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Appendix A: Science Publications

In 2019 AIMS scientists published the following:

Journal Articles

Abdul Wahab MA, Maldonado M, Luter HM, Jones R, Ricardo G (2019) Effects of sediment resuspension on the larval stage of the model sponge Carteriospongia foliascens. Science of the Total Environment 695: 133837

Abdul Wahab MA, Radford B, Fromont J, Hosie AM, Miller K, Heyward A (2019) The diversity and distribution of mesophotic benthic invertebrates at Ningaloo Reef, Western Australia. Marine Biodiversity 49: 2871–2886

Aguilar C, Raina JB, Fôret S, Hayward DC, Lapeyre B, Bourne DG, Miller DJ (2019) Transcriptomic analysis reveals protein homeostasis breakdown in the coral Acropora millepora during hypo-saline stress. BMC Genomics 20: 148

Anderson KD, Cantin NE, Casey JM, Pratchett MS (2019) Independent effects of ocean warming versus acidification on the growth, survivorship and physiology of two Acropora corals. Coral Reefs 38(6): 1225–1240

Andrzejaczek S, Gleiss AC, Lear KO, Pattiaratchi CB, Chapple TK, Meekan MG (2019) Biologging tags reveal links between fine-scale horizontal and vertical movement behaviors in tiger sharks (Galeocerdo cuvier). Frontiers in Marine Science 6: 229

Andrzejaczek S, Gleiss AC, Pattiaratchi CB, Meekan MG (2019) Patterns and drivers of vertical movements of the large fishes of the epipelagic. Reviews in Fish Biology and Fisheries 29(2): 335-354

Aulich MG, McCauley RD, Saunders BJ, Parsons MJG (2019) Fin whale (Balaenoptera physalus) migration in Australian waters using passive acoustic monitoring. Scientific Reports 9: 8840

Bailey K, Steinberg C, Davies C, Galibert G, Hidas M, McManus MA, Murphy T, Newton J, Roughan M, Schaeffer A (2019) Coastal mooring observing networks and their data products: Recommendations for the next decade. Frontiers in Marine Science 6: 180

Bainbridge S (2019) Use of Bayesian models to develop coral bleaching indices and forecasts from in-situ observations for the 2015-16 bleaching event. Journal of Marine Systems 198: 103187

Bainbridge S, Benthuysen J, Depczynski M, Evans-Illidge E, Forester T (2019) Reef Scan: A reef survey system for Indigenous based monitoring. The Journal of Ocean Technology 14(1): 29-36

Barton JA, Hutson KS, Bourne DG, Humphrey C, Dybala C, Rawlinson KA (2019) The life cycle of the Acropora coral-eating flatworm (AEFW), Prosthiostomum acroporae; The influence of temperature and management guidelines. Frontiers in Marine Science 6: 524

Berry KLE, Epstein HE, Lewis PJ, Hall NM, Negri AP (2019) Microplastic contamination has limited effects on fertilisation and larvae. Diversity 11: 228

Birt MJ, Stowar M, Currey-Randall LM, McLean DL, Miller KJ (2019) Comparing the effects of different coloured artificial illumination on diurnal fish assemblages in the lower mesophotic zone. Marine Biology 166:154

Botté ES, Nielsen S, Abdul Wahab MA, Webster J, Robbins S, Thomas T, Webster NS (2019) Changes in the metabolic potential of the sponge microbiome under ocean acidification. Nature Communications 10: 4134

Bouchet PJ, Peterson AT, Zurell D, Dormann CF, Schoeman D, Ross RE, Snelgrove P, Sequeira AMM, Whittingham MJ, Wang LF, Rapacciuolo G, Oppel S, Mellin C, Lauria V, Krishnakumar PK, Jones AR, Heinanen S, Heikkinen RK, Gregr EJ, Fielding AH, Caley MJ, Barbosa AM, Bamford AJ, Lozano-Montes H, Parnell S, Wenger S, Yates KL (2019) Better model transfers require knowledge of mechanisms. Trends in Ecology & Evolution 34(6): 489-490

Brodnicke OB, Bourne DG, Heron SF, Pears RJ, Stella JS, Smith HA, Willis BL (2019) Unravelling the links between heat stress, bleaching and disease: fate of tabular corals following a combined disease and bleaching event. Coral Reefs 38(4): 591-603

Brown CJ, Jupiter SD, Albert S, Anthony KRN, Hamilton RJ, Fredston-Hermann E, Halpern BS, Lin HY, Maina J, Mangubhai S, Mumby PJ, Possingham HP, Saunders MI, Tulloch VJD, Wenger A, Klein CJ (2019) A guide to modelling priorities for managing land-based impacts on coastal ecosystems. Journal of Applied Ecology 56(5): 1106-1116

Browne N, Braoun C, McIlwain J, Nagarajan R, Zinke J (2019) Borneo coral reefs subject to high sediment loads show evidence of resilience to various environmental stressors. PeerJ 7: e7382

Buck JJH, Bainbridge SJ, Burger EF, Kraberg AC, Casari M, Casey KS, Darroch L, Del Rio J, Metfies K, Delory E, Fischer PF, Gardner T, Heffernan R, Jirka S, Kokkinaki A, Loebl M, Buttigieg PL, Pearlman JS, Schewe I (2019) Ocean data product integration through innovation-the next level of data interoperability. Frontiers in Marine Science 6: 32

Buerger P, Weynberg KD, Wood-Charlson EM, Sato Y, Willis BL, van Oppen MJH (2019) Novel T4 bacteriophages associated with black band disease in corals. Environmental Microbiology 21(6): 1969-1979

Burrows DW, Purandare J, Bay L, Cook N, Koopman D, Long S, Lundgren P, Mead D, Morris S, Newlands M, Roth C, Wachenfeld D, Smith AK, McLeod IM (2019) Symposium report: Great Barrier Reef restoration symposium, 2018. Ecological Management & Restoration 20(2): 175-178

