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College of Science and Engineering CSE publications Recent publications in Marine Science & Aquaculture

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Recent publications in Marine Science & Aquaculture

Schlaefer, Jodie A., Wolanski, Eric, Lambrechts, Jonathan, and Kingsford, Michael J. (2021) Behavioural and oceanographic isolation of an island-based jellyfish (Copula sivickisi, Class Cubozoa) population. Scientific Reports, 11. 10280.
Cubozoan jellyfish are classified as plankton despite the strong swimming and orientation abilities of cubomedusae. How these capabilities could affect cubozoan population structures is poorly understood. Medusae of the cubozoan Copula sivickisi can uniquely attach to surfaces with the sticky pads on their bells. Biophysical modelling was used to investigate the spatial scales of connectivity in a C. sivickisi population. When the medusae were active at night they could maintain their observed distribution on fringing reef if they attached to the reef when the current speed exceeded a moderate threshold. This behaviour facilitated the isolation of a C. sivickisi population on reefs fringing Magnetic Island, Queensland, Australia. Within this distribution, there was considerable within bay retention and medusae rarely travelled > 3 km. The few (< 0.1%) medusae lost from the island habitat were largely advected into open water and away from the mainland coast which lies 8 km from the island. Given that successful emigration is unlikely, the island population probably represents a stock that is ecologically distinct from any mainland populations. The cosmopolitan distribution of C. sivickisi could contain incipient or cryptic species given the small scales of connectivity demonstrated here.

Lee, Calvin K.F., Nicholson, Emily, Duncan, Clare, and Murray, Nicholas J. (2021) Estimating changes and trends in ecosystem extent with dense time-series satellite remote sensing. Conservation Biology. (In Press)
Quantifying trends in ecosystem extent is essential to understanding the status of ecosystems. Estimates of ecosystem loss are widely used to track progress toward conservation targets, monitor deforestation, and identify ecosystems undergoing rapid change. Satellite remote sensing has become an important source of information for estimating these variables. Despite regular acquisition of satellite data, many studies of change in ecosystem extent use only static snapshots, which ignores considerable amounts of data. This approach limits the ability to explicitly estimate trend uncertainty and significance. Assessing the accuracy of multiple snapshots also requires time-series reference data which is often very costly and sometimes impossible to obtain. We devised a method of estimating trends in ecosystem extent that uses all available Landsat satellite imagery. We used a dense time series of classified maps that explicitly accounted for covariates that affect extent estimates (e.g., time, cloud cover, and seasonality). We applied this approach to the Hukaung Valley Wildlife Sanctuary, Myanmar, where rapid deforestation is greatly affecting the lowland rainforest. We applied a generalized additive mixed model to estimate forest extent from more than 650 Landsat image classifications (1999-2018). Forest extent declined significantly at a rate of 0.274%/year (SE = 0.078). Forest extent declined from 91.70% (SE = 0.02) of the study area in 1999 to 86.52% (SE = 0.02) in 2018. Compared with the snapshot method, our approach improved estimated trends of ecosystem loss by allowing significance testing with confidence intervals and incorporation of nonlinear relationships. Our method can be used to identify significant trends over time, reduces the need for extensive reference data through time, and provides quantitative estimates of uncertainty.

Marc, Adrien F., Guppy, Jarrod L., Bauer, Paige, Mulvey, Peter, Jerry, Dean R., and Paris, Damien B.B.P. (2021) Validation of advanced tools to evaluate sperm function in barramundi (Lates calcarifer). Aquaculture, 531. 735802.
Barramundi (Lates calcarifer) is a tropical finfish species rapidly growing in popularity for aquaculture production. However, sperm quality tests have yet to be adapted to enable selection of highly fertile male broodstock in this species. Accordingly, in this study advanced tools were optimized to evaluate barramundi sperm function to facilitate the future study of male fertility and address some of the reproductive constraints currently observed in captive-bred broodstock. Sperm morphology data were used to calibrate and validate automated sperm counting and motility detection by computer-assisted sperm analysis (CASA; AndroVision, Minitube). Several parameters were examined to determine the optimum settings for accurate CASA sperm counting and were compared to manual haemocytometer methods including: sample dilution (1:1000, r = 0.87), minimum number of fields (n = 4, CV = 7.5%), and the effect of motile vs. immotile spermatozoa on automated counting (no effect, r = 0.99, P < .001). Assays for cell viability and DNA damage were also validated for barramundi spermatozoa using 70 °C heat-treated controls and a 5-point intact:damaged dilution curve (r = 0.98, P < .001), and DNase-treated sperm controls, respectively. Data from these optimized assessments indicated high variation between individuals for each parameter assessed and the presence of high rates of DNA and membrane damage in sperm samples tested. Further research building upon this preliminary sperm quality data, is required to identify the cause of DNA and membrane damage in barramundi spermatozoa and understand any potential relationships with paternal performance in commercial spawns.

