Explicitly integrating a third dimension in marine species distribution modelling

Duffy, Grant A.; Chown, Steven Loudon

doi:10.3354/meps12011

Cited by 46 publications

(47 citation statements)

References 32 publications

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“…It has generated estimates of occupancy that are considerably greater than occupancy measured from observation alone, for the first time using outputs from a high‐resolution 3‐dimensional hydrodynamic model in such a modeling framework. While the need for species distribution models to consider the 3‐dimensional nature of the marine environment has been documented previously (Duffy & Chown, ), this study reinforces it using modern statistical methods. Using the outputs, this investigation has shown how the behavior of cusk changes in two different environments as a function of current speed.…”

Section: Resultssupporting

confidence: 80%

“…While the need for species distribution models to consider the 3-dimensional nature of the marine environment has been documented previously (Duffy & Chown, 2017), this study reinforces it F I G U R E 7 Observed and median estimated proportions of sites occupied by cusk at Cashes Ledge during the four sampling periods; S1 (Summer 2006), S2 (Spring 2007), S3 (Summer 2007 andS4 (Autumn 2007). Also shown are the 50% and 95% credible intervals for the posterior estimates of the proportion of occupied sites using modern statistical methods.…”

Section: Con Clus Ionsupporting

confidence: 83%

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Dynamic occupancy modeling of temperate marine fish in area‐based closures

Calvert

McGonigle

Sethi

et al. 2018

Ecology and Evolution

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Species distribution models (SDMs) are commonly used to model the spatial structure of species in the marine environment, however, most fail to account for detectability of the target species. This can result in underestimates of occupancy, where nondetection is conflated with absence. The site occupancy model (SOM) overcomes this failure by treating occupancy as a latent variable of the model and incorporates a detection submodel to account for variability in detection rates. These have rarely been applied in the context of marine fish and never for the multiseason dynamic occupancy model (DOM). In this study, a DOM is developed for a designated species of concern, cusk (Brosme brosme), over a four‐season period. Making novel use of a high‐resolution 3‐dimensional hydrodynamic model, detectability of cusk is considered as a function of current speed and algae cover. Algal cover on the seabed is measured from video surveys to divide the study area into two distinct regions: those with canopy forming species of algae and those without (henceforth bottom types). Modeled estimates of the proportion of sites occupied in each season are 0.88, 0.45, 0.74, and 0.83. These are significantly greater than the proportion of occupied sites measured from underwater video observations which are 0.57, 0.28, 0.43, and 0.57. Individual fish are detected more frequently with increasing current speed in areas lacking canopy and less frequently with increasing current speed in areas with canopy. The results indicate that, where possible, SDM studies for all marine species should take account of detectability to avoid underestimating the proportion of sites occupied at a given study area. Sampling closed areas or areas of conservation often requires the use of nonphysical, low impact sampling methods like camera surveys. These methods inherently result in detection probabilities less than one, an issue compounded by time‐varying features of the environment that are rarely accounted for marine studies. This work highlights the use of modeled hydrodynamics as a tool to correct some of this imbalance.

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Section: Resultssupporting

confidence: 80%

Section: Con Clus Ionsupporting

confidence: 83%

Dynamic occupancy modeling of temperate marine fish in area‐based closures

Calvert

McGonigle

Sethi

et al. 2018

Ecology and Evolution

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“…The marine environment is a complex, multidimensional environment, and mapping exercises often do not include a comprehensive set of pertinent data such as physical, geological, biological, and anthropogenic characteristics (Guarinello et al, 2010;Boyd and Brown, 2015). Even more challenging is the integration of appropriate ecological phenomena and interactions that limits our ability to use this crucial information in decision-making, whether it is the synergistic and antagonistic effects of drivers on species distributions (Boyd and Brown, 2015), habitat edges and transitions (Pinn and Robertson, 2003;Ries et al, 2004), or the addition of temporal variability and the third dimension (i.e., depth of phenomenon rather than depth of the seafloor, see Duffy and Chown, 2017). It is time to recognize that in order to improve the representation of marine habitats, establishing or predicting their spatial extent and distribution may not be enough (Spalding et al, 2016).…”

Section: Data Selection and Fitness For Usementioning

confidence: 99%

On the Use of Maps and Models in Conservation and Resource Management (Warning: Results May Vary)

Lecours

2017

Front. Mar. Sci.