Cabrera MDG, Young JM, Roff G, Staples T, Ortiz JC, Pandolfi JM, Cooper A (2019) Broadening the taxonomic scope of coral reef palaeoecological studies using ancient DNA. Molecular Ecology 28(10): 2636-2652

Cade-Menun BJ, Duhamel S, Dodd RJ, Lonborg C, Parsons CT, Taylor WD (2019) Phosphorus along the soil-freshwater-ocean continuum. Frontiers in Marine Science 6: 28

Campbell HA, Micheli-Campbell MA, Udyawer V (2019) Early career researchers embrace data sharing. Trends in Ecology & Evolution 34(2): 95-98

Carlson JK, Heupel MR, Young CN, Cramp JE, Simpfendorfer CA (2019) Are we ready for elasmobranch conservation success? Environmental Conservation 46(4):264-226

Carrea C, Burridge CP, Wienecke B, Emmerson LM, White D, Miller KJ (2019) High vagility facilitates population persistence and expansion prior to the Last Glacial Maximum in an Antarctic top predator: The Snow petrel (Pagodroma nivea). Journal of Biogeography 46(2): 442-453

Cavicchioli R, Ripple WJ, Timmis KN, Azam F, Bakken LR, Baylis M, Behrenfeld MJ, Boetius A, Boyd PW, Classen AT, Crowther TW, Danovaro R, Foreman CM, Huisman J, Hutchins DA, Jansson JK, Karl DM, Koskella B, Welch DBM, Martiny JBH, Moran MA, Orphan VJ, Reay DS, Remais JV, Rich VI, Singh BK, Stein LY, Stewart FJ, Sullivan MB, van Oppen MJH, Weaver SC, Webb EA, Webster NS (2019) Scientists’ warning to humanity: microorganisms and climate change. Nature Reviews Microbiology 17(9): 569-586

Ceccarelli DM, Evans RD, Logan M, Mantel P, Puotinen M, Petus C, Russ GR, Williamson DH (2019) Long-term dynamics and drivers of coral and macroalgal cover on inshore reefs of the Great Barrier Reef Marine Park. Ecological Applications 30(1):e02008

Chakravarti LJ, Negri AP, van Oppen MJH (2019) Thermal and herbicide tolerances of chromerid algae and their ability to form a symbiosis with corals. Frontiers in Microbiology 10: 173

Chan WY, Hoffmann AA, van Oppen MJH (2019) Hybridization as a conservation management tool. Conservation Letters 12(5): e12652

Chan WY, Peplow LM, Menéndez P, Hoffmann AA, van Oppen MJH (2019) The roles of age, parentage and environment on bacterial and algal endosymbiont communities in Acropora corals. Molecular Ecology 28(16): 3830-3843

Chan WY, Peplow LM, van Oppen MJH (2019) Interspecific gamete compatibility and hybrid larval fitness in reef-building corals: Implications for coral reef restoration. Scientific Reports 9: 4757

Conlan JA, Humphrey CA, Severati A, Parrish CC, Francis DS (2019) Elucidating an optimal diet for captive Acropora corals. Aquaculture 513:734420

Cooke I, Mead O, Whalen C, Boote C, Moya A, Ying H, Robbins S, Strugnell JM, Darling A, Miller D, Voolstra CR, Adamska M, Ainsworth T, Andrade NR, Arnold AE, Ball E, Bourne D, Bosch TCG, Butterfield NJ, Chan CX, Cowman PF, Davy SK, Fabricius K, Fortunato SV, Fraune S, Hernandez A, Hoogenboom M, Jaspers C, Mohamed A, Pita L, Ragan MA, Sakamaki K, Schoepf V, Seemann T, Shinzato C, Stolarski J, Takahashi S, Tang SL, Webster N, Whitelaw B, Consortium Australian Acad Sci Bod (2019) Molecular techniques and their limitations shape our view of the holobiont. Zoology 137:125695

Cresswell AK, Langlois TJ, Wilson SK, Claudet J, Thomson DP, Renton M, Fulton CJ, Fisher R, Vanderklift MA, Babcock RC, Stuart-Smith RD, Haywood MDE, Depczynski M, Westera M, Ayling AM, Fitzpatrick B, Halford AR, McLean DL, Pillans RD, Cheal AJ, Tinkler P, Edgar GJ, Graham NAJ, Harvey ES, Holmes TH (2019) Disentangling the response of fishes to recreational fishing over 30 years within a fringing coral reef reserve network. Biological Conservation 237: 514-524

Cristea IM, Dorrestein PC, Eisen JA, Gilbert JA, Huber JA, Jansson JK, Knight R, Pollard KS, Raes J, Silver PA, Webster NS, Xu J (2019) Early-career scientists shaping the world. mSystems 4(3): e00196-19

Crowe-Riddell JM, D’Anastasi BR, Nankivell JH, Rasmussen AR, Sanders KL (2019) First records of sea snakes (Elapidae: Hydrophiinae) diving to the mesopelagic zone (> 200 m). Austral Ecology 44(4): 752-754

Damjanovic K, van Oppen MJH, Menendez P, Blackall LL (2019) Experimental inoculation of coral recruits with marine bacteria indicates scope for microbiome manipulation in Acropora tenuis and Platygyra daedalea. Frontiers in Microbiology 10: 1702