Smallhorn-West, Patrick F., Gordon, Sophie E., Dempsey, Alexandra C., Purkis, Sam J., Malimali, Siola'a, Halafihi, Tu'ikolongahau, Southgate, Paul C., Bridge, Tom C. L., Pressey, Robert L., and Jones, Geoffrey P. (2021) Tongan socio-environmental spatial layers for marine ecosystem management. Pacific Conservation Biology. (In Press)
Environmental conditions and anthropogenic impacts are key influences on ecological processes and associated ecosystem services. Effective management of Tonga's marine ecosystems therefore depends on accurate and up-to-date knowledge of environmental and anthropogenic variables. Although many types of environmental and anthropogenic data are now available in global layers, they are often inaccessible to end users, particularly in developing countries with limited accessibility and analytical training. Furthermore, the resolution of many global layers might not be sufficient to make informed local decisions. Although the near-shore marine ecosystem of Tonga is extensive, the resources available for its management are limited, and little is known about its current ecological state. Here we provide a marine socio-environmental dataset covering Tonga's near-shore marine ecosystem as compiled from various global layers, remote sensing projects, local ministries, and the 2016 national census. The dataset consists of 11 environmental and 6 anthropogenic variables summarised in ecologically relevant ways, spatially overlaid across the near-shore marine ecosystem of Tonga. The environmental variables selected include bathymetry, coral reef density, distance from deep water, distance from land, distance from major terrestrial inputs, habitat, land area, net primary productivity, salinity, sea surface temperature and wave energy. The anthropogenic variables selected include fishing pressure, management status, distance to fish markets, distance from villages, population pressure and a socioeconomic development index based on population density, growth, mean age, mean education level and unemployment. We hope this extensive and accessible dataset will be a useful tool for future assessment and management of marine ecosystems in Tonga.

Domingos, Jose A., Goldsbury, Julie A., Bastos Gomes, Giana, Smith, Brett G., Tomlinson, Christopher, Bade, Tim, Sander, Corey, Forrester, Justin, and Jerry, Dean R. (2021) Genotype by environment interactions of harvest growth traits for barramundi (Lates calcarifer) commercially farmed in marine vs. freshwater conditions. Aquaculture, 532. 735989.
Barramundi (Lates calcarifer), also known as Asian seabass, is a commercially important tropical aquaculture species farmed in diverse culture production systems and salinities (marine to freshwater). Despite adaptability to different culture conditions, selective breeding programs to improve growth rates in barramundi should consider the impact of genotype by environment (GxE) interactions on genetic gains. Barramundi juveniles from 144 families, originating from 24 dams and 54 sires were farmed in a seawater (SW) raceway in Bowen (QLD, Australia) and a freshwater (FW) pond environment in Townsville (QLD, Australia) - both operated under commercial culture conditions. Fish were sampled at 15 months post-hatch (mph) in the SW raceway (mean 1718 ± 309 g weight (W), 454 ± 28 mm total length (Lₜ) and 141 ± 11 mm body depth (BD) (n = 752)) and at 21 mph in the FW pond (mean 1905 ± 426 g W and 451 ± 39 mm Lt and 144 ± 15 mm BD (n = 752)). DNA parentage analyses were used to assign progeny to their respective parents, and the final dataset comprised of 1116 offspring. Moderate-low heritability estimates were found for body traits (W h² = 0.46 ± 0.10; Lt h² = 0.41 ± 0.12; BD h² = 0.49 ± 0.13; body shape H h² = 0.41 ± 0.12; and Fulton's K condition factor h² = 0.15 ± 0.07). Deformities (Def) were observed in 1.8% of fish in SW and 25.1% of fish in FW, although negligible additive genetic effects were evident (Def h² = 0.05 ± 0.04). GxE interactions were found to be moderate for harvest growth traits (W GxE rg = 0.81 ± 0.11; Lt GxE rg = 0.64 ± 0.18; BD GxE rg = 0.78 ± 0.13; H GxE rg = 0.71 ± 0.17), and high for Fulton's K condition factor (K GxE rg = 0.36 ± 0.31; P > 0.05). This study reveals the presence of weak to moderate re-ranking of genotypes for harvest growth traits in L. calcarifer farmed in marine and freshwater conditions, suggesting that GxE interactions should be taken into account in a breeding program servicing multiple environments. Incorporation of sib-information from extreme salinity environments into the selection criteria of a breeding program may therefore optimize the realization of genetic gains across distinct commercial conditions.