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Conservation planning and management typically require accurate and spatially explicit data at scales that are relevant for conservation objectives. In marine conservation, these data are often combined with spatial analytical techniques to produce marine habitat maps. While marine habitat mapping is increasingly used to inform conservation efforts, this field is still relatively young and its methods are rapidly evolving. Because conservation efforts do not always specify standards or guidelines for the production of habitat maps, results can vary dramatically. As representations of real environmental characteristics, habitat maps are highly sensitive to how they are produced. In this review paper, I present four concepts that are known to cause variation in spatial representation and prediction of habitats: the methodology used, the quality and scale of the data, and the choice of variables in regards to fitness for use. I then discuss the potential antinomy associated with the use of habitat maps in conservation: while habitat maps have become an invaluable tool to inform and assist decision-making, maps of the same area built using different methods and data may provide dissimilar representations, thus providing different information and possibly leading to different decisions. Exploring the theories and methods that have proved effective in terrestrial conservation and the spatial sciences, and how they can be integrated in marine habitat mapping practices, could help improve maps used to support marine conservation efforts and result in more reliable products to inform conservation decisions. Having a strong, consistent, transparent, repeatable, and science-based protocol for data collection and mapping is essential for effectively supporting decision-makers in developing conservation and management plans. The development of user-friendly tools to assist in the application of such protocol is crucial to a widespread improvement in practices. I discuss the potential to use interactive and collaborative Geographic Information Systems (GIS) to encourage the conservation and management community, from data collectors and mapmakers to decision-makers, to move toward a digital resilience and to develop such science-based protocol. Until standards and protocols are developed, habitat maps should always be interpreted with care, and the methods and metadata associated with their production should always be explicitly stated.

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“…Applied SDM studies to marine species (Duffy & Chown, 2017;Marshall et al, 2014;Robinson et al, 2011;Ross & Howell, 2013) may be also confronted with substantial limitations. Sampling bias, data availability, quality, and heterogeneous distribution are common issues (Guillera-Arroita et al, 2015;Robinson et al, 2011;Tessarolo, Rangel, Araújo, & Hortal, 2014).…”

Section: Introductionmentioning

confidence: 99%

Benthic species of the Kerguelen Plateau show contrasting distribution shifts in response to environmental changes

Guillaumot

Fabri‐Ruiz

Martin

et al. 2018

Ecology and Evolution

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Marine life of the Southern Ocean has been facing environmental changes and the direct impact of human activities during the past decades. Benthic communities have particularly been affected by such changes although we only slowly understand the effect of environmental changes on species physiology, biogeography, and distribution. Species distribution models (SDM) can help explore species geographic responses to main environmental changes. In this work, we modeled the distribution of four echinoid species with contrasting ecological niches. Models developed for [2005–2012] were projected to different time periods, and the magnitude of distribution range shifts was assessed for recent‐past conditions [1955–1974] and for the future, under scenario RCP 8.5 for [2050–2099]. Our results suggest that species distribution shifts are expected to be more important in a near future compared to the past. The geographic response of species may vary between poleward shift, latitudinal reduction, and local extinction. Species with broad ecological niches and not limited by biogeographic barriers would be the least affected by environmental changes, in contrast to endemic species, restricted to coastal areas, which are predicted to be more sensitive.

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Explicitly integrating a third dimension in marine species distribution modelling

Cited by 46 publications

References 32 publications

Dynamic occupancy modeling of temperate marine fish in area‐based closures

Dynamic occupancy modeling of temperate marine fish in area‐based closures

On the Use of Maps and Models in Conservation and Resource Management (Warning: Results May Vary)

Benthic species of the Kerguelen Plateau show contrasting distribution shifts in response to environmental changes

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