Darling ES, McClanahan TR, Maina J, Gurney GG, Graham NAJ, Januchowski-Hartley F, Cinner JE, Mora C, Hicks CC, Maire E, Puotinen M, Skirving WJ, Adjeroud M, Ahmadia G, Arthur R, Bauman AG, Beger M, Berumen ML, Bigot L, Bouwmeester J, Brenier A, Bridge TCL, Brown E, Campbell SJ, Cannon S, Cauvin B, Chen CA, Claudet J, Denis V, Donner S, Estradivari, Fadli N, Feary DA, Fenner D, Fox H, Franklin EC, Friedlander A, Gilmour J, Goiran C, Guest J, Hobbs JPA, Hoey AS, Houk P, Johnson S, Jupiter SD, Kayal M, Kuo CY, Lamb J, Lee MAC, Low J, Muthiga N, Muttaqin E, Nand Y, Nash KL, Nedlic O, Pandolfi JM, Pardede S, Patankar V, Penin L, Ribas-Deulofeu L, Richards Z, Roberts TE, Rodgers KS, Safuan CDM, Sala E, Shedrawi G, Sin TM, Smallhorn-West P, Smith JE, Sommer B, Steinberg PD, Sutthacheep M, Tan CHJ, Williams GJ, Wilson S, Yeemin T, Bruno JF, Fortin MJ, Krkosek M, Mouillot D (2019) Social-environmental drivers inform strategic management of coral reefs in the Anthropocene. Nature Ecology & Evolution 3: 1341-1350

Davidson J, Thompson A, Logan M, Schaffelke B (2019) High spatio-temporal variability in Acroporidae settlement to inshore reefs of the Great Barrier Reef. PLoS ONE 14(1): e0209771.

Davis KJ, Vianna GMS, Meeuwig JJ, Meekan MG, Pannell DJ (2019) Estimating the economic benefits and costs of highly protected marine protected areas. Ecosphere 10(10): e02879

Depczynski M, Cook K, Cure K, Davies H, Evans-Illidge L, Forester T, George K, Gould J, Howard A, Oades D, Underwood J, Wyatt M (2019) Marine monitoring of Australia’s Indigenous sea country using remote technologies. The Journal of Ocean Technology 14(1): 60-75

Devloo-Delva F, Huerlimann R, Chua G, Matley JK, Heupel MR, Simpfendorfer CA, Maes GE (2019) How does marker choice affect your diet analysis: comparing genetic markers and digestion levels for diet metabarcoding of tropical-reef piscivores. Marine and Freshwater Research 70: 8-18

Diedrich A, Blythe J, Petersen E, Euriga E, Fatchiya A, Shimada T, Jones C (2019) Socio-economic drivers of adoption of small-scale aquaculture in Indonesia. Sustainability 11(6): 1543

Ding K, Zhang LB, Sun LN, Lin CG, Feng QM, Zhang SY, Yang HS, Brinkman R, Lin G, Huang Z (2019) Transcriptome analysis provides insights into the molecular mechanisms responsible for evisceration behavior in the sea cucumber Apostichopus japonicus. Comparative Biochemistry and Physiology D-Genomics & Proteomics 30: 143-157

Ding K, Zhang LB, Zhang T, Yang HS, Brinkman R (2019) The effect of melatonin on locomotor behavior and muscle physiology in the sea cucumber Apostichopus japonicus. Frontiers in Physiology 10: 221

Dutton PH, Komoroske L, Bejder L, Meekan M (2019) Editorial: Integrating emerging technologies into marine megafauna conservation management. Frontiers In Marine Science 6:693

Eakin CM, Sweatman HPA, Brainard RE (2019) The 2014-2017 global-scale coral bleaching event: insights and impacts. Coral Reefs 38(4): 539-545

Emslie MJ, Logan M, Cheal AJ (2019) The distribution of planktivorous damselfishes (Pomacentridae) on the Great Barrier Reef and the relative influences of habitat and predation. Diversity 11(3): 33

Epstein HE, Hallas JM, Johnson RF, Lopez A, Gosliner TM (2019) Reading between the lines: revealing cryptic species diversity and colour patterns in Hypselodoris nudibranchs (Mollusca: Heterobranchia: Chromodorididae). Zoological Journal of the Linnean Society 186: 116-189

Epstein HE, Kingsford MJ (2019) Are soft coral habitats unfavourable? A closer look at the association between reef fishes and their habitat. Environmental Biology of Fishes 102(3): 479-497

Epstein HE, Smith HA, Cantin NE, Mocellin VJL, Torda G, van Oppen MJH (2019) Temporal variation in the microbiome of Acropora coral species does not reflect seasonality. Frontiers in Microbiology 10: 1775

Epstein HE, Smith HA, Torda G, van Oppen MJH (2019) Microbiome engineering: enhancing climate resilience in corals. Frontiers in Ecology and the Environment 17: 100-108

Epstein HE, Torda G, Munday PL, van Oppen MJH (2019) Parental and early life stage environments drive establishment of bacterial and dinoflagellate communities in a common coral. The ISME Journal 13(6): 1635-1638

Epstein HE, Torda G, van Oppen MJH (2019) Relative stability of the Pocillopora acuta microbiome throughout a thermal stress event. Coral Reefs 38(2): 373-386

Erler DV, Shepherd BO, Linsley BK, Nothdurft LD, Hua Q, Lough JM (2019) Has nitrogen supply to coral reefs in the South Pacific Ocean changed over the past 50 thousand years? Paleoceanography and Paleoclimatology 34(4): 567-579

Espinoza M, Matley J, Heupel MR, Tobin AJ, Fisk AT, Simpfendorfer CA (2019) Multi-tissue stable isotope analysis reveals resource partitioning and trophic relationships of large reef-associated predators. Marine Ecology Progress Series 615: 159-176

Espinoza-Rodriguez N, De Turris-Morales K, Shimada T, Barrios-Garrido H (2019) Guiana Dolphin (Sotalia guianensis) in the southern Gulf of Venezuela: Seasonal distribution, group size, and habitat use. Regional Studies in Marine Science 32: 100874

Evensen NR, Doropoulos C, Morrow KM, Motti CA, Mumby PJ (2019) Inhibition of coral settlement at multiple spatial scales by a pervasive algal competitor. Marine Ecology Progress Series 612: 29-42

Feitosa LM, Martins APB, Lessa RPT, Barbieri R, Nunes JLS (2019) Daggernose shark: an elusive species from northern South America. Fisheries 44: 144-147

