Natural variation of physical-habitat conditions among least-disturbed streams of a neotropical river basin in Brazil

The determination of natural variation in physical habitat conditions and the establishment of least-disturbed reference standards is important for ecosystem conservation. Tropical regions hold most of the global freshwater diversity, nevertheless little is known about the natural conditions of their physical habitats. We calculated 255 physical habitat metrics for 31 stream sites in five protected areas of the Brazilian São Francisco River basin to identify the most variable characteristics among tropical streams in least-disturbed areas. We performed principal components analyses (PCA) to find the most relevant metrics for ordination of streams in the following categories: water quality (2); substrate (7); fish shelter (6); riparian vegetation (9); and channel morphology (7). We used distance-based linear models (DISTLM) to test how much of the variation of these metrics could be explained by geographic position, average elevation, and average discharge of stream sites. The best statistically significant models explained 42% of substrate (33% geographic position; 9% average elevation), 26% of channel morphology (22% geographic position; 4% average discharge), 23% of water quality (14% geographic position; 9% average discharge), 17% of fish shelter (9% geographic position; 8% average elevation), and 14% of riparian vegetation (7% geographic position; 7% average elevation) variation. Thus, regional features (e.g. geology and climate) related to the geographic position are of greatest importance, followed by average elevation and discharge for determining physical habitat characteristics. Therefore, we suggest that reference sites should be set for tropical streams in the same regional landscape and with similar average elevation and discharge.