MacKeracher, Tracy, Mizrahi, Me'ira, Bergseth, Brock, Chit Maung, Khin May, Khine, Zin Lin, Phyu, Ei Thal, Simpfendorfer, Colin A., and Diedrich, Amy (2021) Understanding non-compliance in small-scale fisheries: shark fishing in Myanmar's Myeik Archipelago. Ambio, 50. pp. 572-585.
Achieving fisheries compliance is challenging in contexts where enforcement capacity is limited and the incentives for rule-breaking are strong. This challenge is exemplified in Myanmar, where an active shark fishery exists despite a nationwide ban on targeted shark fishing. We used the Kipling method (5W1H) to gather a complete story of non-compliance in five small-scale fishing communities in the Myeik Archipelago. Among 144 fishers surveyed, 49% were aware of the nationwide ban. Shark fishers (24%) tended to be younger individuals who did not own a boat and perceived shark fishing to be prevalent. Compliant fishers were motivated by a fear of sharks and lack of capacity (equipment, knowledge), whereas food and income were cited as key motivations for non-compliance. The results of our study emphasize that in resource-dependent communities, improving compliance for effective shark conservation may require addressing broader issues of poverty, food security and the lack of alternatives.

Martins, A.P.B., Heupel, M.R., Bierwagen, S.L., Chin, A., and Simpfendorfer, C.A. (2021) Tidal-diel patterns of movement, activity and habitat use by juvenile mangrove whiprays using towed-float GPS telemetry. Marine and Freshwater Research, 72. pp. 534-541.
Stingrays are a diverse and widespread group of elasmobranchs. Despite their ecological and economical importance, many aspects of stingray ecology remain poorly understood. Few studies have examined fine-scale movements of juvenile stingrays within nursery areas. This study aimed to examine diel movement patterns in juvenile mangrove whiprays (Urogymnus granulatus) by using towed-float GPS telemetry within a reef flat habitat of the Great Barrier Reef. Juvenile mangrove whiprays travelled distances from 394 to 2189 m, moving at a rate (mean +/- s.e.) of 3.97 m min(-1) +/- 2.5 during tracking periods ranging from 1.35 to 9 h. Movements of juvenile mangrove whiprays were influenced by tidal height and diel period. Individuals chose more direct paths during outgoing and incoming tides and their activity space was significantly larger during the day than at night-time. Individuals showed preference for mangrove areas during high tides, which was likely to reduce predation risk. Our findings have established the use of the towed-float GPS telemetry as an effective tool to assess short-term movement patterns and habitat use of juvenile stingrays, as well as highlighted how juvenile mangrove whiprays use reef-flat environments.

Shimada, Takahiro, Thums, Michele, Hamann, Mark, Limpus, Colin J., Hays, Graeme C., Fitzsimmons, Nancy N., Wildermann, Natalie E., Duarte, Carlos M., Meekan, Mark G., and UNSPECIFIED (2021) Optimising sample sizes for animal distribution analysis using tracking data. Methods in Ecology and Evolution. (In Press)
Knowledge of the spatial distribution of populations is fundamental to management plans for any species. When tracking data are used to describe distributions, it is sometimes assumed that the reported locations of individuals delineate the spatial extent of areas used by the target population. Here we examine existing approaches to validate this assumption, highlight caveats, and propose a new method for a more informative assessment of the number of tracked animals (i.e. sample size) necessary to identify distribution patterns. We show how this assessment can be achieved by considering the heterogeneous use of habitats by a target species using the probabilistic property of a utilisation distribution. Our methods are compiled in the r package SDLfilter. We illustrate and compare the protocols underlying existing and new methods using conceptual models and demonstrate an application of our approach using a large satellite tracking dataset of flatback turtles Natator depressus tagged with accurate Fastloc‐GPS tags (n = 69). Our approach has applicability for the post hoc validation of sample sizes required for the robust estimation of distribution patterns across a wide range of taxa, populations and life‐history stages of animals.

