA of psbA (which encodes the D I protein of photosystem 11) was located within the Symbiodinium plastids by using in situ hybridization at the electron microscopic level, directly indicating that the psbA gene from this genus is plastid encoded. The psbA gene sequences of Symbiodinium strains, which had already been shown to belong to various clades based on the phylogeny of nuclear-encoded small-subunit ribosomal DNA (SSU rDNA), were determined by reverse transcription-polymerase chain reaction (RT-PCR), cloning and sequencing. Based on their sequence data, phylogenetic analyses were then performed. The topologies of the nuclear SSU rDNA and psbA trees were similar, suggesting that these two genes from different organelles (nucleus and plastid) had evolved in parallel in the genus Symbiodinium and that psbA would be useful for inferring the phylogenetic relationship within the genus. In Symbiodinium, the psbA gene evolves 1.2-18.2 times faster than nuclear SSU rDNA.
Article
Full-text available
Giovanni, the Goddard Earth Sciences Data and Information Services Center (GES DISC) Interactive Online Visualization and Analysis Infrastructure, has provided researchers with advanced capabilities to perform data exploration and analysis with observational data from NASA Earth observation satellites. In the past 5-10 years, examining geophysical events and processes with remote-sensing data required a multistep process of data discovery, data acquisition, data management, and ultimately data analysis. Giovanni accelerates this process by enabling basic visualization and analysis directly on the World Wide Web. In the last two years, Giovanni has added new data acquisition functions and expanded analysis options to increase its usefulness to the Earth science research community.
Article
Full-text available
In Japan, zooxanthellate Palythoa tuberculosa Klunzinger and Palythoa mutuki Verrill (Anthozoa: Hexacorallia: Zoantharia) are found over a 1,000+km latitudinal range, often in environments where most other zooxanthellate anthozoans are not found (i.e. tidal lagoon pools, around shallow water hydrothermal vents, subtropical rocky shorelines). Sequences of internal transcribed spacer of ribosomal DNA (ITS-rDNA) of the symbiotic dinoflagellate genus Symbiodinium (zooxanthellae) Freudenthal (Order Suessiales) from P. tuberculosa and P. mutuki from several locations in Japan (34°11′N–24°16′N) were analysed. Unexpectedly, despite the ability of the genus Palythoa to be flexible in association with different Symbiodinium subclades, most (35 of 36) Palythoa investigated here specifically associate with subclade C1 and closely related types. Symbiodinium subclade C1 has been characterized as a “generalist” in terms of the ability to associate with a range of hosts, but present results suggest that subclade C1 may also be a “generalist” in terms of being able to live in a variety of environments over a latitudinal range.
Article
Full-text available
A protocol that takes advantage of length heteroplasmy in domain V of chloroplast large subunit (cp23S)–ribosomal DNA to identify members of the symbiotic dinoflagellate genus Symbiodinium is presented. This protocol is highly specific for Symbiodinium, can provide intercladal and intracladal identification of a particular Symbiodinium isolate, and can detect multiple Symbiodinium chloroplast genotypes simultaneously in the same isolate, making his technique attractive for a variety of research questions. We used this technique to characterize variation among Symbiodinium populations associated with a range of phylogenetically diverse and geographically discrete hosts. We also examined symbiont variation within a single host, the Caribbean gorgonian Pseudopterogorgia elisabethae, from 9 sites in the Bahamas, and we report a previously undocumented level of symbiont specificity for particular members of Symbiodinium clade B in this gorgonian.
Article
Full-text available
The role of symbiont variation in the photobiology of reef corals was addressed by investigating the links among symbiont genetic diversity, function and ecological distribution in a single host species, Madracis pharensis. Symbiont distribution was studied for two depths (10 and 25m), two different light habitats (exposed and shaded) and three host colour morphs (brown, purple and green). Two Symbiodinium genotypes were present, as defined by nuclear internal transcribed spacer 2 ribosomal DNA (ITS2-rDNA) variation. Symbiont distribution was depth- and colour morph-dependent. Type B15 occurred predominantly on the deeper reef and in green and purple colonies, while type B7 was present in shallow environments and brown colonies. Different light microhabitats at fixed depths had no effect on symbiont presence. This ecological distribution suggests that symbiont presence is potentially driven by light spectral niches. A reciprocal depth transplantation experiment indicated steady symbiont populations under environment change. Functional parameters such as pigment composition, chlorophyll a fluorescence and cell densities were measured for 25m and included in multivariate analyses. Most functional variation was explained by two photobiological assemblages that relate to either symbiont identity or light microhabitat, suggesting adaptation and acclimation, respectively. Type B15 occurs with lower cell densities and larger sizes, higher cellular pigment concentrations and higher peridinin to chlorophyll a ratio than type B7. Type B7 relates to a larger xanthophyll-pool size. These unambiguous differences between symbionts can explain their distributional patterns, with type B15 being potentially more adapted to darker or deeper environments than B7. Symbiont cell size may play a central role in the adaptation of coral holobionts to the deeper reef. The existence of functional differences between B-types shows that the clade classification does not necessarily correspond to functional identity. This study supports the use of ITS2 as an ecological and functionally meaningful marker in Symbiodinium.
Article
Full-text available
A new statistical method for estimating divergence dates of species from DNA sequence data by a molecular clock approach is developed. This method takes into account effectively the information contained in a set of DNA sequence data. The molecular clock of mitochondrial DNA (mtDNA) was calibrated by setting the date of divergence between primates and ungulates at the Cretaceous-Tertiary boundary (65 million years ago), when the extinction of dinosaurs occurred. A generalized leastsquares method was applied in fitting a model to mtDNA sequence data, and the clock gave dates of 92.311.7, 13.31.5, 10.91.2, 3.70.6, and 2.70.6 million years ago (where the second of each pair of numbers is the standard deviation) for the separation of mouse, gibbon, orangutan, gorilla, and chimpanzee, respectively, from the line leading to humans. Although there is some uncertainty in the clock, this dating may pose a problem for the widely believed hypothesis that the bipedal creatureAustralopithecus afarensis, which lived some 3.7 million years ago at Laetoli in Tanzania and at Hadar in Ethiopia, was ancestral to man and evolved after the human-ape splitting. Another likelier possibility is that mtDNA was transferred through hybridization between a proto-human and a protochimpanzee after the former had developed bipedalism.
