Sperm dispersal distances estimated by parentage analysis in a brooding scleractinian coral

Replayed reef sounds induce settlement of Favia fragum coral larvae in aquaria and field environmentsa)

Acoustic cues of healthy reefs are known to support critical settlement behaviors for one reef-building coral, but acoustic responses have not been demonstrated in additional species. Settlement of Favia fragum larvae in response to replayed coral reef soundscapes were observed by exposing larvae in aquaria and reef settings to playback sound treatments for 24-72 h. Settlement increased under 24 h sound treatments in both experiments. The results add to growing knowledge that acoustically mediated settlement may be widespread among stony corals with species-specific attributes, suggesting sound could be one tool employed to rehabilitate and build resilience within imperiled reef communities.

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.

PMSeeker: A Scheme Based on the Greedy Algorithm and the Exhaustive Algorithm to Screen Low-Redundancy Marker Sets for Large-Scale Parentage Assignment with Full Parental Genotyping

Parentage assignment is a genetic test that utilizes genetic characteristics, such as molecular markers, to identify the parental relationships within populations, which, in commercial fish farming, are almost always large and where full information on potential parents is known. To accurately find the true parents, the genotypes of all loci in the parentage marker set (PMS) are required for each individual being tested. With the same accuracy, a PMS containing a smaller number of markers will undoubtedly save experimental costs. Thus, this study established a scheme to screen low-redundancy PMSs using the exhaustive algorithm and greedy algorithm. When screening PMSs, the greedy algorithm selects markers based on the parental dispersity index (PDI), a uniquely defined metric that outperforms the probability of exclusion (PE). With the conjunctive use of the two algorithms, non-redundant PMSs were found for more than 99.7% of solvable cases in three groups of random sample experiments in this study. Then, a low-redundancy PMS can be composed using two or more of these non-redundant PMSs. This scheme effectively reduces the number of markers in PMSs, thus conserving human and experimental resources and laying the groundwork for the widespread implementation of parentage assignment technology in economic species breeding.

Rampant asexual reproduction and limited dispersal in a mangrove population of the coral Porites divaricata

Corals are critical to marine biodiversity. Reproduction and dispersal are key to their resilience, but rarely quantified in nature. Exploiting a unique system-a fully censused, longitudinally characterized, semi-isolated population inhabiting mangroves-we used 2bRAD sequencing to demonstrate that rampant asexual reproduction most likely via parthenogenesis and limited dispersal enable the persistence of a natural population of thin-finger coral (Porites divaricata). Unlike previous studies on coral dispersal, knowledge of colony age and location enabled us to identify plausible parent-offspring relationships within multiple clonal lineages and develop tightly constrained estimates of larval dispersal; the best-fitting model indicates dispersal is largely limited to a few metres from parent colonies. Our results explain why this species is adept at colonizing mangroves but suggest limited genetic diversity in mangrove populations and limited connectivity between mangroves and nearby reefs. As P. divaricata is gonochoristic, and parthenogenesis would be restricted to females (whereas fragmentation, which is presumably common in reef and seagrass habitats, is not), mangrove populations likely exhibit skewed sex ratios. These findings suggest that coral reproductive diversity can lead to distinctly different demographic outcomes in different habitats. Thus, coral conservation will require the protection of the entire coral habitat mosaic, and not just reefs.

Soft coral reproductive phenology along a depth gradient: Can "going deeper" provide a viable refuge?

Many species across a wide range of taxa and habitats display phenological shifts and differences in response to both environmental gradients and climate change. Moreover, the wide‐scale decline of numerous ecosystems is leading to increasing efforts to identify zones that might serve as natural refuges from various disturbances, including ocean warming. One such refuge was suggested to be that of the deep coral reefs, but whether depth can provide coral populations with a viable and reproductive refuge remains unclear. Given the global coral‐reef degradation and the key role that corals play as ecosystem engineers, their reproductive ecology has been widely studied. A particular knowledge gap nonetheless exists regarding coral reproductive phenology along a depth gradient. Filling in this gap may uncover the environmental cues that regulate coral reproduction, leading to better predictions of population connectivity, and their possible responses to climate change and other environmental changes. Here, using long‐term in situ observations of the soft coral Rhytisma fulvum's reproductive activity along its entire depth range (0–45 m), we examined the relationship among several environmental factors and the coral's reproductive phenology and activity over five successive annual breeding seasons. Compared with the shallow depths, a lower number of reproducing colonies was found in habitats deeper than 30 m, highlighting possible constraints on coral reproduction at the deeper end of their range. Our results further revealed that an increase in seawater temperature over 1–2‐day intervals during the breeding season correlated with the onset of reproductive activity along the depth gradient, leading to different reproductive periodicities in different depths. These differences suggest that differential temperature regimes and reproductive timing across depth may create intraspecific temporal reproductive segregation, possibly reducing connectivity among populations along a depth gradient. Moreover, we found high variability among years in both the timing of breeding activities and in the level of reproductive synchrony among corals from different depths. Overall, our study questions whether depth can provide a long‐term and viable refuge for corals in the face of global environmental changes.