Hill, Narelle K., Woodworth, Bradley K., Phinn, Stuart R., Murray, Nicholas J., and Fuller, Richard A. (2021) Global protected‐area coverage and human pressure on tidal flats. Conservation Biology. (In Press)
Tidal flats are a globally distributed coastal ecosystem important for supporting biodiversity and ecosystem services. Local to continental‐scale studies have documented rapid loss of tidal habitat driven by human impacts, but assessments of progress in their conservation are lacking. We analysed human pressure on tidal flats, and measured their representation in protected areas using a newly developed, internally‐consistent estimate of distribution and change for the world's tidal flats. We discovered that 68% of the current extent of tidal flats is subject to moderate to very high human pressure (Human Modification Index > 0.1), but that 31% of tidal flat extent occurred within protected areas, far exceeding percent protection of the marine (6%) and terrestrial (13%) realms. Net change of tidal flat extent inside protected areas was similar to tidal flat net change outside protected areas between 1999 and 2016. Substantial shortfalls in tidal flat protection occurred across Asia, where large intertidal extents coincide with high to very high human pressure (Human Modification Index > 0.4‐1), and net tidal flat losses up to 86.4 km² (83.9 km²‐89.0 km²; 95% confidence interval) occurred inside individual protected area boundaries within the study period. Taken together, our results show substantial progress in protected area designation for tidal flats globally, but that protected area status alone does not prevent all habitat loss. Safeguarding the world's tidal flats will thus require deeper understanding of the factors that govern their dynamics and effective policy that promotes holistic coastal and catchment management strategies.

Karnaneedi, Shaymaviswanathan, Huerlimann, Roger, Johnston, Elecia B., Nugraha, Roni, Ruethers, Thimo, Taki, Aya C., Kamath, Sandip D., Wade, Nicholas M., Jerry, Dean R., and Lopata, Andreas L. (2021) Novel allergen discovery through comprehensive de novo transcriptomic analyses of five shrimp species. International Journal of Molecular Sciences, 22 (1). 32.
Shellfish allergy affects 2% of the world's population and persists for life in most patients. The diagnosis of shellfish allergy, in particular shrimp, is challenging due to the similarity of allergenic proteins from other invertebrates. Despite the clinical importance of immunological cross-reactivity among shellfish species and between allergenic invertebrates such as dust mites, the underlying molecular basis is not well understood. Here we mine the complete transcriptome of five frequently consumed shrimp species to identify and compare allergens with all known allergen sources. The transcriptomes were assembled de novo, using Trinity, from raw RNA-Seq data of the whiteleg shrimp (Litopenaeus vannamei), black tiger shrimp (Penaeus monodon), banana shrimp (Fenneropenaeus merguiensis), king shrimp (Melicertus latisulcatus), and endeavour shrimp (Metapenaeus endeavouri). BLAST searching using the two major allergen databases, WHO/IUIS Allergen Nomenclature and AllergenOnline, successfully identified all seven known crustacean allergens. The analyses revealed up to 39 unreported allergens in the different shrimp species, including heat shock protein (HSP), alpha-tubulin, chymotrypsin, cyclophilin, beta-enolase, aldolase A, and glyceraldehyde-3-phosphate dehydrogenase (G3PD). Multiple sequence alignment (Clustal Omega) demonstrated high homology with allergens from other invertebrates including mites and cockroaches. This first transcriptomic analyses of allergens in a major food source provides a valuable resource for investigating shellfish allergens, comparing invertebrate allergens and future development of improved diagnostics for food allergy.

