Influence of habitat degradation on fish replenishment

Temperature-induced coral bleaching is a major threat to the biodiversity of coral reef ecosystems. While reductions in species diversity and abundance of fish communities have been documented following coral bleaching, the mechanisms that underlie these changes are poorly understood. The present study examined the impacts of coral bleaching on the early life-history processes of coral reef fishes. Daily monitoring of fish settlement patterns found that ten times as many fish settled to healthy coral than sub-lethally bleached coral. Species diversity of settling fishes was least on bleached coral and greatest on dead coral, with healthy coral having intermediate levels of diversity. Laboratory experiments using light-trap caught juveniles showed that different damselfish species chose among healthy, bleached and dead coral habitats using different combinations of visual and olfactory cues. The live coral specialist, Pomacentrus moluccensis, preferred live coral and avoided bleached and dead coral, using mostly visual cues to inform their habitat choice. The habitat generalist, Pomacentrus amboinensis, also preferred live coral and avoided bleached and dead coral but selected these habitats using both visual and olfactory cues. Trials with another habitat generalist, Dischistodus sp., suggested that vision played a significant role. A 20 days field experiment that manipulated densities of P. moluccensis on healthy and bleached coral heads found an influence of fish density on juvenile weight and growth, but no significant influence of habitat quality. These results suggests that coral bleaching will affect settlement patterns and species distributions by influencing the visual and olfactory cues that reef fish larvae use to make settlement choices. Furthermore, increased fish density within the remaining healthy coral habitats could play an important role in influencing population dynamics.     

The effect of microhabitat patch size on settlement differs among co-occurring coral reef fishes

Over small spatial scales, coral reefs represent a mosaic of suitable settlement microhabitat patches of varying size for late-stage larval reef fishes. Few studies have specifically examined how variation in patch size influences density of recently settled coral reef fishes (recruits). Using standardized units of coral rubble settlement substrate deployed on sandy bottom, we monitored the concurrent settlement of three reef fish taxa onto differently sized patches (0.28–1.68 m²) at 5-d intervals during a lunar settlement peak. We found marked differences among taxa in how recruit density scaled with patch size. Recruit density of a damselfish and a parrotfish decreased and increased, respectively, with the increase in patch size, while that of a wrasse was similar among patch sizes. Our results highlight the importance of the interaction between taxon-specific settlement behaviour and patch size in establishing initial spatial differences in density within and among coral reef fish taxa in a heterogeneous landscape.

     

Mismatch between shape changes and ecological shifts during the post-settlement growth of the surgeonfish, Acanthurus triostegus

Background

Many coral reef fishes undergo habitat and diet shifts during ontogeny. However, studies focusing on the physiological and morphological adaptations that may prepare them for these transitions are relatively scarce. Here, we explored the body shape variation related to ontogenetic shifts in the ecology of the surgeonfish Acanthurus triostegus (Acanthuridae) from new settler to adult stages at Moorea Island (French Polynesia). Specifically, we tested the relationship between diet and habitat shifts and changes in overall body shape during the ontogeny of A. triostegus using a combination of geometric morphometric methods, stomach contents and stable isotope analysis.

Results

After reef settlement, stable isotope composition of carbon and nitrogen revealed a change from a zooplanktivorous to a benthic algae diet. The large amount of algae (> 75% of stomach contents) found in the digestive tract of small juveniles (25?C30 mm SL) suggested the diet shift is rapid. The post-settlement growth of A. triostegus is highly allometric. The allometric shape changes mainly concern cephalic and pectoral regions. The head becomes shorter and more ventrally oriented during growth. Morphological changes are directly related to the diet shift given that a small mouth ventrally oriented is particularly suited for grazing activities at the adult stage. The pectoral fin is more anteriorely and vertically positioned and its basis is larger in adults than in juveniles. This shape variation had implications for swimming performance, manoeuvrability, turning ability and is related to habitat shift. Acanthurus triostegus achieves its main transformation of body shape to an adult-like form at size of 35?C40 mm SL.

