Beauchesne-eDriversMS.bib

@techreport{aaf2016,
  title = {Marine {{Aquaculture Site Mapping Program}} ({{MASMP}}). {{Department}} of {{Agriculture}}, {{Aquaculture}} and {{Fisheries}} ({{AAF}}), {{Government}} of {{New}}-{{Brunswick}}, {{New}}-{{Brunswick}}, {{Canada}}. {{Available}} at: {{https://www2.gnb.ca/content/gnb/en/departments/10/aquaculture}} /Content/Masmp.Html},
  author = {AAF},
  year = {2016},
  institution = {{Department of Agriculture, Aquaculture and Fisheries}}
}

@book{archambault2017,
  title = {Les Hydrocarbures Dans Le Golfe Du {{Saint}}-{{Laurent}} - {{Enjeux}} Sociaux, {\'E}conomiques et Environnementaux},
  editor = {Archambault, Philippe and Schloss, Irene R. and Grant, Cindy and Plante, Steve},
  year = {2017},
  publisher = {{Notre Golfe, Rimouski, Qc, Canada}}
}

@article{assis2018,
  title = {Bio-{{ORACLE}} v2.0: {{Extending}} Marine Data Layers for Bioclimatic Modelling},
  shorttitle = {Bio-{{ORACLE}} v2.0},
  author = {Assis, Jorge and Tyberghein, Lennert and Bosch, Samuel and Verbruggen, Heroen and Serr{\~a}o, Ester A. and Clerck, Olivier De},
  year = {2018},
  volume = {27},
  pages = {277--284},
  issn = {1466-8238},
  doi = {10.1111/geb.12693},
  abstract = {Motivation The availability of user-friendly, high-resolution global environmental datasets is crucial for bioclimatic modelling. For terrestrial environments, WorldClim has served this purpose since 2005, but equivalent marine data only became available in 2012, with pioneer initiatives like Bio-ORACLE providing data layers for several ecologically relevant variables. Currently, the available marine data packages have not yet been updated to the most recent Intergovernmental Panel on Climate Change (IPCC) predictions nor to present times, and are mostly restricted to the top surface layer of the oceans, precluding the modelling of a large fraction of the benthic diversity that inhabits deeper habitats. To address this gap, we present a significant update of Bio-ORACLE for new future climate scenarios, present-day conditions and benthic layers (near sea bottom). The reliability of data layers was assessed using a cross-validation framework against in situ quality-controlled data. This test showed a generally good agreement between our data layers and the global climatic patterns. We also provide a package of functions in the R software environment (sdmpredictors) to facilitate listing, extraction and management of data layers and allow easy integration with the available pipelines for bioclimatic modelling. Main types of variable contained Surface and benthic layers for water temperature, salinity, nutrients, chlorophyll, sea ice, current velocity, phytoplankton, primary productivity, iron and light at bottom. Spatial location and grain Global at 5 arcmin (c. 0.08\textdegree{} or 9.2 km at the equator). Time period and grain Present (2000\textendash{}2014) and future (2040\textendash{}2050 and 2090\textendash{}2100) environmental conditions based on monthly averages. Major taxa and level of measurement Marine biodiversity associated with sea surface and epibenthic habitats. Software format ASCII and TIFF grid formats for geographical information systems and a package of functions developed for R software.},
  copyright = {\textcopyright{} 2017 John Wiley \& Sons Ltd},
  file = {/Users/davidbeauchesne/Zotero/storage/WGP6S9EZ/Assis et al. - 2018 - Bio-ORACLE v2.0 Extending marine data layers for .pdf},
  journal = {Global Ecology and Biogeography},
  keywords = {Bio-ORACLE,bioclimatic modelling,environmental data,global,kriging,macroecology,marine,species distribution modelling},
  language = {en},
  note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/geb.12693},
  number = {3}
}

@techreport{bates2019,
  title = {Marine Harmful Algal Blooms and Phycotoxins of Concern to {{Canada}}. {{Can}}. {{Tech}}. {{Rep}}. {{Fish}}. {{Aquat}}. {{Sci}}. {{In}} Revision.},
  author = {Bates, S.S. and Beach, D.G. and Comeau, L.A. and Haigh, N. and Lewis, N.I. and Locke, A. and Martin, J.L. and McCarron, P. and McKenzie, C.H. and Michel, C. and Miles, C.O. and Quilliam, M.A. and Rourke, W.A. and Scarratt, M.G. and Starr, Michel and Wells, T.},
  year = {2019},
  institution = {{Department of Fisheries and Oceans}}
}

@article{beauchesne2016,
  title = {{L'{\'e}valuation des impacts cumul{\'e}s dans l'estuaire et le golfe du Saint-Laurent : vers une planification syst{\'e}mique de l'exploitation des ressources}},
  shorttitle = {{L'{\'e}valuation des impacts cumul{\'e}s dans l'estuaire et le golfe du Saint-Laurent}},
  author = {Beauchesne, David and Grant, Cindy and Gravel, Dominique and Archambault, Philippe},
  year = {2016},
  volume = {140},
  pages = {45--55},
  issn = {0028-0798, 1929-3208},
  doi = {10.7202/1036503ar},
  abstract = {L'intensification de l'empreinte humaine dans l'estuaire et le golfe du Saint-Laurent impose une planification syst{\'e}mique de l'exploitation des ressources marines. Une {\'e}valuation r{\'e}gionale des impacts cumul{\'e}s dans le Saint-Laurent demeure pourtant encore attendue. Un nombre important d'activit{\'e}s (p. ex. transport maritime, p{\^e}che, aquaculture) caract{\'e}rise l'exploitation humaine du Saint-Laurent. Ces activit{\'e}s imposent plusieurs stresseurs environnementaux (p. ex. destruction de l'habitat) affichant un chevauchement spatial croissant. Individuellement, ils peuvent affecter la structure et le fonctionnement des {\'e}cosyst{\`e}mes. Impos{\'e}s simultan{\'e}ment, les stresseurs peuvent agir en synergie et entra{\^i}ner des effets non lin{\'e}aires impr{\'e}visibles. Ces effets demeurent largement incompris et cons{\'e}quemment ignor{\'e}s lors d'{\'e}valuations d'impacts environnementaux, qui demeurent orient{\'e}es sur des esp{\`e}ces ou secteurs uniques et l'approbation de projets. Plusieurs d{\'e}fis relatifs aux impacts cumul{\'e}s dans le Saint-Laurent doivent {\^e}tre relev{\'e}s~: 1) am{\'e}liorer l'{\'e}tat des connaissances des impacts de multiples stresseurs sur les {\'e}cosyst{\`e}mes, 2) am{\'e}liorer l'applicabilit{\'e} des m{\'e}thodes d'{\'e}valuation d'impacts cumul{\'e}s, 3) identifier des indicateurs d'impacts cumul{\'e}s, 4) cr{\'e}er un protocole de suivi environnemental et d'impacts humains, et de partage de donn{\'e}es et 5) d{\'e}velopper une capacit{\'e} de gestion adaptative pour le Saint-Laurent. La planification syst{\'e}mique de l'utilisation des ressources naturelles au sein du Saint-Laurent n{\'e}cessitera une vision int{\'e}grative de la structure et du fonctionnement des {\'e}cosyst{\`e}mes ainsi que des vecteurs de stress qui leur sont impos{\'e}s. Une telle approche ne sera r{\'e}alisable que lorsque nous aurons d{\'e}velopp{\'e} les infrastructures et les outils n{\'e}cessaires {\`a} une gestion {\'e}cosyst{\'e}mique du Saint-Laurent.},
  file = {/Users/davidbeauchesne/Zotero/storage/S5WSN98L/Beauchesne et al. - 2016 - L’évaluation des impacts cumulés dans l’estuaire e.pdf;/Users/davidbeauchesne/Zotero/storage/C9XENGVY/1036503ar.html},
  journal = {Le Naturaliste Canadien},
  language = {fr},
  number = {2}
}

@article{belley2010,
  title = {Effects of Hypoxia on Benthic Macrofauna and Bioturbation in the {{Estuary}} and {{Gulf}} of {{St}}. {{Lawrence}}, {{Canada}}},
  author = {Belley, R{\'e}nald and Archambault, Philippe and Sundby, Bjorn and Gilbert, Franck and Gagnon, Jean-Marc},
  year = {2010},
  month = jul,
  volume = {30},
  pages = {1302--1313},
  issn = {0278-4343},
  doi = {10.1016/j.csr.2010.04.010},
  abstract = {The bottom water in the {$>$}300m deep Lower St. Lawrence Estuary (LSLE) is persistently hypoxic in contrast to the normoxic bottom waters in the Gulf of St. Lawrence (GSL). We photographed the seabed at 11 stations in the Estuary and Gulf of St. Lawrence (EGSL) during the summers 2006 and 2007 and analysed the images to identify bioturbation traces (lebensspuren) and benthic macrofauna. The objective was to identify the environmental variables that influence the density and diversity of benthic macrofauna and bioturbation traces, and the differences that exist among regions with high, medium and low oxygen levels in the bottom water. The bottom water oxygen concentration is the variable that best explains the densities of total-traces as well as surface-traces. However, the density of these traces was higher in hypoxic regions than in well-oxygenated regions. The higher density of traces in the hypoxic region of the LSLE is mainly due to the activities of the surface deposit feeder Ophiura sp., which occurs in large numbers in this region. Possible explanations explored are stress behaviour of the organisms in response to hypoxia and different benthic macrofauna community structures between the hypoxic regions of the LSLE and the normoxic regions of the GSL. In the former, surface deposit feeders and low-oxygen tolerant species dominate over suspension feeders and low-oxygen intolerant species.},
  file = {/Users/davidbeauchesne/Zotero/storage/8TI5UP45/S0278434310001494.html},
  journal = {Continental Shelf Research},
  keywords = {Biodiversity,Bioturbation traces,Gulf of St. Lawrence,Hypoxia,Macrofauna,Photography},
  number = {12}
}

@techreport{benoit2012,
  title = {State of the {{Ocean Report}} for the {{Gulf}} of {{St}}. {{Lawrence Integrated Management}} ({{GOSLIM}})},
  author = {Beno{\^i}t, Hugues P. and Gagn{\'e}, Jacques A. and Savenkoff, Claude and Ouellet, Patrick and Bourassa, Marie-No{\"e}lle},
  year = {2012},
  pages = {viii + 73 p},
  institution = {{Department of Fisheries and Oceans}},
  file = {/Users/davidbeauchesne/Zotero/storage/MRCDBBYJ/Benoît et al. - 2012 - State-ofthe-Ocean Report for the Gulf of St. Lawre.pdf},
  number = {2986}
}

@techreport{blais2019,
  title = {Chemical and {{Biological Oceanographic Conditions}} in the {{Estuary}} and {{Gulf}} of {{St}}. {{Lawrence}} during 2017. {{DFO Can}}. {{Sci}}. {{Advis}}. {{Sec}}. {{Res}}. {{Doc}}. 2019/009. Iv + 56 p.},
  author = {Blais, Marjolaine and Galbraith, Peter S. and Plourde, St{\'e}phane and Scarratt, Michael and Devine, Laure and Lehoux, Caroline},
  year = {2019},
  pages = {iv + 56 p.},
  institution = {{Department of Fisheries and Oceans}},
  abstract = {An overview of chemical and biological oceanographic conditions in the Gulf of St. Lawrence (GSL) in 2016 is presented as part of the Atlantic Zone Monitoring Program (AZMP). AZMP data as well as data from regional monitoring programs are analyzed and presented in relation to long-term means in the context of a strong warming event that began in 2010. Nitrate inventories in 2016 were mostly below normal in the 0\textendash{}50 m layer, due to a mild early winter, but strongly above normal in the deeper layer (particularly in the southern and eastern GSL). According to satellite imagery, phytoplankton biomass averaged annually (March\textendash{}November) over the GSL was slightly below the long-term average. A dominance of small cells (flagellates and dinoflagellates) within phytoplankton assemblages, as observed at Shediac Valley station, could explain why annual biomass was generally low. Nevertheless, spring bloom magnitude and amplitude were generally higher than the climatology (1999\textendash{}2010). Spring bloom maximum biomass even reached a record high in the western GSL. Positive diatom anomalies at Rimouski station were responsible for the strong biomass found there all year-round (April\textendash{}October), and high diatom abundance could also explain the strong phytoplankton biomass retrieved elsewhere in western GSL during spring. The spring bloom occurred earlier and lasted longer than normal in the Magdalen Shallows and Cabot Strait, while timing was normal and duration was shorter in the northern GSL. Zooplankton biomass in 2016 was among the lowest recorded so far throughout the GSL, mainly due to the decreased abundance of Calanus finmarchicus, which showed the earliest stage development observed so far at Rimouski station. The large calanoid index was above normal for the first time since 2006 in the western GSL due to a high abundance of C. hyperboreus. The positive anomalies observed since 2008 for the abundances of small calanoids, cyclopoids, warm-water-associated copepods, Pseudocalanus spp., and non-copepod species continued in 2016. They were possibly due to a combination of warm water and reduced competition since abundances of Calanus spp. were generally low.},
  number = {2018/037}
}

@techreport{bourdages2018,
  title = {Assessment of Northern Shrimp Stocks in the {{Estuary}} and {{Gulf}} of {{St}}. {{Lawrence}} in 2017: Data from the Research Survey. {{DFO Can}}. {{Sci}}. {{Advis}}. {{Sec}}. {{Res}}. {{Doc}}. 2018/057. Iv + 67 p.},
  author = {Bourdages, Hugo and Marquis, Marie-Claude and Noz{\`e}res, Claude and {Ouellette-Plante}, Jordan},
  year = {2018},
  pages = {iv + 67 p},
  file = {/Users/davidbeauchesne/Zotero/storage/HP65966V/Bourdages et al. - 2017 - Preliminary results from the groundfish and shrimp.pdf},
  number = {2018/057}
}

@article{bove2019,
  title = {Common {{Caribbean}} Corals Exhibit Highly Variable Responses to Future Acidification and Warming},
  author = {Bove, Colleen B. and Ries, Justin B. and Davies, Sarah W. and Westfield, Isaac T. and Umbanhowar, James and Castillo, Karl D.},
  year = {2019},
  month = apr,
  volume = {286},
  pages = {20182840},
  doi = {10.1098/rspb.2018.2840},
  abstract = {We conducted a 93-day experiment investigating the independent and combined effects of acidification (280-3300 \textmu{}atm pCO2) and warming (28\textdegree{}C and 31\textdegree{}C) on calcification and linear extension rates of four key Caribbean coral species (Siderastrea siderea, Pseudodiploria strigosa, Porites astreoides, Undaria tenuifolia) from inshore and offshore reefs on the Belize Mesoamerican Barrier Reef System. All species exhibited nonlinear declines in calcification rate with increasing pCO2. Warming only reduced calcification in Ps. strigosa. Of the species tested, only S. siderea maintained positive calcification in the aragonite-undersaturated treatment. Temperature and pCO2 had no effect on the linear extension of S. siderea and Po. astreoides, and natal reef environment did not impact any parameter examined. Results suggest that S. siderea is the most resilient of these corals to warming and acidification owing to its ability to maintain positive calcification in all treatments, Ps. strigosa and U. tenuifolia are the least resilient, and Po. astreoides falls in the middle. These results highlight the diversity of calcification responses of Caribbean corals to projected global change.},
  file = {/Users/davidbeauchesne/Zotero/storage/4ZVALJSN/Bove Colleen B. et al. - 2019 - Common Caribbean corals exhibit highly variable re.pdf;/Users/davidbeauchesne/Zotero/storage/J3J6HMT3/rspb.2018.html},
  journal = {Proceedings of the Royal Society B: Biological Sciences},
  keywords = {Skimmed},
  number = {1900}
}

@article{bowler2019,
  title = {Mapping Human Pressures across the Planet Uncovers Anthropogenic Threat Complexes},
  author = {Bowler, D. E. and Bjorkman, A. D. and Dornelas, M. and {Myers-Smith}, I. H. and Navarro, L. M. and Niamir, A. and Supp, S. R. and Waldock, C. and Vellend, M. and Blowes, S. A. and {B{\"o}hning-Gaese}, K. and Bruelheide, H. and Elahi, R. and Ant{\~a}o, L. H. and Hines, J. and Isbell, F. and Jones, H. P. and Magurran, A. E. and Cabral, J. S. and Winter, M. and Bates, A. E.},
  year = {2019},
  month = jul,
  pages = {432880},
  publisher = {{Cold Spring Harbor Laboratory}},
  doi = {10.1101/432880},
  abstract = {{$<$}h3{$>$}Abstract{$<$}/h3{$>$} {$<$}p{$>$}Climate change and other anthropogenic drivers of biodiversity change are unequally distributed across the world. Overlap in the distributions of different drivers have important implications for biodiversity change attribution and the potential for interactive effects. However, the spatial relationships among different drivers, and whether they differ between the terrestrial and marine realm has yet to be examined.{$<$}/p{$><$}p{$>$}We compiled global gridded datasets on climate change, land-use, resource exploitation, pollution, alien species potential, and human population density. We used multivariate statistics to examine the spatial relationships amongst the drivers and to characterize the typical combinations of drivers experienced by different regions of the world.{$<$}/p{$><$}p{$>$}We found stronger positive correlations among drivers in the terrestrial than in the marine realm, leading to areas with high intensities of multiple drivers on land. Climate change tended to be negatively correlated with other drivers in the terrestrial realm (e.g., in the tundra and boreal forest with high climate change but low human use and pollution), whereas the opposite was true in the marine realm (e.g., in the Indo-Pacific with high climate change and high fishing).{$<$}/p{$><$}p{$>$}We show that different regions of the world can be defined by anthropogenic threat complexes (ATCs), distinguished by different sets of drivers with varying intensities. The ATCs can be used to test hypotheses about patterns of biodiversity change, especially in response to the joint effects of multiple drivers. More generally, our global analysis highlights the broad conservation priorities needed to mitigate the impacts of anthropogenic change, with different priorities emerging on land and in the ocean, and in different parts of the world.{$<$}/p{$>$}},
  copyright = {\textcopyright{} 2019, Posted by Cold Spring Harbor Laboratory. This pre-print is available under a Creative Commons License (Attribution-NonCommercial-NoDerivs 4.0 International), CC BY-NC-ND 4.0, as described at http://creativecommons.org/licenses/by-nc-nd/4.0/},
  file = {/Users/davidbeauchesne/Zotero/storage/TBEWVK2W/Bowler et al. - 2019 - Mapping human pressures across the planet uncovers.pdf},
  journal = {bioRxiv},
  language = {en}
}

