Small giants: Tributaries rescue spatially structured populations from extirpation in a highly fragmented stream

Abstract Habitat fragmentation is a pervasive threat to biodiversity. Linearly arranged habitats such as stream networks are particularly vulnerable fragmentation. As the landscape becomes increasingly human dominated, conservation values of fragmented habitat patches cannot be overlooked. It critical understand demographic mechanisms population persistence or extirpation in patches. We studied dynamics spatially structured populations two Japanese landlocked salmonids persisting for >30 years headwater network that highly due low‐head dams mainstem. parameterised and analysed spatial matrix models using 9‐year mark–recapture data. Tributaries supported higher survival rates some life stages, movement was asymmetrical from tributaries Accordingly, growth were tributary than mainstem both species despite occupying only 12% 18% study by surface area. The harboured more physically hydraulically complex instream (i.e. wood density flow refugia), indicating patch quality important size determining these populations. Tributary locations trajectory upstream‐dwelling charr persisted six impassable infrastructures <500 m patch) immigration fish upstream including tributary. However, downstream‐dwelling salmon has been gradually extirpated uppermost section because they could not maintain positive rate after loss emigrants accounted prevented Synthesis applications . conclude small have rescued (charr) at least slowed down (salmon). Legal protection headwaters aquatic weak globally. Our results suggest management plans underestimating value will likely fail conserve inhabitants therefore endanger discuss implications this related connectivity fisheries management.