[93] Arif, S., & MacNeil, M. A. (2023). Applying the structural causal model framework for observational causal inference in ecology. Ecological Monographs, 93(1), e1554.

[92] Robinson, J. P., Mills, D. J., Asiedu, G. A., Byrd, K., Mancha Cisneros, M. D. M., Cohen, P. J., … & Hicks, C. C. (2022). Small pelagic fish supply abundant and affordable micronutrients to low-and middle-income countries. Nature Food, 1-10.

[91] Mellin, C., Hicks, C. C., Fordham, D. A., Golden, C. D., Kjellevold, M., MacNeil, M. A., … & Graham, N. A. (2022). Safeguarding nutrients from coral reefs under climate change. Nature Ecology & Evolution, 6(12), 1808-1817.

[90] Steele, R. W., MacNeil, M. A., & Hankewich, S. (2022). Direct assessment of Giant Red Sea Cucumber (Apostichopus californicus) sustainability through experimental fisheries. Canadian Journal of Fisheries and Aquatic Sciences.

[89] Hicks, C. C., Gephart, J. A., Koehn, J. Z., Nakayama, S., Payne, H. J., Allison, E. H., … & Naylor, R. L. (2022). Rights and representation support justice across aquatic food systems. Nature Food, 1-11.

[88] Hamelin, K. M., MacNeil, M. A., Curran, K., & Bailey, M. (2022). “The people’s fish”: Sociocultural dimensions of recreational fishing for Atlantic mackerel in Nova Scotia. Frontiers in Marine Science, 1716.

[87] Charbonneau, J. A., Keith, D. M., MacNeil, M. A., & Hutchings, J. A. (2022). Effects of fishing mortality on the age structure of marine fishes. Canadian Journal of Fisheries and Aquatic Sciences, 79(12), 2225-2236.

[86] Arif, S., & MacNeil, M. A. (2022). Predictive models aren’t for causal inference. Ecology Letters, 25(8), 1741-1745.

[85] Hamilton, M., Robinson, J. P., Benkwitt, C. E., Wilson, S. K., MacNeil, M. A., Ebrahim, A., & Graham, N. A. (2022). Climate impacts alter fisheries productivity and turnover on coral reefs. Coral Reefs, 41(4), 921-935.

[84] Robinson, J. P., Nash, K. L., Blanchard, J. L., Jacobsen, N. S., Maire, E., Graham, N. A., … & Hicks, C. C. (2022). Managing fisheries for maximum nutrient yield. Fish and Fisheries, 23(4), 800-811.

[83] Lees, K. J., MacNeil, M. A., Hedges, K. J., & Hussey, N. E. (2022). Estimating survival in a remote community-based fishery using acoustic telemetry. Canadian Journal of Fisheries and Aquatic Sciences, 79(11), 1830-1842.

[82] Chapman, D. D., MacNeil, M. A., Heupel, M. R., Meekan, M. G., Harvey, E. S., Simpfendorfer, C. A., & Heithaus, M. R. (2022). The Elasmobranchs of Coral Reefs. In Biology of Sharks and Their Relatives (pp. 635-655). CRC Press.

[81] Arif S, MacNeil MA. (2022) Model selection isn’t causal inference. Ecology Letters In Press

[80] Nash K, MacNeil MA, Blanchard J, Cohen P, Farmery A, Graham NAJ, Thorne-Lyman A, Watson R, Hicks C (2022) Trade and foreign fishing mediate control of global marine nutrient supply. PNAS In press

[79] Arif S, MacNeil MA. (2022) Utilizing causal diagrams across quasi-experimental approaches. Ecosphere

[78] Arif S, Graham NAJ, Wilson SK, MacNeil MA. (2022) Causal factors of a coral reef regime shift after a climate-induced bleaching event. Ecosphere 13(3):e3956.

