Genetic traces of recent long-distance dispersal in a predominantly self-recruiting coral

Population genetics assessment of two pocilloporid coral species from the northern red sea: Implications for urbanized reef sustainability

Understanding the genetic makeup of key coral species is vital for effective coral reef management, as heightened genetic diversity directly influences long-term survival and resilience against environmental changes. This study focused on two widespread Indo-Pacific branching corals, Pocillopora damicornis (referred as Pocillopora cf. damicornis (as identified only morphologically) and Seriatopora hystrix, by genotyping 222 and 195 colonies, respectively, from 10 sites in the northern Gulf of Eilat, Red Sea, using six and five microsatellite markers, respectively. Both species exhibited low observed heterozygosity (0.47 for P. cf. damicornis, 0.32 for S. hystrix) and similar expected heterozygosity (0.576 for P. cf. damicornis, 0.578 for S. hystrix). Pocillopora cf. damicornis showed minimal deviations from Hardy-Weinberg equilibrium (HWE) and low but positive F values, indicating high gene flow, while S. hystrix exhibited higher diversion from HWE and positive F values, suggesting isolation by distance and possible non-random mating or genetic drift. As the Gulf of Eilat undergoes rapid urbanization, this study highlights the anthropogenic impacts on the population genetics of key ecosystem engineering species and emphasizes the importance of managing genetics of Marine Protected Areas while implementing active coral reef restoration. The differences in reproductive traits between the two species (S. hystrix being a brooder, while P. cf. damicornis a broadcast spawner), underscore the need for sustainable population genetics management of the coral reefs for the future and resilience of the coral reef ecosystem of the northern Red Sea region.

Symbiodiniaceae diversity varies by host and environment across thermally distinct reefs

Endosymbiotic dinoflagellates (Symbiodiniaceae) influence coral thermal tolerance at both local and regional scales. In isolation, the effects of host genetics, environment, and thermal disturbances on symbiont communities are well understood, yet their combined effects remain poorly resolved. Here, we investigate Symbiodiniaceae across 1300 km in Australia's Coral Sea Marine Park to disentangle these interactive effects. We identified Symbiodiniaceae to species-level resolution for three coral species (Acropora cf humilis, Pocillopora verrucosa, and Pocillopora meandrina) by sequencing two genetic markers of the symbiont (ITS2 and psbAncr), paired with genotype-by-sequencing of the coral host (DArT-seq). Our samples predominantly returned sequences from the genus Cladocopium, where Acropora cf humilis affiliated with C3k, Pocillopora verrucosa with C. pacificum, and Pocillopora meandrina with C. latusorum. Multivariate analyses revealed that Acropora symbionts were driven strongly by local environment and thermal disturbances. In contrast, Pocillopora symbiont communities were both partitioned 2.5-fold more by host genetic structure than by environmental structure. Among the two Pocillopora species, the effects of environment and host genetics explained four times more variation in symbionts for P. meandrina than P. verrucosa. The concurrent bleaching event in 2020 had variable impacts on symbiont communities, consistent with patterns in P. verrucosa and A. cf humilis, but not P. meandrina. Our findings demonstrate how symbiont macroscale community structure responses to environmental gradients depend on host species and their respective population structure. Integrating host, symbiont, and environmental data will help forecast the adaptive potential of corals and their symbionts amidst a rapidly changing environment.

The effects of marine heatwaves on acute heat tolerance in corals

Scleractinian coral populations are increasingly exposed to conditions above their upper thermal limits due to marine heatwaves, contributing to global declines of coral reef ecosystem health. However, historic mass bleaching events indicate there is considerable inter- and intra-specific variation in thermal tolerance whereby species, individual coral colonies and populations show differential susceptibility to exposure to elevated temperatures. Despite this, we lack a clear understanding of how heat tolerance varies across large contemporary and historical environmental gradients, or the selective pressures that underpin this variation. Here we conducted standardised acute heat stress experiments to identify variation in heat tolerance among species and isolated reefs spanning a large environmental gradient across the Coral Sea Marine Park. We quantified the photochemical yield (F_v /F_m ) of coral samples in three coral species, Acropora cf humilis, Pocillopora meandrina, and Pocillopora verrucosa, following exposure to four temperature treatments (local ambient temperatures, and + 3°C, +6°C and + 9°C above local maximum monthly mean). We quantified the temperature at which F_v /F_m decreased by 50% (termed ED50) and used derived values to directly compare acute heat tolerance across reefs and species. The ED50 for Acropora was 0.4-0.7°C lower than either Pocillopora species, with a 0.3°C difference between the two Pocillopora species. We also recorded 0.9°C to 1.9°C phenotypic variation in heat tolerance among reefs within species, indicating spatial heterogeneity in heat tolerance across broad environmental gradients. Acute heat tolerance had a strong positive relationship to mild heatwave exposure over the past 35 years (since 1986) but was negatively related to recent severe heatwaves (2016-2020). Phenotypic variation associated with mild thermal history in local environments provides supportive evidence that marine heatwaves are selecting for tolerant individuals and populations; however, this adaptive potential may be compromised by the exposure to recent severe heatwaves.