@article{chabot2008,
  title = {Environmental Hypoxia as a Metabolic Constraint on Fish: {{The}} Case of {{Atlantic}} Cod, {{Gadus}} Morhua},
  shorttitle = {Environmental Hypoxia as a Metabolic Constraint on Fish},
  author = {Chabot, D. and Claireaux, G.},
  year = {2008},
  month = jan,
  volume = {57},
  pages = {287--294},
  issn = {0025-326X},
  doi = {10.1016/j.marpolbul.2008.04.001},
  abstract = {Hypoxia is known to provoke a wide range of effects on aquatic animals. Here we use laboratory and field data on Atlantic cod, Gadus morhua, to illustrate that many of these responses can be explained within the metabolic scope (MS) framework, i.e. taking into account the directive and limiting effects of dissolved oxygen (DO) on the ability of animals to acquire energy for growth and activity. A MS model for cod shows that scope for activity (swimming, feeding, etc.) is proportional to DO and becomes nil, jeopardising survival, when DO is {$<\approx$}20\% air saturation. Laboratory studies have confirmed this lethal threshold and demonstrated that growth and food ingestion were significantly reduced below 70\% sat. This loss of appetite has been linked to a reduction of the peak value and an increase in duration of postprandial metabolism, in agreement with the MS model. Dwindling MS during hypoxia imposes an upper limit to swimming performance. Cod may also opt to reduce spontaneous swimming activity to spare oxygen for other activities such as digestion. In the Kattegat, the Baltic Sea, and the Gulf of St. Lawrence, eastern Canada, cod completely avoid waters where their MS is near zero. Furthermore, cod density increases exponentially with DO up to {$\approx$}70\% sat in the Gulf of St. Lawrence. Although hypoxia results in other direct and indirect effects as well, the MS framework allows modelling of many of the responses to hypoxia for individual cod that ought to be reflected at the population and community levels. The MS framework is also useful to compare species responses. We show that the impact of hypoxia on MS is similar, when expressed as a proportion of MS in normoxia, in cod, European sea bass (Dicentrarchus labrax), the common sole (Solea solea) and turbot (Psetta maxima). Data are required for other species to evaluate how general these findings are.},
  file = {/Users/davidbeauchesne/Zotero/storage/PR5QB685/Chabot and Claireaux - 2008 - Environmental hypoxia as a metabolic constraint on.pdf;/Users/davidbeauchesne/Zotero/storage/K8ZTPUVG/S0025326X08001963.html},
  journal = {Marine Pollution Bulletin},
  keywords = {Food ingestion,Growth rate,Hypoxia,Metabolic scope,Survival,Swimming},
  number = {6},
  series = {5th {{International Conference}} on {{Marine Pollution}} and {{Ecotoxicology}}}
}

@article{chion2018,
  title = {A Voluntary Conservation Agreement Reduces the Risks of Lethal Collisions between Ships and Whales in the {{St}}. {{Lawrence Estuary}} ({{Qu{\'e}bec}}, {{Canada}}): {{From}} Co-Construction to Monitoring Compliance and Assessing Effectiveness},
  shorttitle = {A Voluntary Conservation Agreement Reduces the Risks of Lethal Collisions between Ships and Whales in the {{St}}. {{Lawrence Estuary}} ({{Qu{\'e}bec}}, {{Canada}})},
  author = {Chion, Cl{\'e}ment and Turgeon, Samuel and Cantin, Guy and Michaud, Robert and M{\'e}nard, Nadia and Lesage, V{\'e}ronique and Parrott, Lael and Beaufils, Pierre and Clermont, Yves and Gravel, Caroline},
  year = {2018},
  month = sep,
  volume = {13},
  pages = {e0202560},
  issn = {1932-6203},
  doi = {10.1371/journal.pone.0202560},
  abstract = {Lethal collisions with ships are limiting the recovery of several at-risk whale species worldwide. In the St. Lawrence Estuary (Quebec, Canada), the endangered blue whale and of special concern fin whale are among the migratory species subject to collisions with large ships. In 2011, a working group composed of representatives from the maritime industry, the government, non-governmental organizations, and academia was created to explore solutions to mitigate ship-whale collisions in the St. Lawrence Estuary. Adopting an adaptive risk management framework, the working group took advantage of the best available scientific data and tools to co-construct realistic collision mitigation options and evaluate their likely benefits for whale conservation and costs for the industry. In 2013, the working group recommended the implementation of voluntary measures to mitigate collision risks, consisting of a slow-down area, a no-go area, and a caution area; a recommended route was added in 2014. Along with the voluntary framework, the working group agreed to continuously monitor compliance with and assess effectiveness of these mitigation measures. After the fourth year of implementation, voluntary measures showed encouraging results, with a reduction of up to 40\% of lethal collision risks with fin whales in the highest density area. This reduction in risk is mainly related to ship speed reduction in the slow-down area from 14.1 {$\pm$} 2.6 knots in 2012 to 11.3 {$\pm$} 1.7 knots since 2014. The presence of a mandatory pilotage area overlapping with the slow-down area was instrumental to facilitate communication about the mitigation measures, with the pilotage corporation sitting as a regular member of the working group. This resulted in significantly slower speeds in the slow-down area for ships with a pilot from the pilotage corporation onboard compared to those without (-0.8 knots, p-value {$<$} 0.001). It is also likely to explain the weaker compliance of the maritime industry with the no-go area located outside of the mandatory pilotage area. Other factors of success include: the continuous dedication of the government to a voluntary and transparent participatory process; the use of available data, tools and institutions; the presence of an environmental certification program representative in the working group; and the adoption by consensus of an adaptive risk management approach. The traditional regulatory approach to conservation is often blamed for its focus on deterring negative behaviors, doing nothing to encourage and reward positive ones. In agreement with other case studies, the benefits of the voluntary measures implemented in the St. Lawrence Estuary include the pro-active commitment from the industry (which is likely to reduce conflicts with regulators), the greater flexibility and freedom that allowed to come up with cost-effective and tailored-made mitigation measures, and the fast achievement of conservation gains. More importantly perhaps, the human and working capital built throughout the concertation process have the potential to be a fundamental cornerstone in dealing with more complex issues such as the chronically increasing level of underwater noise in whale habitats.},
  file = {/Users/davidbeauchesne/Zotero/storage/2CME47I7/Chion et al. - 2018 - A voluntary conservation agreement reduces the ris.pdf;/Users/davidbeauchesne/Zotero/storage/LZ2RBN9K/metrics.html},
  journal = {PLOS ONE},
  keywords = {Blue whales,Estuaries,Humpback whales,Marine conservation,Navigation,Pilots,Ships,Whales},
  language = {en},
  number = {9}
}

@article{clarke1993,
  title = {Non-Parametric Multivariate Analyses of Changes in Community Structure},
  author = {Clarke, K. R.},
  year = {1993},
  volume = {18},
  pages = {117--143},
  issn = {1442-9993},
  doi = {10.1111/j.1442-9993.1993.tb00438.x},
  abstract = {In the early 1980s, a strategy for graphical representation of multivariate (multi-species) abundance data was introduced into marine ecology by, among others, Field, et al. (1982). A decade on, it is instructive to: (i) identify which elements of this often-quoted strategy have proved most useful in practical assessment of community change resulting from pollution impact; and (ii) ask to what extent evolution of techniques in the intervening years has added self-consistency and comprehensiveness to the approach. The pivotal concept has proved to be that of a biologically-relevant definition of similarity of two samples, and its utilization mainly in simple rank form, for example `sample A is more similar to sample B than it is to sample C'. Statistical assumptions about the data are thus minimized and the resulting non-parametric techniques will be of very general applicability. From such a starting point, a unified framework needs to encompass: (i) the display of community patterns through clustering and ordination of samples; (ii) identification of species principally responsible for determining sample groupings; (iii) statistical tests for differences in space and time (multivariate analogues of analysis of variance, based on rank similarities); and (iv) the linking of community differences to patterns in the physical and chemical environment (the latter also dictated by rank similarities between samples). Techniques are described that bring such a framework into place, and areas in which problems remain are identified. Accumulated practical experience with these methods is discussed, in particular applications to marine benthos, and it is concluded that they have much to offer practitioners of environmental impact studies on communities.},
  file = {/Users/davidbeauchesne/Zotero/storage/YH4LGI42/j.1442-9993.1993.tb00438.html},
  journal = {Australian Journal of Ecology},
  language = {en},
  number = {1}
}

@article{cote2016,
  title = {Interactions among Ecosystem Stressors and Their Importance in Conservation},
  author = {C{\^o}t{\'e}, Isabelle M. and Darling, Emily S. and Brown, Christopher J.},
  year = {2016},
  month = feb,
  volume = {283},
  pages = {20152592},
  issn = {0962-8452, 1471-2954},
  doi = {10.1098/rspb.2015.2592},
  abstract = {Interactions between multiple ecosystem stressors are expected to jeopardize biological processes, functions and biodiversity. The scientific community has declared stressor interactions\textemdash{}notably synergies\textemdash{}a key issue for conservation and management. Here, we review ecological literature over the past four decades to evaluate trends in the reporting of ecological interactions (synergies, antagonisms and additive effects) and highlight the implications and importance to conservation. Despite increasing popularity, and ever-finer terminologies, we find that synergies are (still) not the most prevalent type of interaction, and that conservation practitioners need to appreciate and manage for all interaction outcomes, including antagonistic and additive effects. However, it will not be possible to identify the effect of every interaction on every organism's physiology and every ecosystem function because the number of stressors, and their potential interactions, are growing rapidly. Predicting the type of interactions may be possible in the near-future, using meta-analyses, conservation-oriented experiments and adaptive monitoring. Pending a general framework for predicting interactions, conservation management should enact interventions that are robust to uncertainty in interaction type and that continue to bolster biological resilience in a stressful world.},
  copyright = {\textcopyright{} 2016 The Author(s). http://royalsocietypublishing.org/licencePublished by the Royal Society. All rights reserved.},
  file = {/Users/davidbeauchesne/Zotero/storage/KQJ2JZD5/Côté et al. - 2016 - Interactions among ecosystem stressors and their i.pdf;/Users/davidbeauchesne/Zotero/storage/BI8RH9PD/20152592.html},
  journal = {Proceedings of the Royal Society B: Biological Sciences},
  language = {en},
  number = {1824},
  pmid = {26865306}
}

@article{crain2008,
  title = {Interactive and Cumulative Effects of Multiple Human Stressors in Marine Systems},
  author = {Crain, Caitlin Mullan and Kroeker, Kristy and Halpern, Benjamin S.},
  year = {2008},
  volume = {11},
  pages = {1304--1315},
  issn = {1461-0248},
  doi = {10.1111/j.1461-0248.2008.01253.x},
  abstract = {Humans impact natural systems in a multitude of ways, yet the cumulative effect of multiple stressors on ecological communities remains largely unknown. Here we synthesized 171 studies that manipulated two or more stressors in marine and coastal systems and found that cumulative effects in individual studies were additive (26\%), synergistic (36\%), and antagonistic (38\%). The overall interaction effect across all studies was synergistic, but interaction type varied by response level (community: antagonistic, population: synergistic), trophic level (autotrophs: antagonistic, heterotrophs: synergistic), and specific stressor pair (seven pairs additive, three pairs each synergistic and antagonistic). Addition of a third stressor changed interaction effects significantly in two-thirds of all cases and doubled the number of synergistic interactions. Given that most studies were performed in laboratories where stressor effects can be carefully isolated, these three-stressor results suggest that synergies may be quite common in nature where more than two stressors almost always coexist. While significant gaps exist in multiple stressor research, our results suggest an immediate need to account for stressor interactions in ecological studies and conservation planning.},
  copyright = {\textcopyright{} 2008 Blackwell Publishing Ltd/CNRS},
  file = {/Users/davidbeauchesne/Zotero/storage/HC8DMKQ5/Crain et al. - 2008 - Interactive and cumulative effects of multiple hum.pdf;/Users/davidbeauchesne/Zotero/storage/3KMILXLB/j.1461-0248.2008.01253.html},
  journal = {Ecology Letters},
  keywords = {Antagonisms,cumulative stressors,cumulative threat models,ecosystem-based management,interactions,synergisms,threat-analysis},
  language = {en},
  number = {12}
}

@article{dafforn2016,
  title = {Big Data Opportunities and Challenges for Assessing Multiple Stressors across Scales in Aquatic Ecosystems},
  author = {Dafforn, K. A. and Johnston, E. L. and Ferguson, A. and Humphrey, C. L. and Monk, W. and Nichols, S. J. and Simpson, S. L. and Tulbure, M. G. and Baird, D. J.},
  year = {2016},
  month = apr,
  volume = {67},
  pages = {393--413},
  issn = {1448-6059},
  doi = {10.1071/MF15108},
  abstract = {Aquatic ecosystems are under threat from multiple stressors, which vary in distribution and intensity across temporal and spatial scales. Monitoring and assessment of these ecosystems have historically focussed on collection of physical and chemical information and increasingly include associated observations on biological condition. However, ecosystem assessment is often lacking because the scale and quality of biological observations frequently fail to match those available from physical and chemical measurements. The advent of high-performance computing, coupled with new earth observation platforms, has accelerated the adoption of molecular and remote sensing tools in ecosystem assessment. To assess how emerging science and tools can be applied to study multiple stressors on a large (ecosystem) scale and to facilitate greater integration of approaches among different scientific disciplines, a workshop was held on 10\textendash{}12 September 2014 at the Sydney Institute of Marine Sciences, Australia. Here we introduce a conceptual framework for assessing multiple stressors across ecosystems using emerging sources of big data and critique a range of available big-data types that could support models for multiple stressors. We define big data as any set or series of data, which is either so large or complex, it becomes difficult to analyse using traditional data analysis methods.},
  file = {/Users/davidbeauchesne/Zotero/storage/TR8ENUIH/Dafforn et al. - 2016 - Big data opportunities and challenges for assessin.pdf;/Users/davidbeauchesne/Zotero/storage/BNWM93R3/MF15108.html},
  journal = {Marine and Freshwater Research},
  language = {en},
  number = {4}
}

@article{daigle2017,
  title = {Incorporating Public Priorities in the {{Ocean Health Index}}: {{Canada}} as a Case Study},
  shorttitle = {Incorporating Public Priorities in the {{Ocean Health Index}}},
  author = {Daigle, R{\'e}mi M. and Archambault, Philippe and Halpern, Benjamin S. and Lowndes, Julia S. Stewart and C{\^o}t{\'e}, Isabelle M.},
  year = {2017},
  month = may,
  volume = {12},
  pages = {e0178044},
  issn = {1932-6203},
  doi = {10.1371/journal.pone.0178044},
  abstract = {The Ocean Health Index (OHI) is a framework to assess ocean health by considering many benefits (called `goals') provided by the ocean provides to humans, such as food provision, tourism opportunities, and coastal protection. The OHI framework can be used to assess marine areas at global or regional scales, but how various OHI goals should be weighted to reflect priorities at those scales remains unclear. In this study, we adapted the framework in two ways for application to Canada as a case study. First, we customized the OHI goals to create a national Canadian Ocean Health Index (COHI). In particular, we altered the list of iconic species assessed, added methane clathrates and subsea permafrost as carbon storage habitats, and developed a new goal, 'Aboriginal Needs', to measure access of Aboriginal people to traditional marine hunting and fishing grounds. Second, we evaluated various goal weighting schemes based on preferences elicited from the general public in online surveys. We quantified these public preferences in three ways: using Likert scores, simple ranks from a best-worst choice experiment, and model coefficients from the analysis of elicited choice experiment. The latter provided the clearest statistical discrimination among goals, and we recommend their use because they can more accurately reflect both public opinion and the trade-offs faced by policy-makers. This initial iteration of the COHI can be used as a baseline against which future COHI scores can be compared, and could potentially be used as a management tool to prioritise actions on a national scale and predict public support for these actions given that the goal weights are based on public priorities.},
  file = {/Users/davidbeauchesne/Zotero/storage/5355MWZN/Daigle et al. - 2017 - Incorporating public priorities in the Ocean Healt.pdf;/Users/davidbeauchesne/Zotero/storage/Q28C94V4/Daigle et al. - 2017 - Incorporating public priorities in the Ocean Healt.pdf;/Users/davidbeauchesne/Zotero/storage/C5N6CFQP/article.html},
  journal = {PLOS ONE},
  keywords = {Biodiversity,Canada,Fisheries,Food,Marine ecology,Marine fish,Methane,Oceans},
  language = {en},
  number = {5}
}

@article{darling2008,
  title = {Quantifying the Evidence for Ecological Synergies},
  author = {Darling, Emily S. and C{\^o}t{\'e}, Isabelle M.},
  year = {2008},
  volume = {11},
  pages = {1278--1286},
  issn = {1461-0248},
  doi = {10.1111/j.1461-0248.2008.01243.x},
  abstract = {There is increasing concern that multiple drivers of ecological change will interact synergistically to accelerate biodiversity loss. However, the prevalence and magnitude of these interactions remain one of the largest uncertainties in projections of future ecological change. We address this uncertainty by performing a meta-analysis of 112 published factorial experiments that evaluated the impacts of multiple stressors on animal mortality in freshwater, marine and terrestrial communities. We found that, on average, mortalities from the combined action of two stressors were not synergistic and this result was consistent across studies investigating different stressors, study organisms and life-history stages. Furthermore, only one-third of relevant experiments displayed truly synergistic effects, which does not support the prevailing ecological paradigm that synergies are rampant. However, in more than three-quarters of relevant experiments, the outcome of multiple stressor interactions was non-additive (i.e. synergies or antagonisms), suggesting that ecological surprises may be more common than simple additive effects.},
  copyright = {\textcopyright{} 2008 Blackwell Publishing Ltd/CNRS},
  file = {/Users/davidbeauchesne/Zotero/storage/9B35ITXR/Darling and Côté - 2008 - Quantifying the evidence for ecological synergies.pdf;/Users/davidbeauchesne/Zotero/storage/5493UU9V/j.1461-0248.2008.01243.html},
  journal = {Ecology Letters},
  keywords = {Meta-analysis,mortality,multiple stressors,non-additive effects,synergy},
  language = {en},
  number = {12}
}