Jackson, Micha V., Fuller, Richard A., Gan, Xiaojing, Li, Jing, Mao, Dehua, Melville, David S., Murray, Nicholas, Wang, Zongming, and Choi, Chi-Yeung (2021) Dual threat of tidal flat loss and invasive Spartina alterniflora endanger important shorebird habitat in coastal mainland China. Journal of Environmental Management, 278 (Part 2). 111549.
China's coastal wetlands are critically important to shorebirds. Substantial loss of tidal flats, shorebirds' primary foraging grounds, has occurred from land claim and other processes, and is driving population declines in multiple species. Smooth cordgrass Spartina alterniflora was intentionally introduced to the coast of China in 1979 to promote conversion of tidal flats into dry land and has since spread rapidly. The occurrence of S. alterniflora reduces the availability of foraging and roosting habitat for shorebirds, and may be particularly detrimental in places that have experienced other tidal flat loss. However, the extent to which S. alterniflora is encroaching upon important shorebird habitat throughout coastal mainland China, and its intersection with tidal flat loss, has not been quantified. Here, we i) estimate change in the spatial extent of tidal flats between 2000 and 2015 in coastal mainland China where internationally important numbers of shorebirds have been recorded; ii) map the extent of S. alterniflora coverage in 2015 at the same set of sites; and, iii) investigate where these two threats to important shorebird habitat intersect. Our analysis of remote sensing data indicated a 15% net loss in tidal flat area between 2000 and 2015 across all sites, including a net loss in tidal flat area in 39 of 53 individual sites (74%). Spartina alterniflora occurred at 28 of 53 sites (53%) in 2015, of which 22 sites (79%) also had a net loss in tidal flat area between 2000 and 2015. Combined pressures from tidal flat loss and S. alterniflora invasion were most severe in eastern coastal China. Species highly dependent on migrating through this region, which include the Critically Endangered Spoon-billed Sandpiper and Endangered Nordmann's Greenshank and Far Eastern Curlew, may be particularly impacted. Our results underscore the urgent need to arrest tidal flat declines and develop a comprehensive control program for S. alterniflora in coastal areas of mainland China that are important for shorebirds.

Silva, Catarina N.S., Murphy, Nicholas P., Bell, James J., Green, Bridget S,, Duhamel, Guy, Cockcroft, Andrew C., Hernández, Cristián E., and Strugnell, Jan M. (2021) Global drivers of recent diversification in a marine species complex. Molecular Ecology. (In Press)
Investigating historical gene flow in species complexes can indicate how environmental and reproductive barriers shape genome divergence during speciation. The processes influencing species diversification under environmental change remain one of the central focal points of evolutionary biology, particularly for marine organisms with high dispersal potential. We investigated genome‐wide divergence, introgression patterns and inferred demographic history between species pairs of all six extant rock lobster species (Jasus spp.), which have a long larval duration of up to two years and have populated continental shelf and seamount habitats around the globe at approximately 40oS. Genetic differentiation patterns reflected geographic isolation and the environment (i.e. habitat structure). Eastern Pacific species (J. caveorum and J. frontalis) were geographically more distant and genetically more differentiated from the remaining four species. Species associated with continental shelf habitats shared a common ancestry, but are geographically distant from one another. Similarly, species associated with island/seamount habitats in the Atlantic and Indian Oceans shared a common ancestry, but are also geographically distant. Benthic temperature was the environmental variable that explained most of the genetic differentiation (FST), while controlling for the effects of geographic distance. Eastern Pacific species retained a signal of strict isolation following ancient migration, whereas species pairs from Australia and Africa, and seamounts in the Indian and Atlantic oceans, included events of introgression after secondary contact. Our results reveal important effects of habitat and demographic processes on the recent divergence of species within the genus Jasus, providing one of the first empirical studies of genome‐wide drivers of diversification that incorporates all extant species in a marine genus with long pelagic larval duration.