Article
Full-text available
Numerous marine invertebrates form endosymbiotic relationships with dinoflagellates in the genus Symbiodinium. However, few studies have examined the fine-scale population structure of these symbionts. Here, we describe the genetic structure of Symbiodinium type “B1/B184” inhabiting the gorgonian Gorgonia ventalina along the Florida Keys. Six polymorphic microsatellite loci were utilized to examine 16 populations along the Upper, Middle, and Lower Keys spanning a range of ~200km. Multiple statistical tests detected significant differentiation in 54–92% of the 120 possible pairwise comparisons between localities, suggesting low levels of gene flow in these dinoflagellates. In general, populations clustered by geographic region and/or reefs in close proximity. Some of the sharpest population differentiation was detected between Symbiodinium from deep and shallow sites on the same reef. In spite of the high degree of population structure, alleles and genotypes were shared among localities, indicating some connectivity between Symbiodinium populations associated with G. ventalina.
Article
Full-text available
The program MRBAYES performs Bayesian inference of phylogeny using a variant of Markov chain Monte Carlo. Availability: MRBAYES, including the source code, documentation, sample data files, and an executable, is available at http://brahms.biology.rochester.edu/software.html. Contact: johnh{at}brahms.biology.rochester.edu
Article
Full-text available
Ribosomal DNA sequence data abounds from numerous studies on the dinoflagellate endosymbionts of corals, and yet the multi-copy nature and intragenomic variability of rRNA genes and spacers confound interpretations of symbiont diversity and ecology. Making consistent sense of extensive sequence variation in a meaningful ecological and evolutionary context would benefit from the application of additional genetic markers. Sequences of the non-coding region of the plastid psbA minicircle (psbA(ncr)) were used to independently examine symbiont genotypic and species diversity found within and between colonies of Hawaiian reef corals in the genus Montipora. A single psbA(ncr) haplotype was recovered in most samples through direct sequencing (~80-90%) and members of the same internal transcribed spacer region 2 (ITS2) type were phylogenetically differentiated from other ITS2 types by substantial psbA(ncr) sequence divergence. The repeated sequencing of bacterially-cloned fragments of psbA(ncr) from samples and clonal cultures often recovered a single numerically common haplotype accompanied by rare, highly-similar, sequence variants. When sequence artifacts of cloning and intragenomic variation are factored out, these data indicate that most colonies harbored one dominant Symbiodinium genotype. The cloning and sequencing of ITS2 DNA amplified from these same samples recovered numerically abundant variants (that are diagnostic of distinct Symbiodinium lineages), but also generated a large amount of sequences comprising PCR/cloning artifacts combined with ancestral and/or rare variants that, if incorporated into phylogenetic reconstructions, confound how small sequence differences are interpreted. Finally, psbA(ncr) sequence data from a broad sampling of Symbiodinium diversity obtained from various corals throughout the Indo-Pacific were concordant with ITS lineage membership (defined by denaturing gradient gel electrophoresis screening), yet exhibited substantially greater sequence divergence and revealed strong phylogeographic structure corresponding to major biogeographic provinces. The detailed genetic resolution provided by psbA(ncr) data brings further clarity to the ecology, evolution, and systematics of symbiotic dinoflagellates.
Article
Full-text available
Coral bleaching has been identified as one of the major contributors to coral reef decline, and the occurrence of different symbionts determined by broad genetic groupings (clades A–H) is commonly used to explain thermal responses of reef-building corals. By using Stylophora pistillata as a model, we monitored individual tagged colonies in situ over a two-year period and show that fine level genetic variability within clade C is correlated to differences in bleaching susceptibility. Based on denaturing gradient gel electrophoresis of the internal transcribed spacer region 2, visual bleaching assessments, symbiont densities, host protein, and pulse amplitude modulated fluorometry, we show that subcladal types C78 and C8/a are more thermally tolerant than C79 and C35/a, which suffered significant bleaching and postbleaching mortality. Although additional symbiont types were detected during bleaching in colonies harboring types C79 and C35/a, all colonies reverted back to their original symbionts postbleaching. Most importantly, the data propose that the differential mortality of hosts harboring thermally sensitive versus resistant symbionts rather than symbiont shuffling/switching within a single host is responsible for the observed symbiont composition changes of coral communities after bleaching. This study therefore highlights that the use of broad cladal designations may not be suitable to describe differences in bleaching susceptibility, and that differential mortality results in a loss of both symbiont and host genetic diversity and therefore represents an important mechanism in explaining how coral reef communities may respond to changing conditions. • climate change • coral reefs • Symbiodinium • zooxanthellae • Stylophora
Article
Full-text available
PhyML is a phylogeny software based on the maximum-likelihood principle. Early PhyML versions used a fast algorithm performing nearest neighbor interchanges to improve a reasonable starting tree topology. Since the original publication (Guindon S., Gascuel O. 2003. A simple, fast and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst. Biol. 52:696-704), PhyML has been widely used (>2500 citations in ISI Web of Science) because of its simplicity and a fair compromise between accuracy and speed. In the meantime, research around PhyML has continued, and this article describes the new algorithms and methods implemented in the program. First, we introduce a new algorithm to search the tree space with user-defined intensity using subtree pruning and regrafting topological moves. The parsimony criterion is used here to filter out the least promising topology modifications with respect to the likelihood function. The analysis of a large collection of real nucleotide and amino acid data sets of various sizes demonstrates the good performance of this method. Second, we describe a new test to assess the support of the data for internal branches of a phylogeny. This approach extends the recently proposed approximate likelihood-ratio test and relies on a nonparametric, Shimodaira-Hasegawa-like procedure. A detailed analysis of real alignments sheds light on the links between this new approach and the more classical nonparametric bootstrap method. Overall, our tests show that the last version (3.0) of PhyML is fast, accurate, stable, and ready to use. A Web server and binary files are available from http://www.atgc-montpellier.fr/phyml/.