[77]Robinson JPW, Nash K, Blanchard J, Jacobsen N, Maire E, Graham NAJ, MacNeil MA, et al. (2022) Managing fisheries for Maximum Nutrient Yield. Fish and Fisheries

[76] Robinson JPW, Maire E, Bodin N, Hempson TN, Graham NAJ, Wilson SK, MacNeil MA, Hicks CC (2022) Climate-induced changes in micronutrient availability for small-scale tropical fisheries. One Earth

[75] McLean M, Mouillot D, Maureaud AA, Hattab T, MacNeil MA, Goberville E, Lindegren M, Engelhard G, Pinsky M, Auber, A (2021). Disentangling tropicalization and deborealization in marine ecosystems under climate change. Current Biology 31:4817 4823.

[74] Maire, E., Graham N.A.J., MacNeil A, Lam V.W.Y, Robinson, J.P.W., Cheung, W.W.L. and Hicks, C.C. (2021) Micronutrient supply from global marine fisheries under climate change and overfishing. Current Biology.

[73] Chapman DD, Ali K, MacNeil MA, Heupel MR, Meekan M, Harvey ES, Simpfendorfer CA, Heithaus MR (2021) Long-term investment in shark sanctuaries. Science372(6541):473.

[72] McLean M, Stuart-Smith RD, Villger S, Auber A, Edgar GJ, MacNeil MS, Loiseau N, MouillotD (2021) Trait similarity in reef fish faunas across the world’s oceans. PNAS118 (12) e2012318118 .

[71] Clementi GM, Bakker J, Flowers KI, et al.(2021) Moray eels are more common on coral reefs subject to higher human pressure in the greater Caribbean. iScience 102097.

[70] Lees K, MacNeil MA, Hedges KJ, Hussey NE (2021) Estimating demographic parameters for fisheries management using acoustic telemetry. Reviews in Fish Biology and Fisheries 31:2551.

[69] MacNeil MA, Chapman D, Heupel M, Simpfendorfer CA, Heithaus M, Meekan M, Harvey E, et al. 2020. Global Status and Conservation Potential of Reef Sharks. Nature 583:801806

[68] Charbonneau J, MacNeil MA, Keith D, Sameoto J, Hutchings, J 2020. Pervasive declines in monkfish (Lophius americanus) size structure throughout the northwest Atlantic. Fisheries Research 220:105633.

[67] Cinner JE, Zamborain-Mason J, Gurney GG, Graham NAJ, MacNeil MA, Hoey AS, Mora C, Villéger S, Maire E, McClanahan TR, others (2020) Meeting fisheries, ecosystem function, and biodiversity goals in a human-dominated world. Science 368:307–311

[66] Hicks CC, Cohen PJ, Graham NAJ, MacNeil MA, Nash KL, Allison EH, D´Lima C, Mills D, Roscher M, Thilsted S, Thorne-Lyman A. 2019. Harnessing global fisheries to tackle micronutrient deficiencies. Nature 574:95-98.

[65] Mellin C, Matthews S, Anthony KRN, Brown SC, Caley MJ, Fordham DA, Johns K, Osborne K, Puotinen M, Thompson A, Wolff NH, MacNeil MA. 2019. Spatial resilience of the Great Barrier Reef. Global Change Biology 25:2431-2445.

[64] MacNeil MA, Mellin C, Matthews SA, Wolff NH, McClanahan TR, Devlin M, Drovandi C, Mengersen K, Graham NAJ 2019. Water quality mediated resilience on the Great Barrier Reef. Nature Ecology & Evolution.

[63] Edwards JE, Broell F, Bushnell P, Campana SE, Christiansen JS, Devine BM, Gallant JJ, Hedges K, Hiltz E, MacNeil MA et al. 2019. Advancing our understanding of long-lived species: A case study on the Greenland shark. Frontiers in Marine Science.

[62] Matthews SA, Mellin C, MacNeil MA, Heron SF, Puotinen M. 2018. High-resolution characterization of the abiotic environment and disturbance regimes on the Great Barrier Reef: 1985-2017. Ecology 100(2):e02547.