Fisher R, Bessell-Browne P, Jones R (2019) Synergistic and antagonistic impacts of suspended sediments and thermal stress on corals. Nature Communications 10: 2346

Fisher R, Shiell GR, Sadler RJ, Inostroza K, Shedrawi G, Holmes TH, McGree JM (2019) epower: An r package for power analysis of Before-After-Control-Impact (BACI) designs. Methods in Ecology and Evolution 10 (11):1843-1853

Frassl MA, Abell JM, Botelho DA, Cinque K, Gibbes BR, Johnk KD, Muraoka K, Robson BJ, Wolski M, Xiao M, Hamilton DP (2019) A short review of contemporary developments in aquatic ecosystem modelling of lakes and reservoirs. Environmental Modelling & Software 117: 181-187

Fulton CJ, Abesamis RA, Berkstrom C, Depczynski M, Graham NAJ, Holmes TH, Kulbicki M, Noble MM, Radford BT, Tano S, Tinkler P, Wernberg T, Wilson SK (2019) Form and function of tropical macroalgal reefs in the Anthropocene. Functional Ecology 33(6): 989-999

George LW, Martins APB, Heupel MR, Simpfendorfer CA (2019) Fine-scale movements of juvenile blacktip reef sharks Carcharhinus melanopterus in a shallow nearshore nursery. Marine Ecology Progress Series 623: 85-97

Gillanders BM, Heupel AR (2019) Women in marine science in Australia. Marine and Freshwater Research 70(7): i-iii

Gilmour JP, Cook KL, Ryan NM, Puotinen ML, Green RH, Shedrawi G, Hobbs JPA, Thomson DP, Babcock RC, Buckee J, Foster T, Richards ZT, Wilson SK, Barnes PB, Coutts TB, Radford BT, Piggott CH, Depczynski M, Evans SN, Schoepf V, Evans RD, Halford AR, Nutt CD, Bancroft KP, Heyward AJ, Oades D (2019) The state of Western Australia’s coral reefs. Coral Reefs 38(4): 651-667

Gissi F, Reichelt-Brushett AJ, Chariton AA, Stauber JL, Greenfield P, Humphrey C, Salmon M, Stephenson SA, Cresswell T, Jolley DF (2019) The effect of dissolved nickel and copper on the adult coral Acropora muricata and its microbiome. Environmental Pollution 250: 792-806

Glasl B, Bourne DG, Frade PR, Thomas T, Schaffelke B, Webster NS (2019) Microbial indicators of environmental perturbations in coral reef ecosystems. Microbiome 7: 94

Glasl B, Smith CE, Bourne DG, Webster NS (2019) Disentangling the effect of host-genotype and environment on the microbiome of the coral Acropora tenuis. PeerJ 7: e6377

Goetze JS, Bond T, McLean DL, Saunders BJ, Langlois TJ, Lindfield S, Fullwood LAF, Driessen D, Shedrawi G, Harvey ES (2019) A field and video analysis guide for diver operated stereo-video. Methods in Ecology and Evolution 10(7): 1083-1090

Gordon TAC, Radford AN, Davidson IK, Barnes K, McCloskey K, Nedelec SL, Meekan MG, McCormick MI, Simpson SD (2019) Acoustic enrichment can enhance fish community development on degraded coral reef habitat. Nature Communications 10: 5414

Gouezo M, Golbuu Y, Fabricius K, Olsudong D, Mereb G, Nestor V, Wolanski E, Harrison P, Doropoulos C (2019) Drivers of recovery and reassembly of coral reef communities. Proceedings of the Royal Society B-Biological Sciences 286(1897): 20182908

Green RH, Lowe RJ, Buckley ML, Foster T, Gilmour JP (2019) Physical mechanisms influencing localized patterns of temperature variability and coral bleaching within a system of reef atolls. Coral Reefs 38(4): 759-771

Gruber RK, Lowe RJ, Falter JL (2019) Tidal and seasonal forcing of dissolved nutrient fluxes in reef communities. Biogeosciences 16: 1921-1935

Grutter AS, Blomberg SP, Box S, Bshary R, Ho O, Madin EMP, McClure EC, Meekan MG, Murphy JM, Richardson MA, Sikkel PC, Sims CA, Sun D, Warner RR (2019) Changes in local free-living parasite populations in response to cleaner manipulation over 12 years. Oecologia 190(4): 783-797

Haller-Bull V, Bode M (2019) Superadditive and subadditive dynamics are not inherent to the types of interacting threat. PLoS ONE 14(8): e0211444

Harcourt R, Sequeira AMM, Zhang XL, Roquet F, Komatsu K, Heupel M, McMahon C, Whoriskey F, Meekan M, Carroll G, Brodie S, Simpfendorfer C, Hindell M, Jonsen I, Costa DP, Block B, Muelbert M, Woodward B, Weise M, Aarestrup K, Biuw M, Boehme L, Bograd SJ, Cazau D, Charrassin JB, Cooke SJ, Cowley P, de Bruyn PJN, du Dot TJ, Duarte C, Eguiluz VM, Ferreira LC, Fernandez-Gracia J, Goetz K, Goto Y, Guinet C, Hammill M, Hays GC, Hazen EL, Huckstadt LA, Huveneers C, Iverson S, Jaaman SA, Kittiwattanawong K, Kovacs KM, Lydersen C, Moltmann T, Naruoka M, Phillips L, Picard B, Queiroz N, Reverdin G, Sato K, Sims DW, Thorstad EB, Thums M, Treasure AM, Trites AW, Williamss GD, Yonehara Y, Fedak MA (2019) Animal-borne telemetry: An integral component of the ocean observing toolkit. Frontiers in Marine Science 6: 326

Harding HR, Gordon TAC, Eastcott E, Simpson SD, Radford AN (2019) Causes and consequences of intraspecific variation in animal responses to anthropogenic noise. Behavioral Ecology 30(6): 1501-1511