Banh, Quyen Q.T., Domingos, Jose A., Pinto, Ricardo C.C., Nguyen, Kien T., and Jerry, Dean R. (2021) Dietary 17 β‐oestradiol and 17 α‐ethinyloestradiol alter gonadal morphology and gene expression of the two sex‐related genes, dmrt1 and cyp19a1a , in juvenile barramundi ( Lates calcarifer Bloch). Aquaculture Research. (In Press)
This study investigated the effect of 17 β‐oestradiol (E2) and 17 α‐ethinyloestradiol (EE2) on the feminization of barramundi (Lates calcarifer). Fish were fed pellets containing 10 mg E2/kg food, 20 mg E2/kg food, 5 mg EE2/kg food and 10 mg EE2/kg food from 30 to 160 days post hatch (dph), which covers the period of initial male gonad differentiation. The effect of E2 and EE2 treatment on gonadal morphology and dmrt1 and cyp19a1a gene expression was analysed by histology and RT‐qPCR. Orally delivered E2 and EE2 induced observable changes in gonad morphology. Previtellogenic oocytes (PO) were observed in 33% and 50% of the fish fed with 20 mg E2/kg at 160 dph and 12 months post hatch (mph), respectively, while PO were not observed in control fish. 10 mg E2/kg treatment did not induce feminization, but significantly suppressed testicular development. Treatment with EE2 resulted in fibrosis within gonad tissues at a dose‐dependent rate. E2 administration resulted in upregulation of the gene cyp19a1a and downregulation of dmrt1. EE2 significantly suppressed expression of dmrt1 at 160 dph and 12 mph, while cyp19a1a was not significantly different at 160 dph and was significantly downregulated at 12 mph. The result of this study showed that E2 is a more suitable hormone than EE2 to induce precocious feminization of barramundi, and when delivered through the feed it has a dose‐dependent feminizing effect.

Infante Villamil, Sandra, Huerlimann, Roger, and Jerry, Dean R. (2021) Microbiome diversity and dysbiosis in aquaculture. Reviews in Aquaculture. (In Press)
With the continuous growth of the human population and associated need for high‐quality protein, the aquaculture sector will be required to increase significantly in productivity. This growth in productivity will be achieved through more efficient use of resources like feeds, genetic improvement and limiting the impacts of disease. One of the key links between animal productivity and disease is that of microbial diversity, with high‐throughput sequencing technologies increasing our understanding of the role microorganisms play in health, development and physiology of vertebrate and invertebrate hosts alike. Increasing our understanding of microbial–host interactions will help avoid or manage dysbiosis in aquaculture systems with the final aim of improving productivity. We review the current literature, which indicates that there is an association between productivity and microbial diversity in aquaculture systems, as changes in bacterial microbiomes are implicated in animal performance, in disease development associated with both bacterial and viral origin, and in dysbiosis triggered by environmental stressors or diet choice. Dysbiosis, whether in the form of the loss of beneficial bacteria, or the expansion of pathogens or potentially harmful microorganisms, can be used as an indicator tool for productivity monitoring purposes. Development of management strategies towards preserving the microbial balance, including maintaining or increasing diversity in the host, is critical for the health of cultured aquatic animals and will likely be critical for the expansion of aquaculture.

Thompson, Cassandra A., Hoey, Andrew S., Montanari, Stefano R., Messmer, Vanessa, Doll, Peter C., and Pratchett, Morgan S. (2021) Territoriality and condition of chevron butterflyfish (Chaetodon trifascialis) with varying coral cover on the great barrier reef, Australia. Environmental Biology of Fishes, 104. pp. 53-69.
The chevron butterflyfish, Chaetodon trifascialis, is among the most specialised coral-feeding fish, and while it is known to be very susceptible to extensive depletion of its preferred coral prey (tabular Acropora spp.), their specific responses to changing coral cover are poorly understood. The purpose of this study was to test for variation in territorial behaviour and condition of C. trifascialis relative to spatial variation in coral cover across four mid-shelf reefs on the Great Barrier Reef. Explicit consideration was also given to the territorial arrangement and interactions among sympatric individuals, with a view to better understanding the sociality of this species. Variation in overall coral cover (which ranged from 26.5-73.4% among sites) as well as cover of tabular Acropora (13.3-44.8%) had limited effect on the territoriality or body condition of C. trifascialis. Rather, individual variation in territoriality was attributable to differences in gender and size of fish. Male C. trifascialis were generally larger and also had larger territories than female counterparts. They also interacted with conspecifics (and congenerics) much more than females. Taken together, these results support previous assertions that C. trifascialis is haremic. There was, however, limited evidence of male territories encompassing the territories of >1 female. While the sociality of C. trifascialis is clearly atypical of Chaetodon butterflyfishes, more work is needed to understand their reproductive biology as well as their behavioural responses to changing coral cover.

