A large wild salmon stock shows genetic and life history differentiation within, but not between, rivers

Anadromous salmonid fishes frequently exhibit strong geographic population
structuring. However, population genetic differentiation of Atlantic
salmon (Salmo salar) at fine geographic scales differs across equivalent
spatial extents in different regions. So far, fine-scale genetic
differentiation has not been assessed in rivers of the Baltic Sea, a
region that contains an evolutionarily distinct Atlantic salmon lineage.
Thus, Baltic salmon are currently managed on the river level, without
focus on potential genetic structure and diversity within rivers. Here, we
used microsatellites to characterize the genetic structure of wild
juvenile salmon sampled throughout the interconnected, northern Baltic
Tornio and Kalix Rivers. We found genetic differentiation within the two
rivers, but not between them: salmon in the upper reaches differed from
individuals in the lower reaches, regardless of river system. Further,
examining smolts migrating from the river to the sea and adults returning
from the sea to spawn, we found an association between the genetic
structure and seasonal migration timing. Out-migrating smolts genetically
assigned to upper river reaches were older and tended to reach the sea
later in the season than smolts from the lower reaches. In contrast,
mature adults originating from the upper reaches returned to the river
early in the season. Our observation of genetic population structuring
between downstream and upstream reaches of the large Tornio and Kalix
rivers, and its association with migration timing, implies that careful
temporal management of the northern Baltic fisheries would help to
preserve the diversity and sustainability of the wild salmon stocks of
these rivers.