Elemental signatures of Acanthochromis polyacanthus otoliths from the Great Barrier Reef have significant temporal, spatial, and between-brood variation

We evaluated the spatial and temporal scales over which otolith signatures varied in a reef fish on the Great Barrier Reef (GBR) using the non-dispersing damselfish Acanthochromis polyacanthus. We found a robust multi-element separation in otolith signatures from reef clusters in the northern and southern GBR. Variance components indicated that this spatial scale accounted for the majority of the variation in two elemental ratios (Ba/Ca and Sr/Ca) over the 2 years of the study. There was also significant variation in elemental signatures between otoliths collected over two consecutive years, as well as within a season. Individual reefs within clusters were less distinguishable based on otolith chemistry and were probably observed by differences within reefs (among sites and broods within sites). These results indicate that it may be difficult to determine the reef of origin for individual fish using otolith chemistry, while determining natal region seems a realistic goal.     

DNA microsatellites in Acanthochromis polyacanthus

To determine genetic substructuring in populations of the spiny damselfish Acanthochromis polyacanthus among different reefs of the Great Barrier Reef, Australia, we characterized six polymorphic microsatellite loci.     

STRONG GENETIC DIVERGENCE AMONG POPULATIONS OF A MARINE FISH WITH LIMITED DISPERSAL, ACANTHOCHROMIS POLYACANTHUS, WITHIN THE GREAT BARRIER REEF AND THE CORAL SEA

Abstract Acanthochromis polyacanthus is an unusual tropical marine damselfish that uniquely lacks pelagic larvae and has lost the capacity for broad‐scale dispersal among coral reefs. On the modern Great Barrier Reef (GBR), three color morphs meet and hydridize at two zones of secondary contact. Allozyme electrophoreses revealed strong differences between morphs from the southern zone but few differences between morphs from the northern counterpart, thus suggesting different contact histories. We explore the phylogeography of Acanthochromis polyacanthus with mitochondrial cytochrome b region sequences (alignment of 565 positions) obtained from 126 individuals representing seven to 12 fish from 13 sites distributed over 12 reefs of the GBR and the Coral Sea. The samples revealed three major clades: (1) black fish collected from the southern GBR; (2) bicolored fish collected from the GBR and one reef (Osprey) from the northern Coral Sea; (3) black and white monomorphs collected from six reefs in the Coral Sea. All three clades were well supported (72–100%) by bootstrap analyses. Sequence divergences were very high between the major clades (mean = 7.6%) as well as within them (2.0–3.6%). Within clades, most reefs segregated as monophyletic assemblages. This was revealed both by phylogenetic analyses and AMOVAs that showed that 72–90% of the variance originated from differences among groups, whereas only 5–13% originated within populations. These patterns are discussed in relation to the known geological history of coral reefs of the GBR and the Coral Sea. Finally, we ask whether the monospecific status of Acanthochromis should be revisited because the sequence divergences found among our samples is substantially greater than those recorded among well‐recognized species in other reef fishes.     

Wave-induced abiotic stress shapes phenotypic diversity in a coral reef fish across a geographical cline

While morphological variation across geographical clines has been well documented, it is often unclear whether such changes enhance individual performance to local environments. We examined whether the damselfish Acanthochromis polyacanthus display functional changes in swimming phenotype across a 40-km cline in wave-driven water motion on the Great Barrier Reef, Australia. A. polyacanthus populations displayed strong intraspecific variation in swimming morphology and performance that matched local levels of water motion: individuals on reefs subject to high water motion displayed higher aspect-ratio fins and faster swimming speeds than conspecifics on sheltered reefs. Remarkably, intraspecific variation within A. polyacanthus spanned over half the diversity seen among closely related damselfish species from the same region. We find that local selection driven by wave-induced abiotic stress is an overarching ecological mechanism shaping the inter- and intraspecific locomotor diversity of coral reef fishes.     

