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

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Recent publications in Marine Science & Aquaculture

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.

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.

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.

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.

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.

Whitelaw, Brooke L., Cooke, Ira R., Finn, Julian, da Fonseca, Rute R., Ritschard, Elena A., Gilbert, M. T. P., Simakov, Oleg, and Strugnell, Jan M. (2020) Adaptive venom evolution and toxicity in octopods is driven by extensive novel gene formation, expansion, and loss. GigaScience, 9 (11). giaa120.
Background: Cephalopods represent a rich system for investigating the genetic basis underlying organismal novelties. This diverse group of specialized predators has evolved many adaptations including proteinaceous venom. Of particular interest is the blue-ringed octopus genus (Hapalochlaena), which are the only octopods known to store large quantities of the potent neurotoxin, tetrodotoxin, within their tissues and venom gland. Findings: To reveal genomic correlates of organismal novelties, we conducted a comparative study of 3 octopod genomes, including the Southern blue-ringed octopus (Hapalochlaena maculosa). We present the genome of this species and reveal highly dynamic evolutionary patterns at both non-coding and coding organizational levels. Gene family expansions previously reported in Octopus bimaculoides (e.g., zinc finger and cadherins, both associated with neural functions), as well as formation of novel gene families, dominate the genomic landscape in all octopods. Examination of tissue-specific genes in the posterior salivary gland revealed that expression was dominated by serine proteases in non–tetrodotoxin-bearing octopods, while this family was a minor component in H. maculosa. Moreover, voltage-gated sodium channels in H. maculosa contain a resistance mutation found in pufferfish and garter snakes, which is exclusive to the genus. Analysis of the posterior salivary gland microbiome revealed a diverse array of bacterial species, including genera that can produce tetrodotoxin, suggestive of a possible production source. Conclusions: We present the first tetrodotoxin-bearing octopod genome H. maculosa, which displays lineage-specific adaptations to tetrodotoxin acquisition. This genome, along with other recently published cephalopod genomes, represents a valuable resource from which future work could advance our understanding of the evolution of genomic novelty in this family.

Shiel, Brett P., Cooke, Ira R., Hall, Nathan E., Robinson, Nicholas A., and Strugnell, Jan M. (2020) Gene expression differences between abalone that are susceptible and resilient to a simulated heat wave event. Aquaculture, 526. 735317.
Sudden increases in water temperature can lead to mortality of cultured and wild mollusc communities during the summer months. The frequency and severity of mortality events are expected to increase as climate changes. The molecular basis for individual survival ability is poorly understood. To better understand signatures and mechanisms affecting survival we analyzed the gene expression profiles of greenlip abalone (Haliotis laevigata) classified as susceptible or resilient to laboratory induced heat stress both prior to, and at three time points throughout, the heat stress event. We detected 487 genes that were significantly differentially expressed between resilient and susceptible abalone (28 of these were significantly differentially expressed over all three time points and 26 were significantly differentially expressed throughout two of the three heat stress trial sampling points). These 54 genes also demonstrated a similar relative expression level difference between resilient and susceptible abalone in samples collected six months prior to the heat stress event. Three distinct co-expression networks incorporating these genes were also identified. The most informative transcriptomic differences between resilient and susceptible abalone throughout the heat stress trial were associated with metabolism (e.g. Mitofusin 1) and immune process (e.g. Multiple epidermal growth factor-like domain 10, Lysozyme). These functional mechanisms may enable resilient individuals to endure heat wave events. These signatures could be used to predict an individual's resilience. The findings have application in aiding stock selection for the aquaculture industry, to provide greater resilience to global climate change.