Macro- and micro-scale adaptations allow distinct Stylophora pistillata-symbiodiniaceae holobionts to optimize performance across a broad light habitat

In sessile organisms, phenotypic plasticity represents an important strategy for dealing with environmental variability. Here we test if phenotypic plasticity enables the common coral Stylophora pistillata to occupy a broad niche. We find clear differences in the photo-physiology of four putative species of photosynthetic dinoflagellate symbionts associated with the coral S. pistillata, namely, Cladocopium 'C35a', 'C79', 'C78a' and 'C8a'. Coral phenotypic responses were also tightly linked to symbiont identity. Corals with Cladocopium 'C8a' have more "open" macro-morphology compared to colonies associating with depth-restricted Cladocopium 'C35a' or 'C78a' in the same shallow water habitat. Corals with Cladocopium 'C8a' had 40 to 60% lower symbiont cell densities compared to other holobionts but were more efficient at acclimating over a range of light levels, with clear mechanisms to dissipate excess light energy. This holobiont contains host-based green fluorescent pigments, increased concentrations of symbiont-based mycosporine amino acids, and xanthophyll cycling in high light habitats. Photosynthetic efficiency was also adjusted over the light habitat. In contrast, limited micro-scale responses were observed between three depth-restricted symbionts: Cladocopium 'C79', 'C35a', and 'C78a'. To optimize light levels reaching the photosynthetic unit, these colonies rely on a more closed macro-morphology under high light levels, which reduces incident light levels by up to 43%, and higher symbiont densities . Our results show that distinct macro- and micro-scale adaptations lead to functional differences between four distinct S. pistillata holobionts, allowing them to co-exist by filling specific niches on a small, but environmentally diverse, spatial scale. Key index words: Light, Symbiodiniaceae, coral, pigments, Stylophora pistillata, ITS2, phenotypic plasticity, niche diversification.

A molecular census of early-life stage scleractinian corals in shallow and mesophotic zones

The decline of coral reefs has fueled interest in determining whether mesophotic reefs can shield against disturbances and help replenish deteriorated shallower reefs. In this study, we characterized spatial (horizontal and vertical) and seasonal patterns of diversity in coral recruits from Dabaisha and Guiwan reefs at Ludao, Taiwan. Concrete blocks supporting terra-cotta tiles were placed at shallow (15m) and mesophotic (40m) depths, during 2016-2018. Half of the tiles were retrieved and replaced biannually over three 6-month surveys (short-term); the remainder retrieved at the end of the 18-month (long-term) survey. 451 recruits were located using fluorescent censusing and identified by DNA barcoding. Barcoding the mitochondrial cytochrome oxidase I (COI) gene resulted in 17 molecular operational taxonomic units (MOTUs). To obtain taxonomic resolution to the generic level, Pocillopora were phylotyped using the mitochondrial open reading frame (ORF), resolving eight MOTUs. Acropora, Isopora, and Montipora recruits were identified by the nuclear PaxC intron, yielding ten MOTUs. Overall, 35 MOTUs were generated and were comprised primarily of Pocillopora and, in fewer numbers, Acropora, Isopora, Pavona, Montipora, Stylophora, among others. 40% of MOTUs recruited solely within mesophotic reefs while 20% were shared by both depth zones. MOTUs recruiting across a broad depth distribution appear consistent with the hypothesis of mesophotic reefs acting as a refuge for shallow-water coral reefs. In contrast, Acropora and Isopora MOTUs were structured across depth zones representing an exception to this hypothesis. This research provides an imperative assessment of coral recruitment in understudied mesophotic reefs and imparts insight into the refuge hypothesis.

