ARC Centre of Excellence for Coral Reef Studies

This study investigates the effect of habitat degradation on the interrelationships between morphological, performance, and behavioural traits and their influence on the survival of juvenile Ambon damselfish (Pomacentrus amboinensis). The research combined laboratory measurements with field observations on live or dead-degraded coral reef patches. Fish behavioural traits emerged as key predictors of survival across habitats. Specifically, boldness, bite rate, and maximum distance ventured from the patch reef were key factors. However, the relative importance of specific traits differed between habitats. On live coral, relative lateralization was a significant predictor of survival. In contrast, for fish on dead-degraded coral, routine swimming speed and fast-start response latency were more important. Damselfish in dead-degraded habitats experienced significantly higher mortality. These results indicate that habitat degradation alters the selective pressures on phenotypic traits. This study highlights the importance of considering context-dependent trait selection when predicting how fish communities will respond to changing habitat conditions. Additionally, our findings provide insights for restocking and restoration interventions, suggesting that behavioural conditioning that promotes risk-averse behaviours and predator recognition could improve the survival of reseeded fishes, although further testing within this applied context is required.Supplementary InformationThe online version contains supplementary material available at 10.1038/s41598-025-22578-y.

Abstract With an area covering just under 1 million km2, Australia’s Coral Sea Marine Park (CSMP) is among the largest marine protected areas globally. Yet, the demersal deep-reef fish fauna of the CSMP remains poorly described, due in part to its remote location, as well as its sheer size, much of which is inaccessible below conventional SCUBA diving depths. Recent remotely operated vehicle (ROV) explorations conducted by the Schmidt Ocean Institute provided an opportunity to explore the benthic ichthyofauna of deep mesophotic and rariphotic coral ecosystems. Contributions to the deep, demersal ichthyofauna of Australia’s CSMP are herein supplemented with an integrative dataset consisting of ROV imagery and specimen vouchers. Sixty-two new records of fishes from 26 families are reported from the CSMP. Of these, 45 are new Australian records, one of which is also a new family record for Australia. Four species are new records for the Southern Hemisphere, and 21 species are potentially new to science. We report new voucher material for 29 species, including several species previously identified as new for the CSMP with no voucher specimens.

Changes in biophysical conditions and energetic resource supply across depths are predicted to promote or limit the abundance of different coral reef benthic groups. However, the degree to which regional differences in biophysical processes govern and local human activities might alter naturally occurring depth zonation patterns remains unclear. Here, we used 2239 reef surveys conducted between 0 and 30 m depth around 33 islands (18 unpopulated and 15 populated) across the Pacific Ocean to quantify the percentage cover change of seven broad benthic groups. We tested whether natural depth zonation patterns differed across geographies (using six ecoregions) and whether and how local human impacts might disrupt these natural zonation patterns. We found benthic community depth zonation did not always occur. At the three ecoregions where depth zonation existed, there was no universal ‘natural’ zonation pattern and the benthic groups most responsible for driving patterns of depth zonation differed across geographies. We also found evidence of human-disrupted changes to benthic community depth zonation; patterns were inversed across depths and less distinct at populated compared to unpopulated islands within two ecoregions. We show coral reef communities are naturally highly variable and that human activities can disrupt natural patterns of ecological organization in contemporary ecosystems.

Elasmobranch fishes (i.e., sharks, skates, and rays) exhibit remarkable wound‐healing capabilities and consistently maintain a high capacity for tissue regeneration throughout their lives. This high capacity for wound healing may be particularly important for neonatal elasmobranchs that are still developing their immune system. However, little is known about the costs associated with wound healing and the potential influence of environmental variables or life history. In this study, we explore (1) the impact of minor, external injuries on the growth and body condition of neonatal blacktip reef (Carcharhinus melanopterus) and sicklefin lemon (Negaprion acutidens) sharks using a long‐term fisheries‐independent dataset from Moorea, French Polynesia, (2) the influence of ambient temperature on healing rates in neonatal blacktip reef sharks at two experimental temperatures (25°C and 29°C), and (3) variations in umbilical wound‐healing rates between blacktip reef and sicklefin lemon sharks using an additional long‐term dataset from St. Joseph Atoll, Seychelles. We found no impact of minor, external injuries on growth and body condition in neonatal blacktip reef and sicklefin lemon sharks, accelerated umbilical wound healing in neonatal blacktip reef sharks exposed to elevated ambient temperatures, and distinct umbilical wound‐healing rates between neonatal blacktip reef and sicklefin lemon sharks. Enhancing our understanding of sharks' healing capabilities and the influence of environmental factors on this process is crucial for informing handling practices aimed at improving post‐release survival rates of captured sharks under current and future oceanic conditions.