Fuller, Zachary L., Mocellin, Veronique J. L., Morris, Luke A., Cantin, Neal, Shepherd, Jihanne, Sarre, Luke, Peng, Julie, Liao, Yi, Pickrell, Joseph, Andolfatto, Peter, Matz, Mikhail, Bay, Line K., and Przeworski, Molly (2020) Population genetics of the coral Acropora millepora: toward genomic prediction of bleaching. Science, 369 (6501). eaba4674.
INTRODUCTION Coral reefs worldwide are suffering losses at an alarming rate as a result of anthropogenic climate change. Increased seawater temperatures, even only slightly above long-term maxima, can induce bleaching—the breakdown of the symbiotic relationship between coral hosts and their intracellular photosynthetic dinoflagellates from the family Symbiodiniaceae. Because these symbionts provide the majority of energy required by the coral host, prolonged periods of bleaching can eventually lead to the death of the colony. In the face of rapidly increasing temperatures, new conservation strategies are urgently needed to prevent future mass losses of coral cover, and these benefit from an understanding of the genetic basis of bleaching. RATIONALE Bleaching responses vary within and among coral species; in the reef-building coral Acropora millepora, a commonly distributed species across the Indo-Pacific, these differences have been shown to be at least partly heritable. In principle, therefore, interindividual differences in bleaching should be predictable from genomic data. Here, we demonstrate the feasibility of using a genomics-based approach to predict individual bleaching responses and suggest ways in which this can inform new strategies for coral conservation. RESULTS We first generated a chromosome-scale genome assembly as well as whole-genome sequences for 237 samples collected at 12 reefs distributed across the central Great Barrier Reef during peak bleaching in 2017. We showed that we can reliably impute genotypes in low-coverage sequencing data with a modestly sized reference haplotype panel, demonstrating a cost-effective approach for future large-scale whole-genome sequencing efforts. Very little population structure was detected across the sampled reefs, which was likely the result of the broadcast spawning mode of reproduction in A. millepora. Against this genomic background, we detected unusually old variation at the heat-shock co-chaperone sacsin, which is consistent with long-term balancing selection acting on this gene. Our genomic sequencing approach simultaneously provides a quantitative measure of bleaching and identifies the composition of symbiont species present within individual coral hosts. Testing more than 6.8 million variants for associations with three different measures of bleaching response, no single site reached genome-wide significance, indicating that variation in bleaching response is not due to common loci of large effect. However, a model that incorporates genetic effects estimated from the genome-wide association data, genomic data on relative symbiont species composition, and environmental variables is predictive of individual bleaching phenotypes. CONCLUSION Understanding the genetics of heat and bleaching tolerance will be critical to predict coral adaptation and the future of coral reef ecosystems under climate change. This knowledge also supports both conventional management approaches and the development of new interventions. Our work provides insight into the genetic architecture of bleaching response and serves as a proof of principle for the use of genomic approaches in conservation efforts. We show that a model based on environmental factors, genomic data from the symbiont, and genome-wide association data in the coral host can help distinguish individuals most tolerant to bleaching from those that are most susceptible. These results thus build a foundation toward a genomic predictor of bleaching response in A. millepora and other coral species.

Worthington, Thomas A., Andradi-Brown, Dominic A., Bhargava, Radhika, Buelow, Christina, Bunting, Pete, Duncan, Clare, Fatoyinbo, Lola, Friess, Daniel A., Goldberg, Liza, Hilarides, Lammert, Lagomasino, David, Landis, Emily, Longley-Wood, Kate, Lovelock, Catherine E., Murray, Nicholas J., Narayan, Siddharth, Rosenqvist, Ake, Sievers, Michael, Simard, Marc, Thomas, Nathan, van Eijk, Pieter, Zganjar, Chris, and Spalding, Mark D. (2020) Harnessing big data to support the conservation and rehabilitation of mangrove forests globally. One Earth, 2 (5). pp. 429-443.
Mangrove forests are found on sheltered coastlines in tropical, subtropical, and some warm temperate regions. These forests support unique biodiversity and provide a range of benefits to coastal communities, but as a result of large-scale conversion for aquaculture, agriculture, and urbanization, mangroves are considered increasingly threatened ecosystems. Scientific advances have led to accurate and comprehensive global datasets on mangrove extent, structure, and condition, and these can support evaluation of ecosystem services and stimulate greater conservation and rehabilitation efforts. To increase the utility and uptake of these products, in this Perspective we provide an overview of these recent and forthcoming global datasets and explore the challenges of translating these new analyses into policy action and on-the-ground conservation. We describe a new platform for visualizing and disseminating these datasets to the global science community, non-governmental organizations, government officials, and rehabilitation practitioners and highlight future directions and collaborations to increase the uptake and impact of large-scale mangrove research. This Perspective reviews the role of global-scale research in stimulating policy action and on-the-ground conservation for mangrove ecosystems. We outline the current state of knowledge in terms of global analyses and examine the challenge of translating this research in action.