[61] Emslie MJ, Cheal AJ, MacNeil, MA, Miller IR, Sweatman PA. 2018. Reef fish communities are spooked by scuba surveys and may take hours to recover. PeerJ:

[60] Cinner JE, Huchery C, Maire E, MacNeil MA, Graham, NAJ, et al. 2018. Gravity of human impacts mediates coral reef conservation gains. Proceedings of the National Academy of Sciences USA 115 (27): E6116-E6125.

[59] ∗Graham, NAJ, Wilson SK, Carr P, Hoey AS, Jennings S, MacNeil, MA 2018. Seabirds fuel coral reef productivity and functioning in the absence of invasive rats. Nature 559: 250-253.

[58] Wilson SK, Graham NAJ, Holmes TH, MacNeil MA, Ryan NM 2018. Visual versus video methods for estimating reef fish biomass. Ecological Indicators 85, 146-152.

[57] Hempson TN, Graham NAJ, MacNeil MA, Hoey AS, Wilson SK 2018. Ecosystem regime shifts disrupt trophic structure. Ecological Applications 28(1), 191-200.

[56] Hempson TN, Graham NAJ, MacNeil MA, Hoey AS, Almany GR 2018. Mesopredator trophodynamics on thermally stressed coral reefs. Coral Reefs 37(1), 135-144.

[55] Hempson TN, Graham NAJ, MacNeil MA, Bodin N, Wilson SK, 2018. Regime shifts shorten food chains for mesopredators with potential sublethal effects. Functional Ecology 32(3), 820-830.

[54] ∗Graham NAJ, McClanahan TR, MacNeil MA, Wilson SK, Cinner JE, Hutchery C, Holmes TH 2017. Human Disruption of Coral Reef Trophic Structure. Current Biology 27: 231236.

[53] MacNeil MA, Chong-Seng KM, Pratchett DJ, Thompson C, Messmer V, Pratchett MS 2017. Age and growth of an outbreaking Acanthaster cf. solaris population on the Great Barrier Reef. Diversity 9.1: 18.

[52] ∗†Cheal AJ, MacNeil MA, Emslie MJ, Sweatman H. 2017. The threat to coral reefs from more intense cyclones under climate change. Global Change Biology 23(4), 1511-1524.

[51] Steeves H, McMeans B, Field C, Stewart C, Arts MT, Fisk AT, Lydersen C, Kovacs KM, MacNeil MA. 2016. Non-parametric spatio-temporal variability in the fatty-acid profiles among Greenland Sharks. Journal of the Marine Biological Association of the UK in press.

[50] Hempsen TN, Graham NAJ, MacNeil MA, Williamson DH, Jones GP, Almany GR 2017. Coral reef mesopredators switch prey, shortening food chains, in response to habitat degradation. Ecology & Evoloution 7(8), 2626-2635.

[49] Mellin C, Lurgi M, Matthews S, MacNeil MA, Caley MJ, Bax N, Przeslawski R, Fordham D 2016. Biotic interactions mediate marine invasions under climate change. Biological Conservation 204: 459-467.

[48] MacNeil MA, Mellin, C, Pratchett M, Hoey AJ, et al.. 2016. Joint estimation of crown of thorns (Acanthaster plancii) densities on the Great Barrier Reef. PeerJ 4:e2310; DOI 10.7717/peerj.2310.