Conclusion

Most of the shape changes occurred after the reef colonization but before the transition between juvenile habitat (fringing reef) and adult habitat (barrier reef). A large amount of allometric variation was observed after diet shift from zooplankton to benthic algae. Diet shift could act as an environmental factor favouring or inducing morphological changes. On the other hand, the main shape changes have to be achieved before the recruitment to adult populations and start negotiating the biophysical challenges of locomotion and feeding in wave- and current-swept outer reef habitat.     

Suspended sediment impairs habitat choice and chemosensory discrimination in two coral reef fishes

Increasing sediment onto coral reefs has been identified as a major source of habitat degradation, and yet little is known about how it affects reef fishes. In this study, we tested the hypothesis that sediment-enriched water impairs the ability of larval damselfish to find suitable settlement sites. At three different experimental concentrations of suspended sediment (45, 90, and 180 mg l⁻¹), pre-settlement individuals of two species (Pomacentrus amboinensis and P. moluccensis) were not able to select their preferred habitat. In a clear water environment (no suspended sediment), both species exhibit a strong preference for live coral over partially dead and dead coral, choosing live coral 70 and 80% of the time, respectively. However, when exposed to suspended sediment, no habitat choice was observed, with individuals of both species settling on live coral, partially dead, and dead coral, at the same frequency. To determine a potential mechanism underlying these results, we tested chemosensory discrimination in sediment-enriched water. We demonstrated that sediment disrupts the ability of this species to respond to chemical cues from different substrata. That is, individuals of P. moluccensis prefer live coral to dead coral in clear water, but in sediment-enriched water, chemical cues from live and dead coral were not distinguished. These results suggest that increasing suspended sediment in coral reef environments may reduce settlement success or survival of coral reef fishes. A sediment-induced disruption of habitat choice may compound the effects of habitat loss on coral reefs.     

Herbivory facilitates growth of a key reef‐building Caribbean coral

The decline of reef‐building corals in conjunction with shifts to short‐lived opportunistic species has prompted concerns that Caribbean reef framework‐building capacity has substantially diminished. Restoring herbivore populations may be a potential driver of coral recovery; however, the impact of herbivores on coral calcification has been little studied. We performed an exclusion experiment to evaluate the impact of herbivory on Orbicella faveolata coral growth over 14 months. The experiment consisted of three treatments: full exclusion cages; half cage procedural controls; and uncaged control plates, each with small O. faveolata colonies. We found that herbivorous fish exclusion had a substantial impact on both macroalgal cover and coral growth. Fleshy macroalgae reached 50% cover within some exclusion cages, but were almost absent from uncaged control plates. Critically, O. faveolata calcification rates were suppressed by almost half within exclusion cages, with monthly coral growth negatively related to overgrowth by fleshy macroalgae. These findings highlight the importance of herbivorous fishes for coral growth and the detrimental impact of macroalgal proliferation in the Caribbean. Policy makers and local managers should consider measures to protect herbivorous fishes and reduce macroalgal proliferation to enable coral communities to continue to grow and function.     

Differences in the behavior and diet between shoaling and solitary surgeonfish (Acanthurus triostegus)

Variation in behavior within marine and terrestrial species can influence the functioning of the ecosystems they inhabit. However, the contribution of social behavior to ecosystem function remains underexplored. Many coral reef fish species provide potentially insightful models for exploring how social behavior shapes ecological function because they exhibit radical intraspecific variation in sociality within a shared habitat. Here, we provide an empirical exploration on how the ecological function of a shoaling surgeonfish (Acanthurus triostegus) may differ from that of solitary conspecifics on two Pacific coral reefs combining insight from behavioral observations, stable isotope analysis, and macronutrient analysis of gut and fecal matter. We detected important differences in how the social mode of A. triostegus affected its spatial and feeding ecology, as well as that of other reef fish species. Specifically, we found increased distance traveled and area covered by shoaling fish relative to solitary A. triostegus. Additionally, shoaling A. triostegus primarily grazed within territories of other herbivorous fish and had piscivorous and nonpiscivorous heterospecific fish associated with the shoal, while solitary A. triostegus grazed largely grazed outside of any territories and did not have any such interactions with heterospecific fish. Results from stable isotope analysis show a difference in δ15N isotopes between shoaling and solitary fish, which suggests that these different social modes are persistent. Further, we found a strong interaction between social behavior and site and carbohydrate and protein percentages in the macronutrient analysis, indicating that these differences in sociality are associated with measurable differences in both the feeding ecology and nutrient excretion patterns. Our study suggests that the social behavior of individuals may play an important and underappreciated role in mediating their ecological function.     