Mafic magmatism has repeatedly taken place in Pakistan throughout its geological history from the earliest Proterozoic to Recent. Much of it, however, does not have associated metallic mineralization. This paper concerns mineralization associated with ultramafic–mafic plutonic rock occurrences in the western and northern suture zones of Pakistan, which demarcate the collision boundary between the northwestern Indian plate and Eurasian blocks. We discuss the petrology of the ophiolites and basaltic magma-related chromite deposits, showings of platinum group elements (PGE) and Ni minerals, and secondary mineral deposits (emerald and peridot gems, rodingite and nephrite jade) associated with ultramafic–mafic complexes of the two suture zones. Chromite with high Cr# (68–85) occurs in fair quantity and is mostly considered to be genetically related to basaltic magma of subduction-related environments. PGE and nickeliferous minerals are insignificant in quantity; PGE are formed by a higher degree of partial melting and melt-rock reaction, whereas Ni sulfides are the product of serpentinization of the ultramafic rocks. Emerald occurs in several localities in the Indus Suture Zone, whereas the peridot has so far been reported from only one locality. Emerald is associated with Mg-carbonate ± quartz ± fuchsite ± talc ± serpentine, and peridot (Fo 89–92 ) is associated with chrysotile ± magnesite ± talc ± magnetite ± ludwigite. Both are formed via hydrothermal alteration of ultramafic rocks through the introduction of hydrous fluids incorporating CO 2 , Be, B, K, Al and possibly Na. In view of the undeformed nature of the emerald and peridot, and the 23 Ma age of emerald formation, the mineralization appears to post-date deformation and may be of Late Oligocene–Early Miocene age. The metasomatizing fluids were either derived from the subducting Indian plate crust underneath the Kohistan arc or related to 23–26 Ma silicic magmatism in this area of the NW Indian plate. The nephrite jade in the ophiolite mélange is hosted in serpentinites and has disseminated grains of chrome spinel with elevated Fe 2+ /(Mg 2+ + Fe 2+ ) ratios (0.10–0.18), implying low-grade metamorphism of ultramafic rocks (protolith of serpentinite) with loss of Al and introduction of SiO 2 during accompanying metasomatism. The rodingite in the Dargai ophiolite could have formed by the action of seawater channelled through fractures and cracks in rocks. However, their mineral assemblages indicate that they formed as a result of the influx of Ca-, Al- and Na-bearing hydrothermal fluids related to the intrusion of gabbros/sheeted dykes in the serpentinized ultramafic rocks, resulting in Ca-metasomatism.

Metamorphosis is a critical aspect of coral reef fish ecology. This developmental milestone marks changes in form and function that permit successful transition of pelagic larvae to the demersal lifestyle on coral reefs. However, we know very little about the physiological changes that occur during this period, specifically potential changes in energetics associated with swimming. This is critical, as swimming is the mechanism by which pelagic larvae find a suitable reef on which to settle. Coral grouper larvae (Serranidae: Plectropomas leopardus) were collected at night as they came into the vicinity of a fringing reef to settle, and their physiological metamorphosis was characterized. Larvae and 24 h-settled juveniles were exposed to an endurance swimming test at ecologically relevant swimming speeds, and oxygen uptake rates were measured during activity. To describe how aerobic and anaerobic properties of tissues change during metamorphosis, we also measured whole body citrate synthase and lactate dehydrogenase activity, respectively, as well as mitochondrial density in the trunk and pectoral fins. Our approach accurately measures the oxygen uptake rates these life stages need during the recruitment process, with larvae having a 74% higher mass-specific oxygen uptake rate (ṀO2) than settled juveniles despite swimming at speeds that are only 1.5 body-lengths per second (BLs−1) faster. Citrate synthase activity significantly decreased upon settlement; as larvae had 3.7 times higher activities than juveniles, suggesting that rapid changes in aerobic metabolism of tissues may be an important process during metamorphosis in this species. In contrast, lactate dehydrogenase did not significantly differ upon settlement. These findings highlight some physiological modifications that pelagic coral grouper larvae undertake within 24 h that contribute to successfully settling onto a coral reef.