Clones or clans: the genetic structure of a deep‐sea sponge,Aphrocallistes vastus,in unique sponge reefs of British Columbia,Canada

Understanding patterns of reproduction, dispersal and recruitment in deep‐sea communities is increasingly important with the need to manage resource extraction and conserve species diversity. Glass sponges are usually found in deep water (>1000 m) worldwide but form kilometre‐long reefs on the continental shelf of British Columbia and Alaska that are under threat from trawling and resource exploration. Due to their deep‐water habitat, larvae have not yet been found and the level of genetic connectivity between reefs and nonreef communities is unknown. The genetic structure of Aphrocallistes vastus, the primary reef‐building species in the Strait of Georgia (SoG) British Columbia, was studied using single nucleotide polymorphisms (SNPs). Pairwise comparisons of multilocus genotypes were used to assess whether sexual reproduction is common. Structure was examined 1) between individuals in reefs, 2) between reefs and 3) between sites in and outside the SoG. Sixty‐seven SNPs were genotyped in 91 samples from areas in and around the SoG, including four sponge reefs and nearby nonreef sites. The results show that sponge reefs are formed through sexual reproduction. Within a reef and across the SoG basin, the genetic distance between individuals does not vary with geographic distance (r = ?0.005 to 0.014), but populations within the SoG basin are genetically distinct from populations in Barkley Sound, on the west coast of Vancouver Island. Population structure was seen across all sample sites (global F_ST = 0.248), especially between SoG and non‐SoG locations (average pairwise F_ST = 0.251). Our results suggest that genetic mixing occurs across sponge reefs via larvae that disperse widely.     

GENETIC AND COLOR INTERACTIONS AT A CONTACT ZONE OF ACANTHOCHROMIS POLYACANTHUS: A MARINE FISH LACKING PELAGIC LARVAE

Abstract. — Acanthochromis polyacanthus is an unusual tropical marine damselfish that uniquely lacks pelagic larvae and has lost the capacity for broad-scale dispersal among coral reefs. Different color morphs exist in different regions of the Great Barrier Reef, and morphs from northern and southern regions are genetically distinct. In the Hydrographers Passage area, which is a large break through the reef matrix in the central Great Barrier Reef that may have acted as a bottleneck on the migration of these animals during sea level rise, three morphs recognized from other regions were found on neighboring reefs. The transition between them is abrupt with three loci (AAT-2*, GPI-1*, and PGM*) showing allelic frequency patterns close to fixation between opposite alleles within a few kilometers. On two reefs (Hyde, Bebe), a pair of morphs was found to coexist and exhibited a habitat partitioning pattern with each morph restricted to one side on the reef and steep transitions in between. Outside these transition zones, phenotypes and genotypes matched those on surrounding reefs without coexistence and were little changed from reefs several hundred kilometers away. An electrophoretic survey across one transition zone on Hyde Reef showed steep genetic gradients along one kilometer of reef slope. Significant linkage disequilibria in samples collected in Hyde Reef as a result of dispersal of parental combinations of alleles into the center or because parental combinations of alleles confer greater fitness, allowed us to estimate the dispersal rate (189 m/generation) and the selection pressure on the marker loci (0.411). Finally, we investigated models that could lead to such a steep transition in genotypic and phenotypic combinations. Both contact zones on each side of Hyde Reef were associated with geomorphological discontinuities in the reef structure. We suggest that assortative mating may be a proximal mechanism for maintaining isolated each color morph, which could be reinforced by selective predation against hybrids outside the zone of their formation (i.e., the frequency-dependent selection model of Mallet and Barton (1989). Acanthochromis is a midwater planktivore and, when in coexistence, the two morphs forage in different habitats amid multispecific flocks of other damselfishes of matching colors.     