Morphological stasis masks ecologically divergent coral species on tropical reefs

Coral reefs are the epitome of species diversity, yet the number of described scleractinian coral species, the framework-builders of coral reefs, remains moderate by comparison. DNA sequencing studies are rapidly challenging this notion by exposing a wealth of undescribed diversity, but the evolutionary and ecological significance of this diversity remains largely unclear. Here, we present an annotated genome for one of the most ubiquitous corals in the Indo-Pacific (Pachyseris speciosa) and uncover, through a comprehensive genomic and phenotypic assessment, that it comprises morphologically indistinguishable but ecologically divergent lineages. Demographic modeling based on whole-genome resequencing indicated that morphological crypsis (across micro- and macromorphological traits) was due to ancient morphological stasis rather than recent divergence. Although the lineages occur sympatrically across shallow and mesophotic habitats, extensive genotyping using a rapid molecular assay revealed differentiation of their ecological distributions. Leveraging "common garden" conditions facilitated by the overlapping distributions, we assessed physiological and quantitative skeletal traits and demonstrated concurrent phenotypic differentiation. Lastly, spawning observations of genotyped colonies highlighted the potential role of temporal reproductive isolation in the limited admixture, with consistent genomic signatures in genes related to morphogenesis and reproduction. Overall, our findings demonstrate the presence of ecologically and phenotypically divergent coral species without substantial morphological differentiation and provide new leads into the potential mechanisms facilitating such divergence. More broadly, they indicate that our current taxonomic framework for reef-building corals may be scratching the surface of the ecologically relevant diversity on coral reefs, consequently limiting our ability to protect or restore this diversity effectively.

Population genetics of the brooding coral Seriatopora hystrix reveals patterns of strong genetic differentiation in the Western Indian Ocean

Coral reefs provide essential goods and services but are degrading at an alarming rate due to local and global anthropogenic stressors. The main limitation that prevents the implementation of adequate conservation measures is that connectivity and genetic structure of populations are poorly known. Here, the genetic diversity and connectivity of the brooding scleractinian coral Seriatopora hystrix were assessed at two scales by genotyping ten microsatellite markers for 356 individual colonies. S. hystrix showed high differentiation, both at large scale between the Red Sea and the Western Indian Ocean (WIO), and at smaller scale along the coast of East Africa. As such high levels of differentiation might indicate the presence of more than one species, a haploweb analysis was conducted with the nuclear marker ITS2, confirming that the Red Sea populations are genetically distinct from the WIO ones. Based on microsatellite analyses three groups could be distinguished within the WIO: (1) northern Madagascar, (2) south-west Madagascar together with one site in northern Mozambique (Nacala) and (3) all other sites in northern Mozambique, Tanzania and Kenya. These patterns of restricted connectivity could be explained by the short pelagic larval duration of S. hystrix, and/or by oceanographic factors, such as eddies in the Mozambique Channel (causing larval retention in northern Madagascar but facilitating dispersal from northern Mozambique towards south-west Madagascar). This study provides an additional line of evidence supporting the conservation priority status of the Northern Mozambique Channel and should inform coral reef management decisions in the region.

Population genetic structure and connectivity of the seagrass Thalassia hemprichii in the Western Indian Ocean is influenced by predominant ocean currents

This study is the first large-scale genetic population study of a widespread climax species of seagrass, Thalassia hemprichii, in the Western Indian Ocean (WIO). The aim was to understand genetic population structure and connectivity of T. hemprichii in relation to hydrodynamic features. We genotyped 205 individual seagrass shoots from 11 sites across the WIO, spanning over a distance of ~2,700 km, with twelve microsatellite markers. Seagrass shoots were sampled in Kenya, Tanzania (mainland and Zanzibar), Mozambique, and Madagascar: 4-26°S and 33-48°E. We assessed clonality and visualized genetic diversity and genetic population differentiation. We used Bayesian clustering approaches (TESS) to trace spatial ancestry of populations and used directional migration rates (DivMigrate) to identify sources of gene flow. We identified four genetically differentiated groups: (a) samples from the Zanzibar channel; (b) Mozambique; (c) Madagascar; and (d) the east coast of Zanzibar and Kenya. Significant pairwise population genetic differentiation was found among many sites. Isolation by distance was detected for the estimated magnitude of divergence (D EST), but the three predominant ocean current systems (i.e., East African Coastal Current, North East Madagascar Current, and the South Equatorial Current) also determine genetic connectivity and genetic structure. Directional migration rates indicate that Madagascar acts as an important source population. Overall, clonality was moderate to high with large differences among sampling sites, indicating relatively low, but spatially variable sexual reproduction rates. The strongest genetic break was identified for three sites in the Zanzibar channel. Although isolation by distance is present, this study suggests that the three regionally predominant ocean current systems (i.e., East African Coastal Current, North East Madagascar Current, and the South Equatorial Current) rather than distance determine genetic connectivity and structure of T. hemprichii in the WIO. If the goal is to maintain genetic connectivity of T. hemprichii within the WIO, conservation planning and implementation of marine protection should be considered at the regional scale-across national borders.