Wei, Yujie, Lin, Dongdong, Xu, Zhanning, Gao, Xiaoman, Zeng, Chaoshu, and Ye, Haihui (2020) A possible role of crustacean cardioactive peptide in regulating immune response in hepatopancreas of mud crab. Frontiers in Immunology, 11. 711.
Crustacean cardioactive peptide (CCAP), a cyclic amidated non-apeptide, is widely found in arthropods. The functions of CCAP have been revealed to include regulation of heart rate, intestinal peristalsis, molting, and osmotic pressure. However, to date, there has not been any report on the possible involvement of CCAP in immunoregulation in crustaceans. In this study, a CCAP precursor (designated as Sp-CCAP) was identified in the commercially important mud crab Scylla paramamosain, which could be processed into four CCAP-associated peptides and one mature peptide (PFCNAFTGC-NH2). Bioinformatics analysis indicated that Sp-CCAP was highly conserved in crustaceans. RT-PCR results revealed that Sp-CCAP was expressed in nerve tissues and gonads, whereas the Sp-CCAP receptor gene (Sp-CCAPR) was expressed in 12 tissues of S. paramamosain, including hepatopancreas. In situ hybridization further showed that an Sp-CCAPR-positive signal is mainly localized in the F-cells of hepatopancreas. Moreover, the mRNA expression level of Sp-CCAPR in the hepatopancreas was significantly up-regulated after lipopolysaccharide (LPS) or polyriboinosinic polyribocytidylic acid [Poly (I:C)] challenge. Meanwhile, the mRNA expression level of Sp-CCAPR, nuclear transcription factor NF-kappa B homologs (Sp-Dorsal and Sp-Relish), member of mitogen-activated protein kinase (MAPK) signaling pathway (Sp-P38), pro-inflammatory cytokines factor (Sp-TNFSF and Sp-IL16), and antimicrobial peptide (Sp-Lysozyme, Sp-ALF, Sp-ALF4, and Sp-ALF5) in the hepatopancreas were all up-regulated after the administration of synthetic Sp-CCAP mature peptide both in vivo and in vitro. The addition of synthetic Sp-CCAP mature peptide in vitro also led to an increase in nitric oxide (NO) concentration and an improved bacterial clearance ability in the hepatopancreas culture medium. The present study suggested that Sp-CCAP signaling system might be involved in the immune responses of S. paramamosain by activating immune molecules on the hepatopancreas. Collectively, our findings shed new light on neuroendocrine-immune regulatory system in arthropods and could potentially provide a new strategy for disease prevention and control for mud crab aquaculture.

Lau, Sally C. Y., Wilson, Nerida G., Silva, Catarina N. S., and Strugnell, Jan M. (2020) Detecting glacial refugia in the Southern Ocean. Ecography. (In Press)
Throughout the Quaternary, the continental‐based Antarctic ice sheets expanded and contracted repeatedly. Evidence suggests that during glacial maxima, grounded ice eliminated most benthic (bottom‐dwelling) fauna across the Antarctic continental shelf. However, paleontological and molecular evidence indicates most extant Antarctica benthic taxa have persisted in situ throughout the Quaternary. Where and how the Antarctic benthic fauna survived throughout repeated glacial maxima remain mostly hypothesised. If understood, this would provide valuable insights into the ecology and evolution of Southern Ocean biota over geological timescales. Here we synthesised and appraised recent studies and presented an approach to demonstrate how genetic data can be effective in identifying where and how Antarctic benthic fauna survived glacial periods. We first examined the geological and ecological evidence for how glacial periods influenced past species demography in order to provide testable frameworks for future studies. We outlined past ice‐free areas from Antarctic ice sheet reconstructions that could serve as glacial refugia and discussed how benthic fauna with pelagic or non‐pelagic dispersal strategies moved into and out of glacial refugia. We also reviewed current molecular studies and collated proposed locations of Southern Ocean glacial refugia on the continental shelf around Antarctica, in the deep sea, and around sub‐Antarctic islands. Interestingly, the proposed glacial refugia based on molecular data generally do not correspond to the ice‐free areas identified by Antarctic ice sheet reconstructions. The potential biases in sampling and in the choice of molecular markers in current literature are discussed, along with the future directions for employing testable frameworks and genomic methods in Southern Ocean molecular studies. Continued data syntheses will elucidate greater understanding of where and how Southern Ocean benthic fauna persisted throughout glacial periods and provide insights into their resilience against climate changes in the future.