Habitat selection and juvenile persistence control the distribution of two closely related Caribbean damselfishes

Summary On many Caribbean fringing coral reefs, two closely related and ecologically similar damselfishes, the beaugregory (Stegastes leucostictus Müller and Troschel) and the cocoa damselfish (S. variabilis Castelnau), occupy nonoverlapping vertical distributions. In St. Croix (USVI), beaugregory are very abundant in shallow water back reef habitats (1–2 m depth) while cocoa damselfish are restricted to the base of the forereef (10–15 m depth).In this study, the roles of habitat selection at settlement and juvenile persistence were investigated to determine their influence on this pattern of zonation. Settlement events observed at intervals over a two-year period revealed that habitat selection occurred at settlement and was confined to habitats occupied by adults. In addition, differences in juvenile persistence (due to mortality and/or emigration) were found when species were translocated between depths. Over a period of 100-days, juvenile beaugregory moved from 1 m to 12 m depth suffered four-fold greater losses at the deeper sites than shallow water controls, while translocated cocoa damselfish suffered twice as many losses in shallow water than controls at 12 m depth. Despite these differences in persistence, growth rates of the two species were similar and independent of depth. These results indicate that preferential habitat selection at settlement, perhaps an evolutionary response to differential juvenile mortality, may play a deciding role in determining distributions of ecologically similar species of coral reef fishes.     

Kin recognition in embryonic damselfishes

Predator‐induced mortality rates are highest in early life stages; therefore, early recognition of threats can greatly increase survival chances. Some species of coral reef fishes have been frequently found to recruit back to their natal reefs; in this instance, there is a high chance of juveniles encountering their siblings, among other kin, after hatching. Kin recognition plays an important ecological role in that it allows individuals to protect genetically similar relatives, and hence increase their inclusive fitness. By observing changes in heart rates, we demonstrated that embryos of two damselfish species, Acanthochromis polyacanthus and Amphiprion melanopus, not only possess recognition of kin and damage‐released alarm odours, but also react to them in a graded manner. Such refined olfactory capabilities in embryonic stage organisms (seven and eleven days after fertilisation) suggest identification of threats may provide survival advantages post‐hatching, such as the informed choice of low risk habitats at settlement. To our knowledge this is the first time that kin recognition has been identified in embryos of any species.     

Impact of cyclones on hard coral and metapopulation structure,connectivity and genetic diversity of coral reef fish

Cyclones have one of the greatest effects on the biodiversity of coral reefs and the associated species. But it is unknown how stochastic alterations in habitat structure influence metapopulation structure, connectivity and genetic diversity. From 1993 to 2018, the reefs of the Capricorn Bunker Reef group in the southern part of the Great Barrier Reef were impacted by three tropical cyclones including cyclone Hamish (2009, category 5). This resulted in substantial loss of live habitat-forming coral and coral reef fish communities. Within 6–8 years after cyclones had devastated, live hard corals recovered by 50–60%. We show the relationship between hard coral cover and the abundance of the neon damselfish (Pomacentrus coelestis), the first fish colonizing destroyed reefs. We present the first long-term (2008–2015 years corresponding to 16–24 generations of P. coelestis) population genetic study to understand the impact of cyclones on the meta-population structure, connectivity and genetic diversity of the neon damselfish. After the cyclone, we observed the largest change in the genetic structure at reef populations compared to other years. Simultaneously, allelic richness of genetic microsatellite markers dropped indicating a great loss of genetic diversity, which increased again in subsequent years. Over years, metapopulation dynamics were characterized by high connectivity among fish populations associated with the Capricorn Bunker reefs (2200 km²); however, despite high exchange, genetic patchiness was observed with annual strong genetic divergence between populations among reefs. Some broad similarities in the genetic structure in 2015 could be explained by dispersal from a source reef and the related expansion of local populations. This study has shown that alternating cyclone-driven changes and subsequent recovery phases of coral habitat can greatly influence patterns of reef fish connectivity. The frequency of disturbances determines abundance of fish and genetic diversity within species.