@article{dee2017,
  title = {Operationalizing {{Network Theory}} for {{Ecosystem Service Assessments}}},
  author = {Dee, Laura E. and Allesina, Stefano and Bonn, Aletta and Ekl{\"o}f, Anna and Gaines, Steven D. and Hines, Jes and Jacob, Ute and {McDonald-Madden}, Eve and Possingham, Hugh and Schr{\"o}ter, Matthias and Thompson, Ross M.},
  year = {2017},
  month = feb,
  volume = {32},
  pages = {118--130},
  issn = {0169-5347},
  doi = {10.1016/j.tree.2016.10.011},
  abstract = {Managing ecosystems to provide ecosystem services in the face of global change is a pressing challenge for policy and science. Predicting how alternative management actions and changing future conditions will alter services is complicated by interactions among components in ecological and socioeconomic systems. Failure to understand those interactions can lead to detrimental outcomes from management decisions. Network theory that integrates ecological and socioeconomic systems may provide a path to meeting this challenge. While network theory offers promising approaches to examine ecosystem services, few studies have identified how to operationalize networks for managing and assessing diverse ecosystem services. We propose a framework for how to use networks to assess how drivers and management actions will directly and indirectly alter ecosystem services.},
  file = {/Users/davidbeauchesne/Zotero/storage/3NV4VNAQ/Dee et al. - 2017 - Operationalizing Network Theory for Ecosystem Serv.pdf;/Users/davidbeauchesne/Zotero/storage/XQAFMEXQ/S0169534716301926.html},
  journal = {Trends in Ecology \& Evolution},
  keywords = {ecosystem services,Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem Services (IPBES),natural resource management,network theory},
  number = {2}
}

@article{deleo2017,
  title = {Bottom Trawling and Oxygen Minimum Zone Influences on Continental Slope Benthic Community Structure off {{Vancouver Island}} ({{NE Pacific}})},
  author = {De Leo, Fabio C. and Gauthier, Ma{\'e}va and Nephin, Jessica and Mih{\'a}ly, Steven and Juniper, S. Kim},
  year = {2017},
  month = mar,
  volume = {137},
  pages = {404--419},
  issn = {0967-0645},
  doi = {10.1016/j.dsr2.2016.11.014},
  abstract = {Understanding responses of benthic ecosystems to cumulative impacts of natural stressors, long-term ocean change and increasing resource exploitation is an emerging area of interest for marine ecologists and environmental managers. Few, if any, studies have quantitatively addressed cumulative effects in the deep sea. We report here on a study from the continental slope off Vancouver Island (Canada) in the northeast Pacific Ocean, where the Oxygen Minimum Zone impinges on seabed habitats that are subjected to widespread bottom trawling, primarily by the fishery for thornyhead (Sebastolobus ssp.). We examined how the benthic megafauna in this area was influenced by varying levels of dissolved oxygen and trawling activity, along a depth gradient that was also likely to shape community composition. Continuous video and sonar records from two ROV surveys (50 linear km total; depth range 300\textendash{}1400m) respectively provided data on faunal attributes (composition, abundance and diversity) and the frequency of trawl door marks on the seabed. Faunal and trawl data were compiled in a geo-referenced database along with corresponding dissolved oxygen data, and pooled into 500m segments for statistical analysis. Trawl mark occurrence peaked between 500 and 1100m, corresponding to areas of slope subjected to hypoxia ({$<$}1.4mll-1) and severe hypoxia ({$<$}0.5mll-1). A combined total of 266,251 megafauna organisms from 87 taxa were enumerated in the two transects. Significant megafaunal assemblages according to depth, trawling intensity and bottom water dissolved oxygen concentration were identified by PERMANOVA analyses, with characterizing taxa identified for all three factors. Depth, dissolved oxygen and trawl mark density accounted for 21\% to 52\% of the variability in benthic community structure according to multiple regression (DISTLM) models. Species richness was highest at intermediate depths and in areas subject to intermediate levels of trawling, and higher under hypoxia than under severe hypoxia. These statistically significant trends demonstrate that the structuring influences of bottom trawling on deep-sea benthic communities can be observed even where communities are being shaped by strong environmental gradients.},
  file = {/Users/davidbeauchesne/Zotero/storage/3DEM27HY/De Leo et al. - 2017 - Bottom trawling and oxygen minimum zone influences.pdf;/Users/davidbeauchesne/Zotero/storage/ELRTRZIK/S0967064516303769.html},
  journal = {Deep Sea Research Part II: Topical Studies in Oceanography},
  keywords = {Benthic megafauna,Bottom trawling,Continental slope,Dissolved oxygen,Northeast Pacific},
  series = {Advances in Deep-Sea Biology: Biodiversity, Ecosystem Functioning and Conservation}
}

@article{dempsey2018,
  title = {Explanatory {{Power}} of {{Human}} and {{Environmental Pressures}} on the {{Fish Community}} of the {{Grand Bank}} before and after the {{Biomass Collapse}}},
  author = {Dempsey, Danielle P. and Gentleman, Wendy C. and Pepin, Pierre and {Koen-Alonso}, Mariano},
  year = {2018},
  volume = {5},
  issn = {2296-7745},
  doi = {10.3389/fmars.2018.00037},
  abstract = {Ecosystem based fisheries management will benefit from assessment of how various pressures affect the fish community, including delayed responses. The objective of this study was to identify which pressures are most directly related to changes in the fish community of the Grand Bank, Northwest Atlantic. These changes are characterized by a collapse and partial recovery of fish biomass and shifting trophic structure over the past three decades. All possible subsets of nine fishing and environmental pressure indicators were evaluated as predictors of the fish community structure (represented by the biomasses of six fish functional-feeding groups), for periods Before (1985 \textendash{} 1995) and After (1996 \textendash{} 2013) the collapse, and the Full time series. We modelled these relationships using redundancy analysis, an extension of multiple linear regression that simultaneously evaluates the effect of one or more predictors on several response variables. The analysis was repeated with different lengths (0 to 5 years) and types (moving average vs. lags) of time delays imposed on the predictors. Both fishing and environmental indicators were included in the best models for all types and length of time delays, reinforcing that there is no single type of pressure impacting the fish community in this region. Results show notable differences in the most influential pressures Before and After the collapse, which reflects the changes in harvester behavior in response to the groundfish moratoria in the mid-1990s. The best models for Before the collapse had strikingly high explanatory power when compared to the other periods, which we speculate is because of changes in the relationships among and within the pressures and responses. Moving average predictor sets generally had higher explanatory power than lagged sets, implying that trends in pressures are important for predicting changes in the fish community. Assigning a carefully chosen delay to each predictor further improved the explanatory power, which is indicative of the complexity of interactions between pressures and responses. Here we add to the current understanding of this ecosystem while demonstrating a method for selecting pressures that could be useful to scientists and managers in other ecosystems.},
  file = {/Users/davidbeauchesne/Zotero/storage/M5CD357L/Dempsey et al. - 2018 - Explanatory Power of Human and Environmental Press.pdf},
  journal = {Frontiers in Marine Science},
  keywords = {Ecosystem indicators,lag,moving average,Northwest Atlantic,redundancy analysis (RDA),Regression Analysis,Time delay},
  language = {English}
}

@techreport{dfo2016,
  title = {Zonal {{Interchange File Format}} ({{ZIFF}}) Data. {{A}} Compilation of Landing Data from Logbook Data between 2010 and 2015. {{Gestion}} Des Donn{\'e}es, {{Institut Maurice Lamontagne}}, {{Department}} of {{Fisheries}} and {{Oceans}} ({{DFO}}) {{Mont}}-{{Joli}}, {{Canada}}.},
  author = {DFO},
  year = {2016},
  institution = {{Department of Fisheries and Oceans}}
}

@techreport{dfo2016a,
  title = {Prince {{Edward Island Aquaculture Leases}}. {{Aquaculture Division}}. {{Department}} of {{Fisheries}} and {{Oceans Canada}} ({{DFO}}). {{Prince}}-{{Edward}}-{{Island}}, {{Canada}}. {{Available}} at: {{http://www.arcgis.com/home/item.html?id=16aa8830c7084a8a92ce066b525978b4}}},
  author = {DFO},
  year = {2016},
  institution = {{Department of Fisheries and Oceans}}
}

@article{diaz1995,
  title = {Marine Benthic Hypoxia: A Review of Its Ecological Effects and the Behavioural Responses of Benthic Macrofauna},
  shorttitle = {Marine Benthic Hypoxia},
  author = {Diaz, R. J. and Rosenberg, R.},
  year = {1995},
  volume = {33},
  pages = {245--303},
  issn = {0967-0653},
  abstract = {In this review the effects of hypoxia on benthic fauna are summarized and detailed information is given on: the impact on community structure and function in fjords, estuaries, coastal and offshore areas; behavioural changes; recovery processes; ecosystem energy flow implications; tolerance in experimental studies.},
  file = {/Users/davidbeauchesne/Zotero/storage/FHPJR6XV/Diaz and Rosenberg - 1995 - Marine benthic hypoxia a review of its ecological.pdf;/Users/davidbeauchesne/Zotero/storage/QS25QRZU/bwmeta1.element.html},
  journal = {Oceanography and Marine Biology. An annual review},
  language = {English}
}

@techreport{dickson2007,
  title = {Guide to {{Best Practices}} for {{Ocean CO2 Measurements}}.},
  author = {Dickson, A. G. and Sabine, C. L. and Christian, J. R.},
  year = {2007},
  institution = {{North Pacific Marine Science Organization}},
  abstract = {The collection of extensive, reliable,  
oceanic carbon data was a key component  
of the Joint Global Ocean Flux Study  
(JGOFS) and World Ocean Circulation  
Experiment (WOCE) and continues to be a cornerstone of the global climate  
research effort.  This Guide was originally 
 prepared at the request, and with the  
active participation, of a science team formed by the U.S. Department of Energy  
(DOE) to carry out the first global surv 
ey of carbon dioxide in the oceans (DOE.  
1994. Handbook of methods for the analysis of the various parameters of the  
carbon dioxide system in sea water; version 2, A.G. Dickson and C. Goyet, Eds.  
ORNL/CDIAC-74).  The manual has been  
updated several times since, and the  
current version contains the most up-to-date information available on the  
chemistry of CO 
2 
 in sea water and the methodology of determining carbon  
system parameters.  This revision has been made possible by the generous  
support of the North Pacific Marine Science Organization (PICES), the  
International Ocean Carbon Coordination  
Project (IOCCP) co-sponsored by the   
Scientific Committee on Ocean Research (SCOR) and the Intergovernmental  
Oceanographic Commission (IOC) of UNESCO, and the Carbon Dioxide  
Information Analysis Center (CDIAC).   
The editors are extremely grateful to  
Alex Kozyr and Mikhail Krassovski at CDIAC for their hard work in helping us  
to complete this revised volume.},
  file = {/Users/davidbeauchesne/Zotero/storage/H42KX2KL/Dickson et al. - 2007 - Guide to Best Practices for Ocean CO2 Measurements.pdf;/Users/davidbeauchesne/Zotero/storage/W78AX9DF/249.html},
  language = {en},
  type = {Report}
}

@article{dube2001,
  title = {Integration of {{Effects}}-{{Based}} and {{Stressor}}-{{Based Approaches}} into a {{Holistic Framework}} for {{Cumulative Effects Assessment}} in {{Aquatic Ecosystems}}},
  author = {Dub{\'e}, Monique and Munkittrick, Kelly},
  year = {2001},
  month = mar,
  volume = {7},
  pages = {247--258},
  issn = {1080-7039},
  doi = {10.1080/20018091094367},
  abstract = {As the density of development increases, there is a growing need to address the cumulative effects of project developments on the environment. In Canada this need has been recognized in legislation whereby new project developments that require an environmental assessment under the Canadian Environmental Assessment Act are required to address the cumulative effects of proposed project activities relative to the existing environmental condition. Unfortunately, existing stressor-based and effects-based approaches to environmental assessment do not adequately address cumulative effects as defined under the Act when used in isolation. However, elements from each approach can be conceptually incorporated into a holistic cumulative effects assessment framework. Key framework components include: (1) an effects-based assessment to determine existing accumulated environmental state, (2) a stressor-based assessment to predict potential impacts of new development relative to the existing environmental state, (3) post-development monitoring to assess the accuracy of impact predictions and to provide an avenue for adaptive management, and (4) decision-making frameworks to link scientific information to public opinion and managerial action. The key advantage of this framework is that it provides a more holistic, systematic approach for incorporation of ecological information into a scientific and management framework for cumulative effects assessment.},
  file = {/Users/davidbeauchesne/Zotero/storage/D6PQ8R7R/Dubé and Munkittrick - 2001 - Integration of Effects-Based and Stressor-Based Ap.pdf},
  journal = {Human and Ecological Risk Assessment: An International Journal},
  keywords = {Cumulative Effects Assessment,Environmental Impact Assessment.},
  number = {2}
}

@article{dube2003,
  title = {Cumulative Effect Assessment in {{Canada}}: A Regional Framework for Aquatic Ecosystems},
  shorttitle = {Cumulative Effect Assessment in {{Canada}}},
  author = {Dub{\'e}, Monique G.},
  year = {2003},
  month = oct,
  volume = {23},
  pages = {723--745},
  issn = {0195-9255},
  doi = {10.1016/S0195-9255(03)00113-6},
  abstract = {Sustainable development of the aquatic environment depends upon routine and defensible cumulative effects assessment (CEA). CEA is the process of predicting the consequences of development relative to an assessment of existing environmental quality. Theoretically, it provides an on-going mechanism to evaluate if levels of development exceed the environment's assimilative capacity; i.e., its ability to sustain itself. In practice, the link between CEA and sustainable development has not been realized because CEA concepts and methods have developed along two dichotomous tracks. One track views CEA as an extension of the environmental assessment (EA) process for project developments. Under this track, stressor-based (S-B) methods have been developed where the emphasis is on local, project-related stressors, their link with aquatic indicators, and the potential for environmental effects through stressor-indicator interactions. S-B methods focus on the proposed development and prediction of project-related effects. They lack a mechanism to quantify existing aquatic quality especially at scales broader than an isolated development. This limitation results in the prediction of potential effects relative to a poorly defined baseline state. The other track views CEA as a broader, regional assessment tool where effects-based (E-B) methods specialize in quantification of existing aquatic effects over broad spatial scales. However, the predictive capabilities of E-B methods are limited because they are retrospective, i.e., the stressor causing the effect is identified after the effect has been measured. When used in isolation, S-B and E-B methods do not address CEA in the context necessary for sustainable development. However, if the strengths of these approaches were integrated into a holistic framework for CEA, an operational mechanism would exist to better monitor and assess sustainable development of our aquatic resources. This paper reviews the existing conceptual basis of CEA in Canada including existing methodologies, limitations and strengths. A conceptual framework for integrating project-based and regional-based CEA is presented.},
  file = {/Users/davidbeauchesne/Zotero/storage/5E84VNWX/Dubé - 2003 - Cumulative effect assessment in Canada a regional.pdf},
  journal = {Environmental Impact Assessment Review},
  keywords = {Cumulative effects assessment,Environmental impact assessment,Environmental monitoring,Environmental planning,Sustainable development},
  language = {en},
  number = {6}
}

@techreport{dufour2007,
  title = {Estuary and {{Gulf}} of {{St}}. {{Lawrence}} Marine Ecosystem Overview and Assessment Report. {{Can}}. {{Tech}}. {{Rep}}. {{Fish}}. {{Aquat}}. {{Sci}}. {{2744E}}: Vii + 112 p.},
  author = {Dufour, R{\'e}jean and Ouellet, Patrick},
  year = {2007},
  pages = {vii + 112 p},
  file = {/Users/davidbeauchesne/Zotero/storage/AKTCG6YW/Dufour and Ouellet - 2007 - Estuary and Gulf of St. Lawrence marine ecosystem .pdf},
  number = {2744E}
}