Da Fonseca, Rute R., Couto, Alvarina, Machado, Andre M., Brejova, Brona, Albertin, Carolin B., Silva, Filipe, Gardner, Paul, Baril, Tobias, Hayward, Alex, Campos, Alexandre, Ribeiro, Ângela M., Barrio-Hernandez, Inigo, Hoving, Henk-Jan, Tafur-Jimenez, Ricardo, Chu, Chong, Frazão, Barbara, Petersen, Bent, Peñaloza, Fernando, Musacchia, Francesco, Alexander, Graham C., Osório, Hugo, Winkelmann, Inger, Simakov, Oleg, Rasmussen, Simon, Rahman, M. Ziaur, Pisani, Davide, Vinther, Jakob, Jarvis, Erich, Zhang, Guojie, Strugnell, Jan M., Castro, L. Filipe C., Fedrigo, Olivier, Patricio, Mateus, Li, Qiye, Rocha, Sara, Antunes, Agostinho, Wu, Yufeng, Ma, Bin, Sanges, Remo, Vinar, Tomas, Blagoev, Blagoy, Sicheritz-Ponten, Thomas, Nielsen, Rasmus, and Gilbert, M Thomas P. (2020) A draft genome sequence of the elusive giant squid, Architeuthis dux. GigaScience, 9 (1). giz152.
Background The giant squid (Architeuthis dux; Steenstrup, 1857) is an enigmatic giant mollusc with a circumglobal distribution in the deep ocean, except in the high Arctic and Antarctic waters. The elusiveness of the species makes it difficult to study. Thus, having a genome assembled for this deep-sea–dwelling species will allow several pending evolutionary questions to be unlocked. Findings We present a draft genome assembly that includes 200 Gb of Illumina reads, 4 Gb of Moleculo synthetic long reads, and 108 Gb of Chicago libraries, with a final size matching the estimated genome size of 2.7 Gb, and a scaffold N50 of 4.8 Mb. We also present an alternative assembly including 27 Gb raw reads generated using the Pacific Biosciences platform. In addition, we sequenced the proteome of the same individual and RNA from 3 different tissue types from 3 other species of squid (Onychoteuthis banksii, Dosidicus gigas, and Sthenoteuthis oualaniensis) to assist genome annotation. We annotated 33,406 protein-coding genes supported by evidence, and the genome completeness estimated by BUSCO reached 92%. Repetitive regions cover 49.17% of the genome. Conclusions This annotated draft genome of A. dux provides a critical resource to investigate the unique traits of this species, including its gigantism and key adaptations to deep-sea environments.

Chin, A., Rigby, C., Short, A., and White, W.T. (2020) Verified records of Kuhl's devil ray (Mobula kuhlii) in the Solomon Islands from citizen scientists. Pacific Conservation Biology, 26. pp. 100-101.
Citizen science provides valuable information about species distributions. The Shark Search Indo-Pacific project received photographs of devil rays (Mobula spp.) from the Solomon Islands that were identified as Kuhl’s devil ray (Mobula kuhlii). These records represent new knowledge about the range and distribution of a poorly known species in an undersampled region.