Hays GC, Bailey H, Bograd SJ, Bowen WD, Campagna C, Carmichael RH, Casale P, Chiaradia A, Costa DP, Cuevas E, de Bruyn PJN, Dias MP, Duarte CM, Dunn DC, Dutton PH, Esteban N, Friedlaender A, Goetz KT, Godley BJ, Halpin PN, Hamann M, Hammerschlag N, Harcourt R, Harrison AL, Hazen EL, Heupel MR, Hoyt E, Humphries NE, Kot CY, Lea JSE, Marsh H, Maxwell SM, McMahon CR, di Sciara GN, Palacios DM, Phillips RA, Righton D, Schofield G, Seminoff JA, Simpfendorfer CA, Sims DW, Takahashi A, Tetley MJ, Thums M, Trathan PN, Villegas-Amtmann S, Wells RS, Whiting SD, Wildermann NE, Sequeira AMM (2019) Translating marine animal tracking data into conservation policy and management. Trends in Ecology & Evolution 34(5): 459-473

He S, Robitzch V, Hobbs JPA, Travers MJ, Lozano-Cortes D, Berumen ML, DiBattista JD (2019) An examination of introgression and incomplete lineage sorting among three closely related species of chocolate-dipped damselfish (genus: Chromis). Ecology and Evolution 9(9): 5468-5478

Heupel MR, Kanno S, Martins APB, Simpfendorfer CA (2019) Advances in understanding the roles and benefits of nursery areas for elasmobranch populations. Marine and Freshwater Research 70(7): 897-907

Heupel MR, Munroe SEM, Ledee EJI, Chin A, Simpfendorfer CA (2019) Interspecific interactions, movement patterns and habitat use in a diverse coastal shark assemblage. Marine Biology 166(6): 68

Heupel MR, Papastamatiou YP, Espinoza M, Green ME, Simpfendorfer CA (2019) Reef Shark Science - Key Questions and Future Directions. Frontiers in Marine Science 6: 12

Hoegh-Guldberg O, Skirving WJ, Lough JM, Liu CY, Mann ME, Donner S, Eakin CM, Cantin N, Carilli J, Heron SF, Miller S, Dove S (2019) Commentary: Reconstructing Four Centuries of Temperature-Induced Coral Bleaching on the Great Barrier Reef. Frontiers in Marine Science 6: 86

Holbrook NJ, Scannell HA, Sen Gupta A, Benthuysen JA, Feng M, Oliver ECJ, Alexander LV, Burrows MT, Donat MG, Hobday AJ, Moore PJ, Perkins-Kirkpatrick SE, Smale DA, Straub SC, Wernberg T (2019) A global assessment of marine heatwaves and their drivers. Nature Communications 10: 2624

Hughes TP, Kerry JT, Baird AH, Connolly SR, Chase TJ, Dietzel A, Hill T, Hoey AS, Hoogenboom MO, Jacobson M, Kerswell A, Madin JS, Mieog A, Paley AS, Pratchett MS, Torda G, Woods RM (2019) Global warming impairs stock-recruitment dynamics of corals. Nature 568: 387-390

Hughes TP, Kerry JT, Connolly SR, Baird AH, Eakin CM, Heron SF, Hoey AS, Hoogenboom MO, Jacobson M, Liu G, Pratchett MS, Skirving W, Torda G (2019) Ecological memory modifies the cumulative impact of recurrent climate extremes. Nature Climate Change 9: 40-43

Jaspers C, Fraune S, Arnold AE, Miller DJ, Bosch TCG, Voolstra CR, Adamska M, Ainsworth T, Ball E, Boote C, Bourne D, Butterfield NJ, Chan CX, Cooke I, Cowman PF, Darling A, Davy SK, Mohamed A, Fabricius K, Fortunato SV, Hernandez A, Hoogenboom M, Moya A, Pita L, Ragan MA, Robbins SJ, Andrade NR, Sakamaki K, Schoepf V, Seemann T, Shinzato C, Stolarski J, Strugnell J, Takahashi S, Tang SL, Webster N, Whitelaw B, Ying H (2019) Resolving structure and function of metaorganisms through a holistic framework combining reductionist and integrative approaches. Zoology 133: 81-87

Jensen LH, Motti CA, Garm AL, Tonin H, Kroon FJ (2019) Sources, distribution and fate of microfibres on the Great Barrier Reef, Australia. Scientific Reports 9: 9021

Jensen S, Hovland M, Lynch MDJ, Bourne DG (2019) Diversity of deep-water coral-associated bacteria and comparison across depth gradients. FEMS Microbiology Ecology 95: fiz091

Jewell OJD, Gleiss AC, Jorgensen SJ, Andrzejaczek S, Moxley JH, Beatty SJ, Wikelski M, Block BA, Chapple TK (2019) Cryptic habitat use of white sharks in kelp forest revealed by animal-borne video. Biology Letters 15(4): 20190085

Johnson GB, Taylor BM, Robbins WD, Franklin EC, Toonen R, Bowen B, Choat JH (2019) Diversity and structure of parrotfish assemblages across the northern Great Barrier Reef. Diversity 11(1): 14

Jones R, Fisher R, Bessell-Browne P (2019) Sediment deposition and coral smothering. PLoS ONE 14(6): e0216248

Jonker MJ, Thompson AA, Menéndez, Osborne K (2019) Cross-shelf variation among juvenile and adult coral assemblages on Australia’s Great Barrier Reef. Diversity 11(6): 85

Kanno S, Schlaff AM, Heupel MR, Simpfendorfer CA (2019) Stationary video monitoring reveals habitat use of stingrays in mangroves. Marine Ecology Progress Series 621: 155-168

Kim SW, Sampayo EM, Sommer B, Sims CA, Gomez-Cabrera MD, Dalton SJ, Beger M, Malcolm HA, Ferrari R, Fraser N, Figueira WF, Smith SDA, Heron SF, Baird AH, Byrne M, Eakin CM, Edgar R, Hughes TP, Kyriacou N, Liu G, Matis PA, Skirving WJ, Pandolfi JM (2019) Refugia under threat: Mass bleaching of coral assemblages in high-latitude eastern Australia. Global Change Biology 25(11): 3918-3931