Population Connectivity in the Common Reef Zoantharian Zoanthus sansibaricus (Anthozoa: Hexacorallia) in Southern Japan

Tropical and subtropical shallow benthic marine communities are highly diverse and balanced systems that constitute an important natural resource. Knowledge of the genetic diversity, connectivity and reproduction mode of each population is critical to understanding the fate of whole assemblages in times of disturbances. Importantly, the capability of populations to adapt to environmental challenges will be crucial to determining their survival. Here, we report on the population structure of the common reef zoantharian Zoanthus sansibaricus in the northwestern Pacific, by examining populations at three different locations in southern Japan using five highly variable microsatellite markers. Analyses of a population at the species' northern distribution limit combined with analyses of two subtropical populations suggest that habitat characteristics and ocean currents influence the connectivity and genetic diversity of this species. Our findings emphasize the adaptive ability of Z. sansibaricus to different environmental conditions and may help explain the wide distribution and generalist nature of this species.

Unexpected mixed-mode transmission and moderate genetic regulation of Symbiodinium communities in a brooding coral

Determining the extent to which Symbiodinium communities in corals are inherited versus environmentally acquired is fundamental to understanding coral resilience and to predicting coral responses to stressors like warming oceans that disrupt this critical endosymbiosis. We examined the fidelity with which Symbiodinium communities in the brooding coral Seriatopora hystrix are vertically transmitted and the extent to which communities are genetically regulated, by genotyping the symbiont communities within 60 larvae and their parents (9 maternal and 45 paternal colonies) using high-throughput sequencing of the ITS2 locus. Unexpectedly, Symbiodinium communities associated with brooded larvae were distinct from those within parent colonies, including the presence of types not detected in adults. Bayesian heritability (h²) analysis revealed that 33% of variability in larval Symbiodinium communities was genetically controlled. Results highlight flexibility in the establishment of larval symbiont communities and demonstrate that symbiont transmission is not exclusively vertical in brooding corals. Instead, we show that Symbiodinium transmission in S. hystrix involves a mixed-mode strategy, similar to many terrestrial invertebrate symbioses. Also, variation in the abundances of common Symbiodinium types among adult corals suggests that microhabitat differences influence the structure of in hospite Symbiodinium communities. Partial genetic regulation coupled with flexibility in the environmentally acquired component of Symbiodinium communities implies that corals with vertical transmission, like S. hystrix, may be more resilient to environmental change than previously thought.

Reproductive biology of the deep brooding coral Seriatopora hystrix: Implications for shallow reef recovery

Mesophotic coral ecosystems (MCEs, between 30 and 150 m depth) are hypothesized to contribute to the recovery of degraded shallow reefs through sexually produced larvae (referred to as Deep Reef Refuge Hypothesis). In Okinawa, Japan, the brooder coral Seriatopora hystrix was reported to be locally extinct in a shallow reef while it was found abundant at a MCE nearby. In this context, S. hystrix represents a key model to test the Deep Reef Refuge Hypothesis and to understand the potential contribution of mesophotic corals to shallow coral reef recovery. However, the reproductive biology of mesophotic S. hystrix and its potential to recolonize shallow reefs is currently unknown. This study reports for the first time, different temporal scales of reproductive periodicity and larval settlement of S. hystrix from an upper mesophotic reef (40 m depth) in Okinawa. We examined reproductive seasonality, lunar, and circadian periodicity (based on polyp dissection, histology, and ex situ planula release observations) and larval settlement rates in the laboratory. Mesophotic S. hystrix reproduced mainly in July and early August, with a small number of planulae being released at the end of May, June and August. Compared to shallow colonies in the same region, mesophotic S. hystrix has a 4-month shorter reproductive season, similar circadian periodicity, and smaller planula size. In addition, most of the planulae settled rapidly, limiting larval dispersal potential. The shorter reproductive season and smaller planula size may result from limited energy available for reproduction at deeper depths, while the similar circadian periodicity suggests that this reproductive aspect is not affected by environmental conditions differing with depth. Overall, contribution of mesophotic S. hystrix to shallow reef rapid recovery appears limited, although they may recruit to shallow reefs through a multistep process over a few generations or through random extreme mixing such as typhoons.

Planning Marine Reserve Networks for Both Feature Representation and Demographic Persistence Using Connectivity Patterns