Article
Full-text available
Coral reefs are hotspots of biodiversity, yet processes of diversification in these ecosystems are poorly understood. The environmental heterogeneity of coral reef environments could be an important contributor to diversification, however, evidence supporting ecological speciation in corals is sparse. Here, we present data from a widespread coral species that reveals a strong association of host and symbiont lineages with specific habitats, consistent with distinct, sympatric gene pools that are maintained through ecologically-based selection. Populations of a common brooding coral, Seriatopora hystrix, were sampled from three adjacent reef habitats (spanning a approximately 30 m depth range) at three locations on the Great Barrier Reef (n = 336). The populations were assessed for genetic structure using a combination of mitochondrial (putative control region) and nuclear (three microsatellites) markers for the coral host, and the ITS2 region of the ribosomal DNA for the algal symbionts (Symbiodinium). Our results show concordant genetic partitioning of both the coral host and its symbionts across the different habitats, independent of sampling location. This study demonstrates that coral populations and their associated symbionts can be highly structured across habitats on a single reef. Coral populations from adjacent habitats were found to be genetically isolated from each other, whereas genetic similarity was maintained across similar habitat types at different locations. The most parsimonious explanation for the observed genetic partitioning across habitats is that adaptation to the local environment has caused ecological divergence of distinct genetic groups within S. hystrix.
Article
Full-text available
Dinoflagellates in the genus Symbiodinium are crucial components of coral reef ecosystems in their roles as endosymbionts of corals and other marine invertebrates. The genus Symbiodinium encompasses eight lineages (clades A-H), and multiple sub-clade types. Symbiodinium in clades A, B, C, and D are most commonly associated with metazoan hosts while clades C, D, F, G, and H with large soritid foraminifera. Recent studies have described a diversity of new Symbiodinium types within each clades, but no new clades have been reported since 2001. Here, we describe a new clade of Symbiodinium isolated from soritid foraminifera from Hawai'i.
Article
Full-text available
The diversity and community structures of symbiotic dinoflagellates are described from reef invertebrates in southern and central provinces of the Great Barrier Reef (GBR), Australia, and Zamami Island, Okinawa, Japan. The symbiont assemblages from region to region were dominated by Clade C Symbiodinium spp. and consisted of numerous host-specific and/or rare types (specialists), and several types common to many hosts (generalists). Prevalence in the host community among certain host-generalist symbionts differed between inshore and offshore environments, across latitudinal (central versus southern GBR) gradients, and over wide geographic ranges (GBR versus Okinawa). One particular symbiont (C3h) from the GBR had a dramatic shift in dominance. Its prevalence ranged from being extremely rare, or absent on high-latitude reefs to dominating the scleractinian diversity on a mid-latitude inshore reef. These changes occurred among coral fauna whose larvae must acquire symbionts from environmental sources (horizontal symbiont acquisition). Such differences did not occur among 'vertical transmitters' such as Porites spp., Montipora spp. and pocilloporids (corals that directly transmit symbionts to their offspring) or among those hosts displaying 'horizontal acquisition', but that associate with specific symbionts. Most host-specialized types were found to be characteristic of a particular geographic region (i.e. Okinawa versus Central GBR versus Southern GBR). The mode of symbiont acquisition may play an important role in how symbiont composition may shift in west Pacific host communities in response to climate change. There is no indication that recent episodes of mass bleaching have provoked changes in host-symbiont combinations from the central GBR.
Article
Full-text available
We have analyzed the genetic profiles of dinoflagellate populations obtained from the Pacific coast sea anemone Anthopleura elegantissima (Brandt) at collection sites from Washington to California. Genetic differences within the symbiont populations of California anemones have been uncovered by restriction length polymorphism (RFLP) analysis of the small subunit (SSU) and large subunit (LSU) ribosomal RNA genes, and by denaturing gradient gel electrophoresis (DGGE) of the internal transcribed spacer region 2 (ITS 2). The existence of two Symbiodinium species is substantiated by sequence analysis of the variable regions V1, V2, and V3 of the SSUrDNA, which also establishes their phylogenetic relatedness to other members of the genus Symbiodinium. Anemones from Washington and Oregon harbor a single dinoflagellate species, for which we propose the name S. muscatinei sp. nov. At these northern locations, S. muscatinei either exists alone or co-occurs with the Chlorella-like green algal symbiont. Our results indicate that S. muscatinei co-occurs with a second dinoflagellate, S. californium, in mixed populations in central and southern California. We suggest that the geographic distribution of these dinoflagellates is related to the temperature cline created by latitude.