Growth history and intrinsic factors influence risk assessment at a critical life transition for a fish

Making the appropriate decision in the face of predation risk dictates the fate of prey, and predation risk is highest at life history boundaries such as settlement. At the end of the larval phase, most coral reef fishes enter patches of reef containing novel predators. Since vision is often obscured in the complex surroundings, chemical information released from damaged conspecific is used to forewarn prey of an active predator. However, larvae enter the reef environment with their own feeding and growth histories, which will influence their motivation to feed and take risks. The present study explored the link between recent growth, feeding history, current performance and behavioural risk taking in newly settling stages of a coral reef damselfish (Pomacentrus amboinensis). Older and larger juveniles in good body condition had a stronger response to chemical alarm cues of injured conspecifics; these fish spent a longer time in shelter and displayed a more dramatic decrease in foraging behaviour than fish in lower body condition. Feeding experiments supported these findings and emphasized the importance of body condition in affecting risk assessment. Evidently, larval growth history and body condition influences the likelihood of taking risks under the threat of predation immediately after settlement, thereby affecting the probability of survival in P. amboinensis.     

Promoting larval settlement of coral Pocillopora damicornis by calcium

Larval settlement is a critical bottleneck in the process of coral sexual propagation. Promoting coral larval settlement by inducers is a promising strategy in coral reef restoration engineering. In this study, the settlement-promoting effect of Ca²⁺ on larvae of the brooding coral Pocillopora damicornis was investigated for the first time. Treatment with 40 mM CaCl₂ for 24 h effectively promoted coral larval settlement (~ 80%). Moreover, CaCl₂ is comparable with the natural inducer, crustose coralline algae (CCA), in both promoting coral larval settlement and post-settlement growth. CaCl₂ showed toxic effects on larval survival and growth at high concentrations, and this could be minimized by optimizing CaCl₂ concentration and shortening the exposure period. Our study suggests that applying Ca²⁺ to effectively and efficiently induce coral larval settlement is viable for laboratory research and small-scale aquaculture systems, and it might become a useful tool in future coral reef restoration engineering.

     

Rising CO2 concentrations affect settlement behaviour of larval damselfishes

Reef fish larvae actively select preferred benthic habitat, relying on olfactory, visual and acoustic cues to discriminate between microhabitats at settlement. Recent studies show exposure to elevated carbon dioxide (CO₂) impairs olfactory cue recognition in larval reef fishes. However, whether this alters the behaviour of settling fish or disrupts habitat selection is unknown. Here, the effect of elevated CO₂ on larval behaviour and habitat selection at settlement was tested in three species of damselfishes (family Pomacentridae) that differ in their pattern of habitat use: Pomacentrus amboinensis (a habitat generalist), Pomacentrus chrysurus (a rubble specialist) and Pomacentrus moluccensis (a live coral specialist). Settlement-stage larvae were exposed to current-day CO₂ levels or CO₂ concentrations that could occur by 2100 (700 and 850 ppm) based on IPCC emission scenarios. First, pair-wise choice tests were performed using a two-channel flume chamber to test olfactory discrimination between hard coral, soft coral and coral rubble habitats. The habitat selected by settling fish was then compared among treatments using a multi-choice settlement experiment conducted overnight. Finally, settlement timing between treatments was compared across two lunar cycles for one of the species, P. chrysurus. Exposure to elevated CO₂ disrupted the ability of larvae to discriminate between habitat odours in olfactory trials. However, this had no effect on the habitats selected at settlement when all sensory cues were available. The timing of settlement was dramatically altered by CO₂ exposure, with control fish exhibiting peak settlement around the new moon, whereas fish exposed to 850 ppm CO₂ displaying highest settlement rates around the full moon. These results suggest larvae can rely on other sensory information, such as visual cues, to compensate for impaired olfactory ability when selecting settlement habitat at small spatial scales. However, rising CO₂ could cause larvae to settle at unfavourable times, with potential consequences for larval survival and population replenishment.     