Settling in aggregation: Spatial planning consideration for brooding coral transplants

Aggregated larval co-settlement has been documented in myriad marine invertebrate taxa, shaping adult population structures. Still, kinship settlement patterns in brooding corals have not been studied in detail, especially under scenarios of enhanced larval assemblies. Employing two sets of ex-situ experiments, planulae staining for kinship resolution and a computer random settlement simulation, we show that larval settlement of the coral Stylophora pistillata, a brooding species in the Gulf of Aqaba/Eilat, is mostly affected by the number of larval donors, and that larvae tend to aggregate (up to 50% tissue-contacts; distances <3 mm), compared to 3% predicted in a computer simulation, all without a kinship-bias. Field surveys on juvenile colonies revealed a similar clustering pattern. Although aggregated settlement inevitably carries disadvantages such as intraspecific competition, it may be bracketed in adult colonies with benefits such as enhanced fertilization and chimerism-related ecological advantages, including augmented colony size and survivorship. These improved life-history traits of brooding coral species that aggregate could be harnessed as applied ecological engineering tools in reef restoration acts.

Deep connections: divergence histories with gene flow in mesophotic Agaricia corals

Largely understudied, mesophotic coral ecosystems lie below shallow reefs (at >30 m depth) and comprise ecologically distinct communities. Brooding reproductive modes appear to predominate among mesophotic‐specialist corals and may limit genetic connectivity among populations. Using reduced representation genomic sequencing, we assessed spatial population genetic structure at 50 m depth in an ecologically important mesophotic‐specialist species Agaricia grahamae, among locations in the Southern Caribbean. We also tested for hybridisation with the closely related (but depth‐generalist) species Agaricia lamarcki, within their sympatric depth zone (50 m). In contrast to our expectations, no spatial genetic structure was detected between the reefs of Curaçao and Bonaire (~40 km apart) within A. grahamae. However, cryptic taxa were discovered within both taxonomic species, with those in A. lamarcki (incompletely) partitioned by depth and those in A. grahamae occurring sympatrically (at the same depth). Hybrid analyses and demographic modelling identified contemporary and historical gene flow among cryptic taxa, both within and between A. grahamae and A. lamarcki. These results (1) indicate that spatial connectivity and subsequent replenishment may be possible between islands of moderate geographic distances for A. grahamae, an ecologically important mesophotic species, (2) that cryptic taxa occur in the mesophotic zone and environmental selection along shallow to mesophotic depth gradients may drive divergence in depth‐generalists such as A. lamarcki, and (3) highlight that gene flow links taxa within this relativity diverse Caribbean genus.

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.

Parentage analyses identify local dispersal events and sibling aggregations in a natural population of Millepora hydrocorals, a free-spawning marine invertebrate

Dispersal is a critical process for the persistence and productivity of marine populations. For many reef species, there is increasing evidence that local demography and self-recruitment have major consequences on their genetic diversity and adaptation to environmental change. Yet empirical data of dispersal patterns in reef-building species remain scarce. Here, we document the first genetic estimates of self-recruitment and dispersal distances in a free-spawning marine invertebrate, the hydrocoral Millepora cf. platyphylla. Using twelve microsatellite markers, we gathered genotypic information from 3,160 georeferenced colonies collected over 27,000 m² of a single reef in three adjacent habitats in Moorea, French Polynesia; the mid slope, upper slope, and back reef. Although the adult population was predominantly clonal (85% were clones), our parentage analysis revealed a moderate self-recruitment rate with a minimum of 8% of sexual propagules produced locally. Assigned offspring often settled at <10 m from their parents and dispersal events decrease with increasing geographic distance. There were no discrepancies between the dispersal distances of offspring assigned to parents belonging to clonal versus nonclonal genotypes. Interhabitat dispersal events via cross-reef transport were also detected for sexual and asexual propagules. Sibship analysis showed that full siblings recruit nearby on the reef (more than 40% settled at <30 m), resulting in sibling aggregations. Our findings highlight the importance of self-recruitment together with clonality in stabilizing population dynamics, which may ultimately enhance local sustainability and resilience to disturbance.