Article
Full-text available
Current efforts to reconstruct the tree of life and histories of multigene families demand the inference of phylogenies consisting of thousands of gene sequences. However, for such large data sets even a moderate exploration of the tree space needed to identify the optimal tree is virtually impossible. For these cases the neighbor-joining (NJ) method is frequently used because of its demonstrated accuracy for smaller data sets and its computational speed. As data sets grow, however, the fraction of the tree space examined by the NJ algorithm becomes minuscule. Here, we report the results of our computer simulation for examining the accuracy of NJ trees for inferring very large phylogenies. First we present a likelihood method for the simultaneous estimation of all pairwise distances by using biologically realistic models of nucleotide substitution. Use of this method corrects up to 60% of NJ tree errors. Our simulation results show that the accuracy of NJ trees decline only by ≈5% when the number of sequences used increases from 32 to 4,096 (128 times) even in the presence of extensive variation in the evolutionary rate among lineages or significant biases in the nucleotide composition and transition/transversion ratio. Our results encourage the use of complex models of nucleotide substitution for estimating evolutionary distances and hint at bright prospects for the application of the NJ and related methods in inferring large phylogenies. • phylogenetics • molecular evolution • distance estimation • tree of life • maximum likelihood
Article
AimThe Red Sea presents an ideal setting to explore the variability of Symbiodinium over environmental, latitudinal and geographical gradients. We used sequences from two molecular markers to examine genetic diversity of Symbiodinium associated with the widely distributed zoantharian Palythoa tuberculosa in the northern and central Red Sea. LocationNorthern and central Red Sea. Methods Specimens (n=329) were collected from 15 locations. Sequence data from nuclear ribosomal ITS2 (n=269) and chloroplast minicircle psbA(ncr) (n=173) were phylogenetically analysed (maximum likelihood, neighbour joining), and Symbiodinium types identified for each P. tuberculosa colony. To establish whether environment was a strong predictor of Symbiodinium psbA(ncr) lineage, SST, chlorophyll-a, salinity, and depth data were fit into a multinomial logistic regression using the package VGAM in the R statistical environment. ResultsBased on ITS2 and psbA(ncr) results, P. tuberculosa colonies were shown to be in symbioses with Symbiodinium clade C (n=172) and clade D (n=1). Within clade C, four psbA(ncr) lineages were observed; closely related lineages designated Pt-1-a and Pt-1-b, and closely related lineages Pt-3-a and Pt-3-b. By location, Pt-1-a dominated the sites within the Gulf of Aqaba (c.86%, 37/43 colonies). At the entrance to the Gulf of Aqaba, Pt-3-a dominated (c.88%, 15/17), while the more southern remaining sites in the Red Sea were dominated by Pt-3-b (c.78%, 89/113). Main conclusionsMultinomial logistic regression analyses established that predictions based on the combination of temperature, chlorophyll-a and salinity accurately reflected symbiont distributions in the central and northern Red Sea. Palythoa tuberculosa host Pt-1-a in the coldest region, the Gulf of Aqaba (annual average SST=24.5-25.0 degrees C), while immediately to the south Pt-3-a dominates (SST=26.0-26.5 degrees C), with warmest southern sites dominated by Pt-3-b (SST >26.5 degrees C). The Gulf of Aqaba is a unique environment, and more research on Symbiodinium outside the Gulf is required to understand symbiont diversity patterns within the Red Sea.
Article
Coral reef bleaching events are expected to become more frequent and severe in the near future as climate changes. The zoantharian Palythoa tuberculosa bleaches earlier than many scleractinian corals and may serve as an indicator species. Basic monitoring of such species could help to detect and even anticipate bleaching events, especially in areas where more sophisticated approaches that rely on buoy or satellite measurements of sea surface temperature are unavailable or too coarse. One simple and inexpensive monitoring method involves training volunteers to record observations of host color as a proxy for symbiosis quality. Here, we trained university students to take the ‘color fingerprint’ of a reef by assessing the color of multiple randomly selected colonies of P. tuberculosa at one time point in Okinawa Island, Japan. We tested the reliability of the students’ color scores and whether they matched expectations based on previous monthly monitoring of tagged colonies at the same locations. We also measured three traditional metrics of symbiosis quality for comparison: symbiont morphological condition, cell density, and chlorophyll a content. We found that P. tuberculosa color score, although highly correlated among observers, provided little predictive power for the other variables. This was likely due to inherent variation in colony color among generally healthy zoantharians in midwinter, as well as low sample size and brief training owing to the course structure. Despite certain limitations of P. tuberculosa as a focal organism, the citizen science approach to color monitoring has promise, and we outline steps that could improve similar efforts in the future.
Article
Understanding the factors that help shape the association between corals and their algal symbionts, zooxanthellae (Symbiodinium), is necessary to better understand the functional diversity and acclimatization potential of the coral host. However, most studies focus on tropical zooxanthellate corals and their obligate algal symbionts, thus limiting our full comprehension of coral–algal symbiont associations. Here, we examine algal associations in a facultative zooxanthellate coral. We survey the Symbiodinium communities associated with Oculina corals in the western North Atlantic and the Mediterranean using one clade-level marker (psbA coding region) and three fine-scale markers (cp23S–rDNA, b7sym15 flanking region, and b2sym17). We ask whether Oculina spp. harbor geographically different Symbiodinium communities across their geographic range and, if so, whether the host’s genetics or habitat differences are correlated with this geographical variation. We found that Oculina corals harbor different Symbiodinium communities across their geographical range. Of the habitat differences (including chlorophyll a concentration and depth), sea surface temperature is better correlated with this geographical variation than the host’s genetics, a pattern most evident in the Mediterranean. Our results suggest that although facultative zooxanthellate corals may be less dependent on their algal partners compared to obligate zooxanthellate corals, the Symbiodinium communities that they harbor may nevertheless reflect acclimatization to environmental variation among habitats.
Article
We have developed a World Wide Web (WWW) version of the sequence retrieval system Query: WWW-Query. This server allows to query nucleotide sequence banks in the EMBL/GenBank/DDBJ formats and protein sequence banks in the NBRF/PIR format. WWW-Query includes all the features of the on-line sequences browsers already available: possibility to build complex queries, integration of cross-references with different data banks, and access to the functional zones of biological interest. It also provides original services not available elsewhere: introduction of the notion of re-usable sequence lists, integration of dedicated helper applications for visualizing alignments and phylogenetic trees and links with multivariate methods for studying codon usage or for complementing phylogenies.