Klein AH, Ballard KR, Storey KB, Motti CA, Zhao M, Cummins SF (2019) Multi-omics investigations within the Phylum Mollusca, Class Gastropoda: from ecological application to breakthrough phylogenomic studies. Briefings in Functional Genomics 18(6): 377-394

Korsvig-Nielsen C, Hall M, Motti C, Garm A (2019) Eyes and negative phototaxis in juvenile crown-of-thorns starfish, Acanthaster species complex. Biology Open 8: bio041814

Laffy PW, Botté ES, Wood-Charlson EM, Weynberg KD, Rattei T, Webster NS (2019) Thermal stress modifies the marine sponge virome. Environmental Microbiology Reports 11(5): 690-698

Lechene MAA, Haberstroh AJ, Byrne M, Figueira W, Ferrari R (2019) Optimising sampling strategies in coral reefs using large-area mosaics. Remote Sensing 11:2907

Lee MA, Duarte CM, Eguiluz VM, Heller DA, Langer R, Meekan MG, Sikes HD, Srivastava MB, Strano MS, Wilson R (2019) Can Fish and Cell Phones Teach Us about Our Health? ACS Sensors 4(10): 2566-2570

Lee MA, Nguyen FT, Scott K, Chan NYL, Bakh NA, Jones KK, Pham C, Garcia-Salinas P, Garcia-Parraga D, Fahlman A, Marco V, Koman VB, Oliver RJ, Hopkins LW, Rubio C, Wilson RP, Meekan MG, Duarte CM, Strano MS (2019) Implanted nanosensors in marine organisms for physiological biologging: Design, feasibility, and species variability. ACS Sensors 4(1): 32-43

Levin LA, Bett BJ, Gates AR, Heimbach P, Howe BM, Janssen F, McCurdy A, Ruhl HA, Snelgrove P, Stocks KI, Bailey D, Baumann-Pickering S, Beaverson C, Benfield MC, Booth DJ, Carreiro-Silva M, Colaco A, Eble MC, Fowler AM, Gjerde KM, Jones DOB, Katsumata K, Kelley D, Le Bris N, Leonardi AP, Lejzerowicz F, Macreadie PI, McLean D, Meitz F, Morato T, Netburn A, Pawlowski J, Smith CR, Sun S, Uchida H, Vardaro MF, Venkatesan R, Weller RA (2019) Global observing needs in the deep ocean. Frontiers in Marine Science 6: 241

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Fisher R, van Dam RA, Batley GE, Fox DR, Harford AJ, Humphrey CL, King CK, Menendez P, Negri AP, Proctor A, Shao Q, Stauber JL, van Dam JW, Warne MStJ (2019). Key issues in the derivation of water quality guideline values: a workshop report. Australian Institute of Marine Science Report, Perth (59 pp)

Galaiduk R, Huang Z, Miller K, Nanson R, Przeslawski R, Nichol S (2019) An eco-narrative of Joseph Bonaparte Gulf Marine Park: North-west marine region. Marine Park Eco-Narrative Series. Report to the National Environmental Science Programme, Marine Biodiversity Hub. Geoscience Australia (21pp)

Gilmour J, Ryan N, Cook K, Underwood J, Richards Z, Case M, Foster T, Puotinen M, Thomas L (2019) Long term monitoring at Scott Reef and Rowley Shoals 2017. Report prepared for Woodside Energy Ltd as operator for and on behalf of the Browse Joint Venture Development. Australian Institute of Marine Science, Perth (201pp)

Gilmour J, Ryan N, Cook K, Radford B, Case M, Foster T (2019) Long-term monitoring of benthic communities at Ashmore Reef, 2016-2017. Report prepared for Parks Australia. Australian Institute of Marine Science, Perth (32 pp)

Gruber R, Waterhouse J, Logan M, Petus C, Howley C, Lewis S, Tracey D, Langlois L, Tonin H, Skuza M, Costello P, Davidson J, Gunn K, Lefevre C, Shanahan M,Wright M, Zagorskis I, Kroon F, Neilen A (2019) Marine Monitoring Program: Annual report for inshore water quality monitoring 2017-2018. Report for the Great Barrier Reef Marine Park Authority, Townsville (288pp)

Heupel MR, Kyne PM, White WT, Simpfendorfer CA (2019) Shark Action Plan Policy Report. Report to the National Environmental Science Programme, Marine Biodiversity Hub. Australian Institute of Marine Science, Townsville (62pp)

Heyward A, Miller K, Fromont J, Keesing J, Parnum I (Eds) (2019) Kimberley Benthic Biodiversity Synthesis Report of Project 1.1.1 prepared for the Kimberley Marine Research Program, Western Australian Marine Science Institution, Perth, Western Australia (57pp)

Heyward A, Wakeford M, Currey-Randall L, Colquhoun J, Galaiduk R, Fisher R, Menéndez P, Case M, Radford B, Stowar M, Vaughan B, Cure K, Birt M, Puotinen M (2019) Browse Island reef: Quantitative information on the abundance, diversity and temporal variability of benthos and associated fish. Final report for ARP7-1 Subtidal Benthos, prepared for Shell/INPEX Applied Research Program in accordance with Shell Contract No U124206 and INPEX Contract No 800950. Australian Institute of Marine Science, Perth (162pp)

Jones R, Twomey L (2019) WAMSI Dredging Science Node Theme 1. Review and consolidation of environmental monitoring data collected by industry. Final Report prepared for the Dredging Science Node, Western Australian Marine Science Institution, Perth, Western Australia (14 pp)