The Lockhart Limestone is evaluated for its reservoir potential by utilizing wireline logs of Shakardara-01well from Kohat Basin, Pakistan. The analyses showed 28.03% average volume of shale (Vsh), 25.57% average neutron porosity (NPHI), 3.31% average effective porosity (PHIE), 76% average water saturation (Sw), and 24.10% average hydrocarbon saturation (Sh) of the Lockhart Limestone in Shakardara-01 well. Based on variation in petrophysical character, the reservoir units of the Lockhart Limestone are divided into three zones i.e., zone-1, zone-2 and zone-3. Out of these zones, zone-1 and zone-2 possess a poor reservoir potential for hydrocarbons as reflected by very low effective porosity (1.40 and 2.02% respectively) and hydrocarbon saturation (15 and 5.20%), while zone-3 has a moderate reservoir potential due to its moderate effective porosity (6.50%) and hydrocarbon saturation (52%) respectively. Overall, the average effective porosity of 3.31% and hydrocarbon saturation of 24.10% as well as 28.03% volume of shale indicated poor reservoir potential of the Lockhart Limestone. Lithologically, this formation is dominated by limestone and shale interbeds in the Shakardara-01 well. Cross-plots of the petrophysical parameters versus depth showed that the Lockhart Limestone is a poor to tight reservoir in Shakardara-01 well and can hardly produce hydrocarbons under conventional drilling conditions.

ABSTRACT The social and cultural elements of human interactions with nature remain among the least-studied and least understood elements of social-ecological systems. Although the conceptual framework of the Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem Services (IPBES) provides an entry point into assessing nature’s contributions to people (NCP), at face value IPBES has limited capacity to capture subjective elements of values and culture as influences on important socio-cultural processes that underpin social-ecological interactions. We propose that integrating cultural ecosystem services more explicitly into the IPBES conceptual framework can help fill its existing gaps by 1) elucidating the social-cultural mechanisms that underpin the production and valuation of non-material NCP, 2) explaining the role of heterogeneity in cultural, social and environmental processes, 3) identifying the two-way interactions between nature and people that co-produce NCP, and 4) identifying synergies between the IPBES conceptual framework and the cultural ecosystem services approach that will facilitate the application of the IPBES framework in more diverse settings. We use recently published work on cultural ecosystem services associated with birds to illustrate our suggestions in action. Assessing social-ecological systems through this adapted framework makes implicit connections easier to draw out, thereby providing holistic insight into the feedbacks and linkages that should be considered at all levels of environmental decision-making.

Considerable gaps in our understanding of cubozoan ecology exist due to challenges associated with their detection. Environmental DNA (eDNA) removes the need for physical identification, offering a new approach to detect and study these elusive taxa. The objective of this study was to utilise eDNA as an ecological tool to test hypotheses surrounding the ecology of the Australian box jellyfish Chironex fleckeri, through examining the presence of both polyp and medusa life history stages. Additionally, the utility of eDNA as a proxy of abundance was explored. This study was conducted within and outside of Port Musgrave, a semi-enclosed estuarine system in northern Australia. eDNA proved successful in detecting both life history stages. Polyps were detected during winter when medusae were absent. This detection allowed investigation into potential polyp habitat. Polyps were exclusively detected in habitats characterised by nearby patches of rocky substrata and shallow carbonate reefs, with no detection occurring in mangrove habitats. The highest frequency of medusa detections occurred within Port Musgrave, while detections outside were more sporadic. Through comparing the distributions of both life history stages, evidence suggests that Port Musgrave is likely a population stock of the species, aligning with predictions from biophysical models. Finally, use of eDNA as a proxy of abundance showed a poor relationship, which can be attributed to likely higher variance in eDNA concentrations resulting from the spatially dispersed nature of the jellyfish. We conclude that eDNA provides a new approach to study cubozoan ecology and will provide critical information needed to mitigate against their threat of envenomation.

The abundance and distribution of demersal fishes rely on larvae successfully settling from the pelagic environment to a benthic habitat and their subsequent survival. With high mortality rates during this life stage, settling to a habitat that maximizes survival is critical. However, relationships between settlement choices and subsequent survival are poorly understood and may vary among species with different habitat preferences. To test this, we focused on five congeneric (Pomacentrus) damselfish species that are known to differ in their habitat choices and explored whether habitat associations at settlement influenced survival. Newly settled individuals were tagged and monitored daily for two weeks to estimate natural mortality rates. Morphological attributes of fish and characteristics of settlement habitats, including depth, rugosity, benthic substrata, and local fish assemblages, were used to predict mortality. We found that some species displayed stronger associations with specific benthic substrata at settlement, but contrary to expectations, these selected habitat characteristics were relatively weak predictors of survivorship. Our survival analysis revealed that the best predictors of survivorship were rugosity (P. adelus and P. amboinensis) and two morphological traits, body depth and ocellus size (P. chrysurus and P. adelus). Interestingly, we found that P. moluccensis that settled in areas of high coverage of mounding coral experienced increased mortality. Of the remaining substrata, analysis showed that instead of associating with habitat characteristics enhancing survivorship, individuals tended not to associate with habitats characteristics that increased mortality (e.g., Turbinaria and sand). This study highlights the species-specific drivers of early post-settlement mortality in coral reef fishes.