@article{dupont-prinet2013,
  title = {Impact of Hypoxia on the Metabolism of {{Greenland}} Halibut ({{Reinhardtius}} Hippoglossoides)},
  author = {{Dupont-Prinet}, Aur{\'e}lie and Vagner, Marie and Chabot, Denis and Audet, C{\'e}line},
  year = {2013},
  month = jan,
  volume = {70},
  pages = {461--469},
  issn = {0706-652X},
  doi = {10.1139/cjfas-2012-0327},
  abstract = {Greenland halibut (Reinhardtius hippoglossoides), especially juveniles, are frequently found in severely hypoxic areas (18\%\textendash{}25\% saturation) of the St. Lawrence Estuary. We investigated the tolerance of this species to hypoxia and evaluated the consequences of low oxygen levels on metabolic capacity. At 5 \textdegree{}C, juveniles had a higher critical oxygen threshold than adults (15\% versus 11\% saturation), indicating that they were less tolerant to hypoxia. Severe hypoxia (19\% saturation) did not affect the juveniles' standard metabolic rate but significantly reduced (by 55\%) their maximum metabolic rate compared with normoxia. Consequently, the aerobic scope was reduced by 72\% in hypoxia compared with normoxia. In juveniles, severe hypoxia increased the duration of digestive processes. The decrease in aerobic scope in hypoxia and the determination of critical oxygen threshold at a saturation level close to actual field dissolved oxygen values strongly suggest that juveniles from the St. Lawrence Estuary are living..., Les fl{\'e}tans du Groenland (Reinhardtius hippoglossoides), en particulier les juv{\'e}niles, sont fr{\'e}quemment p{\^e}ch{\'e}s dans les zones hypoxiques (18 \%\textendash{}25 \% saturation) de l'estuaire du Saint-Laurent. L'objectif de cette {\'e}tude {\'e}tait d'{\'e}valuer la tol{\'e}rance {\`a} l'hypoxie chez cette esp{\`e}ce ainsi que les cons{\'e}quences des faibles niveaux d'oxyg{\`e}ne sur sa capacit{\'e} m{\'e}tabolique. {\`A} 5 \textdegree{}C, les juv{\'e}niles ont un seuil critique d'oxyg{\`e}ne sup{\'e}rieur {\`a} celui des adultes (15 \% versus 11 \% saturation), indiquant qu'ils sont moins tol{\'e}rants {\`a} l'hypoxie. L'hypoxie s{\'e}v{\`e}re (19 \% saturation) n'a pas affect{\'e} le taux m{\'e}tabolique standard des juv{\'e}niles, mais a r{\'e}duit significativement (de 55 \%) leur taux m{\'e}tabolique maximal par rapport {\`a} la normoxie. Par cons{\'e}quent, le registre a{\'e}robie a {\'e}t{\'e} r{\'e}duit de 72 \% en hypoxie par rapport {\`a} la normoxie. Chez les juv{\'e}niles, l'hypoxie s{\'e}v{\`e}re augmente la dur{\'e}e du processus de digestion. La r{\'e}duction du registre a{\'e}robie en hypoxie et la d{\'e}termination du seuil critique d'oxyg{\`e}ne {\`a} des niveaux pr{\`e}s de ceux a...},
  file = {/Users/davidbeauchesne/Zotero/storage/NHKPMP3N/Dupont-Prinet et al. - 2013 - Impact of hypoxia on the metabolism of Greenland h.pdf;/Users/davidbeauchesne/Zotero/storage/GQM3SRES/cjfas-2012-0327.html},
  journal = {Canadian Journal of Fisheries and Aquatic Sciences},
  number = {3}
}

@techreport{dutil2011,
  title = {A Hierarchical Classification of the Seabed Based on Physiographic and Oceanographic Features in the {{St}}. {{Lawrence}}. {{Can}}. {{Tech}}. {{Rep}}. {{Fish}}. {{Aquat}}. {{Sci}}. 2916: Vii + 72 p.},
  author = {Dutil, Jean-Denis and Proulx, Serge and Chouinard, Pierre-Marc and Borcard, Daniel},
  year = {2011},
  pages = {vii + 72 p},
  file = {/Users/davidbeauchesne/Zotero/storage/T43IRE6F/Dutil et al. - 2011 - A Hierarchical Classification of the Seabed Based .pdf},
  number = {2916}
}

@techreport{dutil2012,
  title = {Coastal and Epipelagic Habitats of the Estuary and {{Gulf}} of {{St}}. {{Lawrence}}. {{Can}}. {{Tech}}. {{Rep}}. {{Fish}}. {{Aquat}}. {{Sci}}. 3009: Ix + 87 Pp.},
  author = {Dutil, Jean-Denis and Proulx, Serge and Galbraith, Peter S. and Chass{\'e}, Jo{\"e}l and Lambert, Nicolas and Laurian, Catherine},
  year = {2012},
  pages = {ix + 87 pp},
  file = {/Users/davidbeauchesne/Zotero/storage/UISYTHDC/Dutil et al. - 2012 - Coastal and epipelagic habitats of the estuary and.pdf},
  number = {3009}
}

@techreport{earthobservationgroup2019,
  title = {Version 1 {{VIIRS Day}}/{{Night Band Nighttime Lights}}},
  author = {{Earth observation group}},
  year = {2019},
  institution = {{NOAA National Centers for Environmental Information (NCEI)}}
}

@article{eby2005,
  title = {Habitat Degradation from Intermittent Hypoxia: Impacts on Demersal Fishes},
  shorttitle = {Habitat Degradation from Intermittent Hypoxia},
  author = {Eby, Lisa A. and Crowder, Larry B. and McClellan, Catherine M. and Peterson, Charles H. and Powers, Monica J.},
  year = {2005},
  month = apr,
  volume = {291},
  pages = {249--262},
  issn = {0171-8630, 1616-1599},
  doi = {10.3354/meps291249},
  abstract = {As eutrophication of estuaries and coastal oceans increases worldwide, the resulting expansion of hypoxic zones represents an increasingly frequent form of habitat degradation. Although impacts of prolonged hypoxia on benthic invertebrate species are well-documented, there is little understanding of how those effects subsequently influence the motile upper trophic levels in estuarine ecosystems. Quantitative nekton surveys in the Neuse River Estuary and field experiments in June and August
1999 using Atlantic croaker Micropogonias undulatus demonstrated that intermittent hypoxia decreased habitat quality for juvenile, demersal fish through 3 pathways: (1) hypoxia restricted the fishes in estuaries to shallow, oxygenated areas, where in the early part of the summer about 1/3 fewer prey resources were available. (2) This contraction of suitable habitat crowded the fish into smaller areas and may have resulted in density-dependent reduction of growth rates. (3) Most importantly, mortality of sessile infauna in deeper areas exposed to intermittent hypoxia decreased prey densities about 8-fold between the June and August experiments. Through these mechanisms, intermittent hypoxia may result in ecological crunches or bottlenecks. Field data collected from May to October in 3 yr (1998 to 2000) with differing levels of hypoxia support the conclusion that intermittent hypoxia may decrease habitat quality and result in {$\geq$}50\% declines in juvenile fish growth rate. Incorporation of these indirect effects of hypoxia on juvenile growth rates into a population model demonstrated the potential for significant (\textasciitilde{}4\%) reductions in population growth rate. Thus, sublethal effects of hypoxia-driven habitat degradation may impact fisheries production not only through reduced size at age, but also through reduced abundance of demersal fish populations.},
  file = {/Users/davidbeauchesne/Zotero/storage/TGF6D7DW/Eby et al. - 2005 - Habitat degradation from intermittent hypoxia imp.pdf;/Users/davidbeauchesne/Zotero/storage/N7HA83GU/p249-262.html},
  journal = {Marine Ecology Progress Series},
  keywords = {Demersal fishes,Habitat degradation,Hypoxia,Indirect effects,Leiostomus xanthurus,Micropogonias undulatus,Neuse River Estuary,Population dynamics},
  language = {en}
}

@misc{eccc2018,
  title = {Environment and {{Climate Change Canada}}'s ({{ECCC}}) {{Atlantic Shoreline Classification Available}} from {{https://open.canada.ca/data/en/dataset/30449352-2556-42df-9ffe-47ea8e696f91}} {{Accessed}} 2019-09-19},
  author = {ECCC},
  year = {2018}
}

@book{el-sabh1990a,
  title = {Oceanography of a {{Large}}-{{Scale Estuarine System}}},
  author = {{El-Sabh}, Mohammed I. and Silverberg, Norman},
  editor = {{El-Sabh}, Mohammed I. and Silverberg, Norman},
  year = {1990},
  publisher = {{Springer New York}},
  doi = {10.1007/978-1-4615-7534-4}
}

@article{eppler2004,
  title = {The {{Concept}} of {{Information Overload}}: {{A Review}} of {{Literature}} from {{Organization Science}}, {{Accounting}}, {{Marketing}}, {{MIS}}, and {{Related Disciplines}}},
  shorttitle = {The {{Concept}} of {{Information Overload}}},
  author = {Eppler, Martin J. and Mengis, Jeanne},
  year = {2004},
  month = nov,
  volume = {20},
  pages = {325--344},
  issn = {0197-2243},
  doi = {10.1080/01972240490507974},
  abstract = {Based on literature from the domains of organization science, marketing, accounting, and management information systems, this review article examines the theoretical basis of the information overload discourse and presents an overview of the main definitions, situations, causes, effects, and countermeasures. It analyzes the contributions from the last 30 years to consolidate the existing research in a conceptual framework and to identify future research directions.},
  file = {/Users/davidbeauchesne/Zotero/storage/6MVRDXCY/Eppler and Mengis - 2004 - The Concept of Information Overload A Review of L.pdf;/Users/davidbeauchesne/Zotero/storage/GBXPN5BJ/01972240490507974.html},
  journal = {The Information Society},
  keywords = {information explosion,information management strategies,information overload,information processing,information skills,information technology},
  number = {5}
}

@techreport{fa2016,
  title = {Aquaculture {{Site Mapping Tool}}. {{Department}} of {{Fisheries}} and {{Aquaculture}} ({{FA}}), {{Department}} of {{Agriculture}}, {{Government}} of {{Nova}}-{{Scotia}}. {{Nova}}-{{Scotia}}, {{Canada}}. {{Available}} at: {{https://novascotia.ca/fish/aquaculture/site-mapping-tool/}}},
  author = {FA},
  year = {2016},
  institution = {{Department of Fisheries and Aquaculture}}
}

@article{fabry2008,
  title = {Impacts of Ocean Acidification on Marine Fauna and Ecosystem Processes},
  author = {Fabry, Victoria J. and Seibel, Brad A. and Feely, Richard A. and Orr, James C.},
  year = {2008},
  month = apr,
  volume = {65},
  pages = {414--432},
  issn = {1054-3139},
  doi = {10.1093/icesjms/fsn048},
  abstract = {Abstract.  Fabry, V. J., Seibel, B. A., Feely, R. A., and Orr, J. C. 2008. Impacts of ocean acidification on marine fauna and ecosystem processes. \textendash{} ICES Journa},
  file = {/Users/davidbeauchesne/Zotero/storage/KXQQJHN3/Fabry et al. - 2008 - Impacts of ocean acidification on marine fauna and.pdf;/Users/davidbeauchesne/Zotero/storage/FTI2DGQF/789605.html},
  journal = {ICES Journal of Marine Science},
  language = {en},
  number = {3}
}

@article{feist2016,
  title = {Novel {{Indicators}} of {{Anthropogenic Influence}} on {{Marine}} and {{Coastal Ecosystems}}},
  author = {Feist, Blake E. and Levin, Phillip S.},
  year = {2016},
  volume = {3},
  issn = {2296-7745},
  doi = {10.3389/fmars.2016.00113},
  abstract = {Human populations are concentrated along coastal regions worldwide, placing a disproportionate stress on coastal marine ecosystems. Ironically, biogenic habitats may be adversely affected by human activities though they serve to attenuate the impacts of global change on coastal cities. Surprisingly, simple, coastwide indicators of anthropogenic influences in relation to the spatial distribution of biogenic habitats are relatively underdeveloped. In this paper, we introduce a spatially explicit index of coastal as well as upland riverine human population proximity, based on human population and river dynamics datasets on the West- and Gulf-Coasts of the US. We then examine the relationship between these indices and biogenic habitats (kelp and mangrove forests). Finally, we identify patterns of landscape-scale biodiversity with human populations, and explore occurrence of biogenic habitats within and outside of marine protected areas (MPAs). We found that biogenic habitats were negatively associated with human populations and that MPAs were generally placed away from people. Landscape-scale patterns of biodiversity did not differ within and outside kelp forests and MPAs on the West Coast, but had a negative association with mangroves and a positive association with MPAs on the Gulf Coast. This index can be used anywhere in the world, can project into the future using various human population growth forecasts, and can serve as an important method for conservation triage.},
  file = {/Users/davidbeauchesne/Zotero/storage/YQBACW4L/Feist and Levin - 2016 - Novel Indicators of Anthropogenic Influence on Mar.pdf},
  journal = {Frontiers in Marine Science},
  keywords = {Biogenic habitat,Coastal marine,ecosystem based management,human populations,indicators,marine protected areas,Nearshore},
  language = {English}
}

@techreport{ffa2016,
  title = {Description of Aquaculture Sites in {{Newfoundland}}. {{Department}} of {{Fisheries}}, {{Forestry}} and {{Agrifoods}} ({{FFA}}), {{Government}} of {{Newfoundland}} and {{Labrador}}. {{Newfoundland}}, {{Canada}}.},
  author = {FFA},
  year = {2016},
  institution = {{Department of Fisheries, Forestry and Agrifoods}}
}

@techreport{force112014,
  title = {Data {{Citation Synthesis Group}}: {{Joint Declaration}} of {{Data Citation Principles}}. {{Martone M}}. (Ed.) {{San Diego CA}}},
  author = {FORCE11},
  year = {2014}
}

@article{frank2005,
  title = {Trophic {{Cascades}} in a {{Formerly Cod}}-{{Dominated Ecosystem}}},
  author = {Frank, Kenneth T. and Petrie, Brian and Choi, Jae S. and Leggett, William C.},
  year = {2005},
  month = jun,
  volume = {308},
  pages = {1621--1623},
  issn = {0036-8075, 1095-9203},
  doi = {10.1126/science.1113075},
  abstract = {Removal of top predators from ecosystems can result in cascading effects through the trophic levels below, completely restructuring the food web. Cascades have been observed in small-scale or simple food webs, but not in large, complex, open-ocean ecosystems. Using data spanning many decades from a once cod-dominated northwest Atlantic ecosystem, we demonstrate a trophic cascade in a large marine ecosystem. Several cod stocks in other geographic areas have also collapsed without recovery, suggesting the existence of trophic cascades in these systems.
Severe overfishing of cod, a top predator, in the northwest Atlantic has led to an increase in small fishes and invertebrates and has altered plankton dynamics and ocean chemistry.
Severe overfishing of cod, a top predator, in the northwest Atlantic has led to an increase in small fishes and invertebrates and has altered plankton dynamics and ocean chemistry.},
  copyright = {American Association for the Advancement of Science},
  file = {/Users/davidbeauchesne/Zotero/storage/XFU93457/Frank et al. - 2005 - Trophic Cascades in a Formerly Cod-Dominated Ecosy.pdf;/Users/davidbeauchesne/Zotero/storage/DRMHGQGU/1621.html},
  journal = {Science},
  language = {en},
  number = {5728},
  pmid = {15947186}
}

@article{franzoni2014,
  title = {Crowd Science: {{The}} Organization of Scientific Research in Open Collaborative Projects},
  shorttitle = {Crowd Science},
  author = {Franzoni, Chiara and Sauermann, Henry},
  year = {2014},
  month = feb,
  volume = {43},
  pages = {1--20},
  issn = {0048-7333},
  doi = {10.1016/j.respol.2013.07.005},
  abstract = {A growing amount of scientific research is done in an open collaborative fashion, in projects sometimes referred to as ``crowd science'', ``citizen science'', or ``networked science''. This paper seeks to gain a more systematic understanding of crowd science and to provide scholars with a conceptual framework and an agenda for future research. First, we briefly present three case examples that span different fields of science and illustrate the heterogeneity concerning what crowd science projects do and how they are organized. Second, we identify two fundamental elements that characterize crowd science projects \textendash{} open participation and open sharing of intermediate inputs \textendash{} and distinguish crowd science from other knowledge production regimes such as innovation contests or traditional ``Mertonian'' science. Third, we explore potential knowledge-related and motivational benefits that crowd science offers over alternative organizational modes, and potential challenges it is likely to face. Drawing on prior research on the organization of problem solving, we also consider for what kinds of tasks particular benefits or challenges are likely to be most pronounced. We conclude by outlining an agenda for future research and by discussing implications for funding agencies and policy makers.},
  file = {/Users/davidbeauchesne/Zotero/storage/QR79JF2X/Franzoni and Sauermann - 2014 - Crowd science The organization of scientific rese.pdf;/Users/davidbeauchesne/Zotero/storage/YQDELSHJ/S0048733313001212.html},
  journal = {Research Policy},
  keywords = {Citizen science,Community-based production,Crowd science,Crowdsourcing,Funding,Open innovation,Problem solving},
  number = {1}
}

@techreport{galbraith2018,
  title = {Physical {{Oceanographic Conditions}} in the {{Gulf}} of {{St}}. {{Lawrence}} during 2017. {{DFO Can}}. {{Sci}}. {{Advis}}. {{Sec}}. {{Res}}. {{Doc}}. 2018/050. v + 79 p.},
  author = {Galbraith, Peter S. and Chass{\'e}, Jo{\"e}l and Caverhill, Carla and Nicot, Paul and Gilbert, Denis and Lefaivre, Denis and Lafleur, Caroline},
  year = {2018},
  pages = {v + 79 p.},
  institution = {{Department of Fisheries and Oceans}},
  abstract = {An overview of physical oceanographic conditions in the Gulf of St. Lawrence (GSL) in 2017 is presented as part of the Atlantic Zone Monitoring Program (AZMP). AZMP data as well as data from regional monitoring programs are analysed and presented in relation to long-term means. The annual average freshwater runoff of the St. Lawrence River measured at Qu{\'e}bec City and its combination with rivers flowing into the Estuary (RIVSUM II) were both at the highest level since 1974. Above-normal January air temperatures led to late onset of sea-ice and the sixth lowest sea ice cover maximum volume since 1969, but the winter mixed layer volume was nearnormal. The August cold intermediate layer (CIL) showed warmer than normal minimum temperature (+0.8 SD) and less than normal volume of water colder than 1\textdegree{}C (-0.6 SD), but the seasonally average minimum temperature index was near normal. Sea-surface temperatures averaged over the Gulf were near normal or above normal from May to November 2017, leading to an above-normal May-November average (+0.6\textdegree{}C, +0.9 SD). The timing of summer warming onset and fall cooling were respectively slightly sooner (-0.7 weeks) and later than normal (+1.7 weeks). Deep water temperatures have been increasing overall in the Gulf, with inward advection from Cabot Strait. Gulf average temperature decreased from 2015 record highs at 150 and 200 m, remaining above-normal (2.7\textdegree{}C, +0.5 SD and 5.0\textdegree{}C, +1.4 SD), decreased slightly at 250 m (6.0\textdegree{}C, +2.7 SD) from the 2016 record high but increased to a new record level at 300 m (6.3\textdegree{}C, +5.0 SD). The bottom area covered by waters warmer than 6\textdegree{}C decreased in 2017 in Anticosti Channel and Esquiman Channel, but increased sharply in Central Gulf and made its first appearance in the northwest Gulf.},
  file = {/Users/davidbeauchesne/Zotero/storage/6JYH2MR3/galbraith2018.pdf;/Users/davidbeauchesne/Zotero/storage/QKGNR6J8/Galbraith et al. - 2018 - Physical Oceanographic Conditions in the Gulf of S.pdf;/Users/davidbeauchesne/Zotero/storage/ZR445X6F/2018_050-fra.html},
  number = {2018/050}
}