Article
Preliminary phylogenetic analyses of specimens of a leucothoid amphipod, Leucothoe vulgaris, collected from sponges, ascidians, and coral rubble from Okinawa, Japan, were completed using mitochondrial COI and nuclear 18S ribosomal DNA sequences. Analyses of sequences from 83 specimens demonstrate that populations of L. vulgaris likely entail at least two cryptic species, which are reciprocally monophyletic and reproductively isolated. These two potentially cryptic species live in sympatry but are apparently morphologically identical, suggesting a geographically driven divergence process and secondary contact. Within each clade, two major subclades corresponding to the east and west coast of Okinawa Island were present, with divergence times of approximately 1.61–1.83 mya. This last result suggests a role of Pleistocene sea level changes in the current patterns of intra-specific genetic structure and highlights the need for a more comprehensive sampling of L. vulgaris throughout the Indo-west Pacific. © The Trustees of the Natural History Museum, London 2015. All Rights Reserved.
Book
— We studied sequence variation in 16S rDNA in 204 individuals from 37 populations of the land snail Candidula unifasciata (Poiret 1801) across the core species range in France, Switzerland, and Germany. Phylogeographic, nested clade, and coalescence analyses were used to elucidate the species evolutionary history. The study revealed the presence of two major evolutionary lineages that evolved in separate refuges in southeast France as result of previous fragmentation during the Pleistocene. Applying a recent extension of the nested clade analysis (Templeton 2001), we inferred that range expansions along river valleys in independent corridors to the north led eventually to a secondary contact zone of the major clades around the Geneva Basin. There is evidence supporting the idea that the formation of the secondary contact zone and the colonization of Germany might be postglacial events. The phylogeographic history inferred for C. unifasciata differs from general biogeographic patterns of postglacial colonization previously identified for other taxa, and it might represent a common model for species with restricted dispersal.
Article
The mutualistic symbioses between reef-building corals and micro-algae form the basis of coral reef ecosystems, yet recent environmental changes threaten their survival. Diversity in host-symbiont pairings on the sub-species level could be an unrecognized source of functional variation in response to stress. The Caribbean elkhorn coral, Acropora palmata, associates predominantly with one symbiont species (Symbiodinium 'fitti'), facilitating investigations of individual-level (genotype) interactions. Individual genotypes of both host and symbiont were resolved across the entire species' range. Most colonies of a particular animal genotype were dominated by one symbiont genotype (or strain) that may persist in the host for decades or more. While Symbiodinium are primarily clonal, the occurrence of recombinant genotypes indicates sexual recombination is the source of this genetic variation, and some evidence suggests this happens within the host. When these data are examined at spatial scales spanning the entire distribution of A. palmata, gene flow among animal populations was an order of magnitude greater than among populations of the symbiont. This suggests that independent micro-evolutionary processes created dissimilar population genetic structures between host and symbiont. The lower effective dispersal exhibited by the dinoflagellate raises questions regarding the extent to which populations of host and symbiont can co-evolve during times of rapid and substantial climate change. However, these findings also support a growing body of evidence, suggesting that genotype-by-genotype interactions may provide significant physiological variation, influencing the adaptive potential of symbiotic reef corals to severe selection.
Article
Shallow water anthozoans, the major builders of modern coral reefs, enhance their metabolic and calcification rates with algal symbionts. Controversy exists over whether these anthozoan-algae associations are flexible over the lifetimes of individual hosts, promoting acclimative plasticity, or are closely linked, such that hosts and symbionts coevolve across generations. Given the diversity of algal symbionts and the morphological plasticity of many host species, cryptic variation within either partner could potentially confound studies of anthozoan-algal associations. Here, we used ribosomal, organelle, and nuclear sequences, along with microsatellite variation, to study the relationship between lineages of a common Caribbean gorgonian and its algal symbionts. The gorgonian Eunicea flexuosa is a broadcast spawner, composed of two recently diverged, genetically distinct lineages largely segregated by depth. We sampled colonies of the two lineages across depth gradients at three Caribbean locations. We find that each host lineage is associated with a unique Symbiodinium B1/184 phylotype. This relationship between host and symbiont is maintained when host colonies are reciprocally transplanted, although cases of within phylotype switching were also observed. Even when the phylotypes of both partners are present at intermediate depths, the specificity between host and symbiont lineages remained absolute. Unrecognized cryptic diversity may mask host-symbiont specificity and change the inference of evolutionary processes in mutualistic associations. Symbiotic specificity thus likely contributes to the ecological divergence of the two partners, generating species diversity within coral reefs.This article is protected by copyright. All rights reserved.
Article
Despite extensive work on the genetic diversity of reef invertebrate-dinoflagellate symbioses on the Great Barrier Reef (Australia), large information gaps exist from northern and inshore regions. Therefore, a broad survey was done comparing the community of inshore, mid-shelf and outer reefs at the latitude of Lizard Island. Symbiodinium (Freudenthal) diversity was characterized using DGGE fingerprinting and sequencing of the ITS2 region of the ribosomal DNA. Thirty-nine distinct Symbiodinium types were identified from four sub-generic clades (B, C, D and G). Several Symbiodinium types originally characterized from the Indian Ocean were discovered as well as eight novel types (C1kk, C1LL, C3nn, C26b, C161a, C162, C165, C166). Multivariate analyses on the Symbiodinium species diversity data showed a strong link with host identity, consistent with previous findings. Of the four environmental variables tested, mean austral winter SST influenced Symbiodinium distribution across shelves most significantly. A similar result was found when the analysis was performed on Symbiodinium diversity data of genera with an open symbiont transmission mode separately with Chl-a and PAR explaining additional variation. This study underscores the importance of SST and water quality related variables as factors driving Symbiodinium distribution on cross-shelf scales. Furthermore this study expands our knowledge on Symbiodinium species diversity, ecological partitioning (including host-specificity) and geographic ranges across the GBR. The accelerating rate of environmental change experienced by coral reef ecosystems emphasizes the need to comprehend the full complexity of cnidarian symbioses, including the biotic and abiotic factors that shape their current distributions.This article is protected by copyright. All rights reserved.