Mashkour, Narges, Jones, Karina, Kophamel, Sara, Hipolito, Teresa, Ahasan, Shamim, Walker, Grant, Jakob-Hoff, Richard, Whittaker, Maxine, Hamann, Mark, Bell, Ian, Elliman, Jennifer, Owens, Leigh, Saladin, Claire, Crespo-Picazo, Jose Luis, Gardner, Brett, Loganathan, Aswini Leela, Bowater, Rachel, Young, Erina, Robinson, David, Baverstock, Warren, Blyde, David, March, Duan, Eghbali, Maryam, Mohammadi, Maryam, Freggi, Daniela, Giliam, Jane, Hale, Mike, Nicolle, Nicholas, Spiby, Kevin, Wrobel, Daphne, Parga, Mariluz, Mobaraki, Asghar, Rajakaruna, Rupika, Hyland, Kevin P., Read, Mark, and Ariel, Ellen (2020) Disease risk analysis in sea turtles: a baseline study to inform conservation efforts. PLoS ONE, 15 (10). e0230760..
The impact of a range of different threats has resulted in the listing of six out of seven sea turtle species on the IUCN Red List of endangered species. Disease risk analysis (DRA) tools are designed to provide objective, repeatable and documented assessment of the disease risks for a population and measures to reduce these risks through management options. To the best of our knowledge, DRAs have not previously been published for sea turtles, although disease is reported to contribute to sea turtle population decline. Here, a comprehensive list of health hazards is provided for all seven species of sea turtles. The possible risk these hazards pose to the health of sea turtles were assessed and “One Health” aspects of interacting with sea turtles were also investigated. The risk assessment was undertaken in collaboration with more than 30 experts in the field including veterinarians, microbiologists, social scientists, epidemiologists and stakeholders, in the form of two international workshops and one local workshop. The general finding of the DRA was the distinct lack of knowledge regarding a link between the presence of pathogens and diseases manifestation in sea turtles. A higher rate of disease in immunocompromised individuals was repeatedly reported and a possible link between immunosuppression and environmental contaminants as a result of anthropogenic influences was suggested. Society based conservation initiatives and as a result the cultural and social aspect of interacting with sea turtles appeared to need more attention and research. A risk management workshop was carried out to acquire the insights of local policy makers about management options for the risks relevant to Queensland and the options were evaluated considering their feasibility and effectiveness. The sea turtle DRA presented here, is a structured guide for future risk assessments to be used in specific scenarios such as translocation and head-starting programs.

Tebbett, Sterling B., Streit, Robert P., and Bellwood, David R. (2020) A 3D perspective on sediment accumulation in algal turfs: implications of coral reef flattening. Journal of Ecology, 108 (1). pp. 70-80.
Globally, coral reefs are being transformed by a suite of stressors, the foremost being climate change. Increasingly, it is expected that these reconfigured reef systems will emerge with lower-complexity and will be dominated by algal turfs. Understanding this new operating space is vital if we are to maintain the services, such as fishable biomass production, that reefs provide. However, the functionality of these systems appears to depend on the nature of the algal turfs themselves, which is in-turn, intimately linked to the sediments they contain. As reefs are losing complexity, we need to understand if, and to what extent, algal turf condition and complex reef structure are connected. To address this issue we took advantage of recent developments in 3D structure-from-motion technology to examine how complexity metrics (elevation and surface angle) related to the nature of algal turfs on a heavily climate-impacted coral reef. This represents a novel application of this technology in the context of coral reef ecosystems. We found that as both elevation and surface angle decreased, the nutritional value of the epilithic algal matrix also decreased while sediment accumulation increased. Furthermore, we showed that elevated surfaces were characterized by far shorter algal turfs, and are potentially herbivory hotspots, offering fertile grounds for further exploration of herbivory dynamics at sub-metre spatial scales. Synthesis. This study yields new insights into the operating-space of future reefs, and suggests that as reefs flatten, sediment accumulation is likely to increase even if sediment inputs remain unchanged, altering algal turfs fundamentally. Maintaining key services provided by climate-transformed, low-complexity algal turf-dominated reefs of the future, will depend on managing the complex interactions between herbivory, sediments, algal turfs and reef structural complexity.

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