     

Fine‐scale structure among mesophotic populations of the great star coral Montastraea cavernosa revealed by SNP genotyping

Mesophotic reefs (30‐150 m) have been proposed as potential refugia that facilitate the recovery of degraded shallow reefs following acute disturbances such as coral bleaching and disease. However, because of the technical difficulty of collecting samples, the connectivity of adjacent mesophotic reefs is relatively unknown compared with shallower counterparts. We used genotyping by sequencing to assess fine‐scale genetic structure of Montastraea cavernosa at two sites at Pulley Ridge, a mesophotic coral reef ecosystem in the Gulf of Mexico, and downstream sites along the Florida Reef Tract. We found differentiation between reefs at Pulley Ridge (~68 m) and corals at downstream upper mesophotic depths in the Dry Tortugas (28–36 m) and shallow reefs in the northern Florida Keys (Key Biscayne, ~5 m). The spatial endpoints of our study were distinct, with the Dry Tortugas as a genetic intermediate. Most striking were differences in population structure among northern and southern sites at Pulley Ridge that were separated by just 12km. Unique patterns of clonality and outlier loci allele frequency support these sites as different populations and suggest that the long‐distance horizontal connectivity typical of shallow‐water corals may not be typical for mesophotic systems in Florida and the Gulf of Mexico. We hypothesize that this may be due to the spawning of buoyant gametes, which commits propagules to the surface, resulting in greater dispersal and lower connectivity than typically found between nearby shallow sites. Differences in population structure over small spatial scales suggest that demographic constraints and/or environmental disturbances may be more variable in space and time on mesophotic reefs compared with their shallow‐water counterparts.     

Alloparental care in the sea: Brood parasitism and adoption within and between two species of coral reef Altrichthys damselfish?

The evolution of parental care opens the door for the evolution of brood parasitic strategies that allow individuals to gain the benefits of parental care without paying the costs. Here we provide the first documentation for alloparental care in coral reef fish and we discuss why these patterns may reflect conspecific and interspecific brood parasitism. Species‐specific barcodes revealed the existence of low levels (3.5% of all offspring) of mixed interspecific broods, mostly juvenile Amblyglyphidodon batunai and Pomacentrus smithi damselfish in Altrichthys broods. A separate analysis of conspecific parentage based on microsatellite markers revealed that mixed parentage broods are common in both species, and the genetic patterns are consistent with two different modes of conspecific brood parasitism, although further studies are required to determine the specific mechanisms responsible for these mixed parentage broods. While many broods had offspring from multiple parasites, in many cases a given brood contained only a single foreign offspring, perhaps a consequence of the movement of lone juveniles between nests. In other cases, broods contained large numbers of putative parasitic offspring from the same parents and we propose that these are more likely to be cases where parasitic adults laid a large number of eggs in the host nest than the result of movements of large numbers of offspring from a single brood after hatching. The evidence that these genetic patterns reflect adaptive brood parasitism, as well as possible costs and benefits of parasitism to hosts and parasites, are discussed.     

Large‐scale,multidirectional larval connectivity among coral reef fish populations in the Great Barrier Reef Marine Park

Larval dispersal is the key process by which populations of most marine fishes and invertebrates are connected and replenished. Advances in larval tagging and genetics have enhanced our capacity to track larval dispersal, assess scales of population connectivity, and quantify larval exchange among no‐take marine reserves and fished areas. Recent studies have found that reserves can be a significant source of recruits for populations up to 40 km away, but the scale and direction of larval connectivity across larger seascapes remain unknown. Here, we apply genetic parentage analysis to investigate larval dispersal patterns for two exploited coral reef groupers (Plectropomus maculatus and Plectropomus leopardus) within and among three clusters of reefs separated by 60–220 km within the Great Barrier Reef Marine Park, Australia. A total of 69 juvenile P. maculatus and 17 juvenile P. leopardus (representing 6% and 9% of the total juveniles sampled, respectively) were genetically assigned to parent individuals on reefs within the study area. We identified both short‐distance larval dispersal within regions (200 m to 50 km) and long‐distance, multidirectional dispersal of up to ~250 km among regions. Dispersal strength declined significantly with distance, with best‐fit dispersal kernels estimating median dispersal distances of ~110 km for P. maculatus and ~190 km for P. leopardus. Larval exchange among reefs demonstrates that established reserves form a highly connected network and contribute larvae for the replenishment of fished reefs at multiple spatial scales. Our findings highlight the potential for long‐distance dispersal in an important group of reef fishes, and provide further evidence that effectively protected reserves can yield recruitment and sustainability benefits for exploited fish populations.     

