Effects of longitudinal and lateral stream channel complexity on native and non‐native fishes in an invaded desert stream

Summary Understanding how habitat heterogeneity influences the structure of communities has been a longstanding goal of ecologists. Identifying how stream channel complexity affects fishes will be particularly important in systems simplified by anthropogenic activities and encroachment of non-native riparian vegetation. Here, we assessed how large-scale longitudinal distribution of lateral stream channel complexity from anthropogenically channelised, naturally braided and canyon-bound reaches of the San Juan River in New Mexico and Utah, U.S.A., correlated with species richness, evenness and the relative abundance of small-bodied native and non-native fishes. We also contrasted fish assemblages at a smaller scale, in the most laterally complex reach of the river, by comparing fish assemblages between primary channel and secondary channel habitats as well as in newly restored secondary channels. Rarefied fish species richness was generally highest in the braided reach of the river and the longitudinal distribution of total fish densities varied temporally. Contrary to our predictions, native fish densities were highest in the most upstream and anthropogenically channelised reach of the river. Non-native fish densities tended to be highest in the downstream braided reach, and all fishes were sparse in the least complex canyon-bound reach. Total fish densities were higher in secondary channels compared with primary channels, and non-native fishes were responsible for this difference. Fish assemblages in recently restored secondary channels were generally similar to those in naturally occurring ones. Our results suggest that lateral channel complexity can facilitate greater species richness at larger scales and is likely to provide habitats for fishes that are rare or not found in larger primary channels. These findings also suggest reduced channel complexity may lower the ability of riverine systems to support diverse fish assemblages.