Marine reserve networks must ensure the representation of important conservation features, and also guarantee the persistence of key populations. For many species, designing reserve networks is complicated by the absence or limited availability of spatial and life-history data. This is particularly true for data on larval dispersal, which has only recently become available. However, systematic conservation planning methods currently incorporate demographic processes through unsatisfactory surrogates. There are therefore two key challenges to designing marine reserve networks that achieve feature representation and demographic persistence constraints. First, constructing a method that efficiently incorporates persistence as well as complementary feature representation. Second, incorporating persistence using a mechanistic description of population viability, rather than a proxy such as size or distance. Here we construct a novel systematic conservation planning method that addresses both challenges, and parameterise it to design a hypothetical marine reserve network for fringing coral reefs in the Keppel Islands, Great Barrier Reef, Australia. For this application, we describe how demographic persistence goals can be constructed for an important reef fish species in the region, the bar-cheeked trout (Plectropomus maculatus). We compare reserve networks that are optimally designed for either feature representation or demographic persistence, with a reserve network that achieves both goals simultaneously. As well as being practically applicable, our analyses also provide general insights into marine reserve planning for both representation and demographic persistence. First, persistence constraints for dispersive organisms are likely to be much harder to achieve than representation targets, due to their greater complexity. Second, persistence and representation constraints pull the reserve network design process in divergent directions, making it difficult to efficiently achieve both constraints. Although our method can be readily applied to the data-rich Keppel Islands case study, we finally consider the factors that limit the method's utility in information-poor contexts common in marine conservation.

De Novo Assembly and Characterization of Four Anthozoan (Phylum Cnidaria) Transcriptomes

Many nonmodel species exemplify important biological questions but lack the sequence resources required to study the genes and genomic regions underlying traits of interest. Reef-building corals are famously sensitive to rising seawater temperatures, motivating ongoing research into their stress responses and long-term prospects in a changing climate. A comprehensive understanding of these processes will require extending beyond the sequenced coral genome (Acropora digitifera) to encompass diverse coral species and related anthozoans. Toward that end, we have assembled and annotated reference transcriptomes to develop catalogs of gene sequences for three scleractinian corals (Fungia scutaria, Montastraea cavernosa, Seriatopora hystrix) and a temperate anemone (Anthopleura elegantissima). High-throughput sequencing of cDNA libraries produced ~20-30 million reads per sample, and de novo assembly of these reads produced ~75,000-110,000 transcripts from each sample with size distributions (mean ~1.4 kb, N50 ~2 kb), comparable to the distribution of gene models from the coral genome (mean ~1.7 kb, N50 ~2.2 kb). Each assembly includes matches for more than half the gene models from A. digitifera (54-67%) and many reasonably complete transcripts (~5300-6700) spanning nearly the entire gene (ortholog hit ratios ≥0.75). The catalogs of gene sequences developed in this study made it possible to identify hundreds to thousands of orthologs across diverse scleractinian species and related taxa. We used these sequences for phylogenetic inference, recovering known relationships and demonstrating superior performance over phylogenetic trees constructed using single mitochondrial loci. The resources developed in this study provide gene sequences and genetic markers for several anthozoan species. To enhance the utility of these resources for the research community, we developed searchable databases enabling researchers to rapidly recover sequences for genes of interest. Our analysis of de novo assembly quality highlights metrics that we expect will be useful for evaluating the relative quality of other de novo transcriptome assemblies. The identification of orthologous sequences and phylogenetic reconstruction demonstrates the feasibility of these methods for clarifying the substantial uncertainties in the existing scleractinian phylogeny.

A population genetic assessment of coral recovery on highly disturbed reefs of the Keppel Island archipelago in the southern Great Barrier Reef

Coral reefs surrounding the islands lying close to the coast are unique to the Great Barrier Reef (GBR) in that they are frequently exposed to disturbance events including floods caused by cyclonic rainfall, strong winds and occasional periods of prolonged above-average temperatures during summer. In one such group of islands in the southern GBR, the Keppel Island archipelago, climate-driven disturbances frequently result in major coral mortality. Whilst these island reefs have clearly survived such dramatic disturbances in the past, the consequences of extreme mortality events may include the loss of genetic diversity, and hence adaptive potential, and a reduction in fitness due to inbreeding, especially if new recruitment from external sources is limited. Here we examined the level of isolation of the Keppel Island group as well as patterns of gene flow within the Keppel Islands using 10 microsatellite markers in nine populations of the coral, Acropora millepora. Bayesian cluster analysis and assignment tests indicated gene flow is restricted, but not absent, between the outer and inner Keppel Island groups, and that extensive gene flow exists within each of these island groups. Comparison of the Keppel Island data with results from a previous GBR-wide study that included a single Keppel Island population, confirmed that A. millepora in the Keppel Islands is genetically distinct from populations elsewhere on the GBR, with exception of the nearby inshore High Peak Reef just north of the Keppel Islands. We compared patterns of genetic diversity in the Keppel Island populations with those from other GBR populations and found them to be slightly, but significantly lower, consistent with the archipelago being geographically isolated, but there was no evidence for recent bottlenecks or deviation from mutation-drift equilibrium. A high incidence of private alleles in the Keppel Islands, particularly in the outer islands, supports their relative isolation and contributes to the conservation value of the archipelago. The lack of evidence for genetic erosion, in combination with our observation that the North Keppel Island population samples collected in 2002 and 2008, respectively, exhibited a pairwise genetic distance of zero, supports previous published work indicating that, following bleaching, Acropora corals in the Keppel Islands predominantly recover from regrowth of small amounts of remaining live tissue in apparently dead coral colonies. This is likely supplemented by recruitment of larvae from genetically similar, less disturbed populations at nearby reefs, particularly following extreme flood events.