Article
Bursts in species diversification are well documented among animals and plants, yet few studies have assessed recent adaptive radiations of eukaryotic microbes. Consequently, we examined the radiation of the most ecologically dominant group of endosymbiotic dinoflagellates found in reef-building corals, Symbiodinium Clade C, using nuclear ribosomal (ITS2), chloroplast (psbA(ncr) ), and multilocus microsatellite genotyping. Through a hierarchical analysis of high-resolution genetic data, we assessed whether ecologically distinct Symbiodinium, differentiated by seemingly equivocal rDNA sequence differences, are independent species lineages. We also considered the role of host specificity in Symbiodinium speciation and the correspondence between endosymbiont diversification and Caribbean paleo-history. According to phylogenetic, biological, and ecological species concepts, Symbiodinium Clade C comprises many distinct species. Although regional factors contributed to population-genetic structuring of these lineages, Symbiodinium diversification was mainly driven by host specialization. By combining patterns of the endosymbiont's host specificity, water depth distribution, and phylogeography with paleo-historical signals of climate change, we inferred that present-day species diversity on Atlantic coral reefs stemmed mostly from a post-Miocene adaptive radiation. Host-generalist progenitors spread, specialized, and diversified during the ensuing epochs of prolonged global cooling and change in reef-faunal assemblages. Our evolutionary reconstruction thus suggests that Symbiodinium undergoes "boom and bust" phases in diversification and extinction during major climate shifts.
Article
Zoanthids of the genus Palythoa are common in coral reef environments worldwide, particularly in the intertidal zone. However, their taxonomy remains problematic, resulting in an incomplete understanding of their diversity. Palythoa caesia Dana, 1846 is found in Fiji, Australia, and the Indian Ocean, while P. tuberculosa (Esper, 1805) has been reported from India, the Red Sea, Singapore, Madagascar, and Japan. The lack of obvious characters differentiating the two species, their wide distributions and high levels of intraspecific variation raise the possibility that these species are in fact one. Based on specimens from Australia, the Red Sea, and Japan, we used three DNA markers (mitochondrial cytochrome oxidase I, 16S ribosomal DNA, and the nuclear internal transcribed spacer region of ribosomal DNA) combined with morphological analyses of tentacle numbers, and cnidae to re-examine the identity of these two taxa. Phylogenetic results showed sequences from all specimens for all markers formed one monophyly, and morphological results showed little differentiation between the two putative taxa. Overall, it is apparent these two taxa are the same species, and the senior synonym P. tuberculosa should be used for specimens for the entire Indo-Pacific region.
Article
Traditional approaches for describing species of morphologically cryptic and often unculturable forms of endosymbiotic dinoflagellates are problematic. Two new species in the genus Symbiodinium Freudenthal 1962 are described using an integrative evolutionary genetics approach: Symbiodinium minutum sp. nov. are harbored by widespread tropical anemones in the genus Aiptasia; and Symbiodinium psygmophilum sp. nov. are harbored by subtropical and temperate stony corals (e.g., Astrangia, Cladocora, and Oculina) from the Atlantic Ocean and Mediterranean Sea. Both new species are readily distinguished from each other by phylogenetic disparity and reciprocal monophyly of several nucleic acid sequences including nuclear ribosomal internal transcribed spacers 1 and 2, single copy microsatellite flanker Sym15, mitochondrial cytochrome b, and the chloroplast 23S rRNA gene. Such molecular evidence, combined with well-defined differences in cell size, physiology (thermal tolerance), and ecology (host compatibility) establishes these organisms as distinct species. Future descriptions of Symbiodinium spp. will need to emphasize genetics-based descriptions because significant morphological overlap in this group obscures large differences in ecology and evolutionary divergence. By using molecular evidence based on conserved and rapidly evolving genes analyzed from a variety of samples, species boundaries are defined under the precepts of Evolutionary and Biological Species Concepts without reliance on an arbitrary genetic distance metric. Because ecological specialization arises through genetic adaptations, the Ecological Species Concept can also serve to delimit many host-specific Symbiodinium spp.
Article
Zooxanthellate zoanthid colonies of the species Zoanthus sansibaricus (Cnidaria: Anthozoa: Hexacorallia) are present both in the intertidal zone and at depths greater than 7 m at three locations (Manza, Zanpa, Sunabe) along the west coast of Okinawa, Japan. In this study, the identity of Z. sansibaricus colonies from various depths as the same species was confirmed using morphological analyses of tentacle numbers, polyp diameter, and nematocyst examination. In addition, molecular analyses of sequences of mitochondrial cytochrome oxidase subunit I and the internal transcribed spacer region 2 of ribosomal DNA (ITS2-rDNA) were performed. Surveys from 0 to 35 m depths at Manza indicated that the populations of Z. sansibaricus were discontinuous in their bathymetrical distribution, with few or no Z. sansibaricus colonies found at depths of 4–7 m. Examination of Symbiodinium (=zooxanthellae) types within Z. sansibaricus colonies by phylogenetic analyses of Symbiodinium ITS2-rDNA showed clear differences between the two populations, with some (=27 %) intertidal colonies having Symbiodinium clade A, while all deeper subtidal (>7 m depth) colonies possessed Symbiodinium clade C (n = 18). Detailed phylogenetic analyses further indicated significant differences within Symbiodinium clade C populations over depth. From this study, it is clear that the zoanthid Z. sansibaricus has some variation in its symbiosis with Symbiodinium, potentially allowing the species to colonize different depths in the subtropical coral reef environment of Okinawa, and that its range extends far past the shallow subtidal zone as previously believed.