[47] ∗Cinner JE, Hutchery C, MacNeil MA, Graham NAJ, McClanahan TR et al.. 2016. Bright spots among the world’s coral reefs. Nature Cover Story 21 July 2016. (Nature News and Views; Nature Podcast; international print and television media; Altmetric score >1100)

[46] ∗Mellin C, MacNeil MA, Cheal AJ, Emslie MJ, Caley, MJ 2016. Marine protected areas increase resilience among coral reef communities. Ecology Letters 19(6): 629-637. (International media coverage; Altmetric score >180)

[45]∗†MacNeil MA, Graham NAJ, Cinner JE, Wilson SK, Williams ID, Maina J, Newman S, Fried- lander AM, Jupiter S, Polunin, NVC, McClanahan TR 2015. Recovery potential of the world’s coral reef fishes. Nature 520:341-344. (Nature News and Views; international print media; Altmetric score >370; Featured article in Nature Masterclass: how to write a Nature paper)

[44]∗‡Graham NAJ, Jennings S, MacNeil MA, Mouillot D, Wilson SK 2015. Predicting climate driven regime shifts versus rebound potential in coral reefs. Nature 518:94-97. (Nature News and Views; Nature Publishing Hot Topic; international print media; Altmetric score >470)

[43] Hussey NE, MacNeil MA, Siple MC, Popp BN, Dudley SFJ, Fisk AT 2015. Expanded trophic structure and limited functional redundancy among a large shark community. Food Webs 4:1-7.

[42]∗Emslie MJ, Logan M, Williamson DH, Ayling T, MacNeil MA, et al. 2015. Expectations and Outcomes of Reserve Network Performance following Re-zoning of the Great Barrier Reef Marine Park. Current Biology 25(8):983-992. (international print media; Altimetric score > 150)

[41] McClanahan TR, Graham NAJ, MacNeil MA, and Cinner JE 2015. Biomass-based management of multi species coral reef fisheries. Conservation Biology, 29(2):409-417.

[40] MacNeil MA, and Connolly SR 2015. Multi-scale patterns and processes in reef fish abundance. In Mora, C. Ed. Ecology of fishes on coral reefs: the functioning of an ecosystem in a changing world. Cambridge University Press, Cambridge, UK.

[39] Mengersen, K, Caley MJ, and MacNeil MA 2015. The Potential for Meta-Analysis to Support Decision Analysis in Ecology. Research Methods 6.2 (2015): 111-121.

[38]∗Connolly SR, MacNeil MA, Caley MJ, Cripps E, and et al. 2014. Commonness and rarity in the marine biosphere. Proceedings of the National Academy of Sciences USA 111:85248-529.

[37] Burgess GH, Bruce BD, Cailliet GM, Goldman KJ, Grubbs RD, Lowe CG, MacNeil MA, Mollet HF, O’Sullivan JB, and Weng KC 2014. A re-evaluation of the size of the white shark (Carcharodon carcharias) population off California, USA. PLoS ONE 9(6):e98078.

[36]∗†Hussey NE, MacNeil MA, McMeans BC, Olin JA, Dudley SFJ, Cliff G, Wintner SP, Fennessy ST, and Fisk AT 2014. Rescaling the trophic structure of marine food webs. Ecology Letters 17(2): 239-250.

[35] MacNeil MA 2013. The politics, science, and policy of reference points for resource management. Environmental Conservation 40(04) 297-301. [34] Cinner JE, MacNeil MA, Basurto X and Gelcich S 2013. Looking beyond the fisheries crisis: Cumulative learning from small-scale fisheries through diagnostic approaches. Global Environmental Change 23(6) 1359-1365.

[33] MacNeil MA and Cinner JE 2013. Hierarchical livelihood outcomes among co-managed fisheries. Global Environmental Change 23(6) 1393-1401.

[32] Holt BG, Rioja Nieto R, Lupton J, Rahbek C, and MacNeil MA 2013. Assessing the value of volunteer survey protocols for biodiversity studies: a case study with Caribbean fish assemblages. Methods in Ecology and Evolution 4: 383-392.

[31] Cinner JE, Graham NAJ, Huchery C, and MacNeil MA 2013. Global Impacts of Local Human Population Density and Distance to Markets on the Condition of Coral Reef Fisheries. Conservation Biology 27(3):453-8.

[30] McClanahan TR, Donner SD, Maynard JA, MacNeil MA, Graham NAJ, Maina JM, Baker AC et al.. Evidence-based Prioritizing key resilience assessments indicators to support coral reef management in a changing climate. PLoS ONE 7(8): e42884.