Barton, Jonathan A., Neil, Rachel C., Humphrey, Craig, Bourne, David G., and Hutson, Kate S. (2021) Efficacy of chemical treatments for Acropora-eating flatworm infestations. Aquaculture, 532. 735978.
Pest management is a critical component of aquaculture operations since high stocking densities can facilitate rapid pest infestation and high stock losses. The Acropora eating-flatworm, Prosthiostomum acroporae impact the health of captive Acropora colonies, which are commonly grown as part of coral aquaculture for trade, research and the hobbyist sector. We investigated the efficacy of anthelmintics levamisole and praziquantel for the removal of Acropora-eating flatworms from A. millepora using one-hour chemical immersions and assessed if these treatments negatively impacted coral growth and/or caused bleaching. Coral fragments (194 total) were spread across eight treatments; levamisole infested (LI; n = 20), levamisole uninfested (LU; n = 20), praziquantel (in EtOH) infested (PI; n = 20), praziquantel (in EtOH) uninfested (PU; n = 20), handling control infested (HCI; n = 14), handling control uninfested (HCU; n = 20), EtOH control (EC; n = 40), control with no handling (NHC; n = 40). To test the efficacy of flatworm removal by short, one-hour chemical immersions, A. millepora fragments (54 total) were manually infested (three P. acroporae per fragment) and immersed separately to uninfested A. millepora fragments (60 total). All fragments were shaken in in a bath of seawater following immersion, then mechanically screened to recover any flatworms not removed from either immersion or shaking to determine the removal efficacy of the treatments. Furthermore, coral fragments (194 total) were photographed before treatment and four weeks following treatments to compare coral basal growth and visual signs of bleaching between infested and uninfested fragments. Levamisole and praziquantel immersions removed significantly more flatworms from A. millepora fragments (93% +/- 3.8 and 95.0% +/- 2.6 respectively; mean +/- SE; p 0.05) compared to the handling control (26% +/- 7.5%). Chemical treatments had no significant effect on basal growth, with fragments across all treatments (including controls) increasing basal area by 73.31 +/- 3.82% (mean +/- SE). Furthermore, bleaching was not observed for any A. millepora fragments across the treatments and controls. Results from this study demonstrate that levamisole and praziquantel used in conjunction with water movement were effective at removing 90% of Acropora eating-flatworms with no observable negative impacts on coral health on treated coral fragments relative to controls.

Silva, Catarina N. S., Young, Emma F., Murphy, Nicholas P., Bell, James J., Green, Bridget S., Morley, Simon A., Duhamel, Guy, Cockcroft, Andrew C., and Strugnell, Jan M. (2021) Climatic change drives dynamic source–sink relationships in marine species with high dispersal potential. Ecology and Evolution. (In Press)
While there is now strong evidence that many factors can shape dispersal, the mechanisms influencing connectivity patterns are species‐specific and remain largely unknown for many species with a high dispersal potential. The rock lobsters Jasus tristani and Jasus paulensis have a long pelagic larval duration (up to 20 months) and inhabit seamounts and islands in the southern Atlantic and Indian Oceans, respectively. We used a multidisciplinary approach to assess the genetic relationships between J. tristani and J. paulensis, investigate historic and contemporary gene flow, and inform fisheries management. Using 17,256 neutral single nucleotide polymorphisms we found low but significant genetic differentiation. We show that patterns of connectivity changed over time in accordance with climatic fluctuations. Historic migration estimates showed stronger connectivity from the Indian to the Atlantic Ocean (influenced by the Agulhas Leakage). In contrast, the individual‐based model coupled with contemporary migration estimates inferred from genetic data showed stronger inter‐ocean connectivity in the opposite direction from the Atlantic to the Indian Ocean driven by the Subtropical Front. We suggest that the J. tristani and J. paulensis historical distribution might have extended further north (when water temperatures were lower) resulting in larval dispersal between the ocean basis being more influenced by the Agulhas Leakage than the Subtropical Front. As water temperatures in the region increase in accordance with anthropogenic climate change, a southern shift in the distribution range of J. tristani and J. paulensis could further reduce larval transport from the Indian to the Atlantic Ocean, adding complexity to fisheries management.

