Understanding immediate and carry-over effects to prioritise habitat protection and restoration: a case study of threatened Atlantic salmon

As habitat degradation threatens global biodiversity and conservation efforts are resource limited, maximising the effectiveness of habitat protection and thus restoration of wild populations is essential. For animals that occupy multiple habitats throughout their lifetime, understanding how the immediate (i.e., affecting a given life stage) and carry-over (i.e., affecting a subsequent life stage) effects of habitat quality impact their population dynamics could help prioritise effective habitat protection. Here, we use a bespoke integrated path analysis model that simultaneously accounts for effects of habitat characteristics, density-dependent regulation, and random effect structures, to draw inference from a case study dataset for the threatened diadromous fish, Atlantic salmon (Salmo salar). We show that higher quality growing habitat promotes greater young-of-year (YOY) body length by the end of the growing season that results in a subsequent higher probability of them surviving to be detected as seaward migrating juveniles. Further, these growing habitat characteristics, along with instream macrophyte cover, promote higher YOY abundance at the end of the growing season. Higher YOY abundance is associated with, on average, shorter YOY and a lower probability of subsequent survival, suggesting density-dependent processes are evident throughout these juvenile life stages. Our study demonstrates that detailed population and habitat monitoring data can be used to disentangle and quantify immediate and carry-over effects from myriad other regulatory processes. We postulate that such findings are useful to prioritise effective habitat management that maximises its beneficial (or minimises its detrimental) immediate and carry-over effects to different life stages of the target population.