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Brown trout (Salmo trutta L.) population genetic structure and its temporal stability were studied within a small forest stream in central Sweden using five microsatellite loci. Both resident and migrating brown trout are present in the watershed. Tissue samples were collected from seven sections of the stream during two consecutive years. No differences were found in multilocus FST estimates between years within sections except in one case. Moreover, differences between age cohorts within sample sections were rare. The low interannual variation and the low heterogeny between cohorts is interpreted as indications of temporal stability. Pairwise multilocus FST estimates increased with increasing geographic distance, indicating isolation by distance. It is argued that the brown trout of the Farsan stream represent a population complex. The structure is probably maintained by precise natal homing and a limited, but important, amount of gene flow between closely situated sections within the stream supporting a stepping-stone model of gene flow.