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

Habitat fragmentation is a pervasive threat to biodiversity. Linearly arranged habitats such as stream networks are particularly vulnerable to fragmentation. As the landscape becomes increasingly human dominated, conservation values of fragmented habitat patches cannot be overlooked. It is critical to understand the demographic mechanisms of population persistence or extirpation in fragmented patches. We studied dynamics of spatially structured populations of two Japanese landlocked salmonids persisting for >30 years in a headwater stream network that is highly fragmented due to low‐head dams in the mainstem. We parameterised and analysed spatial matrix population models using 9‐year mark–recapture data. Tributaries supported higher survival rates in some life stages, and movement was asymmetrical from the tributaries to the mainstem. Accordingly, population growth rates were higher in the tributary patches than the mainstem in both species despite the tributaries occupying only 12% or 18% of the study stream network by surface area. The tributaries harboured more physically and hydraulically complex instream habitats (i.e. higher wood density and flow refugia), indicating that habitat patch quality was more important than habitat patch size in determining the dynamics of these spatially structured populations. Tributary locations in the stream network were important in the trajectory of these populations. The upstream‐dwelling charr persisted in the highly fragmented mainstem patch (i.e. six impassable infrastructures in a