Habitat variability and the individual variability of juvenile Atlantic salmon (Salmo salar)

Spatiotemporal flow variability contributes to create a dynamic habitat mosaic sustaining ecological diversity. One of the most important topics in ecohydraulic research is to identify the relevant scales of flow variability affecting organisms at different life stages. The general objective of the thesis is to examine the links between habitat variability and the behaviour of juvenile Atlantic salmon. More specifically, three themes are addressed: turbulence as a fish habitat variable, the spatial and temporal scales of habitat selection and individual variability in fish behaviour. Through detailed field measurements incorporating a variety of sampling techniques and statistical analyses our objectives were to: 1) Quantify the causal links between standard habitat variables and flow turbulence at multiple scales; 2) Test a new in situ portable flume to analyse the effect of turbulent flow properties on the prey capture probability and foraging behaviour of juvenile Atlantic salmon; 3) Analyse the spatial and temporal scale dependence of fish-habitat associations within a reach during the summer and autumn; 4) Examine individual variation of seasonal and daily activity patterns and habitat use and their interaction; 5) Investigate the individual variation in seasonal daily movement behaviour in relation to environmental fluctuations.  The thesis provides a detailed characterization of turbulence in pools and riffles and showed that the capacity of ‘standard’ fish habitat variables to explain turbulent properties was relatively low, especially at smaller spatial scales, but varied greatly between the units. From a practical point of view, this level of complexity suggested that turbulence should be considered as a ‘distinct’ ecological variable within this range of spatial scales. In a second experiment, using an in situ portable flume and underwater videotaping of fish, we did not conclusively confirm or rule out the effect of turbulence on prey capture probability, but observed a preferential selection of locations where flow velocity was downward and turbulence intensity was lower. The selection of lower turbulence habitat was also observed in natural habitat conditions in an observational field study, in which 66 PIT-tagged fish were tracked for three months in a river reach using a high resolution network of antennas buried in the bed.   Juvenile salmon habitat selection was dependant on the scale of observations. Fish were associated with moderate depth micro-scale habitats, but also with higher depth patch-scale habitats. Furthermore, the range of habitat used by individuals increased asymptotically with the temporal scale. The scale of one hour was considered as optimal to describe the range of habitats used in a day and three days optimal to describe the range of habitat used in a month.  Individual tracking revealed high inter-individual variability in activity patterns, as some individuals were predominantly nocturnal whereas others frequently changed their daily activity pattern. Changes in activity patterns were linked to environmental fluctuations, but also to individual habitat use patterns, which might signify that lower quality habitats require fish to increase daytime activity when food intake and the risk of predation are both high. High inter-individual variability was also observed in the fish movement behaviour. It appeared that most fish exhibited low mobility on most days, but also showed occasional bouts of high mobility. Between-individual variability accounted for only 12-17% of the variability in the mobility data. These results challenge the assumption of a population composed of a sedentary and mobile fraction. Individual variation on a daily basis suggested that movement behaviour is a response to changing environmental conditions rather than an individual behavioural trait.

Keyphrases: Rivers, Habitats, Salmon, Scales, Turbulence, Turbulence, Mobility, Activity cycles, Habitat use, fish