Adding coral rubble to substrata enhances settlement of Pocillopora?damicornis larvae

Settlement preferences of Pocillopora damicornis larvae were examined on artificial substrata. Planulation of P. damicornis followed a lunar cycle and the release of larvae occurred after new moon. P. damicornis larvae had the highest rates of settlement within 3 days of being presented settlement substrata. Cumulative settlement gradually increased from 3 to 8 days, and post-settlement mortality was most frequent after 8 days. Settlement experiments showed greatest settlement preference to cement tiles containing 10% coral rubble. This study suggests that physical cues are important in the settlement process, which may be useful for coral reef rehabilitation projects.     

Auditory sensitivity in settlement-stage larvae of coral reef fishes

The larval phase of most species of coral reef fishes is spent away from the reef in the pelagic environment. At the time of settlement, these larvae need to locate a reef, and recent research indicates that sound emanating from reefs may act as a cue to guide them. Here, the auditory abilities of settlement-stage larvae of four species of coral reef fishes (families Pomacentridae, Lutjanidae and Serranidae) and similar-sized individuals of two pelagic species (Carangidae) were tested using an electrophysiological technique, auditory brainstem response (ABR). Five of the six species heard frequencies in the 100–2,000 Hz range, whilst one carangid species did not detect frequencies higher than 800 Hz. The audiograms of the six species were of similar shape, with best hearing at lower frequencies between 100 and 300 Hz. Strong within-species differences were found in hearing sensitivity both among the coral reef species and among the pelagic species. Larvae of the coral reef species had significantly more sensitive hearing than the larvae of the pelagic species. The results suggest that settlement-stage larval reef fishes may be able to detect reef sounds at distances of a few 100 m. If true hearing thresholds are lower than ABR estimates, as indicated in some comparisons of ABR and behavioural methods, the detection distances would be much larger.     

Trawl fishery resources in the “southern waters” of Japan

Settlement-stage larvae of the coral reef fishes Ostorhinchus doederleini (Apogonidae) and Pomacentrus coelestis (Pomacentridae) prefer the odor of their settlement reef to that of other nearby reefs. It was unknown whether these olfactory preferences are temporally stable or the result of recent olfactory experience. Ostorhinchus doederleini and P. coelestis larvae were held in aquaria and exposed to water from either their settlement reef or a neighboring reef for 5–9 days and their olfactory preference was tested. We show that exposure to water from another reef did not influence olfactory preference. Ostorhinchus doederleini olfactory preference declined slightly over time whereas P. coelestis preference was gradually lost after 2–3 days in captivity. Neither species switched their preference to the new reef odor. While we cannot determine conclusively the time window of odor learning, imprinting at or shortly after birth is logical and has been demonstrated in other fish species.     

Intraspecific variability in the life histories of endemic coral-reef fishes between photic and mesophotic depths across the Central Pacific Ocean

Mesophotic coral ecosystems (MCEs) represent the lowest depth distribution inhabited by many coral reef-associated organisms. Research on fishes associated with MCEs is sparse, leading to a critical lack of knowledge of how reef fish found at mesophotic depths may vary from their shallow reef conspecifics. We investigated intraspecific variability in body condition and growth of three Hawaiian endemics collected from shallow, photic reefs (5–33 m deep) and MCEs (40–75 m) throughout the Hawaiian Archipelago and Johnston Atoll: the detritivorous goldring surgeonfish, Ctenochaetus strigosus, and the planktivorous threespot chromis, Chromis verater, and Hawaiian dascyllus, Dascyllus albisella. Estimates of body condition and size-at-age varied between shallow and mesophotic depths; however, these demographic differences were outweighed by the magnitude of variability found across the latitudinal gradient of locations sampled within the Central Pacific. Body condition and maximum body size were lowest in samples collected from shallow and mesophotic Johnston Atoll sites, with no difference occurring between depths. Samples from the Northwestern Hawaiian Islands tended to have the highest body condition and reached the largest body sizes, with differences between shallow and mesophotic sites highly variable among species. The findings of this study support newly emerging research demonstrating intraspecific variability in the life history of coral-reef fish species whose distributions span shallow and mesophotic reefs. This suggests not only that the conservation and fisheries management should take into consideration differences in the life histories of reef-fish populations across spatial scales, but also that information derived from studies of shallow fishes be applied with caution to conspecific populations in mesophotic coral environments.