Siqueira, Alexandre C., Morais, Renato A., Bellwood, David R., and Cowman, Peter F. (2021) Planktivores as trophic drivers of global coral reef fish diversity patterns. Proceedings of the National Academy of Sciences of the United States of America, 118 (9). e2019404118.
One of the most prominent features of life on Earth is the uneven number of species across large spatial scales. Despite being inherently linked to energetic constraints, these gradients in species richness distribution have rarely been examined from a trophic perspective. Here we dissect the global diversity of over 3,600 coral reef fishes to reveal patterns across major trophic groups. By analyzing multiple nested spatial scales, we show that planktivores contribute disproportionally to the formation of the Indo-Australian Archipelago (IAA) marine biodiversity hotspot. Besides being “hotter” at the hotspot, planktivorous fishes display the steepest decline in species numbers with distance from the IAA when compared to other trophic groups. Surprisingly, we did not detect differences in diversification, transition, and dispersal rates in extant species phylogenies that would explain this remarkable gradient in planktivorous fish richness. Thus, we identify two potential complementary drivers for this pattern. First, exceptional levels of partitioning among planktivorous coral reef fishes were driven by temporally stable oceanographic conditions and abundant planktonic resources in the IAA. Second, extinctions of planktivores outside the IAA have been particularly pronounced during Quaternary climate fluctuations. Overall, our results highlight trophic ecology as an important component of global species richness gradients.

Hillcoat, Suzanne K., Curnock, Matthew I., Gardiner, Naomi M., and Birtles, R. Alastair (2021) Developing protocols for in‐water morphometric measurements of cetaceans using stereo‐videogrammetry. Marine Mammal Science, 37 (1). pp. 45-63.
Morphometry underpins the basic knowledge of any organism's population demographics and dynamics. Such understanding enables the investigation of trends with important conservation implications including monitoring the health of individuals and changes in population dynamics over time. By detecting declines in health prior to the onset of significant mortality, monitoring of body condition can potentially allow time for a management response to avert population decline. We trialed the use of a diver‐operated stereo‐video (SDOV) system for making morphometric measurements of dwarf minke whales (Balaenoptera acutorostrata subsp.), a small oceanic rorqual, in the Great Barrier Reef, Australia. The SDOV system produced 68% more precise replicate total body length measurements than a single‐camera system, while both systems achieved a mean error below 0.5%. The increased precision offered by a SDOV system is desirable for longitudinal monitoring of growth rates and body condition. Optimal application of this method relied on adherence to protocols for both data collection and analysis beyond those dictated by the equipment user manuals. We provide recommendations for these field and analytical protocols, which may be suitable for use with other cetaceans when in‐water access is available.

Xiao, Hui, Chadès, Iadine, Hill, Narelle, Murray, Nicholas, Fuller, Richard A., and Mcdonald-Madden, Eve (2021) Conserving migratory species while safeguarding ecosystem services. Ecological Modelling, 442. 109442.
Many migratory shorebird species are undergoing severe population declines due to habitat loss. Selecting sites for protection along migratory shorebird flyways requires accounting for connectivity between sites and representing all migratory cycle stages within a protected area network. Site protection decisions often additionally account for the economic value of habitat-related ecosystem services, as shorebird habitats often provide services such as fisheries and recreational opportunities. In this study, we develop a new approach which combines graph theory, decision science, and stochastic dynamic optimization, to investigate whether habitat protection strategies aimed at safeguarding ecosystem services can also deliver efficient protection for migratory shorebirds. We use graph theory to empirically model migration routes for two shorebird species, the Curlew Sandpiper (Calidris ferruginea) and Eastern Curlew (Numenius madagascariensis), linking their migratory networks with data on habitat-related ecosystem services within the East Asian - Australasian Flyway (EAAF). Using dynamic optimization, we calculate the optimal habitat protection strategy for both ecosystem services and shorebird conservation objectives for both species. We further investigate if, and how, these two strategies can converge to achieve both objectives, and whether there is a trade-off between strategies. Our results show that the biodiversity outcome from strategies maximizing ecosystem services provided by shorebird habitat could align closely with a species-focused conservation plan. More specifically, the optimal ecosystem services oriented strategy maintains a similar level of shorebird populations as the optimal conservation strategy, while protecting an additional 45% (Curlew Sandpiper) and 42% (Eastern Curlew) of ecosystem services throughout the network. Conservation budget also matters, as small budgets would lead to inefficient protection for biodiversity. Our research shows that conservation planning can simultaneously achieve conservation and ecosystem services objectives for migratory species. By accounting for the value of ecosystem services within shorebird habitats, we provide quantitative evidence of a win-win scenario in which both shorebird conservation and ecosystem service provision can be achieved. Our model could be applied to other migratory species to improve spatially explicit planning for both biodiversity and ecosystem service targets.

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