@article{gari2015,
  title = {A Review of the Application and Evolution of the {{DPSIR}} Framework with an Emphasis on Coastal Social-Ecological Systems},
  author = {Gari, Sirak Robele and Newton, Alice and Icely, John D.},
  year = {2015},
  month = jan,
  volume = {103},
  pages = {63--77},
  issn = {0964-5691},
  doi = {10.1016/j.ocecoaman.2014.11.013},
  abstract = {The applications of the Driver-Pressure-State-Impact-Response (DPSIR) framework were reviewed for several Social-Ecological Systems (SES), with an emphasis on the coastal environment. The evolution of DPSIR was traced from the Stress-Response framework to its present form. Discrepancies in the definitions of the DPSIR's information categories are presented. The application of the framework was explored both as a discrete tool and combined with other methods for different coastal and estuarine systems and biodiversity. The overall merits and limitations of the DPSIR framework are discussed in a critique. Several recommendations are suggested for refining the framework to overcome its limitations. Finally it is concluded that an updated DPSIR framework is a useful adaptive management tool for analyzing and identifying solutions to environmental problems.},
  file = {/Users/davidbeauchesne/Zotero/storage/B4VQF8RS/Gari et al. - 2015 - A review of the application and evolution of the D.pdf},
  journal = {Ocean \& Coastal Management},
  keywords = {Coasts,Driver-pressure-state-impact-response,Social-ecological systems},
  language = {en}
}

@article{gilbert2007,
  title = {Appauvrissement En Oxyg{\`e}ne Dans Les Eaux Profondes Du {{Saint}}-{{Laurent}} Marin: Causes Possibles et Impacts {\'E}cologiques},
  shorttitle = {Appauvrissement En Oxyg{\`e}ne Dans Les Eaux Profondes Du {{Saint}}-{{Laurent}} Marin},
  author = {Gilbert, D. and Chabot, D. and Archambault, P. and Rondeau, B. and H{\'e}bert, S.},
  year = {2007},
  volume = {131},
  pages = {67--75},
  file = {/Users/davidbeauchesne/Zotero/storage/887BZNHC/Gilbert et al. - 2007 - Appauvrissement en oxygène dans les eaux profondes.pdf},
  journal = {Naturaliste Canadien}
}

@misc{governmentofcanada2018,
  title = {Marine {{Spatial Data Infrastructure}} Portal {{Available}} from {{http://msdi-idsm.maps.arcgis.com/home/index.html}} {{Accessed}} 2019-09-19},
  author = {{Government of Canada}},
  year = {2018}
}

@techreport{governmentofquebec2015,
  title = {Strat{\'e}gie Maritime, {{The}} Maritime Strategy by the Year 2030. 2015-2020 Action {{Plan}}.},
  author = {{Government of Qu{\'e}bec}},
  year = {2015},
  pages = {vii + 78 p}
}

@article{halpern2008a,
  title = {A {{Global Map}} of {{Human Impact}} on {{Marine Ecosystems}}},
  author = {Halpern, Benjamin S. and Walbridge, Shaun and Selkoe, Kimberly A. and Kappel, Carrie V. and Micheli, Fiorenza and D'Agrosa, Caterina and Bruno, John F. and Casey, Kenneth S. and Ebert, Colin and Fox, Helen E. and Fujita, Rod and Heinemann, Dennis and Lenihan, Hunter S. and Madin, Elizabeth M. P. and Perry, Matthew T. and Selig, Elizabeth R. and Spalding, Mark and Steneck, Robert and Watson, Reg},
  year = {2008},
  month = feb,
  volume = {319},
  pages = {948--952},
  doi = {10.1126/science.1149345},
  file = {/Users/davidbeauchesne/Zotero/storage/KUJAFP6S/Halpern_SOM.pdf;/Users/davidbeauchesne/Zotero/storage/U7RAVYR2/Halpern et al. - 2008 - A global map of human impact on marine ecosystems.pdf},
  journal = {Science},
  number = {5865}
}

@article{halpern2012,
  title = {An Index to Assess the Health and Benefits of the Global Ocean},
  author = {Halpern, Benjamin S. and Longo, Catherine and Hardy, Darren and McLeod, Karen L. and Samhouri, Jameal F. and Katona, Steven K. and Kleisner, Kristin and Lester, Sarah E. and O'Leary, Jennifer and Ranelletti, Marla and Rosenberg, Andrew A. and Scarborough, Courtney and Selig, Elizabeth R. and Best, Benjamin D. and Brumbaugh, Daniel R. and Chapin, F. Stuart and Crowder, Larry B. and Daly, Kendra L. and Doney, Scott C. and Elfes, Cristiane and Fogarty, Michael J. and Gaines, Steven D. and Jacobsen, Kelsey I. and Karrer, Leah Bunce and Leslie, Heather M. and Neeley, Elizabeth and Pauly, Daniel and Polasky, Stephen and Ris, Bud and Martin, Kevin St and Stone, Gregory S. and Sumaila, U. Rashid and Zeller, Dirk},
  year = {2012},
  month = aug,
  volume = {488},
  pages = {615--620},
  issn = {1476-4687},
  doi = {10.1038/nature11397},
  abstract = {The ocean plays a critical role in supporting human well-being, from providing food, livelihoods and recreational opportunities to regulating the global climate. Sustainable management aimed at maintaining the flow of a broad range of benefits from the ocean requires a comprehensive and quantitative method to measure and monitor the health of coupled human\textendash{}ocean systems. We created an index comprising ten diverse public goals for a healthy coupled human\textendash{}ocean system and calculated the index for every coastal country. Globally, the overall index score was 60 out of 100 (range 36\textendash{}86), with developed countries generally performing better than developing countries, but with notable exceptions. Only 5\% of countries scored higher than 70, whereas 32\% scored lower than 50. The index provides a powerful tool to raise public awareness, direct resource management, improve policy and prioritize scientific research.},
  copyright = {2012 Nature Publishing Group},
  file = {/Users/davidbeauchesne/Zotero/storage/7WUWNAEU/Halpern et al. - 2012 - An index to assess the health and benefits of the .pdf;/Users/davidbeauchesne/Zotero/storage/BSHU95DA/nature11397.html},
  journal = {Nature},
  language = {en},
  number = {7413}
}

@misc{halpern2015,
  title = {Cumulative Human Impacts: Raw Stressor Data (2008 and 2013). {{Knowledge Network}} for {{Biocomplexity}}.},
  author = {Halpern, Benjamin S. and Frazier, Melanie and Potapenko, John and Casey, Kenneth S. and Koenig, Kellee and Longo, Catherine and Lowndes, Julia Stewart and Rockwood, R. Cotton and Selig, Elizabeth R. and Selkoe, Kimberly A. and Walbridge, Shaun},
  year = {2015},
  doi = {10.5063/f1s180fs},
  howpublished = {https://knb.ecoinformatics.org/\#view/doi:10.5063/F1S180FS}
}

@article{halpern2015a,
  title = {Spatial and Temporal Changes in Cumulative Human Impacts on the World's Ocean},
  author = {Halpern, Benjamin S. and Frazier, Melanie and Potapenko, John and Casey, Kenneth S. and Koenig, Kellee and Longo, Catherine and Lowndes, Julia Stewart and Rockwood, R. Cotton and Selig, Elizabeth R. and Selkoe, Kimberly A. and Walbridge, Shaun},
  year = {2015},
  month = jul,
  volume = {6},
  doi = {10.1038/ncomms8615},
  file = {/Users/davidbeauchesne/Zotero/storage/VC2N9FQM/ncomms8615-s1.pdf;/Users/davidbeauchesne/Zotero/storage/WSCBRP5N/Halpern et al. - 2015 - Spatial and temporal changes in cumulative human i.pdf},
  journal = {Nature Communications},
  keywords = {Skimmed},
  number = {1}
}

@article{halpern2019,
  title = {Recent Pace of Change in Human Impact on the World's Ocean},
  author = {Halpern, Benjamin S. and Frazier, Melanie and Afflerbach, Jamie and Lowndes, Julia S. and Micheli, Fiorenza and O'Hara, Casey and Scarborough, Courtney and Selkoe, Kimberly A.},
  year = {2019},
  month = dec,
  volume = {9},
  pages = {11609},
  issn = {2045-2322},
  doi = {10.1038/s41598-019-47201-9},
  file = {/Users/davidbeauchesne/Zotero/storage/4HIUVCSY/41598_2019_47201_MOESM1_ESM.docx;/Users/davidbeauchesne/Zotero/storage/LNVEXVS7/Halpern et al. - 2019 - Recent pace of change in human impact on the world.pdf},
  journal = {Scientific Reports},
  language = {en},
  number = {1}
}

@article{jones2016,
  title = {Cumulative Effects Assessment: Theoretical Underpinnings and Big Problems},
  shorttitle = {Cumulative Effects Assessment},
  author = {Jones, F. Chris},
  year = {2016},
  month = feb,
  volume = {24},
  pages = {187--204},
  issn = {1181-8700},
  doi = {10.1139/er-2015-0073},
  abstract = {Cumulative effects assessment (CEA) is a sub-discipline of environmental impact assessment that is concerned with appraising the collective effects of human activities and natural processes on the environment. Aspirations for CEA have been expressed by many authors since 1969, when the foundation of environmental appraisal was laid by the US National Environmental Policy Act. This paper's purposes are (i) to review aspirations for CEA, relative to current practice; and (ii) to fully explain and critique the logic that connects CEA's operational steps and underlying philosophies. A literature review supports the following statements: Some conceptualizations emphasize the delivery of information to support decision making as the key purpose of CEA; others deem collaboration, debate, and learning as most important. Consensus on CEA's operational steps has been reached, but each step requires practitioners to make analytical decisions (e.g., about the scope of issues to include or the time horizon to consider) and objective rules for how to approach those decisions are lacking. Numerical methods for assessing cumulative effects are largely available, meaning that CEA's biggest problems are not scientific. CEA cannot succeed without substantive public engagement, monitoring, and adaptive management. CEA is best undertaken regionally, rather than project-by-project. CEA and planning are complementary, and should be merged. In its most enlightened form, CEA is a useful tool for ensuring that human undertakings ultimately conform to Earth's finite biosphere, but current practice falls short of the ideal, and CEA's logical derivation is not entirely sound. As regards CEA's big problems, sustainability has not been defined clearly enough to make criteria for judging the significance of cumulative effects indisputable; legal, regulatory, and institutional frameworks are poorly aligned for CEA; and objective criteria for judging the adequacy of CEA's scope, scale, and thresholds do not exist, which makes the question of how to provide general guidance to practitioners intractable. Recommendations call for sustainability goals to be clearly expressed as measurable targets. Furthermore, precaution in human enterprise should be exercised by avoiding, minimizing, restoring, and offsetting negative cumulative effects. CEA can assist by quantifying and optimizing trade-offs.},
  file = {/Users/davidbeauchesne/Zotero/storage/FQURVNEF/Jones - 2016 - Cumulative effects assessment theoretical underpi.pdf;/Users/davidbeauchesne/Zotero/storage/YEGYVIDI/er-2015-0073.html},
  journal = {Environmental Reviews},
  keywords = {conceptual model,environmental impact assessment,environmental management,planning,precautionary principle,sustainability},
  number = {2}
}

@inproceedings{kaufman1990,
  title = {Finding {{Groups}} in {{Data}}: {{An Introduction}} to {{Cluster Analysis}}},
  author = {Kaufman, L. and Rousseeuw, Peter},
  year = {1990},
  pages = {342},
  publisher = {{Wiley, New York}}
}

@article{keith2011,
  title = {Uncertainty and Adaptive Management for Biodiversity Conservation},
  author = {Keith, David A. and Martin, Tara G. and {McDonald-Madden}, Eve and Walters, Carl},
  year = {2011},
  month = apr,
  volume = {144},
  pages = {1175--1178},
  issn = {0006-3207},
  doi = {10.1016/j.biocon.2010.11.022},
  abstract = {Adaptive management of natural resources is widely supported, but in biodiversity conservation there have been few practical applications of the approach in its entirety. Some of the contributions to this special publication examine progress in the implementation of adaptive approaches into conservation policy, while others explore novel theoretical and modeling approaches that seek to accommodate the complexities of real-world applications. Several of the papers address the treatment of uncertainty in adaptive management through innovative approaches to experimentation and monitoring, use and characterisation of expert knowledge and reconciliation of differences of opinion about parameters or systems. Drawing on these contributions, we discuss the major impediments to implementing adaptive management, why adaptive management has been slow to be implemented and how this can be redressed.},
  file = {/Users/davidbeauchesne/Zotero/storage/P5RBIAK5/Keith et al. - 2011 - Uncertainty and adaptive management for biodiversi.pdf;/Users/davidbeauchesne/Zotero/storage/2ZZJDCK5/S0006320710004933.html},
  journal = {Biological Conservation},
  keywords = {Conflict resolution,Conservation policy,Decision making,Ecosystem management,Experimental management,Learning by doing,Management goals,Monitoring,Process model},
  number = {4},
  series = {Adaptive Management for Biodiversity Conservation in an Uncertain World}
}

@techreport{kleypas2006,
  title = {Impacts of {{Ocean Acidification}} on {{Coral Reefs}} and {{Other Marine Calcifiers}}: {{A Guide}} for {{Future Research}}, Report of a Workshop Held 18\textendash{}20 {{April}} 2005, {{St}}. {{Petersburg}}, {{FL}}, Sponsored by {{NSF}}, {{NOAA}}, and the {{US Geological Survey}}, 88 Pp},
  shorttitle = {Impacts of {{Ocean Acidification}} on {{Coral Reefs}} and {{Other Marine Calcifiers}}},
  author = {Kleypas, J. A. and Feely, R. A. and Fabry, V. J. and Langdon, C. and Sabine, C. L. and Robbins, L. L.},
  year = {2006},
  file = {/Users/davidbeauchesne/Zotero/storage/LYGTCJHP/54b577eb0cf2318f0f998b54.pdf}
}

@article{kristensen2004,
  title = {The {{DPSIR}} Framework},
  author = {Kristensen, Peter},
  year = {2004},
  volume = {10},
  file = {/Users/davidbeauchesne/Zotero/storage/RNC47QVC/Kristensen - 2004 - The DPSIR framework.pdf},
  journal = {National Environmental Research Institute, Denmark}
}

@article{kroeker2013,
  title = {Impacts of Ocean Acidification on Marine Organisms: Quantifying Sensitivities and Interaction with Warming},
  shorttitle = {Impacts of Ocean Acidification on Marine Organisms},
  author = {Kroeker, Kristy J. and Kordas, Rebecca L. and Crim, Ryan and Hendriks, Iris E. and Ramajo, Laura and Singh, Gerald S. and Duarte, Carlos M. and Gattuso, Jean-Pierre},
  year = {2013},
  volume = {19},
  pages = {1884--1896},
  issn = {1365-2486},
  doi = {10.1111/gcb.12179},
  abstract = {Ocean acidification represents a threat to marine species worldwide, and forecasting the ecological impacts of acidification is a high priority for science, management, and policy. As research on the topic expands at an exponential rate, a comprehensive understanding of the variability in organisms' responses and corresponding levels of certainty is necessary to forecast the ecological effects. Here, we perform the most comprehensive meta-analysis to date by synthesizing the results of 228 studies examining biological responses to ocean acidification. The results reveal decreased survival, calcification, growth, development and abundance in response to acidification when the broad range of marine organisms is pooled together. However, the magnitude of these responses varies among taxonomic groups, suggesting there is some predictable trait-based variation in sensitivity, despite the investigation of approximately 100 new species in recent research. The results also reveal an enhanced sensitivity of mollusk larvae, but suggest that an enhanced sensitivity of early life history stages is not universal across all taxonomic groups. In addition, the variability in species' responses is enhanced when they are exposed to acidification in multi-species assemblages, suggesting that it is important to consider indirect effects and exercise caution when forecasting abundance patterns from single-species laboratory experiments. Furthermore, the results suggest that other factors, such as nutritional status or source population, could cause substantial variation in organisms' responses. Last, the results highlight a trend towards enhanced sensitivity to acidification when taxa are concurrently exposed to elevated seawater temperature.},
  copyright = {\textcopyright{} 2013 Blackwell Publishing Ltd},
  file = {/Users/davidbeauchesne/Zotero/storage/YP4T6BWH/Kroeker et al. - 2013 - Impacts of ocean acidification on marine organisms.pdf;/Users/davidbeauchesne/Zotero/storage/U2YS8TJW/gcb.html},
  journal = {Global Change Biology},
  keywords = {calcification,carbonate chemistry,climate change,cumulative effects,pH},
  language = {en},
  number = {6}
}