Jones R, Fisher R, Bessell-Browne P, Negri A, Duckworth A (2019) WAMSI Dredging Science Node Theme 4. Synthesis report: Defining thresholds and indicators of coral response to dredging-related pressures. Final Synthesis Report prepared for the Dredging Science Node, Western Australian Marine Science Institution, Perth, Western Australia (36 pp)

Jones R, Miller KJ (2019) Greater Western Flank-2 – Rankin Bank: Environmental Research and Monitoring Program. Report prepared for Woodside Energy Ltd. Australian Institute of Marine Science, Perth (155 pp)

Klein A, Zhao M, Motti C, Cummins S (2019) Gene expression analysis of the giant triton snail, Charonia tritonis, during larval development. Report prepared for Reef2050 Grant Id: 3600000775. Department of the Environment and Energy. University of the Sunshine Coast, Sippy Downs (19 pp)

Lucieer V, Monk J, Huang Z, Nichol S, Miller K, Barrett N, Williams A (2019) An eco-narrative of Huon Marine Park – South-east marine region. Marine Park Eco-Narrative Series. Report to the National Environmental Science Programme, Marine Biodiversity Hub. Geoscience Australia (34pp)

McLean D (2019) Assessing the scientific value of historical industrial ROV video: Santos North West Shelf assets. Report prepared for Santos Ltd. Australian Institute of Marine Science, Perth (16 pp) (Rev 0 February 2019)

Meekan MG, Lester E (2019) Recent research on whale sharks at Ningaloo Reef. Report prepared for Woodside Energy Limited. Australian Institute of Marine Science, Perth. (40 pp) (Rev 0 March 2019)

Motti C, Armstrong T, Cummins S, Francis D, Hall M, Hillberg A, Klein A, Menéndez P, Rudd D, Thomas-Hall P (2019) Charonia tritonis: A natural biocontrol agent for Crown-of-Thorns Starfish. Final Report prepared for Reef2050 Grant Id: 3600000775. Department of the Environment and Energy. Australian Institute of Marine Science, Townsville (172 pp)

Negri AP, Luter HM, Brinkman DL, Nordborg M, Langtry S, Jones R (2019) Ecotoxicological thresholds of petroleum hydrocarbons for modelling risk to tropical marine species. Final report prepared for Shell/INPEX Applied Research Program 8 in accordance with Shell Contract No U124206 and INPEX Contract No 800950. Australian Institute of Marine Science, Perth (48 pp)

Negri A, Ricardo G, Jones R (2019) WAMSI Dredging Science Node Theme 7. Synthesis report: Effects of dredging-related pressures on critical ecological processes for corals. Final synthesis report prepared for the Dredging Science Node, Western Australian Marine Science Institution, Perth, Western Australia (23 pp)

Przeslawski R, Falkner I, Foster S, Mancini S, Bainbridge S, Bax N, Carroll A, Flukes E, Gonzalez-Rivero M, Langlois T, Moore K, Rehbein M, Tattersall K, Watts D, Williams A, Wyatt M (2019) Data discoverability and accessibility. Report from workshops on marine imagery and biological specimen data, September 2018. Report to the National Environmental Science Programme, Marine Biodiversity Hub. Geoscience Australia (42pp)

Puotinen M, Galaiduk R, Miller K, Nanson R, Huang Z, Nichol S (2019) An eco-narrative of Kimberley Marine Park: North-west marine region. Marine Park Eco-Narrative Series. Report to the National Environmental Science Programme, Marine Biodiversity Hub. Geoscience Australia (36pp)

Radford B, Heyward A, Birt MJ, Case M, Colquhoun J, Currey-Randall LM, Stowar MJ, Vaughan BI, Wyatt M (2019) Oceanic Shoals MP benthic habitat and fish diversity assessment 2017. Final report prepared for ConocoPhillips Pty Ltd. Australian Institute of Marine Science, Perth (98pp)

Robson B, Canto M, Collier C, di Perna S, Logan M, Menéndez P, McKinna L, Noonan S, Fabricius K (2019) Benthic light as ecologically validated GBR-wide indicator for water quality. Tropical Water Quality Hub Project 2.3.1. Final technical report to the National Environmental Science Program. Reef and Rainforest Research Centre Limited, Cairns (40 pp)

Schlaff A, Menéndez P, Heupel M, Hall M, Armstrong T, Miller M, Motti C (2019) Mitigation of Crown-of-Thorns Starfish on the Great Barrier Reef: Modelling the Release of Giant Triton Snails. Report prepared for Reef2050 Grant Id: 3600000775. Department of the Environment and Energy. Australian Institute of Marine Science, Townsville (72 pp)

Schlaff A, Menéndez P, Hall M, Heupel M, Armstrong T, Thomas-Hall P, Motti C (2019) The movement ecology of Charonia tritonis. Report prepared for Reef2050 Grant ID: 3600000775. Department of the Environment and Energy. Australia Institute of Marine Science, Townsville.

Streten C, Davies H, Galaiduk, R (2019) AIMS – Indigenous marine habitat workshop - Mapping of Indigenous values and knowledge of sea country. Final report to ENI and Thamarrurr Rangers. Australian Institute of Marine Science, Darwin

Streten C (2019) Presentation of participatory mapping results to the Thamarrurr Development Corporation, Rangers and Traditional Owners. Report to ENI and Thamarrurr Rangers. Australian Institute of Marine Science, Darwin

Streten C, Harries S, Bartlett C (2019) Alternative discharge study stage 2 – model validation, habitat mapping and ecotoxicology. Field and Water Chemistry Report 1 – December 2018. Report to Rio Tinto, Gove. Australian Institute of Marine Science, Darwin (42 pp)

Streten C, Harries S, Bartlett C, van Dongen-Vogels V, Tonin H (2019) Alternative discharge study stage 2 – model validation, habitat mapping and ecotoxicology. Field and Water Chemistry Report 2 – March 2019. Report to Rio Tinto, Gove. Australian Institute of Marine Science, Darwin (69 pp)