[29] Cheal AJ, Emslie M, MacNeil MA, Miller I, and Sweatman H 2013. Spatial variation in the functional characteristics of herbivorous fish communities and the resilience of coral reefs. Ecological Applications 23(1):174-88.

[28]∗†Cinner JE, McClanahan TR, MacNeil MA, Graham NAJ, Daw T, Mukminin A, Feary D, Rabearisoa A, Wamukota A, Jiddawi N, Campbell S, Baird A, Januchowski-Hartley F, Hamed S, Lahari R, Morove T, and Kuange K 2012. Co-management of coral reef social-ecological systems. Proceedings of the National Academy of Sciences USA 109: 52195222.

[27]∗MacNeil MA, McMeans BC, Hussey N, Treble M, Vecsei P, Skomal GB, Svavarsson J, Kovacs K, Lyderson C, Ramsey M, and Fisk AT 2012. Biology of the Greenland shark Somniosus microcephalus Bloch and Schneider, 1801. Journal of Fish Biology 80:991-1018.

[26] Hussey NE, MacNeil MA, Olin JA, McMeans BC, Kinney MJ, Chapman DD and Fisk AT 2012. Stable isotopes and elasmobranchs: tissue types, methods, applications and assumptions. Journal of Fish Biology 80:1449-1484.

[25] Mellin C, Parrott L, Andr ́efou ̈et S, Bradshaw CAJ, MacNeil MA, and Caley MJ 2012. Multi- scale marine biodiversity patterns inferred efficiently from habitat image processing. Ecological Applications 22:792803.

[24] Olin JA, MacNeil MA, Rush SA, and Fisk AT 2012. Isotopic Ratios Reveal Mixed Seasonal Variation Among Fishes from Two Subtropical Estuarine Systems. Estuaries and Coasts 3:811-820.

[23] McClanahan TR, Graham NAJ., MacNeil MA, Muthiga NA, Cinner JE, Bruggemann JH and Wilson SK 2011 Critical thresholds and tangible targets for ecosystem-based management of coral reefs. Proceedings of the National Academy of Sciences USA 108(41):17230-17233.

[22] Graham NAJ.; Chabanet, P., Evans, R.D., Jennings, S., Letourneur, Y., MacNeil MA, Mc- Clanahan TR, O ̈hman, M.C., Polunin, N.V.C., and Wilson SK 2011. Extinction risk in coral reef fishes. Ecology Letters 14: 341-348.

[21] Dennis, C., MacNeil MA, Rosati, J., Pitcher, T. and Fisk AT 2010. Diet discrimination factors are inversely related to δ15N and δ13C values of food for fish under controlled conditions. Rapid Communications in Mass Spectrometry 24: 3515-3520.

[20] MacNeil MA, Graham NAJ., Cinner JE, Loring, P.A., Jennings, S., Dulvy, N.K., Fisk AT, Polunin, N.V.C., and McClanahan TR 2010. Transitional states in marine fisheries: adapting to predicted global change. Philosophical Transactions of the Royal Society 365: 3753-3763.

[19] Hussey NE, MacNeil MA, and Fisk AT 2010. The requirement for accurate diet-tissue discrim- ination factors for interpreting stable isotopes in sharks. Comment on ‘Stable isotope dynamics in elasmobranch fishes.’ Hydrobiologia 654(1): 1-5.

[18] Cheal AJ, MacNeil MA, Cripps E, Emslie M, Jonker M, Shaffelke B, and Sweatman H 2010. First evidence of a coral-macroalgal phase shift on the Great Barrier Reef highlights the importance of herbivorous fishes. Coral Reefs 29: 1005-1015.

[17] MacNeil MA and Graham NAJ. 2010. Enabling Coral-reef management in a changing cli- mate through predictive Bayesian meta-analysis of large-scale disturbance. Global Ecology and Biogeography 19: 412-421.

