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

Abstract

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.

Harnessing environmental DNA to reveal biogeographical patterns of non-indigenous species for improved co-governance of the marine environment in Aotearoa New Zealand

“…These observed patterns were also largely supported by the occupancy model outputs. Occupancy models are increasingly used to refine detection probabilities 20 , 49 , support decision making around study designs and aid in spatial interpretation of eDNA-based species detections 50 – 53 . In the present study, predicted NIS eDNA occupancy values differed significantly between the pre-determined factor groups: harbor proximity and latitudinal gradient.…”