Otolith growth of Springer's demoiselle, Chrysiptera springeri (Pomacentridae, Allen & Lubbock), on a protected and non-protected coral reef

The structural complexity of coral reefs is important for their function as shelter and feeding habitats for coral reef fishes, but physical disturbance by human activities often reduce complexity of the reefs by selectively destroying fragile and more complex coral species. The damselfish Springer's demoiselle Chrysiptera springeri primarily utilize complex coral heads for shelter and are hence vulnerable to human disturbance. In order to evaluate the potential effect of habitat degradation on juvenile fish growth, coral reef cover, fish age at settling and otolith growth, juvenile Springer's demoiselle was investigated on a protected and non‐protected coral reef in Darvel Bay, Borneo. The protected reef had higher coverage of complex branching corals and exhibited a more complex 3‐dimensional structure than the non‐protected reef. Springer's demoiselle settled at the same age on non‐protected and protected reefs. The growth rates of the otoliths from Springer's demoiselle were similar during the pre‐settlement period on the two reefs (manova , P > 0.05), but from age 20 to 48 days (post‐settlement period) the otolith growth rate of juveniles on the non‐protected reef was reduced compared to those from the protected reef (manova , P = 0.017). However, the differences in the otolith size, and by inference, fish size, after 48 days were small. The small effect of habitat degradation on growth is likely related to the fact that the Springer's demoiselles collected on the non‐protected reef were associated with the few remaining complex coral heads. Increased foraging‐predation tradeoffs on the non‐protected reef may decrease food intake and growth of juvenile Springer's demoiselle, but the main effect of habitat degradation on their abundance is likely to be related to lack of suitable shelter, and consequently reduced carrying capacity, on disturbed reefs.     

Polymorphic microsatellite loci for population studies of the bicolor damselfish,Stegastes partitus (Pomacentridae)

The extent of dispersal between populations of Caribbean reef fish remains largely unknown. Resolution of this issue is critical for managing populations and designing marine reserves. As part of a larger study of reef fish dispersal, we developed and characterized 11 polymorphic microsatellite loci for the bicolor damselfish (Stegastes partitus), an abundant reef fish found throughout the Caribbean. These loci will be useful for population genetic and relatedness studies of this species and also appear to be useful in other Caribbean members of the Pomacentridae.     

Genetic structure of juvenile cohorts of bicolor damselfish ( Stegastes partitus ) along the Mesoamerican barrier reef: chaos through time

Dispersal in marine systems is a critical component of the ecology, evolution, and conservation of such systems; however, estimating dispersal is logistically difficult, especially in coral reef fish. Juvenile bicolor damselfish (Stegastes partitus) were sampled at 13 sites along the Mesoamerican Barrier Reef System (MBRS), the barrier reefs on the east coast of Central America extending from the Yucatan, Mexico to Honduras, to evaluate genetic structure among recently settled cohorts. Using genotype data at eight microsatellite loci genetic structure was estimated at large and small spatial scales using exact tests for allele frequency differences and hierarchical analysis of molecular variance (AMOVA). Isolation-by-distance models of divergence were assessed at both spatial scales. Results showed genetic homogeneity of recently settled S. partitus at large geographic scales with subtle, but significant, genetic structure at smaller geographic scales. Genetic temporal stability was tested for using archived juvenile S. partitus collected earlier in the same year (nine sites), and in the previous year (six sites). The temporal analyses indicated that allele frequency differences among sites were not generally conserved over time, nor were pairwise genetic distances correlated through time, indicative of temporal instability. These results indicate that S. partitus larvae undergo high levels of dispersal along the MBRS, and that the structure detected at smaller spatial scales is likely driven by stochastic effects on dispersal coupled with microgeographic effects. Temporal variation in juvenile cohort genetic signature may be a fundamental characteristic of connectivity patterns in coral reef fishes, with various species and populations differing only in the magnitude of that instability. Such a scenario provides a basis for the reconciliation of conflicting views regarding levels of genetic structuring in S. partitus and possibly other coral reef fish species.     