Linking demographic processes of juvenile corals to benthic recovery trajectories in two common reef habitats

Tropical reefs are dynamic ecosystems that host diverse coral assemblages with different life-history strategies. Here, we quantified how juvenile (<50 mm) coral demographics influenced benthic coral structure in reef flat and reef slope habitats on the southern Great Barrier Reef, Australia. Permanent plots and settlement tiles were monitored every six months for three years in each habitat. These environments exhibited profound differences: the reef slope was characterised by 95% less macroalgal cover, and twice the amount of available settlement substrata and rates of coral settlement than the reef flat. Consequently, post-settlement coral survival in the reef slope was substantially higher than that of the reef flat, and resulted in a rapid increase in coral cover from 7 to 31% in 2.5 years. In contrast, coral cover on the reef flat remained low (~10%), whereas macroalgal cover increased from 23 to 45%. A positive stock-recruitment relationship was found in brooding corals in both habitats; however, brooding corals were not directly responsible for the observed changes in coral cover. Rather, the rapid increase on the reef slope resulted from high abundances of broadcast spawning Acropora recruits. Incorporating our results into transition matrix models demonstrated that most corals escape mortality once they exceed 50 mm, but for smaller corals mortality in brooders was double those of spawners (i.e. acroporids and massive corals). For corals on the reef flat, sensitivity analysis demonstrated that growth and mortality of larger juveniles (21–50 mm) highly influenced population dynamics; whereas the recruitment, growth and mortality of smaller corals (<20 mm) had the highest influence on reef slope population dynamics. Our results provide insight into the population dynamics and recovery trajectories in disparate reef habitats, and highlight the importance of acroporid recruitment in driving rapid increases in coral cover following large-scale perturbation in reef slope environments.

Oceanographic and behavioural assumptions in models of the fate of coral and coral reef fish larvae

A predictive model of the fate of coral reef fish larvae in a reef system is proposed that combines the oceanographic processes of advection and turbulent diffusion with the biological process of horizontal swimming controlled by olfactory and auditory cues within the timescales of larval development. In the model, auditory cues resulted in swimming towards the reefs when within hearing distance of the reef, whereas olfactory cues resulted in the larvae swimming towards the natal reef in open waters by swimming against the concentration gradients in the smell plume emanating from the natal reef. The model suggested that the self-seeding rate may be quite large, at least 20% for the larvae of rapidly developing reef fish species, which contrasted with a self-seeding rate less than 2% for non-swimming coral larvae. The predicted self-recruitment rate of reefs was sensitive to a number of parameters, such as the time at which the fish larvae reach post-flexion, the pelagic larval duration of the larvae, the horizontal turbulent diffusion coefficient in reefal waters and the horizontal swimming behaviour of the fish larvae in response to auditory and olfactory cues, for which better field data are needed. Thus, the model suggested that high self-seeding rates for reef fish are possible, even in areas where the 'sticky water' effect is minimal and in the absence of long-term trapping in oceanic fronts and/or large-scale oceanic eddies or filaments that are often argued to facilitate the return of the larvae after long periods of drifting at sea.

Population genetic structure and demographic history of Atrina pectinata based on mitochondrial DNA and microsatellite markers

The pen shell, Atrina pectinata, is one of the commercial bivalves in East Asia and thought to be recently affected by anthropogenic pressure (habitat destruction and/or fishing pressure). Information on its population genetic structure is crucial for the conservation of A. pectinata. Considering its long pelagic larval duration and iteroparity with high fecundity, the genetic structure for A. pectinata could be expected to be weak at a fine scale. However, the unusual oceanography in the coasts of China and Korea suggests potential for restricted dispersal of pelagic larvae and geographical differentiation. In addition, environmental changes associated with Pleistocene sea level fluctuations on the East China Sea continental shelf may also have strongly influenced historical population demography and genetic diversity of marine organisms. Here, partial sequences of the mitochondrial Cytochrome c oxidase subunit I (COI) gene and seven microsatellite loci were used to estimate population genetic structure and demographic history of seven samples from Northern China coast and one sample from North Korea coast. Despite high levels of genetic diversity within samples, there was no genetic differentiation among samples from Northern China coast and low but significant genetic differentiation between some of the Chinese samples and the North Korean sample. A late Pleistocene population expansion, probably after the Last Glacial Maximum, was also demonstrated for A. pectinata samples. No recent genetic bottleneck was detected in any of the eight samples. We concluded that both historical recolonization (through population range expansion and demographic expansion in the late Pleistocene) and current gene flow (through larval dispersal) were responsible for the weak level of genetic structure detected in A. pectinata.