     

Comparison between community structures of fishes in <Emphasis Type="Italic">Enhalus acoroides</Emphasis>- and <Emphasis Type="Italic">Thalassia hemprichii</Emphasis>-dominated seagrass beds on fringing coral reefs in the Ryukyu Islands,Japan

To clarify differences in community structures and habitat utilization patterns of fishes in Enhalus acoroides- and Thalassia hemprichii-dominated seagrass beds on fringing coral reefs, visual censuses were conducted at Iriomote and Ishigaki islands, southern Japan. The numbers of fish species and individuals were significantly higher in the E. acoroides bed than in the T. hemprichii bed, although the 15 most dominant fishes in each seagrass bed were similar. Cluster and ordination analyses based on the number of individuals of each fish species also demonstrated that fish community structures were similar in the two seagrass beds. Species and individual numbers of coral reef fishes which utilized the seagrass beds numbered less than about 15% of whole coral reef fish numbers, although they comprised about half of the seagrass bed fishes. Of the 15 most dominant species, 5 occurred only in the two seagrass beds, including seagrass feeders. Ten other species were reef species, their habitat utilization patterns not differing greatly between the two seagrass beds. Some reef species, such as Lethrinus atkinsoni and L. obsoletus, showed ontogenetic habitat shifts with growth, from the seagrass beds to the coral areas. These results indicate that community structures and habitat utilization patterns of fishes were similar between E. acoroides- and T. hemprichii-dominated seagrass beds, whereas many coral reef fishes hardly utilized the seagrass beds.     

Coral mortality versus structural collapse as drivers of corallivorous butterflyfish decline

As climate change increasingly threatens biodiversity, identifying specific drivers of species loss as well as the attributes of species most vulnerable to climatic disturbances is a key challenge to ecologists and conservationists. Here we assess the effects of coral loss versus declines in structural complexity on obligate and facultative coral feeding butterflyfishes on coral reefs in the central and western Indian Ocean. In the inner Seychelles, the abundance of the obligate coral feeding group declined markedly in response to live coral mortality (r ² = 0.48), but showed no further decline with respect to erosion of the physical matrix of the reef. Conversely, the facultative feeding group showed no decline in response to live coral loss, reflecting their feeding versatility; however they did decline in response to structural erosion of the reef framework (r ² = 0.26). There were no significant changes in either obligate or facultative corallivore abundances at a reference location (Chagos archipelago), highlighting that butterflyfish populations are stable in the absence of habitat disturbance. While specialised coral dependant fishes are highly vulnerable to coral loss caused by climate-induced coral bleaching, the structural collapse of dead coral colonies may have significant, but more variable, impacts across a wide range of fishes. If conservation and mitigation planning are to be effective, there is a clear need to better understand the mechanisms of reef structural collapse and the dynamics of system recovery following large-scale disturbance.     

Early life history and settlement of the slender filefish, <Emphasis Type="Italic">Monacanthus tuckeri</Emphasis> (Monacanthidae), at Calabash Caye,Turneffe Atoll,Belize

Synopsis We examined early life history traits and patterns of settlement of the slender filefish, Monacanthus tuckeri, at Calabash Caye, Turneffe Atoll, Belize. A settlement peak was evident at the new moon, and no settlement occurred at the full moon. However, settlement rates at the quarter moons could not be estimated due to sampling gaps. Many reef fishes show new moon settlement peaks, so M. tuckeri shares some characteristics with the primarily perciform species on coral reefs. Pelagic larval duration was long (mean = 42 days) and variable, suggesting that dispersal patterns might be diverse. Size at settlement was large (mean = 32 mm total length) and also variable. Larval duration and size at settlement were outside of the average values exhibited by reef fishes, but are not beyond the extreme end of the range, and might be explained by association with pelagic debris prior to settlement. There were no differences in overall settlement rates on reef and seagrass habitats, and fish settling to either habitat did not differ in larval duration, size at settlement, or larval growth rate. This suggests that settlement to alternative habitats may be random, or driven by availability of suitable microhabitat, rather than habitat quality or individual traits.     