Article
Distribution patterns of five zoanthid species at Okinawa Island, Japan. Zoological Studies 50(4): 426-433. Zoanthids (Anthozoa, Hexacorallia) are distributed worldwide, especially in shallow tropical and subtropical waters. In fringing reefs of Okinawa I., southwestern Japan, zoanthids are common benthic organisms. Despite their abundance, even basic ecological information such as favorable habitats based on quantitative surveys is still lacking. Accordingly, we investigated the distribution patterns of 5 common zooxanthellate zoanthid species in shallow reef waters (< 10 m) of Okinawa I.: Palythoa tuberculosa, P. mutuki, Zoanthus sansibaricus, Z. kuroshio, and Z. gigantus. The survey was conducted using the belt transect method in 3 reef environments (moat, reef crest, and reef slope) at 10 reef sites in 2008. As a result, 2404 zoanthid colonies were observed, and Z. sansibaricus and P. tuberculosa were the 2 most dominant species, respectively comprising 52% and 41% of the total zoanthids observed. The environment where the highest numbers of colonies were observed was the reef crest (1615 colonies) followed by the reef slope (687 colonies), while zoanthids were rare in the moat environment (102 colonies). There were significantly more Z. sansibaricus colonies on reef crests than reef slopes, but no significant difference was seen in the frequencies of the other 4 species between the reef crest and reef slope. As to the zoanthid colony size, most colonies (> 86%) of the 5 zoanthid species were < 10 cm in diameter, and only 2 colonies of > 50 cm in diameter were observed in the survey. The absence of zoanthids in moats suggested that sedimentation or weak currents may be factors limiting zoanthid distribution; however, detailed investigations are necessary to confirm this. Since zooxanthellate zoanthids are a major benthic group on coral reefs, further research focusing on the relationships between zoanthid distribution and environmental conditions will foster a better understanding of coral reef ecosystems.
Article
1. The hermatypic coral, Pocillopora damicornis was incubated in the laboratory and in its reef habitat with Na2(14)CO3 for 1-24 hours. Controls were incubated in darkness. (14)C fixation in light exceeded that in darkness. 2. Fractionation of corals labeled on the reef for 24 hours revealed that 35-50% of the total (14)C fixed appeared in the animal tissue lipid (as (14)C-glycerol) and protein. From a comparison with dark controls it is concluded that photosynthetic products of zooxanthellae are translocated to host coral tissue. The skeletal organic matrix also acquires (14)C. 3. Zooxanthehellae isolated from corals and incubated in a homogenate of host coral tissue selectively release glycerol and traces of other organic material including glucose, alanine, and glycolic acid confirming previous observations.
Article
The internal transcribed spacer (ITS) regions from 47 Symbiodinium (Freudenthal) isolates cultured from 34 different host species and two populations sampled from nature were sequenced and compared. Of these, 17 distinct ITS types were identified. The described species Symbiodinium goreaui , S. kawagutii , S. pilosum (Trench and Blank), S. microadriaticum (Freudenthal), and S. ( � Gymnodinium ) linucheae (Trench and Thinh) had ITS sequences distinct from each other. Four of these species share identical ITS sequences with un- characterized isolates. Sequence differences among other isolates indicate that at least seven other cul- tured types await formal species descriptions, whereas numerous others most likely exist in nature. The Sym- biodinium phylogeny is positively correlated with cell size, mycosporine-like amino acid production (UV pro- tection), and host infectivity, whereas the production of water-soluble peridinin-chl a- protein homodimer and monomer apoproteins and isoenzyme similarity do not correlate. There is evidence, based on the lack of phylogenetic congruency with allelic variability, that sexual recombination occurs at some frequency among Symbiodinium populations. Symbiodinium isolates from the Caribbean possess identical ITS sequences to iso- lates originating from the Red Sea or the western Pa- cific. These findings indicate that some Symbiodinium species may have global biogeographic distributions.
Article
tion of the stress-tolerant zooxanthellae, Symbiodinium clade D, with the low-temperature-tolerant coral, Oulastrea crispata (Scleractinia: Faviidae) in subtropical non-reefal coral communities. Zoological Studies 42(4): 540-550. We examined spatial and temporal zooxanthellae diversity in a low-temperature-tolerant coral, Oulastrea crispata, from 2 subtropical non-reefal coral communities, the Penghu Islands (the Pescadores), Taiwan and from Hong Kong, China using restriction fragment length polymorphism (RFLP) of partial nuclear small subunit ribosomal DNA (nssrDNA) and large subunit ribosomal DNA (nlsrDNA), together with phylogenet- ic analyses of DNA sequences. Oulastrea crispata occurs commonly on shallow reef depressions and on tur- bid bay bedrock inhabited by only a few other corals, and is a pioneer coral colonizing artificial substrates where environmental disturbance is high. This study demonstrates that the zooxanthellae associated with O. crispata, in Penghu and in Hong Kong belong to Symbiodinium clade D, a clade of zooxanthellae formally pro- posed to be stress tolerant in marginal habitats (Toller et al. 2001a). Analyses of zooxanthellae diversity showed no apparent symbiosis polymorphism on either a spatial or temporal scale, suggesting that the associ- ation with Symbiodinium clade D is stable in O. crispata. Oulastrea crispata possesses opportunistic life history traits, including a variety of reproductive strategies and physiological tolerances, enabling it to colonize a variety of substrata unfavorable to other corals. Our finding showed a stable association with a stress-tolerant sym- biont which may provide a key to how O. crispata can achieve such physiological adaptability. http://www.sinica.edu.tw/zool/zoolstud/42.4/540.pdf
Article
▪ Abstract Reef corals (and other marine invertebrates and protists) are hosts to a group of exceptionally diverse dinoflagellate symbionts in the genus Symbiodinium. These symbionts are critical components of coral reef ecosystems whose loss during stress-related “bleaching” events can lead to mass mortality of coral hosts and associated collapse of reef ecosystems. Molecular studies have shown these partnerships to be more flexible than previously thought, with different hosts and symbionts showing varying degrees of specificity in their associations. Further studies are beginning to reveal the systematic, ecological, and biogeographic underpinnings of this flexibility. Unusual symbionts normally found only in larval stages, marginal environments, uncommon host taxa, or at latitudinal extremes may prove critical in understanding the long-term resilience of coral reef ecosystems to environmental perturbation. The persistence of bleaching-resistant symbiont types in affected ecosystems, and the possibilit...