Mixed mating system and variable mating patterns in tropical woody bamboos

BACKGROUND

So far, little is known in detail about mating systems of woody bamboos. Paternity analysis of offspring improved our understanding of these systems, and contributed to their germplasm conservation and genetic improvement.

RESULTS

In this study, a paternity analysis of offspring from two consecutive mass or sporadically flowering events of Dendrocalamus membranaceus and D. sinicus were conducted to determine their mating system and pollen dispersal using the program COLONY based on simple sequence repeat (SSR) markers. Two sporadically flowering populations of D. sinicus (C1, C2) obtained relatively high paternity assignments rates (69.0-71.4%). Meanwhile, among three populations of D. membranaceus, the sporadically flowering population A also had much higher paternity assignments rates (56.4%) than mass flowering populations B1(28.6%) and B2 (42.5%). Both D. membranaceus and D. sinicus had mixed mating systems while their mating patterns were variable depending on pollination conditions. The maximum pollen dispersal distances were 90 m and 4378 m for D. membranaceus and D. sinicus populations, respectively, and the mating distances of these two species focused on ranges of ca. 0-50 m and 0-1500 m, respectively.

CONCLUSIONS

These results revealed for the first time variable mating patterns in woody bamboos. This suggests half-sib seeds from the same bamboo clump may have different male parents and it is crucial to clarify genetic origin in woody bamboos' breeding programs. The results also indicate the importance of pollinators in the mating systems of tropical woody bamboos.

Genetic diversity, connectivity and gene flow along the distribution of the emblematic Atlanto-Mediterranean sponge Petrosia ficiformis (Haplosclerida, Demospongiae)

BACKGROUND

Knowledge about the distribution of the genetic variation of marine species is fundamental to address species conservation and management strategies, especially in scenarios with mass mortalities. In the Mediterranean Sea, Petrosia ficiformis is one of the species most affected by temperature-related diseases. Our study aimed to assess its genetic structure, connectivity, and bottleneck signatures to understand its evolutionary history and to provide information to help design conservation strategies of sessile marine invertebrates.

RESULTS

We genotyped 280 individuals from 19 locations across the entire distribution range of P. ficiformis in the Atlanto-Mediterranean region at 10 microsatellite loci. High levels of inbreeding were detected in most locations (especially in the Macaronesia and the Western Mediterranean) and bottleneck signatures were only detected in Mediterranean populations, although not coinciding entirely with those with reported die-offs. We detected strong significant population differentiation, with the Atlantic populations being the most genetically isolated, and show that six clusters explained the genetic structure along the distribution range of this sponge. Although we detected a pattern of isolation by distance in P. ficiformis when all locations were analyzed together, stratified Mantel tests revealed that other factors could be playing a more prominent role than isolation by distance. Indeed, we detected a strong effect of oceanographic barriers impeding the gene flow among certain areas, the strongest one being the Almeria-Oran front, hampering gene flow between the Atlantic Ocean and the Mediterranean Sea. Finally, migration and genetic diversity distribution analyses suggest a Mediterranean origin for the species.

CONCLUSIONS

In our study Petrosia ficiformis showed extreme levels of inbreeding and population differentiation, which could all be linked to the poor swimming abilities of the larva. However, the observed moderate migration patterns are highly difficult to reconcile with such poor larval dispersal, and suggest that, although unlikely, dispersal may also be achieved in the gamete phase. Overall, because of the high genetic diversity in the Eastern Mediterranean and frequent mass mortalities in the Western Mediterranean, we suggest that conservation efforts should be carried out specifically in those areas of the Mediterranean to safeguard the genetic diversity of the 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.