Streten C, Steinberg C (2019) Summary of the order of magnitude studies to assess management options for contaminated sediment in Inner Gove Harbour. Report to Rio Tinto Gove. Australian Institute of Marine Science, Darwin (27 pp)

van Dam JW (2019) Direct toxicity assessment of QAL RMD discharge 2019. Report to Queensland Alumina Limited. Australian Institute of Marine Science, Darwin (57 pp)

van Dam JW (2019) Direct toxicity assessment of RT Yarwun W1 discharge 2019. Report to Rio Tinto Yarwun. Australian Institute of Marine Science, Darwin (57 pp)

van Dam JW (2019) Amelioration of toxicity in alumina refinery discharge using a moving bed biofilm reactor. Report to Queensland Alumina Limited. Australian Institute of Marine Science, Darwin (35 pp)

van Dam JW, Streten C (2019) Toxicity assessment of phosphonium ionic liquid, stage II. Report to Rio Tinto. Australian Institute of Marine Science, Darwin (36 pp)

WAMSI (2019) Dredging Science Node – Final Synthesis Report. Western Australian Marine Science Institution, Perth, Western Australia (89 pp)

Wolfe K, Anthony K, Babcock RC, Bay L, Bourne DG, Bradford T, Burrows D, Byrne M, Deaker D, Diaz-Pulido G, Frade PF, González-Rivero M, Hoey A, Hoogenboom M, McCormick M, Ortiz J, Razak T, Richardson AJ, Sheppard-Brennand H, Stella J, Thompson A, Watson S, Webster N, Audas D, Beeden R, Bonanno V, Carver J, Chong-Seng K, Cowlishaw M, Dryden J, Dyer M, Groves P, Horne D, Mattocks N, Thiault L, Vains J, Wachenfeld D, Weekers D, Williams G, Mumby PJ (2019) Recommendations to maintain functioning of the Great Barrier Reef. Project 4.6 Final report to the National Environmental Science Program. Reef and Rainforest Research Centre Limited, Cairns (330 pp)

Books and Book Chapters

Alderslade P, Fabricius K (2019) Chapter 23. Octocorals. pp 283-310. In: Hutchings P, Kingsford M, Hoegh-Guldberg O (Eds) The Great Barrier Reef. Biology, Environment and Management (Second Edition). CSIRO Publishing (488 p) ISBN: 9781486308194

Boyd PW, Collins S, Dupont S, Fabricius K, Gattuso J-P, Havenhand J, Hutchins DA, McGraw CM, Riebesell U, Vichi M, Biswas H, Ciotti A, Dillingham P, Gao K, Gehlen M, Hurd CL, Kurihawa H, Navarro J, Nilsson GE, Passow U, Portner H-O (2019) SCOR WG149 Handbook to support the SCOR Best Practice Guide for ‘Multiple Drivers’ Marine Research. University of Tasmania, on behalf of Scientific Committee on Oceanic Research (SCOR) (48 pp) (http://dx.doi.org/10.25959/5c92fdf0d3c7a
ISBN 978-1-925646-72-6

Brodie J, Fabricius K (2019) Chapter 13. Terrestrial runoff to the Great Barrier Reef and the implications for its long-term ecological status. pp 161-168. In: Hutchings P, Kingsford M, Hoegh-Guldberg O (Eds) The Great Barrier Reef. Biology, Environment and Management (Second Edition). CSIRO Publishing (488 p)
ISBN: 9781486308194

Heyward A, Radford B (2019) Chapter 19. Northwest Australia. pp 337-349. In: Loya Y, Puglise KA, Bridge TCL (Eds) Mesophotic Coral Ecosystems. Coral Reefs of the World Volume 12. Springer, Cham. (1003 pp).
ISBN 978-3-319-92734-3 https://doi.org/10.1007/978-3-319-92735-0

Kingsford MJ, McKinnon AD (2019) Chapter 16. Plankton. pp 191-206. In: Hutchings P, Kingsford M, Hoegh-Guldberg O (Eds) The Great Barrier Reef. Biology, Environment and Management (Second Edition). CSIRO Publishing (488 p)
ISBN: 9781486308194

Pitcher CR, Doherty PJ, Anderson TJ (2019) Chapter 6. Seabed environments, habitats and biological assemblages. pp 63-72. In: Hutchings P, Kingsford M, Hoegh-Guldberg O (Eds) The Great Barrier Reef. Biology, Environment and Management (Second Edition). CSIRO Publishing (488 p)
ISBN: 9781486308194

Pratchett MS, Bridge TCL, Brodie J, Cameron DS, Day JC, Emslie M, Grech A, Hamann M, Heron SF, Hoey AS, Hoogenboom MO, Lough JM, Morrison TH, Osborne K, Read MA, Schauble C, Smithers SG, Sweatman HPA, Waterhouse J (2019) Chapter 15. Australia’s Great Barrier Reef. pp 333-362. In: Sheppard C (Ed) World Seas. An Environmental Evaluation. Volume II the Indian Ocean to the Pacific (2nd Edition). Academic Press. 932 p.
ISBN 9780081008539

Przeslawski R, Nichol S, Alvarez B, Carroll A, Glasby C, Picard K, Radford B (2019) Carbonate banks and terraces of the Oceanic Shoals Marine Park region, Northern Australia. pp 545-558 In: Harris PT, Baker E (Eds) Seafloor Geomorphology as Benthic Habitat. Elsevier, Amsterdam. 1078 p. (
ISBN: 978-0-12-814960-7

National Academies of Sciences, Engineering, and Medicine (2019) A Research Review of Interventions to Increase the Persistence and Resilience of Coral Reefs. Washington, DC: The National Academies Press. doi: https://doi.org/10.17226/25279.

Committee members: Palumbi SR, Anthony KRN, Baker AC, Baskett ML, Bhattacharya D, Bourne DG, Knowlton N, Logan CA, Naish KA, Richmond RH, Smith TB, von Stackelberg K