@article{lavoie2016,
  title = {Large-{{Scale Atmospheric}} and {{Oceanic Control}} on {{Krill Transport}} into the {{St}}. {{Lawrence Estuary Evidenced}} with {{Three}}-{{Dimensional Numerical Modelling}}},
  author = {Lavoie, Diane and Chass{\'e}, Jo{\"e}l and Simard, Yvan and Lambert, Nicolas and Galbraith, Peter S. and Roy, Nathalie and Brickman, Dave},
  year = {2016},
  month = may,
  volume = {54},
  pages = {299--325},
  issn = {0705-5900},
  doi = {10.1080/07055900.2015.1082965},
  abstract = {A three-dimensional circulation model, coupled to a Lagrangian particle drift model, is used to understand the processes leading to krill transport from the northwest Gulf of St. Lawrence (nwGSL) towards the head of the Lower St. Lawrence Estuary (LSLE), a well-known site of krill accumulation. An analysis of the circulation at the scale of the Gulf of St. Lawrence (GSL) over five years (2006 to 2010) evidenced four major findings. (i) There are two main seasonal circulation patterns, one in winter\textendash{}spring and one in summer\textendash{}fall, driven by local wind forcing and transport at Cabot Strait and at the Strait of Belle Isle. (ii) The freshwater runoff variability does not control the observed inflow events at the mouth of the LSLE. (iii) Extratropical storms passing over the GSL are important for the transport of krill into the LSLE through the generation of inflow events at Pointe-des-Monts. (iv) The contribution of the transport in the surface layer (where krill are found at night) during these inflow events is also important in modulating the variability of the transport of krill into the LSLE. The inflow events, combined with the presence or absence of high krill densities in the nwGSL, partly control the interannual variability of the transport of krill into the LSLE.},
  file = {/Users/davidbeauchesne/Zotero/storage/LM2D8S3P/Lavoie et al. - 2016 - Large-Scale Atmospheric and Oceanic Control on Kri.pdf;/Users/davidbeauchesne/Zotero/storage/J8BDUJFE/07055900.2015.html},
  journal = {Atmosphere-Ocean},
  keywords = {biophysical interactions,circulation,diel vertical migration,marginal seas,modelling,seasonal cycle,zooplankton aggregation},
  number = {3}
}

@book{legendre2012,
  title = {Numerical {{Ecology}}},
  author = {Legendre, Pierre and Legendre, Loic F. J.},
  year = {2012},
  month = jul,
  publisher = {{Elsevier}},
  abstract = {The book describes and discusses the numerical methods which are successfully being used for analysing ecological data, using a clear and comprehensive approach. These methods are derived from the fields of mathematical physics, parametric and nonparametric statistics, information theory, numerical taxonomy, archaeology, psychometry, sociometry, econometry and others.An updated, 3rd English edition of the most widely cited book on quantitative analysis of multivariate ecological dataRelates ecological questions to methods of statistical analysis, with a clear description of complex numerical methodsAll methods are illustrated by examples from the ecological literature so that ecologists clearly see how to use the methods and approaches in their own researchAll calculations are available in R language functions},
  isbn = {978-0-444-53869-7},
  keywords = {Science / Environmental Science,Science / Life Sciences / Ecology},
  language = {en}
}

@techreport{lewis1998,
  title = {Program Developed for {{CO}}\{sub 2\} System Calculations},
  author = {Lewis, E. and Wallace, D. and Allison, L. J.},
  year = {1998},
  month = feb,
  institution = {{Brookhaven National Lab., Dept. of Applied Science, Upton, NY (United States); Oak Ridge National Lab., Carbon Dioxide Information Analysis Center, TN (United States)}},
  doi = {10.2172/639712},
  abstract = {The U.S. Department of Energy's Office of Scientific and Technical Information},
  file = {/Users/davidbeauchesne/Zotero/storage/3BFQSK48/Lewis et al. - 1998 - Program developed for CO sub 2 system calculation.pdf;/Users/davidbeauchesne/Zotero/storage/AQTYP5PI/639712.html},
  language = {English},
  number = {ORNL/CDIAC-105}
}

@article{lloyd1982,
  title = {Least Squares Quantization in {{PCM}}},
  author = {Lloyd, S.},
  year = {1982},
  month = mar,
  volume = {28},
  pages = {129--137},
  issn = {0018-9448},
  doi = {10.1109/TIT.1982.1056489},
  journal = {IEEE Transactions on Information Theory},
  keywords = {Least-squares approximation,PCM communication,Quantization (signal),Signal quantization},
  number = {2}
}

@article{lubchenco2015,
  title = {Making Waves: {{The}} Science and Politics of Ocean Protection},
  shorttitle = {Making Waves},
  author = {Lubchenco, Jane and {Grorud-Colvert}, Kirsten},
  year = {2015},
  month = oct,
  volume = {350},
  pages = {382--383},
  issn = {0036-8075, 1095-9203},
  doi = {10.1126/science.aad5443},
  abstract = {The ocean has recently taken a more prominent role on the international policy stage. In June, the United Nations (UN) initiated development of a treaty for conservation of biodiversity on the High Seas. One of the Sustainable Development Goals (SDGs) adopted by the UN in September focuses on the ocean. In early October, the second Our Ocean Conference (OO-2015) provided a high-profile platform for nations to tout progress or make promises to protect and restore the ocean. We discuss recent progress in creating and enforcing strongly protected areas, and we emphasize the need to accelerate the pace and draw on scientific knowledge.
Mature science reveals opportunities for policy progress
Mature science reveals opportunities for policy progress},
  copyright = {Copyright \textcopyright{} 2015, American Association for the Advancement of Science},
  file = {/Users/davidbeauchesne/Zotero/storage/PET5RS2M/Lubchenco and Grorud-Colvert - 2015 - Making waves The science and politics of ocean pr.pdf;/Users/davidbeauchesne/Zotero/storage/NK9FU6IN/382.html},
  journal = {Science},
  language = {en},
  number = {6259},
  pmid = {26472764}
}

@article{mach2017,
  title = {Assessment and Management of Cumulative Impacts in {{California}}'s Network of Marine Protected Areas},
  author = {Mach, Megan E. and Wedding, Lisa M. and Reiter, Sarah M. and Micheli, Fiorenza and Fujita, Rod M. and Martone, Rebecca G.},
  year = {2017},
  month = mar,
  volume = {137},
  pages = {1--11},
  issn = {0964-5691},
  doi = {10.1016/j.ocecoaman.2016.11.028},
  abstract = {In response to concerns about human impacts to coastal ecosystems, conservationists and practitioners are increasingly turning to networks of marine protected areas (MPAs). Although MPAs manage for fishing pressure, many species and habitats in MPAs remain exposed to a multitude of stressors, including stressors from global climate change and regional land- and ocean-based activities. To support the adaptive management of MPAs that are subject to multiple interacting stressors, coastal managers need to understand the potential impacts from other single and multiple stressors. To demonstrate how this can be done, we quantify and map cumulative impacts resulting from multiple stressors to California's network of MPAs, using a widely available cumulative impacts mapping tool. Among individual stressors, those related to climate, including ocean acidification, UV radiation increases, and SST anomalies, were found to have the most intense impacts, especially on surface waters and in the rocky intertidal. Climate stressors are challenging to limit at the local MPA scale, but intense land- and ocean-based impacts that were found to affect a majority of MPAs, such as sediment increases, invasive species, organic pollutants and pollution from shipping and ports, may be more easily regulated at a regional or local scale. This is especially relevant for South and Central coast MPAs where these impacts are the greatest on beaches, tidal flats, and coastal marshes. Accounting for cumulative impacts from these and other stressors when developing monitoring and management plans in California and across the world, would help to improve the efficacy of MPAs.},
  file = {/Users/davidbeauchesne/Zotero/storage/YDLP9QC2/Mach et al. - 2017 - Assessment and management of cumulative impacts in.pdf;/Users/davidbeauchesne/Zotero/storage/8KYT565H/S0964569116303647.html},
  journal = {Ocean \& Coastal Management},
  keywords = {Coasts and beaches,Cumulative impacts,Marine protected area,Marine reserves,Multiple stressors}
}

@book{maechler2018,
  title = {Cluster: {{Cluster Analysis Basics}} and {{Extensions}}},
  author = {Maechler, Martin and Rousseeuw, Peter and Struyf, Anja and Hubert, Mia and Hornik, Kurt},
  year = {2018}
}

@techreport{mapaq2016,
  title = {Description Des Sites Maricoles de La Province de {{Qu{\'e}bec}}. {{Sous}}-Minist{\'e}riat Aux P{\^e}ches et {\`a} l'aquaculture Commerciales, {{Direction}} R{\'e}gionale Des {{{\^I}les}}-de-La-{{Madeleine}}. {{Minist{\`e}re}} de l'{{Agriculture}}, Des {{P{\^e}cheries}} et de l'{{Alimentation}} Du {{Qu{\'e}bec}} ({{MAPAQ}}). {{Qu{\'e}bec}}, {{Canada}}},
  author = {MAPAQ},
  year = {2016},
  institution = {{Minist{\`e}re de l'Agriculture, des P{\^e}cheries et de l'Alimentation du Qu{\'e}bec}}
}

@misc{margules2000,
  title = {Systematic Conservation Planning},
  author = {Margules, C. R. and Pressey, R. L.},
  year = {2000},
  month = may,
  doi = {10.1038/35012251},
  abstract = {The realization of conservation goals requires strategies for managing whole landscapes including areas allocated to both production and protection. Reserves alone are not adequate for nature conservation but they are the cornerstone on which regional strategies are built. Reserves have two main roles. They should sample or represent the biodiversity of each region and they should separate this biodiversity from processes that threaten its persistence. Existing reserve systems throughout the world contain a biased sample of biodiversity, usually that of remote places and other areas that are unsuitable for commercial activities. A more systematic approach to locating and designing reserves has been evolving and this approach will need to be implemented if a large proportion of today's biodiversity is to exist in a future of increasing numbers of people and their demands on natural resources.},
  copyright = {2000 Nature Publishing Group},
  file = {/Users/davidbeauchesne/Zotero/storage/XCEGLFLU/35012251.html},
  howpublished = {https://www.nature.com/articles/35012251},
  journal = {Nature},
  language = {en},
  type = {Special {{Features}}}
}

@article{micheli2016,
  title = {Combined Impacts of Natural and Human Disturbances on Rocky Shore Communities},
  author = {Micheli, Fiorenza and Heiman, Kimberly W. and Kappel, Carrie V. and Martone, Rebecca G. and Sethi, Suresh A. and Osio, Giacomo C. and Fraschetti, Simonetta and Shelton, Andrew O. and Tanner, Jacqui M.},
  year = {2016},
  month = jun,
  volume = {126},
  pages = {42--50},
  issn = {0964-5691},
  doi = {10.1016/j.ocecoaman.2016.03.014},
  abstract = {Most ecosystems are subject to both natural and human disturbances that can combine to influence populations and assemblages in complex ways. Assessing the relative influences and combined impacts of natural and human disturbance is crucial for managing human uses of ecosystems against the backdrop of their natural variability. We evaluated the separate and combined influences of disturbance from storm waves and disturbance associated with human trampling of rocky shores by conducting an experiment mimicking controlled levels of trampling at sites with different wave exposures, and before and after a major storm event in central California, USA. Results show that trampling and storm waves affected the same taxa and have comparable and additive effects on rocky shore assemblages. Both disturbance types caused significant reduction in percent cover of mussels and erect macroalgae, and resulted in significant re-organization of assemblages associated with these habitat-forming taxa. A single extreme storm event caused similar percent cover losses of mussels and erect macroalgae as did 6\textendash{}12 months of trampling. Contrary to a predicted synergistic effect of trampling and storm damage, we found that impacts from each disturbance combined additively. Mussel beds in wave-exposed sites are more vulnerable to trampling impacts than algal beds at protected sites. Mussels and erect macroalgae recovered within five years after trampling stopped. These results suggest that impacts from local human use can be reversed in relatively short time frames, and that cumulative impacts can be reduced by setting recreational carrying capacities more conservatively when ecosystems are already exposed to frequent and/or intense natural disturbances.},
  file = {/Users/davidbeauchesne/Zotero/storage/FLL7933R/S0964569116300394.html},
  journal = {Ocean \& Coastal Management},
  keywords = {Coastal management,Marine conservation,Multiple stressors,Trampling,Waves}
}

@article{millero1986,
  title = {The {{pH}} of Estuarine Waters},
  author = {Millero, Frank J.},
  year = {1986},
  volume = {31},
  pages = {839--847},
  issn = {1939-5590},
  doi = {10.4319/lo.1986.31.4.0839},
  abstract = {The emf measurements for the TRIS buffer in seawater have been used to define buffer solutions that can be used to determine the pH on a free or total proton scale for estuarine waters. The pH is related to the stoichiometric dissociation constant (K*) of TRISH, the concentration of buffer (mTRIS) and salinity (S) by where a = -9.73 \texttimes{} 10-5 and b = 6.988 \texttimes{} 10-5. The values of pK* were fit to equations of the form where A, B, and C are functions of salinity and T is the absolute temperature. An electrode system with liquid junction was used to measure these buffers to compare the various pH scales.},
  copyright = {\textcopyright{} 1986, by the Association for the Sciences of Limnology and Oceanography, Inc.},
  file = {/Users/davidbeauchesne/Zotero/storage/A7IYSGR8/Millero - 1986 - The pH of estuarine waters.pdf;/Users/davidbeauchesne/Zotero/storage/Y9SVB2DL/lo.1986.31.4.html},
  journal = {Limnology and Oceanography},
  language = {en},
  number = {4}
}

@article{moritz2015,
  title = {No More Detectable Fishing Effect on {{Northern Gulf}} of {{St Lawrence}} Benthic Invertebrates},
  author = {Moritz, C. and Gravel, D. and Savard, L. and McKindsey, C. W. and Br{\^e}thes, J.-C. and Archambault, P.},
  year = {2015},
  month = oct,
  volume = {72},
  pages = {2457--2466},
  issn = {1054-3139},
  doi = {10.1093/icesjms/fsv124},
  abstract = {Abstract.  Trawling has been reported worldwide to alter seabed structure, and thus benthic habitats and ecosystems. Usually, a decrease in species richness and},
  file = {/Users/davidbeauchesne/Zotero/storage/5T2M4PN6/Moritz et al. - 2015 - No more detectable fishing effect on Northern Gulf.pdf;/Users/davidbeauchesne/Zotero/storage/UXNKNI6J/2459097.html},
  journal = {ICES Journal of Marine Science},
  language = {en},
  number = {8}
}

@article{mucci2011,
  title = {Acidification of {{Lower St}}. {{Lawrence Estuary Bottom Waters}}},
  author = {Mucci, Alfonso and Starr, Michel and Gilbert, Denis and Sundby, Bjorn},
  year = {2011},
  month = sep,
  volume = {49},
  pages = {206--218},
  issn = {0705-5900},
  doi = {10.1080/07055900.2011.599265},
  abstract = {Accumulation of metabolic CO2 can acidify marine waters above and beyond the ongoing acidification of the ocean by anthropogenic CO2. The impact of respiration on carbonate chemistry and pH is most acute in hypoxic and anoxic basins, where metabolic CO2 accumulates to high concentrations. The bottom waters of the Lower St. Lawrence Estuary (LSLE), where persistently severe hypoxia has developed over the last 80 years, is one such case. We have reconstructed the evolution of pH in the bottom waters from historical and recent data, and from first principles relating the stoichiometry of CO2 produced to oxygen consumed during microbial degradation of organic matter. Based on the value of the atmospheric partial pressure of CO2 that best reproduces the preformed dissolved inorganic carbon concentration in the bottom waters, we estimate the average ventilation age of the bottom waters to be 16 {$\pm$} 3 years. The pH of the bottom waters has decreased by 0.2 to 0.3 over the last 75 years, which is four to six times greater than can be attributed to the uptake of anthropogenic CO2. The pH decrease is accompanied by a decline in the saturation state with respect to both calcite and aragonite. As of 2007, bottom waters in the LSLE are slightly supersaturated with respect to calcite ({$\Omega$}c {$\approx$} 1.06 {$\pm$} 0.04) but are strongly undersaturated with respect to aragonite ({$\Omega$}a {$\approx$} 0.67 {$\pm$} 0.03).},
  file = {/Users/davidbeauchesne/Zotero/storage/TS8UNGQA/Mucci et al. - 2011 - Acidification of Lower St. Lawrence Estuary Bottom.pdf;/Users/davidbeauchesne/Zotero/storage/GELAXWGU/07055900.2011.html},
  journal = {Atmosphere-Ocean},
  keywords = {acidification,metabolic CO2,oxygen depletion,St. Lawrence Estuary},
  number = {3}
}

@article{mucci2017,
  title = {Tidally Induced Variations of {{pH}} at the Head of the {{Laurentian Channel}}},
  author = {Mucci, Alfonso and Levasseur, Maurice and Gratton, Yves and Martias, Chlo{\'e} and Scarratt, Michael and Gilbert, Denis and Tremblay, Jean-{\'E}ric and Ferreyra, Gustavo and Lansard, Bruno},
  year = {2017},
  month = sep,
  volume = {75},
  pages = {1128--1141},
  issn = {0706-652X},
  doi = {10.1139/cjfas-2017-0007},
  abstract = {The head of the Laurentian Channel is a very dynamic region of exceptional biological richness. To evaluate the impact of freshwater discharge, tidal mixing, and biological activity on the pH of surface waters in this region, a suite of physical and chemical variables was measured throughout the water column over two tidal cycles. The relative contributions to the water column of the four source-water types that converge in this region were evaluated using an optimum multiparameter algorithm (OMP). Results of the OMP analysis were used to reconstruct the water column properties assuming conservative mixing, and the difference between the model properties and field measurements served to identify factors that control the pH of the surface waters. These surface waters are generally undersaturated with respect to aragonite, mostly due to the intrusion of waters from the Upper St. Lawrence Estuary and the Saguenay Fjord. The presence of a cold intermediate layer impedes the upwelling of the deeper, hypoxic, l..., La t{\^e}te du chenal Laurentien est une r{\'e}gion tr{\`e}s dynamique d'une richesse biologique exceptionnelle. Afin d'{\'e}valuer l'impact des apports en eaux douces, du m{\'e}lange tidal, et de l'activit{\'e} biologique sur le pH des eaux de surface dans cette r{\'e}gion, une suite de variables physiques et chimiques a {\'e}t{\'e} mesur{\'e}e dans la colonne d'eau sur deux cycles de mar{\'e}e. La contribution relative des quatre sources d'eau-type qui convergent dans cette r{\'e}gion a {\'e}t{\'e} {\'e}valu{\'e}e {\`a} l'aide d'un algorithme d'optimisation multi-param{\'e}trique (OMP). Les r{\'e}sultats de l'OMP ont {\'e}t{\'e} utilis{\'e}s pour reconstruire les propri{\'e}t{\'e}s de la colonne d'eau en assumant un m{\'e}lange conservateur et la diff{\'e}rence entre les propri{\'e}t{\'e}s issues du mod{\`e}le et des mesures effectu{\'e}es sur le terrain ont servies {\`a} identifier les facteurs qui contr{\^o}lent le pH des eaux de surface. Les eaux de surface sont g{\'e}n{\'e}ralement sous-satur{\'e}es par rapport {\`a} l'aragonite, surtout {\`a} cause de l'intrusion d'eau provenant de l'estuaire fluvial du Saint-Laurent et du fjord du Saguenay. L...},
  file = {/Users/davidbeauchesne/Zotero/storage/GLENYLFJ/Mucci et al. - 2017 - Tidally induced variations of pH at the head of th.pdf;/Users/davidbeauchesne/Zotero/storage/AAD5ZST5/cjfas-2017-0007.html},
  journal = {Canadian Journal of Fisheries and Aquatic Sciences},
  number = {7}
}