Depth distributions of coral reef fishes: the influence of microhabitat structure,settlement, and post-settlement processes

Many coral reef fishes have restricted depth ranges that are established at settlement or soon after, but the factors limiting these distributions are largely unknown. This study examines whether the availability of microhabitats (reef substrata) explains depth limits, and evaluates whether juvenile growth and survival are lower beyond these limits. Depth-stratified surveys of reef fishes at Kimbe Bay (Papua New Guinea) showed that the abundance of new settlers and the cover of coral substrata differed significantly among depths. A field experiment investigated whether settling coral reef fishes preferred particular depths, and whether these depth preferences were dependent on microhabitat. Small patch reefs composed of identical coral substrata were set up at five depths (3, 6, 10, 15 and 20 m), and settlement patterns were compared to those on unmanipulated reef habitat at the same five depths. For all species, settlement on patch reefs differed significantly among depths despite uniform substratum composition. For four of the six species tested, depth-related settlement patterns on unmanipulated habitat and on patch reefs did not differ, while for the other two, depth ranges were greater on the patch reefs than on unmanipulated habitat. A second experiment examined whether depth preferences reflected variation in growth and survival when microhabitat was similar. Newly settled individuals of Chrysiptera parasema and Dascyllus melanurus were placed, separately, on patch reefs at five depths (as above) and their survival and growth monitored. D. melanurus, which is restricted to shallow depths, had highest survival and growth at the shallowest depth. Depth did not affect either survival or growth of C. parasema, which has a broader depth range than D. melanurus (between 6 and 15 m). This suggests that the fitness costs potentially incurred by settling outside a preferred depth range may depend on the strength of the depth preference.     

Genetic evidence of closed life-cycles for some coral reef fishes within Taiaro Lagoon (Tuamotu Archipelago, French Polynesia)

 Taiaro Lagoon has no permanent or regular connection with the ocean (ingress is restricted to episodes of high sea-level and/or strong wave action) raising the question of how fish populations with normally dispersive larvae are maintained inside this lagoon. We compared the genetic population structures of two coral reef fishes, Acanthurus triostegus and Chaetodon ulietensis, present on both sides of the atoll rim to determine whether there is evidence of reproductive isolation. Genetic surveys showed that the lagoonal and oceanic populations were statistically different at five loci (AAT ^* -3, GDA ^*, HPD ^*, MDH ^* and SDH ^*) in A. triostegus and three loci (PGI-2^*, IDH ^* and PGD ^*) in C. ulietensis, producing high F _st values of 0.055 and 0.021, respectively. Our genetic and demographic data on these species suggest that both may be completing their life-cycles inside the lagoon, which leads us to question the common assumption that coral reef fishes require oceanic conditions for larval development. Accepted: 28 August 1997     

Indirect consequences of fishing: reduction of coralline algae suppresses juvenile coral abundance

Removing predatory fishes has effects that cascade through ecosystems via interactions between species and functional groups. In Kenyan reef lagoons, fishing-induced trophic cascades produce sea urchin-dominated grazing communities that greatly reduce the overall cover of crustose coralline algae (CCA). Certain species of CCA enhance coral recruitment by chemically inducing coral settlement. If sea urchin grazing reduces cover of settlement-inducing CCA, coral recruitment and hence juvenile coral abundance may also decline on fished reefs. To determine whether fishing-induced changes in CCA influence coral recruitment and abundance, we compared (1) CCA taxonomic compositions and (2) taxon-specific associations between CCA and juvenile corals under three fisheries management systems: closed, gear-restricted, and open-access. On fished reefs (gear-restricted and open-access), abundances of two species of settlement-inducing CCA, Hydrolithon reinboldii and H. onkodes, were half those on closed reefs. On both closed and fished reefs, juveniles of four common coral families (Poritidae, Pocilloporidae, Agariciidae, and Faviidae) were more abundant on Hydrolithon than on any other settlement substrate. Coral densities were positively correlated with Hydrolithon spp. cover and were significantly lower on fished than on closed reefs, suggesting that fishing indirectly reduces coral recruitment or juvenile success over large spatial scales via reduction in settlement-inducing CCA. Therefore, managing reefs for higher cover of settlement-inducing CCA may enhance coral recruitment or juvenile survival and help to maintain the ecological and structural stability of reefs.     

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.