Subtle genetic structure reveals restricted connectivity among populations of a coral reef fish inhabiting remote atolls

We utilized a spatial and temporal analyses of genetic structure, supplemented with ecological and oceanographic analysis, to assess patterns of population connectivity in a coral reef fish Chromis margaritifer among the unique and remote atolls in the eastern Indian Ocean. A subtle, but significant genetic discontinuity at 10 microsatellite DNA loci was detected between atoll systems corresponding with a low (≤ 1%) probability of advection across the hundreds of kilometers of open ocean that separates them. Thus, although genetic connections between systems are likely maintained by occasional long-distance dispersal of C. margaritifer larvae, ecological population connectivity at this spatial scale appears to be restricted. Further, within one of these atoll systems, significant spatial differentiation among samples was accompanied by a lack of temporal pairwise differentiation between recruit and adult samples, indicating that restrictions to connectivity also occur at a local scale (tens of kilometers). In contrast, a signal of panmixia was detected at the other atoll system studied. Lastly, greater relatedness and reduced genetic diversity within recruit samples was associated with relatively large differences among them, indicating the presence of sweepstakes reproduction whereby a small proportion of adults contributes to recruitment in the next generation. These results are congruent with earlier work on hard corals, suggesting that local production of larvae drives population replenishment in these atoll systems for a range of coral reef species.

Rarity and genetic diversity in Indo-Pacific Acropora corals

Among various potential consequences of rarity is genetic erosion. Neutral genetic theory predicts that rare species will have lower genetic diversity than common species. To examine the association between genetic diversity and rarity, variation at eight DNA microsatellite markers was documented for 14 Acropora species that display different patterns of distribution and abundance in the Indo-Pacific Ocean. Our results show that the relationship between rarity and genetic diversity is not a positive linear association because, contrary to expectations, some rare species are genetically diverse and some populations of common species are genetically depleted. Our data suggest that inbreeding is the most likely mechanism of genetic depletion in both rare and common corals, and that hybridization is the most likely explanation for higher than expected levels of genetic diversity in rare species. A significant hypothesis generated from our study with direct conservation implications is that as a group, Acropora corals have lower genetic diversity at neutral microsatellite loci than may be expected from their taxonomic diversity, and this may suggest a heightened susceptibility to environmental change. This hypothesis requires validation based on genetic diversity estimates derived from a large portion of the genome.

Maternal-larval population genetic traits in Stylophora pistillata, a hermaphroditic brooding coral species

Aspects of maternal-planula larval genetics in the monoecious scleractinian coral Stylophora pistillata (Red Sea, Eilat) were studied by amplified fragment length polymorphism (AFLP) methodology in two successive reproductive seasons. In total, 293 planulae and 10 adult colonies were analyzed. In June 2006, 147 planulae were collected from 10 shallow water colonies. In March, April and June 2007, 146 additional planulae were sampled from five of the ten 2006 sampled colonies. All AFLP products showed unalike band profiles indicating a fully sexual production pattern. We used 181 and 210 putative AFLP loci, of which the overall level of polymorphism in 2006 was 92 and 99  % in 2007 (respectively). Differences were also observed between 2006 and 2007 reproductive seasons in terms of total average gene diversity (0.191 vs. 0.247, respectively), suggesting fast turnover of sperm donor genotypes. In addition, increased numbers of potential sperm donor colonies in the vicinity of gravid females showed no impact on genetic differentiation levels in released larvae. UPGMA tree revealed clustering of maternal genotypes and their offspring, suggesting, as expected, high relatedness between planulae and their mothers. In addition, the average heterozygosity of each group of siblings was persistently lower than heterozygosity calculated for the respective maternal colony, suggesting the possibility of partial inbreeding. This trend of reduced genetic heterogeneity in Stylophora pistillata is an alarming sign for populations residing in the northern Red Sea coral reefs.

An assessment of residence times of land-sourced contaminants in the Great Barrier Reef lagoon and the implications for management and reef recovery

We argue that the residence times of key pollutants exported to the Great Barrier Reef (GBR) are greater in the GBR lagoon than those of the water itself, in contradiction to some previous assumptions. Adverse effects of the pollutant discharge will be greater and longer lasting than previously considered, in turn requiring stronger or more urgent action to remediate land practices. Residence times of fine sediments, nitrogen and phosphorus, pesticides and trace metals are suggested to be from years to decades in the GBR lagoon and highly likely to be greater than the residence time of water, estimated at around 15-365days. The recovery of corals and seagrass in the central region of the GBR following current land-use remediation in the catchment depends on the residence time of these contaminants. Ecohydrological modeling suggests that this recovery may take decades even with adequate levels of improved land management practices.