@article{nicholls2010,
  title = {Sea-{{Level Rise}} and {{Its Impact}} on {{Coastal Zones}}},
  author = {Nicholls, Robert J. and Cazenave, Anny},
  year = {2010},
  month = jun,
  volume = {328},
  pages = {1517--1520},
  issn = {0036-8075, 1095-9203},
  doi = {10.1126/science.1185782},
  abstract = {Global sea levels have risen through the 20th century. These rises will almost certainly accelerate through the 21st century and beyond because of global warming, but their magnitude remains uncertain. Key uncertainties include the possible role of the Greenland and West Antarctic ice sheets and the amplitude of regional changes in sea level. In many areas, nonclimatic components of relative sea-level change (mainly subsidence) can also be locally appreciable. Although the impacts of sea-level rise are potentially large, the application and success of adaptation are large uncertainties that require more assessment and consideration.},
  copyright = {Copyright \textcopyright{} 2010, American Association for the Advancement of Science},
  file = {/Users/davidbeauchesne/Zotero/storage/KRDKLIYI/Nicholls and Cazenave - 2010 - Sea-Level Rise and Its Impact on Coastal Zones.pdf;/Users/davidbeauchesne/Zotero/storage/R62B8384/1517.html},
  journal = {Science},
  language = {en},
  number = {5985},
  pmid = {20558707}
}

@misc{obis2019,
  title = {Ocean {{Biogeographic Information System}}. {{Intergovernmental Oceanographic Commission}} of {{UNESCO}}. Www.Iobis.Org. {{Accessed}} 2019-04-19},
  author = {{OBIS}},
  year = {2019},
  language = {en}
}

@article{obrien2019,
  title = {After Decades of Stressor Research in Urban Estuarine Ecosystems the Focus Is Still on Single Stressors: {{A}} Systematic Literature Review and Meta-Analysis},
  shorttitle = {After Decades of Stressor Research in Urban Estuarine Ecosystems the Focus Is Still on Single Stressors},
  author = {O'Brien, A. L. and Dafforn, K. A. and Chariton, A. A. and Johnston, E. L. and {Mayer-Pinto}, M.},
  year = {2019},
  month = feb,
  issn = {0048-9697},
  doi = {10.1016/j.scitotenv.2019.02.131},
  abstract = {Natural systems are threatened by a variety of anthropogenic stressors and so understanding the interactive threats posed by multiple stressors is essential. In this study we focused on urban stressors that are ubiquitous to urban estuarine systems worldwide: elevated nutrients, toxic chemical contaminants, built infrastructure and non-indigenous species (NIS). We investigated structural (abundance, diversity and species richness) and functional endpoints (productivity, primary production (chlorophyll-a) and metabolism) commonly used to determine responses to these selected stressors. Through a systematic review of global literature, we found 579 studies of our selected stressors; 93\% measured responses to a single stressor, with few assessing the effects of multiple stressors (7\%). Structural endpoints were commonly used to measure the effects of stressors (49\% of the total 579 studies). Whereas, functional endpoints were rarely assessed alone (10\%) but rather in combination with structural endpoints (41\%). Elevated nutrients followed by NIS were the most studied single stressors (43\% and 16\% of the 541 single stressor studies), while elevated nutrients and toxic contaminants were overwhelmingly the most common stressor combination (79\% of the 38 multiple stressor studies); with NIS and built infrastructure representing major gaps in multi-stressor research. In the meta-analysis, structural endpoints tended to decrease, while functional endpoints increased and/or decreased in response to different types of organisms or groups. We predicted an antagonistic effect of elevated nutrients and toxic contaminants based on the opposing enriching versus toxic effects of this stressor combination. Of note, biodiversity was the only endpoint that revealed such an antagonistic response. Our results highlight the continuing paucity of multiple stressor studies and provide evidence for opposing patterns in the responses to single and interacting stressors depending on the measured endpoint. The latter is of significant consequence to understanding relevant impacts of stressors in coastal monitoring and management.},
  file = {/Users/davidbeauchesne/Zotero/storage/9AAR8RAH/O'Brien et al. - 2019 - After decades of stressor research in urban estuar.pdf;/Users/davidbeauchesne/Zotero/storage/YV3LUZBF/S0048969719306199.html},
  journal = {Science of The Total Environment},
  keywords = {Built infrastructure,Contaminants,Function,Invasive species,Nutrients,Structure}
}

@article{pillet2016,
  title = {Effects of Exposure to Hypoxia on Metabolic Pathways in Northern Shrimp ({{Pandalus}} Borealis) and {{Greenland}} Halibut ({{Reinhardtius}} Hippoglossoides)},
  author = {Pillet, Marion and {Dupont-Prinet}, Aur{\'e}lie and Chabot, Denis and Tremblay, R{\'e}jean and Audet, C{\'e}line},
  year = {2016},
  month = oct,
  volume = {483},
  pages = {88--96},
  issn = {0022-0981},
  doi = {10.1016/j.jembe.2016.07.002},
  abstract = {In the Estuary and Gulf of St. Lawrence, northern shrimp (Pandalus borealis) and Greenland halibut (Reinhardtius hippoglossoides) are usually found at depths {$>$}150m and thus frequently inhabit hypoxic areas (18\textendash{}50\% saturation). The impact of a one-week exposure to different levels of dissolved oxygen (100, 40, 30, and 20\% saturation) at 5\textdegree{}C was evaluated in adult shrimp and juvenile Greenland halibut; the effect of acute exposure to severe hypoxia was also assessed in Greenland halibut. The activities of key enzymes involved in aerobic (citrate synthase [CS], cytochrome c oxidase [COX]) and anaerobic (pyruvate kinase [PK], phosphoenolpyruvate carboxykinase [PEPCK], lactate dehydrogenase [LDH]) pathways, and of enzymes involved in antioxidant defence (superoxide dismutase, glutathione peroxidase [GPx], and catalase [CAT]) were measured. Quantitative real-time PCR analysis was also performed in Greenland halibut. In northern shrimp exposed to chronic hypoxia, muscle CS activity decreased by \textasciitilde{}40\%. Muscle LDH activity was significantly reduced, with a more intense reduction in males. At the same time, hepatopancreas GPx activity increased under hypoxia, and this response was stronger in males. Overall, the results suggest the presence of a threshold above 40\% saturation and higher hypoxia tolerance in males. In juvenile Greenland halibut, exposure to chronic hypoxia elicited a more wide-ranging enzymatic response than did acute exposure to severe hypoxia. Under chronic hypoxia, CS activity decreased and PK and LDH activity were respectively 46\% and 57\% lower than in normoxia. There were no major changes in the activity of antioxidant enzymes, but activity in normoxia was high compared to other fish species. Interestingly, the relative expression of genes coding for muscle COX (severe hypoxia), liver PEPCK (chronic), and CAT (chronic) activities were triggered in hypoxia. The absence of a corresponding change in enzyme activity makes the interpretation of these results difficult, but clearly there was a response at the transcription level. Overall, the results indicate that these two species are particularly well adapted to withstand severe hypoxia.},
  file = {/Users/davidbeauchesne/Zotero/storage/HXEH9888/S0022098116301113.html},
  journal = {Journal of Experimental Marine Biology and Ecology},
  keywords = {Aerobic pathway,Anaerobic pathway,Antioxidant defence,Enzyme activity,Gene expression,Metabolic capacity}
}

@techreport{plourde2014,
  title = {Ecosystem Perspective on Changes and Anomalies in the {{Gulf}} of {{St}}. {{Lawrence}}: A Context in Support of the Management of the {{St}}. {{Lawrence}} Beluga Whale Population. {{DFO Can}}. {{Sci}}. {{Advis}}. {{Sec}}. {{Res}}. {{Doc}}. 2013/129. v + 29 p.},
  author = {Plourde, St{\'e}phane and Galbraith, Peter S. and Lesage, V{\'e}ronique and Gr{\'e}goire, Fran{\c c}ois and Bourdages, Hugo and Gosselin, Jean-Fran{\c c}ois and McQuinn, Ian and Scarratt, Michael},
  year = {2014},
  pages = {v + 29 p},
  file = {/Users/davidbeauchesne/Zotero/storage/FKML3H3S/Plourde et al. - 2014 - Ecosystem perspective on changes and anomalies in .pdf},
  number = {2013/129}
}

@article{reichman2011,
  title = {Challenges and {{Opportunities}} of {{Open Data}} in {{Ecology}}},
  author = {Reichman, O. J. and Jones, Matthew B. and Schildhauer, Mark P.},
  year = {2011},
  month = feb,
  volume = {331},
  pages = {703--705},
  issn = {0036-8075, 1095-9203},
  doi = {10.1126/science.1197962},
  abstract = {Ecology is a synthetic discipline benefiting from open access to data from the earth, life, and social sciences. Technological challenges exist, however, due to the dispersed and heterogeneous nature of these data. Standardization of methods and development of robust metadata can increase data access but are not sufficient. Reproducibility of analyses is also important, and executable workflows are addressing this issue by capturing data provenance. Sociological challenges, including inadequate rewards for sharing data, must also be resolved. The establishment of well-curated, federated data repositories will provide a means to preserve data while promoting attribution and acknowledgement of its use.},
  copyright = {Copyright \textcopyright{} 2011, American Association for the Advancement of Science},
  file = {/Users/davidbeauchesne/Zotero/storage/8G6H9GQT/Reichman et al. - 2011 - Challenges and Opportunities of Open Data in Ecolo.pdf;/Users/davidbeauchesne/Zotero/storage/CGM3W3G5/703.html},
  journal = {Science},
  language = {en},
  number = {6018},
  pmid = {21311007}
}

@article{rice2011,
  title = {Managing Fisheries Well: Delivering the Promises of an Ecosystem Approach},
  shorttitle = {Managing Fisheries Well},
  author = {Rice, Jake},
  year = {2011},
  volume = {12},
  pages = {209--231},
  issn = {1467-2979},
  doi = {10.1111/j.1467-2979.2011.00416.x},
  abstract = {The four general components of an ecosystem approach to fisheries (EAF) are reviewed. In taking account of environment forcing in stock dynamics, arguments are presented that effects of environmental forcing on growth, maturation and natural mortality are often more important to management than effects on recruitment. In holding fisheries accountable for the ecosystem effects of fishing, it is argued that direct effects of fishing are generally known and can be managed. However, interactions among fisheries and between fisheries and other sectors pose difficult challenges to equitable decisions in managing these impacts, and many traditional incentives function differently in EAF than in target-stock management. Achieving inclusiveness in decision-making and stewardship is also made more complex in EAF, because of the much larger number of interests with a legitimate role in decision-making. As a result, integrated management (IM) becomes a necessary component of EAF, although EAF and IM are not interchangeable concepts. The treatment of all four components of an EAF considers the need for a balanced and stable outcome on all three dimensions of sustainability \textendash{} ecological, economic and social. It also highlights that different participant groups in governance display different risk tolerances for misses (not taking conservation action when needed) and false alarms (restraining access to social or economic benefits when little ecological benefit results). These differences in tolerances for different kinds of management errors often complicate decision-making an EAF setting and raise transaction costs greatly.},
  copyright = {\textcopyright{} 2011 Crown in the right of Canada},
  file = {/Users/davidbeauchesne/Zotero/storage/9D7IMTV9/j.1467-2979.2011.00416.html},
  journal = {Fish and Fisheries},
  keywords = {Ecosystem approach to fisheries,ecosystem effects of fishing,environmental forcing,inclusive governance,integrated management,risk tolerance,sustainable use},
  language = {en},
  number = {2}
}

@misc{rqm2018,
  title = {R{\'e}seau {{Qu{\'e}bec Maritime}} ({{RQM}}). {{Available}} from {{http://rqm.quebec/en/home/.}} {{Accessed}} 2019-09-19},
  author = {{RQM}},
  year = {2018},
  language = {en}
}

@article{saucier2003,
  title = {Modeling the Formation and Circulation Processes of Water Masses and Sea Ice in the {{Gulf}} of {{St}}. {{Lawrence}}, {{Canada}}},
  author = {Saucier, Fran{\c c}ois J. and Roy, Fran{\c c}ois and Gilbert, Denis and Pellerin, Pierre and Ritchie, Harold},
  year = {2003},
  month = aug,
  volume = {108},
  issn = {0148-0227},
  doi = {10.1029/2000JC000686},
  abstract = {The seasonal cycle of water masses and sea ice in the Gulf of St. Lawrence is examined using a three-dimensional coastal ice-ocean model with realistic tidal, atmospheric, hydrologic, and oceanic forcing. The model includes a level 2.5 turbulent kinetic energy equation. A model simulation over 1997?1998 is verified against available data on sea ice, temperature, and salinity. The results demonstrate a consistent seasonal cycle in atmosphere-ocean exchanges and the formation and circulation of water masses and sea ice. The accuracy of radiative, momentum, and sensible heat exchanges at the sea surface, and the production of turbulent kinetic energy from winds and tides, are critical to the accuracy of the modeled circulation. The analysis of the mean error on near-surface temperature and salinity in the late summer and fall using standard bulk exchange coefficients and radiation (about 1\textdegree{}C too cold and 1 salinity unit too fresh) shows the tradeoff between tidal mixing at the head of the Laurentian Channel, and wind-driven circulation and mixing in the surface waters. The results suggest year-long stratification in the estuary and northwestern Gulf, with little mixing except near the head region, where relatively deep warmer waters are mixed to the surface during winter, and cold intermediate waters are efficiently withdrawn during summer. The results suggest that the summer cold waters found at intermediate depths in the estuary and northwestern Gulf are not formed in situ. A significant fraction of these waters enters through the Strait of Belle Isle in wintertime, eventually reaching the estuary within about 6 months.},
  file = {/Users/davidbeauchesne/Zotero/storage/YHN8QWCU/Saucier et al. - 2003 - Modeling the formation and circulation processes o.pdf;/Users/davidbeauchesne/Zotero/storage/24XG475X/2000JC000686.html},
  journal = {Journal of Geophysical Research: Oceans},
  keywords = {air-sea interactions,circulation,numerical modeling,sea ice,seasonal cycle,St. Lawrence,tide},
  number = {C8}
}

@article{savenkoff2000,
  title = {Export of Biogenic Carbon and Structure and Dynamics of the Pelagic Food Web in the {{Gulf}} of {{St}}. {{Lawrence Part}} 1. {{Seasonal}} Variations},
  author = {Savenkoff, C and V{\'e}zina, A. F and Roy, S and Klein, B and Lovejoy, C and Therriault, J. -C and Legendre, L and Rivkin, R and B{\'e}rub{\'e}, C and Tremblay, J. -E and Silverberg, N},
  year = {2000},
  month = apr,
  volume = {47},
  pages = {585--607},
  issn = {0967-0645},
  doi = {10.1016/S0967-0645(99)00119-8},
  abstract = {The seasonal changes in photosynthetic production, respiration, sinking flux of organic carbon, and food web structure are described in the Gulf of St. Lawrence over a two-year period during the Canadian Joint Global Ocean Flux Study (JGOFS) program. The results show contrasts in net metabolism between periods of low (winter and spring) and high (summer and fall) vertical stability. The winter\textendash{}spring period was associated with an autotrophic pelagic food web: predominance of large phytoplankton cells, large zooplankton, and high herbivorous potential transfers towards the zooplankton. The stratified summer-fall period was associated with a heterotrophic food web: dominance of small phytoplankton cells, replacement of the size class occupied by large phytoplankton with large heterotrophic dinoflagellates and ciliates, smaller zooplankton, and dominance of omnivorous transfers towards the zooplankton. Despite differences in algal size and composition as well as in size structure of the trophic compartments between winter\textendash{}spring and summer\textendash{}fall, the particulate organic carbon fluxes observed at 50 m depth was quantitatively similar during these two periods. Even though winter photosynthetic production was relatively low, the high chlorophyll a concentration, the size structure of the trophic compartments, and the high contribution of large phytoplankton cells (mainly diatoms) to biological activity were similar to those observed during the spring and could explain the high heterotrophic biomass observed during winter.},
  file = {/Users/davidbeauchesne/Zotero/storage/K6G3R3P8/Savenkoff et al. - 2000 - Export of biogenic carbon and structure and dynami.pdf;/Users/davidbeauchesne/Zotero/storage/3CRIT4SI/S0967064599001198.html},
  journal = {Deep Sea Research Part II: Topical Studies in Oceanography},
  number = {3\textendash{}4}
}

@incollection{schloss2017,
  title = {Cumulative Potential Impacts of the Stress Factors Associated with Human Activities on the {{St}}. {{Lawrence}} Marine Ecosystem},
  booktitle = {Hydrocarbon in the {{Gulf}} of {{St}}. {{Lawrence}} - {{Social}}, Economic and Environmental Issues},
  author = {Schloss, Irene R. and Archambault, Philippe and Beauchesne, David and Cusson, Mathieu and Ferreyra, Gustavo and Levasseur, Maurice and Pelletier, {\'E}milien and {St-Louis}, Richard and Tremblay, R{\'e}jean},
  editor = {Archambault, Philippe and Schloss, Irene R. and Grant, Cindy and Plante, Steve},
  year = {2017},
  pages = {133--165},
  publisher = {{Notre Golfe, Rimouski, Qc, Canada}}
}