[16] Hussey NE, Wintner SP, Dudley SFJ, Cocks DT, Cliff G, and MacNeil MA. 2009. Maternal investment and size-specific reproductive output in carcharhinid sharks. Journal of Animal Ecology 79: 184-193.

[15] Dennard S, MacNeil MA, Treble M, Campana SE, and Fisk AT 2009. Hierarchical Analysis of a Remote, Arctic, Artisanal Longline Fishery. ICES Journal of Marine Science 67: 41-51.

[14] MacNeil MA, Carlson JK and Beerkircher LR 2009. Shark depredation rates in pelagic longline fisheries: a case study from the Northwest Atlantic. ICES Journal of Marine Science 66: 708-719.

[13] MacNeil MA, Graham NAJ., Polunin, N.V.C., Kulbicki, M., Galzin, R., Harmelin-Vivien, M. and Rushton, S.P. 2009. Hierarchical drivers of reef-fish metacommunity structure. Ecology 90(1): 252-264.

[12] Fisk AT, Sash, K., Maerz, J., Palmer, W., Carroll, J.P., and MacNeil MA 2009. Metabolic turnover rates of carbon and nitrogen stable isotopes in captive juvenile snakes. Rapid Communi- cations in Mass Spectrometry 23: 1-8.

[11] MacNeil MA, Graham NAJ, Conroy MJ, Fonnesbeck CJ, Polunin NVC, Rushton SP, Chabanet P, and McClanahan TR 2008. Detection heterogeniety in underwater visual census data. Journal of Fish Biology 73: 1748-1763.

[10] MacNeil MA, Tyler E, Fonnesbeck CJ, Rushton SP, and Conroy MJ 2008. Accounting for Detectability in Reef-Fish Biodiversity Estimates. Marine Ecology Progress Series 367: 249-260.

[9] Graham NAJ, McClanahan TR, MacNeil MA, Wilson SK, Polunin, N.V.C., Jennings, S. Le- tourner, Y., Galzin, R., Chabanet, P., Bigot, L., Spalding, M.D., Ohman, M.C., Garpe, K.C., Clark, S. Edwards, A.J., and Sheppard, C.R.C. 2008. Climate warming and the Ocean-scale integrity of coral reef ecosystems. PLoS ONE 3(8): 1-9.

[8] MacNeil MA 2008. Making empirical progress in observational ecology. Environmental Conser- vation 35(2): 1-4.

[7] Overmyer J, MacNeil MA, and Fisk AT 2008. Stable Isotope Turnover in the Black Fly, Simulium vittatum IS-7. Rapid Communications in Mass Spectrometry 22: 694-700.

[6] Mill AC, Sweeting CJ, Barnes C, Al-Habsi S, and MacNeil MA 2008. Mass-spectrometer bias in stable isotope ecology. Limnology and Oceanography: Methods 6: 34-39.

[5] MacNeil MA, Fonnesbeck CJ and McClanahan TR 2008. Occupancy models for estimating the size of reef fish communities. Proceedings of the 11th International Coral Reef Symposium.

[4] McClanahan TR, Graham NAJ, Calnan J. and MacNeil MA 2007. Towards pristine biomass: reef fish recovery in coral reef marine protected areas. Ecological Applications 17(4): 1055-1067.

[3] MacNeil MA, Drouillard KG, and Fisk AT 2006. Variable uptake and elimination of stable nitrogen isotopes. Canadian Journal of Fisheries and Aquatic Sciences 63: 345-353.

[2] MacNeil MA, Skomal GB, and Fisk AT 2005. Stable isotopes from multiple tissues reveal diet switching in sharks. Marine Ecology Progress Series 302: 199-206.

[1] MacNeil MA and Campana SE 2002. Comparison of whole and sectioned vertebrae for determin- ing the age of young blue shark (Prionace glauca). Journal of Northwest Atlantic Fisheries Science 30: 77-82.