Hydrodynamics and spatial separation between two clades of a copepod species complex

•We successfully compared modelled drifter trajectories to real drifter trajectories.•We computed finite-time Lyapunov exponents (FTLEs).•A ridge of high FTLE values separates two different Eurytemora affinis clades.

The purpose of this study was to explore the importance of hydrodynamics in the spatial distribution of a dominant calanoid copepod, Eurytemora affinis, in the middle St. Lawrence Estuary. To do this, we used a 3D numerical model of the region. We successfully compared modelled trajectories to real trajectories obtained from surface drifters. Multiple trajectories were then generated to compute finite-time Lyapunov exponents (FTLEs). A ridge of high FTLE values, which starts downstream close to the shoal between Île-aux-Coudres and Ste-Anne's Bay and reaches its upstream extremity on the south shore near Montmagny, separates two groups of modelled particles. This ridge seems to separate two distinct water masses that will not mix together. It appears 1 h after high tide and is persistent for 3 to 4 h during every ebb tide, suggesting that hydrodynamics is an important factor maintaining the separation between the two genetically different E. affinis clades.