Genomic analysis of a cardinalfish with larval homing potential reveals genetic admixture in the Okinawa Islands

Discrepancies between potential and observed dispersal distances of reef fish indicate the need for a better understanding of the influence of larval behaviour on recruitment and dispersal. Population genetic studies can provide insight on the degree to which populations are connected, and the development of restriction site‐associated sequencing (RAD‐Seq) methods has made such studies of nonmodel organisms more accessible. We applied double‐digest RAD‐Seq methods to test for population differentiation in the coral reef‐dwelling cardinalfish, Siphamia tubifer, which based on behavioural studies, have the potential to use navigational cues to return to natal reefs. Analysis of 11,836 SNPs from fish collected at coral reefs in Okinawa, Japan, from eleven locations over 3 years reveals little genetic differentiation between groups of S. tubifer at spatial scales from 2 to 140 km and between years at one location: pairwise F_ST values were between 0.0116 and 0.0214. These results suggest that the Kuroshio Current largely influences larval dispersal in the region, and in contrast to expectations based on studies of other cardinalfishes, there is no evidence of population structure for S. tubifer at the spatial scales examined. However, analyses of outlier loci putatively under selection reveal patterns of temporal differentiation that indicate high population turnover and variable larval supply from divergent source populations between years. These findings highlight the need for more studies of fishes across various geographic regions that also examine temporal patterns of genetic differentiation to better understand the potential connections between early life‐history traits and connectivity of reef fish populations.     

In situ settlement behaviour of damselfish (Pomacentridae) larvae

Settlement‐stage damselfish (Pomacentridae) larvae of 13 species in seven genera were obtained from light traps at Lizard Island, Great Barrier Reef, Australia. Behaviour, observed in situ by SCUBA divers, of 245 larvae (6–13 mm, L_S; 5–60 individuals per species) released individually within a few m of reefs during the day differed markedly among species. From 0–28% (range among 13 species) of individuals of each species swam away from the adjacent reefs without swimming to the reefs. Of those that swam to a reef, 0–75% settled. For three species, sufficient data were available to test the hypothesis that these percentages did not differ amongst reefs: the hypothesis was rejected in one species. From 0–75% of larvae that reached the reef were eaten, 0–63% subsequently left the reef and 0–60% were still swimming over the reef at the end of the observation period. Swimming speeds of all but one species were greater when swimming away from the reef than toward it. Most species exceeded average current speeds when swimming away from reefs, but not when swimming toward and over them. Average swimming depths were in the upper half of the water column for most species, and were somewhat greater where the water depths were greater. The time the larvae swam over the reef before settling and the distance swum varied greatly among species from 0 to a mean of 5.5 min and 43 m. Settlement habitats chosen differed amongst species, and in some species, they were very specific. Average settlement depth varied among species from 6–13.5 m. In one species, settlement depth varied between reefs. About half of the 53 observed interactions between larvae and reef resident fishes were predation attempts: fishes of eight species (six families) attacked larvae. The other interactions were aggressive approaches by 11 species of resident fishes, all but one of which were pomacentrids. Many of these aggressive interactions discouraged settlement attempts. Larvae of some species experienced no predatory or aggressive interactions, whereas in other species interactions averaged >0.6 per released larva. Species that swam more‐or‐less directly to settlement sites near the reef edge experienced more interactions. Even within the same family, settlement behaviour differed among species in nearly all measures.     