Article
In order to determine boundaries of genetic recombination among putative ‘species’ of endosymbiotic dinoflagellates, nine polymorphic microsatellite loci were developed and optimized for clade B Symbiodinium designated as type 7 (B7) and two related types, B13 and B13a. Together, they form a subclade in clade B that is specific to Caribbean corals in the genus Madracis. A total of 52 samples were analysed (including 43 B7, 2 B13, 7 B13a) originating from seven Caribbean locations. Diversity indices at each haploid locus ranged from 0.302 to 0.836 and four to 14 alleles were found per locus. The loci were preliminarily cross-tested on closely related ‘ancestral’ B1 populations found in maze coral Meandrina meandrites and that of another host specialist, B5, from the lesser starlet coral Siderastrea radians.
Article
Previous phylogenetic studies based on mitochondrial DNA markers have suggested that the zoanthid genus Palythoa may consist of both Palythoa species (Palythoa tuberculosa) and species formerly assigned to the genus Protopalythoa (Palythoa mutuki, Palythoa heliodiscus). In the present study various Palythoa spp. samples collected primarily from southern Japan with additional samples from the Indo-Pacific and Caribbean Sea were examined. The nuclear internal transcribed spacer of ribosomal DNA (ITS-rDNA) was sequenced and aligned for phylogenetic analyses to further investigate the relationship between P. tuberculosa, P. mutuki, and P. heliodiscus. ITS-rDNA analyses showed species groups forming monophylies with similar topology but with much higher resolution than seen for mitochondrial phylogenetic analyses. The results also confirmed the very close relationship of P. tuberculosa and P. mutuki. Some specimens appeared to be a potentially undescribed Palythoa species (designated Palythoa sp. sakurajimensis). Additionally, ITS-rDNA sequences of P. mutuki and P. tuberculosa showed additive polymorphic site, demonstrating for the first time a potential history of reticulate evolution in Palythoa.
Article
Aim This study examines the importance of geographic proximity, host life history and regional and local differences in environment (temperature and water clarity) in driving the ecological and evolutionary processes underpinning the global patterns of diversity and distribution of symbiotic dinoflagellates. By comparing and contrasting coral–algal symbioses from isolated regions with differing environmental conditions, we may assess the potential of coral communities to respond to significant changes in climate.
Article
Zooxanthellae are unicellular algae that occur as endosymbionts in many hundreds of common marine invertebrates. The issue of zooxanthella diversity has been difficult to address. Most zooxanthellae have been placed in the dinoflagellate genus Symbiodinium as one or several species that are not easily distinguished. We compared Symbiodinium and nonsymbiotic dinoflagellates using small ribosomal subunit RNA sequences. Surprisingly, small ribosomal subunit RNA diversity within the genus Symbiodinium is comparable to that observed among different orders of nonsymbiotic dinoflagellates. These data reinforce the conclusion that Symbiodinium-like zooxanthellae represent a collection of distinct species and provide a precedent for a molecular genetic taxonomy of the genus Symbiodinium.
Article
Some simple formulae were obtained which enable us to estimate evolutionary distances in terms of the number of nucleotide substitutions (and, also, the evolutionary rates when the divergence times are known). In comparing a pair of nucleotide sequences, we distinguish two types of differences; if homologous sites are occupied by different nucleotide bases but both are purines or both pyrimidines, the difference is called type I (or "transition" type), while, if one of the two is a purine and the other is a pyrimidine, the difference is called type II (or "transversion" type). Letting P and Q be respectively the fractions of nucleotide sites showing type I and type II differences between two sequences compared, then the evolutionary distance per site is K = -(1/2) ln [(1-2P-Q) square root of 1-2Q]. The evolutionary rate per year is then given by k = K/(2T), where T is the time since the divergence of the two sequences. If only the third codon positions are compared, the synonymous component of the evolutionary base substitutions per site is estimated by K'S = -(1/2) ln (1-2P-Q). Also, formulae for standard errors were obtained. Some examples were worked out using reported globin sequences to show that synonymous substitutions occur at much higher rates than amino acid-altering substitutions in evolution.
Article
Zooxanthellae are unicellular algae that occur as endosymbionts in many hundreds of marine invertebrate species. Because zooxanthellae have traditionally been difficult to classify, little is known about the natural history of these symbioses. Zooxanthellae were isolated from 131 individuals in 22 host taxa and characterized by the use of restriction fragment length polymorphisms (RFLPs) in nuclear genes that encode small ribosomal subunit RNA (ssRNA). Six algal RFLPs, distributed host species specifically, were detected. Individual hosts contained one algal RFLP. Zooxanthella phylogenetic relationships were estimated from 22 algal ssRNA sequences—one from each host species. Closely related algae were found in dissimilar hosts, suggesting that animal and algal lineages have maintained a flexible evolutionary relation with each other.
Article
Symbiotic algae in coral species distributed over a large depth range are confronted with major differences in light conditions. We studied the genetic variation of Symbiodinium in the coral genus Madracis over depth (5-40 m) and at two different colony surface positions. Using polymerase chain reaction-denaturing gradient gel electrophoresis ITS2 nuclear ribosomal DNA analyses, we consistently identified three symbiont genotypes with distributions that reveal patterns of host specificity and depth-based zonation. ITS2 type B7 Symbiodinium is the generalist type, occurring in all zooxanthellate Madracis corals and at all depths. Type B13 is restricted to the shallow water specialist Madracis mirabilis. Type B15 is typical of deep reef environments and replaces B7 in the depth generalist Madracis pharensis. Contrasting with variation over depth, we found strong functional within-colony uniformity in symbiont diversity. Relating symbiont distributions to measured physical factors (irradiance, light spectral distribution, temperature), suggests depth-based ecological function and host specificity for Symbiodinium ITS2 types, even among closely related coral species.