@article{simard2009,
  title = {{Le Parc Marin Saguenay\textendash{}Saint-Laurent : processus oc{\'e}anographiques {\`a} la base de ce site unique d'alimentation des baleines du Nord-Ouest Atlantique}},
  shorttitle = {{Le Parc Marin Saguenay\textendash{}Saint-Laurent}},
  author = {Simard, Yvan},
  year = {2009},
  volume = {22},
  pages = {177--197},
  issn = {0992-7158, 1718-8598},
  doi = {https://doi.org/10.7202/037481ar},
  abstract = {The results from an ecosystem research program are summarized. It was conducted in the Saguenay\textendash{}St. Lawrence Marine Park to understand the basic processes responsible for the existence of this traditional whale feeding ground, discovered by the Basques whalers 450~years ago. Persistent processes maintain aggregated whale preys at the head of the main deep-water channel of eastern Canada continental shelf. What are they?},
  file = {/Users/davidbeauchesne/Zotero/storage/J68ZYGTX/Simard - 2009 - Le Parc Marin Saguenay–Saint-Laurent  processus o.pdf;/Users/davidbeauchesne/Zotero/storage/N9T9JNUD/037481ar.html},
  journal = {Revue des sciences de l'eau / Journal of Water Science},
  keywords = {« upwelling »,canyon,channel head,courants,critical habitat,currents,ecosystem hot spot,estuaire,estuary,habitat critique,site d’alimentation des baleines,tête de chenal,upwelling,whale feeding ground},
  language = {fr},
  number = {2}
}

@techreport{starr2019,
  title = {Distribution of Omega Aragonite in the {{Estuary}} and {{Gulf}} of {{St}}. {{Lawrence}} in Eastern {{Canada}}. {{Department}} of {{Fisheries}} and {{Oceans}}.},
  author = {Starr, Michel and Chass{\'e}, Jo{\"e}l},
  year = {2019},
  institution = {{Department of Fisheries and Oceans}}
}

@techreport{statistics-canada2017,
  title = {Population and {{Dwelling Count Highlight Tables}}.  2016 {{Census}}. {{Statistics Canada Catalogue}} No. 98-402-{{X2016001}}. {{Ottawa}}. {{Released February}} 8, 2017.},
  author = {{Statistics-Canada}},
  year = {2017},
  institution = {{Statistics Canada}}
}

@article{stock2018,
  title = {Mapping Ecological Indicators of Human Impact with Statistical and Machine Learning Methods: {{Tests}} on the {{California}} Coast},
  shorttitle = {Mapping Ecological Indicators of Human Impact with Statistical and Machine Learning Methods},
  author = {Stock, A. and Haupt, A. J. and Mach, M. E. and Micheli, F.},
  year = {2018},
  month = nov,
  volume = {48},
  pages = {37--47},
  issn = {1574-9541},
  doi = {10.1016/j.ecoinf.2018.07.007},
  abstract = {Coastal ecosystems are exposed to multiple anthropogenic stressors such as fishing, pollution, and climate change. Ecosystem-based coastal management requires understanding where the combination of multiple stressors has large cumulative effects and where actions to address impacts are most urgently needed. However, the effects of multiple stressors on coastal and marine ecosystems are often non-linear and interactive. This complexity is not captured by commonly used spatial models for mapping human impacts. Flexible statistical and machine learning models like random forests have thus been used as an alternative modeling approach to identify important stressors and to make spatial predictions of their combined effects. However, tests of such models' prediction skill have been limited. Therefore, we tested how well ten statistical and machine learning methods predicted three ecological indicators of coastal marine ecosystem condition (kelp biodiversity, fish biomass, and rocky intertidal biodiversity) off California, USA. Spatial data representing anthropogenic stressors and ocean uses as well as natural gradients were used as predictors. The models' prediction errors were estimated by double spatial block cross-validation. The best models achieved mean squared errors about 25\% lower than a null model for kelp biodiversity and fish biomass; none of the tested models worked well for rocky intertidal biodiversity. The models captured general trends, but not local variability of the indicators. For kelp biodiversity, the best performing method was principal components regression. For fish biomass, the best performing method was boosted regression trees. However, after tuning, this model did not include any interactions between stressors, and ridge regression (a constrained linear model) performed almost as well. While in theory flexible machine learning methods are required to represent the complex stressor-ecosystem state relationships revealed by experimental ecologists, with our data, this flexibility could not be harnessed because more flexible models overfitted due to small sample sizes and low signal-to-noise ratio. The main challenge for harnessing the flexibility of statistical and machine learning methods to link ecological indicators and anthropogenic stressors is obtaining more suitable data. In particular, better data describing the spatial and temporal distribution of human uses and stressors are needed. We conclude by discussing methodological implications for future research.},
  file = {/Users/davidbeauchesne/Zotero/storage/NIM5U6RZ/Stock et al. - 2018 - Mapping ecological indicators of human impact with.pdf;/Users/davidbeauchesne/Zotero/storage/SCEVU9XA/S1574954118300736.html},
  journal = {Ecological Informatics},
  keywords = {Cumulative impacts,Kelp forests,Model selection,Multiple stressors,Regression,Spatial prediction}
}

@article{sutherland2004,
  title = {The Need for Evidence-Based Conservation},
  author = {Sutherland, William J. and Pullin, Andrew S. and Dolman, Paul M. and Knight, Teri M.},
  year = {2004},
  month = jun,
  volume = {19},
  pages = {305--308},
  issn = {0169-5347},
  doi = {10.1016/j.tree.2004.03.018},
  file = {/Users/davidbeauchesne/Zotero/storage/5VMDA3MX/Sutherland et al. - 2004 - The need for evidence-based conservation.pdf;/Users/davidbeauchesne/Zotero/storage/VVH6A3WU/S0169-5347(04)00073-4.html},
  journal = {Trends in Ecology \& Evolution},
  language = {English},
  number = {6},
  pmid = {16701275}
}

@article{taskgroupondatacitationstandardsandpractoutofciteoutofmindthecurrentsices2013,
  title = {Out of {{Cite}}, {{Out}} of {{Mind}}: {{The Current State}} of {{Practice}}, {{Policy}}, and {{Technology}} for the {{Citation}} of {{Data}}},
  shorttitle = {Out of {{Cite}}, {{Out}} of {{Mind}}},
  author = {{Task Group on Data Citation Standards {and} PractOut of Cite, Out of Mind: The Current Sices}, CODATA-ICSTI and {PractOut of Mind: The Current Sices}, C.-I.},
  year = {2013},
  month = sep,
  volume = {12},
  pages = {CIDCR1-CIDCR7},
  issn = {1683-1470},
  doi = {10.2481/dsj.OSOM13-043},
  abstract = {The CODATA\&nbsp;Data Science Journal\&nbsp;is a peer-reviewed, open access, electronic journal, publishing papers on the management, dissemination, use and reuse of research data and databases across all research domains, including science, technology, the humanities and the arts. The scope of the journal includes descriptions of data systems, their implementations and their publication, applications, infrastructures, software, legal, reproducibility and transparency issues, the availability and usability of complex datasets, and with a particular focus on the principles, policies and practices for open data.All data is in scope, whether born digital or converted from other sources.},
  copyright = {Authors who publish with this journal agree to the following terms:    Authors retain copyright and grant the journal right of first publication with the work simultaneously licensed under a  Creative Commons Attribution License  that allows others to share the work with an acknowledgement of the work's authorship and initial publication in this journal.  Authors are able to enter into separate, additional contractual arrangements for the non-exclusive distribution of the journal's published version of the work (e.g., post it to an institutional repository or publish it in a book), with an acknowledgement of its initial publication in this journal.  Authors are permitted and encouraged to post their work online (e.g., in institutional repositories or on their website) prior to and during the submission process, as it can lead to productive exchanges, as well as earlier and greater citation of published work (See  The Effect of Open Access ).  All third-party images reproduced on this journal are shared under Educational Fair Use. For more information on  Educational Fair Use , please see  this useful checklist prepared by Columbia University Libraries .   All copyright  of third-party content posted here for research purposes belongs to its original owners.  Unless otherwise stated all references to characters and comic art presented on this journal are \textcopyright, \textregistered{} or \texttrademark{} of their respective owners. No challenge to any owner's rights is intended or should be inferred.},
  file = {/Users/davidbeauchesne/Zotero/storage/DYY5CA52/Cite and Sices - 2013 - Out of Cite, Out of Mind The Current State of Pra.pdf;/Users/davidbeauchesne/Zotero/storage/NGWUD7WS/dsj.html},
  journal = {Data Science Journal},
  language = {en},
  number = {0}
}

@book{tukey1977,
  title = {Exploratory {{Data Analysis}}.},
  author = {Tukey, J. W.},
  year = {1977},
  publisher = {{Reading, Massachusetts: Addison-Wesley.}}
}

@article{tyberghein2012,
  title = {Bio-{{ORACLE}}: A Global Environmental Dataset for Marine Species Distribution Modelling},
  shorttitle = {Bio-{{ORACLE}}},
  author = {Tyberghein, Lennert and Verbruggen, Heroen and Pauly, Klaas and Troupin, Charles and Mineur, Frederic and Clerck, Olivier De},
  year = {2012},
  month = feb,
  volume = {21},
  pages = {272--281},
  issn = {1466-8238},
  doi = {10.1111/j.1466-8238.2011.00656.x},
  abstract = {Aim The oceans harbour a great diversity of organisms whose distribution and ecological preferences are often poorly understood. Species distribution modelling (SDM) could improve our knowledge and inform marine ecosystem management and conservation. Although marine environmental data are available from various sources, there are currently no user-friendly, high-resolution global datasets designed for SDM applications. This study aims to fill this gap by assembling a comprehensive, uniform, high-resolution and readily usable package of global environmental rasters. Location Global, marine. Methods We compiled global coverage data, e.g. satellite-based and in situ measured data, representing various aspects of the marine environment relevant for species distributions. Rasters were assembled at a resolution of 5 arcmin (c. 9.2 km) and a uniform landmask was applied. The utility of the dataset was evaluated by maximum entropy SDM of the invasive seaweed Codium fragile ssp. fragile. Results We present Bio-ORACLE (ocean rasters for analysis of climate and environment), a global dataset consisting of 23 geophysical, biotic and climate rasters. This user-friendly data package for marine species distribution modelling is available for download at http://www.bio-oracle.ugent.be. The high predictive power of the distribution model of C. fragile ssp. fragile clearly illustrates the potential of the data package for SDM of shallow-water marine organisms. Main conclusions The availability of this global environmental data package has the potential to stimulate marine SDM. The high predictive success of the presence-only model of a notorious invasive seaweed shows that the information contained in Bio-ORACLE can be informative about marine distributions and permits building highly accurate species distribution models.},
  copyright = {\textcopyright{} 2011 Blackwell Publishing Ltd},
  file = {/Users/davidbeauchesne/Zotero/storage/HXSZ78JZ/j.1466-8238.2011.00656.html},
  journal = {Global Ecology and Biogeography},
  keywords = {Bio-ORACLE,Codium fragile,ecological niche modelling,environmental data,global,macroecology,marine,oceanography,species distribution modelling},
  language = {en},
  number = {2}
}

@article{uthicke2016,
  title = {Echinometra Sea Urchins Acclimatized to Elevated {{pCO2}} at Volcanic Vents Outperform Those under Present-Day {{pCO2}} Conditions},
  author = {Uthicke, Sven and Ebert, Thomas and Liddy, Michelle and Johansson, Charlotte and Fabricius, Katharina E. and Lamare, Miles},
  year = {2016},
  volume = {22},
  pages = {2451--2461},
  issn = {1365-2486},
  doi = {10.1111/gcb.13223},
  abstract = {Rising atmospheric CO2 concentrations will significantly reduce ocean pH during the 21st century (ocean acidification, OA). This may hamper calcification in marine organisms such as corals and echinoderms, as shown in many laboratory-based experiments. Sea urchins are considered highly vulnerable to OA. We studied an Echinometra species on natural volcanic CO2 vents in Papua New Guinea, where they are CO2-acclimatized and also subjected to secondary ecological changes from elevated CO2. Near the vent site, the urchins experienced large daily variations in pH ({$>$}1 unit) and pCO2 ({$>$}2000 ppm) and average pH values (pHT 7.73) much below those expected under the most pessimistic future emission scenarios. Growth was measured over a 17-month period using tetracycline tagging of the calcareous feeding lanterns. Average-sized urchins grew more than twice as fast at the vent compared with those at an adjacent control site and assumed larger sizes at the vent compared to the control site and two other sites at another reef near-by. A small reduction in gonad weight was detected at the vents, but no differences in mortality, respiration, or degree of test calcification were detected between urchins from vent and control populations. Thus, urchins did not only persist but actually `thrived' under extreme CO2 conditions. We suggest an ecological basis for this response: Increased algal productivity under increased pCO2 provided more food at the vent, resulting in higher growth rates. The wider implication of our observation is that laboratory studies on non-acclimatized specimens, which typically do not consider ecological changes, can lead to erroneous conclusions on responses to global change.},
  copyright = {\textcopyright{} 2016 John Wiley \& Sons Ltd},
  file = {/Users/davidbeauchesne/Zotero/storage/86IMIXSV/Uthicke et al. - 2016 - Echinometra sea urchins acclimatized to elevated p.pdf;/Users/davidbeauchesne/Zotero/storage/GENH3EYT/gcb.html},
  journal = {Global Change Biology},
  keywords = {calcifying invertebrates,carbon dioxide vents,indirect effects,Ocean acidification},
  language = {en},
  number = {7}
}

@book{walbridge2013,
  title = {Assessing Ship Movements Using Volunteered Geographic Information},
  author = {Walbridge, Shaun},
  year = {2013},
  publisher = {{University of California, Santa Barbara}},
  file = {/Users/davidbeauchesne/Zotero/storage/MNIFJICT/1.html}
}

@book{white1997,
  title = {Marine {{Environmental Assessment}} of the {{Estuary}} and {{Gulf}} of {{St}}. {{Lawrence}}},
  author = {White, Louise and Johns, Frank},
  year = {1997},
  publisher = {{Department of Fisheries and Oceans}},
  abstract = {This assessment is a summary of the accumulated scientific understanding of the Estuary and Golf of St. Lawrence. It discusses the extent of anthropogenic modifications to this marine environment, points out principle uncertainties that hinder our understanding, and identifies important regional environmental issues.},
  file = {/Users/davidbeauchesne/Zotero/storage/JYHM6PGZ/White and Johns - 1997 - Marine Environmental Assessment of the Estuary and.pdf},
  isbn = {978-0-660-20297-6},
  series = {Fisheries and {{Oceans Canada Toxic Chemicals Program}} 1997}
}

@article{wilkinson2016,
  title = {The {{FAIR Guiding Principles}} for Scientific Data Management and Stewardship},
  author = {Wilkinson, Mark D. and Dumontier, Michel and Aalbersberg, IJsbrand Jan and Appleton, Gabrielle and Axton, Myles and Baak, Arie and Blomberg, Niklas and Boiten, Jan-Willem and {da Silva Santos}, Luiz Bonino and Bourne, Philip E. and Bouwman, Jildau and Brookes, Anthony J. and Clark, Tim and Crosas, Merc{\`e} and Dillo, Ingrid and Dumon, Olivier and Edmunds, Scott and Evelo, Chris T. and Finkers, Richard and {Gonzalez-Beltran}, Alejandra and Gray, Alasdair J. G. and Groth, Paul and Goble, Carole and Grethe, Jeffrey S. and Heringa, Jaap and {'t Hoen}, Peter A. C. and Hooft, Rob and Kuhn, Tobias and Kok, Ruben and Kok, Joost and Lusher, Scott J. and Martone, Maryann E. and Mons, Albert and Packer, Abel L. and Persson, Bengt and {Rocca-Serra}, Philippe and Roos, Marco and {van Schaik}, Rene and Sansone, Susanna-Assunta and Schultes, Erik and Sengstag, Thierry and Slater, Ted and Strawn, George and Swertz, Morris A. and Thompson, Mark and {van der Lei}, Johan and {van Mulligen}, Erik and Velterop, Jan and Waagmeester, Andra and Wittenburg, Peter and Wolstencroft, Katherine and Zhao, Jun and Mons, Barend},
  year = {2016},
  month = mar,
  volume = {3},
  pages = {160018},
  issn = {2052-4463},
  doi = {10.1038/sdata.2016.18},
  abstract = {There is an urgent need to improve the infrastructure supporting the reuse of scholarly data. A diverse set of stakeholders\textemdash{}representing academia, industry, funding agencies, and scholarly publishers\textemdash{}have come together to design and jointly endorse a concise and measureable set of principles that we refer to as the FAIR Data Principles. The intent is that these may act as a guideline for those wishing to enhance the reusability of their data holdings. Distinct from peer initiatives that focus on the human scholar, the FAIR Principles put specific emphasis on enhancing the ability of machines to automatically find and use the data, in addition to supporting its reuse by individuals. This Comment is the first formal publication of the FAIR Principles, and includes the rationale behind them, and some exemplar implementations in the community.},
  copyright = {2016 Nature Publishing Group},
  file = {/Users/davidbeauchesne/Zotero/storage/QR8P3NY3/Wilkinson et al. - 2016 - The FAIR Guiding Principles for scientific data ma.pdf;/Users/davidbeauchesne/Zotero/storage/QRTXHWKY/sdata201618.html},
  journal = {Scientific Data},
  language = {en}
}

@book{zeebe2001,
  title = {{{CO2}} in Seawater: Equilibrium, Kinetics, Isotopes},
  shorttitle = {{{CO2}} in Seawater},
  author = {Zeebe, Richard E. and {Wolf-Gladrow}, Dieter},
  year = {2001},
  publisher = {{Gulf Professional Publishing}},
  file = {/Users/davidbeauchesne/Zotero/storage/S3ZLY9XV/books.html},
  number = {65}
}