Dynamic occupancy modelling of temperate marine fish in area-based closures

Jay Calvert, C McGonigle, Suresh Sethi, Bradley Harris, Rory Quinn, Jonathan Grabowski

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1. 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 non-detection 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 sub-model to account for variability in detection rates. These have rarely been applied in the context of marine fish, and never for the multi-season dynamic occupancy model (DOM).

2. 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).

3. Modelled 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.

4. 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 non-physical, 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 in marine studies. This work highlights the use of modelled hydrodynamics as a tool to correct some of this imbalance.
Original languageEnglish
Pages (from-to)10192-10205
Number of pages14
JournalEcology and Evolution
Issue number20
Early online date21 Sept 2018
Publication statusPublished (in print/issue) - 29 Oct 2018


  • detectability
  • dynamic occupancy model
  • hydrodynamics
  • temperate marine fish


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