Gene flow and genetic diversity of a broadcast-spawning coral in northern peripheral populations

Recently, reef-building coral populations have been decreasing worldwide due to various disturbances. Population genetic studies are helpful for estimating the genetic connectivity among populations of marine sessile organisms with metapopulation structures such as corals. Moreover, the relationship between latitude and genetic diversity is informative when evaluating the fragility of populations. In this study, using highly variable markers, we examined the population genetics of the broadcast-spawning coral Acropora digitifera at 19 sites in seven regions along the 1,000 km long island chain of Nansei Islands, Japan. This area includes both subtropical and temperate habitats. Thus, the coral populations around the Nansei Islands in Japan are northern peripheral populations that would be subjected to environmental stresses different from those in tropical areas. The existence of high genetic connectivity across this large geographic area was suggested for all sites (F_ST≤0.033) although small but significant genetic differentiation was detected among populations in geographically close sites and regions. In addition, A. digitifera appears to be distributed throughout the Nansei Islands without losing genetic diversity. Therefore, A. digitifera populations in the Nansei Islands may be able to recover relatively rapidly even when high disturbances of coral communities occur locally if populations on other reefs are properly maintained.

Genetic divergence across habitats in the widespread coral Seriatopora hystrix and its associated Symbiodinium

BACKGROUND

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.

METHODOLOGY/PRINCIPAL FINDINGS

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.

CONCLUSIONS/SIGNIFICANCE

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.

Patterns of genetic structuring in the coral Pocillopora damicornis on reefs in East Africa

Background

Studies of population genetic structures provide an indication of direction and magnitude of larval transport and hence are an important component in the assessment of the ability of reefs to recover from severe disturbance. This paper reports data on population genetic structures in the coral Pocillopora damicornis from 26 reefs in Kenya and Tanzania.

Results

Gene flow among reefs was found to be variable, with a significant overall genetic subdivision (F_ST = 0.023 ± 0.004 SE; p < 0.001), however, only 34% of all pairwise population comparisons showed significant differentiation. Panmixia could not be rejected between reefs separated by as much as 697 km, while other sites, separated by only a single kilometre, were found to be significantly differentiated. An analysis of molecular variance indicated that population genetic differentiation was significant only at the smaller spatial scale (< 10 km), whereas panmixia could not be rejected between groups of samples separated by over 100 km. Estimates of contemporary gene flow showed similar results, with numbers of first generation migrants within each population ranging from 0 to 4 (~5% of the total number of colonies sampled) and likely dispersal distances ranging between 5 and 500 km.

Conclusion

This study showed that population differentiation in P. damicornis varied over spatial scales and that this variability occurred at both evolutionary and ecological time scales. This paradox is discussed in light of stochastic recruitment and small scale population structures found in other species of coral. The study also identifies potential source reefs, such as those within Mnemba Conservation area near Zanzibar and genetically isolated reefs such as those within Malindi Marine National Park and Reserve in northern Kenya.

Genetic diversity and connectivity in a brooding reef coral at the limit of its distribution

Remote populations are predicted to be vulnerable owing to their isolation from potential source reefs, and usually low population size and associated increased extinction risk. We investigated genetic diversity, population subdivision and connectivity in the brooding reef coral Seriatopora hystrix at the limits of its Eastern Australian (EA) distribution and three sites in the southern Great Barrier Reef (GBR). Over the approximately 1270 km survey range, high levels of population subdivision were detected (global F(ST) = 0.224), with the greatest range in pairwise F(ST) values observed among the three southernmost locations: Lord Howe Island, Elizabeth Reef and Middleton Reef. Flinders Reef, located between the GBR and the more southerly offshore reefs, was highly isolated and showed the signature of a recent bottleneck. High pairwise F(ST) values and the presence of multiple genetic clusters indicate that EA subtropical coral populations have been historically isolated from each other and the GBR. One putative first-generation migrant was detected from the GBR into the EA subtropics. Occasional long-distance dispersal is supported by changes in species composition at these high-latitude reefs and the occurrence of new species records over the past three decades. While subtropical populations exhibited significantly lower allelic richness than their GBR counterparts, genetic diversity was still moderately high. Furthermore, subtropical populations were not inbred and had a considerable number of private alleles. The results suggest that these high-latitude S. hystrix populations are supplemented by infrequent long-distance migrants from the GBR and may have adequate population sizes to maintain viability and resist severe losses of genetic diversity.