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

Within populations of brooding sessile corals, sperm dispersal constitutes the mechanism by which gametes interact and mating occurs, and forms the first link in the network of processes that determine specieswide connectivity patterns. However, almost nothing is known about sperm dispersal for any internally fertilizing coral. In this study, we conducted a parentage analysis on coral larvae collected from an area of mapped colonies, to measure the distance sperm disperses for the first time in a reef‐building coral and estimated the mating system characteristics of a recently identified putative cryptic species within the Seriatopora hystrix complex (ShA; Warner et al. 2015). We defined consensus criteria among several replicated methods (colony 2.0, cervus 3.0, mltr v3.2) to maximize accuracy in paternity assignments. Thirteen progeny arrays indicated that this putative species produces exclusively sexually derived, primarily outcrossed larvae (mean t_m = 0.999) in multiple paternity broods (mean r_p = 0.119). Self‐fertilization was directly detected at low frequency for all broods combined (2.8%), but comprised 23% of matings in one brood. Although over 82% of mating occurred between colonies within 10 m of each other (mean sperm dispersal = 5.5 m ± 4.37 SD), we found no evidence of inbreeding in the established population. Restricted dispersal of sperm compared to slightly greater larval dispersal appears to limit inbreeding among close relatives in this cryptic species. Our findings establish a good basis for further work on sperm dispersal in brooding corals and provide the first information about the mating system of a newly identified and abundant cryptic species.     

Distributions and habitat associations of the bridled monocle bream Scolopsis bilineatus (Nemipteridae): a demographic approach

This study focussed on the demography and ecology of Scolopsis bilineatus at three locations on the Great Barrier Reef: the Lizard Island Group, Orpheus Island and One Tree Island. Scolopsis bilineatus lived for up to 16 years and had four distinct life‐history stages, which varied in their distribution patterns, habitat use and reproductive behaviour. Pre‐maturational sex change occurred whereby all males were derived from immature females, and males grew faster and larger than females. Small females and larger males generally formed pairs, which influenced their spatial distributions at small scales. Distributions of S. bilineatus were influenced by depth and exposure within reefs, particularly for juveniles, and most fish were found in shallow, sheltered habitats. Abundance was influenced by benthic cover, and was higher in areas of high coral cover and low where algae were abundant. Habitat associations were stronger at the microhabitat scale, and shelter sites were important for adults. Ontogenetic changes in microhabitat associations were found: juveniles occupied sand and rubble, and adults occupied shelters such as caves and overhangs. Adults showed site fidelity for shelter sites over a period of 4 days and returned to specific shelter sites repeatedly. These findings illustrate the importance of understanding the spatial ecology and habitat use of coral reef fishes, particularly with reference to size‐based changes within species.     

Population structure and connectivity of the mountainous star coral,Orbicella faveolata,throughout the wider Caribbean region

As coral reefs continue to decline worldwide, it becomes ever more necessary to understand the connectivity between coral populations to develop efficient management strategies facilitating survival and adaptation of coral reefs in the future. Orbicella faveolata is one of the most important reef‐building corals in the Caribbean and has recently experienced severe population reductions. Here, we utilize a panel of nine microsatellite loci to evaluate the genetic structure of O. faveolata and to infer connectivity across ten sites spanning the wider Caribbean region. Populations are generally well‐mixed throughout the basin (F_ST = 0.038), although notable patterns of substructure arise at local and regional scales. Eastern and western populations appear segregated with a genetic break around the Mona Passage in the north, as has been shown previously in other species; however, we find evidence for significant connectivity between Curaçao and Mexico, suggesting that the southern margin of this barrier is permeable to dispersal. Our results also identify a strong genetic break within the Mesoamerican Barrier Reef System associated with complex oceanographic patterns that promote larval retention in southern Belize. Additionally, the diverse genetic signature at Flower Garden Banks suggests its possible function as a downstream genetic sink. The findings reported here are relevant to the ongoing conservation efforts for this important and threatened species, and contribute to the growing understanding of large‐scale coral reef connectivity throughout the wider Caribbean.