Can mesophotic reefs replenish shallow reefs? Reduced coral reproductive performance casts a doubt

Mesophotic coral ecosystems (i.e., deep coral reefs at 30-120 m depth) appear to be thriving while many shallow reefs in the world are declining. Amid efforts to understand and manage their decline, it was suggested that mesophotic reefs might serve as natural refuges and a possible source of propagules for the shallow reefs. However, our knowledge of how reproductive performance of corals alters with depth is sparse. Here, we present a comprehensive study of the reproductive phenology, fecundity, and abundance of seven reef-building conspecific corals in shallow and mesophotic habitats. Significant differences were found in the synchrony and timing of gametogenesis and spawning between shallow and mesophotic coral populations. Thus, mesophotic populations exhibited delayed or protracted spawning events, which led to spawning of the mesophotic colonies in large proportions at times where the shallow ones had long been depleted of reproductive material. All species investigated demonstrated a substantial reduction in fecundity and/or oocyte sizes at mesophotic depths (40-60 m). Two species (Seriatopora hystrix and Galaxea fascicularis) displayed a reduction in both fecundity and oocyte size at mesophotic depths. Turbinaria reniformis had only reduced fecundity and Acropora squarrosa and Acropora valida only reduced oocyte size. In Montipora verrucosa, reduced fecundity was found during one annual reproductive season while, in the following year, only reduced oocyte size was found. In contrast, reduced oocyte size in mesophotic populations of Acropora squarrosa was consistent along three studied years. One species, Acropora pharaonis, was found to be infertile at mesophotic depths along two studied years. This indicates that reproductive performance decreases with depth; and that although some species are capable of reproducing at mesophotic depths, their contribution to the replenishment of shallow reefs may be inconsequential. Reduced reproductive performance with depth, combined with the possible narrower tolerance to environmental factors, further suggests that mesophotic corals may in fact be more vulnerable than previously conceived. Furthermore, we posit that the observed temporal segregation in reproduction could lead to assortative mating, and this, in turn, may facilitate adaptive divergence across depth.

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.

Genetic diversity and differentiation in reef-building Millepora species, as revealed by cross-species amplification of fifteen novel microsatellite loci

Quantifying the genetic diversity in natural populations is crucial to address ecological and evolutionary questions. Despite recent advances in whole-genome sequencing, microsatellite markers have remained one of the most powerful tools for a myriad of population genetic approaches. Here, we used the 454 sequencing technique to develop microsatellite loci in the fire coral Millepora platyphylla, an important reef-builder of Indo-Pacific reefs. We tested the cross-species amplification of these loci in five other species of the genus Millepora and analysed its success in correlation with the genetic distances between species using mitochondrial 16S sequences. We succeeded in discovering fifteen microsatellite loci in our target species M. platyphylla, among which twelve were polymorphic with 2–13 alleles and a mean observed heterozygosity of 0.411. Cross-species amplification in the five other Millepora species revealed a high probability of amplification success (71%) and polymorphism (59%) of the loci. Our results show no evidence of decreased heterozygosity with increasing genetic distance. However, only one locus enabled measures of genetic diversity in the Caribbean species M. complanata due to high proportions of null alleles for most of the microsatellites. This result indicates that our novel markers may only be useful for the Indo-Pacific species of Millepora. Measures of genetic diversity revealed significant linkage disequilibrium, moderate levels of observed heterozygosity (0.323–0.496) and heterozygote deficiencies for the Indo-Pacific species. The accessibility to new polymorphic microsatellite markers for hydrozoan Millepora species creates new opportunities for future research on processes driving the complexity of their colonisation success on many Indo-Pacific reefs.

Deep reefs are not universal refuges: Reseeding potential varies among coral species

Deep coral reefs (that is, mesophotic coral ecosystems) can act as refuges against major disturbances affecting shallow reefs. It has been proposed that, through the provision of coral propagules, such deep refuges may aid in shallow reef recovery; however, this "reseeding" hypothesis remains largely untested. We conducted a genome-wide assessment of two scleractinian coral species with contrasting reproductive modes, to assess the potential for connectivity between mesophotic (40 m) and shallow (12 m) depths on an isolated reef system in the Western Atlantic (Bermuda). To overcome the pervasive issue of endosymbiont contamination associated with de novo sequencing of corals, we used a novel subtraction reference approach. We have demonstrated that strong depth-associated selection has led to genome-wide divergence in the brooding species Agaricia fragilis (with divergence by depth exceeding divergence by location). Despite introgression from shallow into deep populations, a lack of first-generation migrants indicates that effective connectivity over ecological time scales is extremely limited for this species and thus precludes reseeding of shallow reefs from deep refuges. In contrast, no genetic structuring between depths (or locations) was observed for the broadcasting species Stephanocoenia intersepta, indicating substantial potential for vertical connectivity. Our findings demonstrate that vertical connectivity within the same reef system can differ greatly between species and that the reseeding potential of deep reefs in Bermuda may apply to only a small number of scleractinian species. Overall, we argue that the "deep reef refuge hypothesis" holds for individual coral species during episodic disturbances but should not be assumed as a broader ecosystem-wide phenomenon.