This PDF file includes:

• Fig. S1. Names, sampling effort, and longitudinal position of the 97 sub-basins.
• Fig. S2. Principal water quality of major subdrainages within the Amazon basin.
• Fig. S3. Delimitation of the Pebas lake ∼23 to 10 Ma ago and Purus Arch.
• Fig. S4. Surfaces of the current Amazon basin covered by seawater under 25- and 100-m sea-level rises.
• Table S1. Environmental predictors used to explain fish diversity and endemism in the Amazon basin.
• Table S2. Correlation coefficients among input variables and components for each of the PCAs performed.
• Table S3. Coefficients and SEs from the GLMs performed for total and endemic richness.
• Table S4. Coefficients and SEs (log link scale) from the GLMs for the richness of each of the 15 most abundant families (raw data).
• Table S5. Coefficients and SEs (log link scale) from the GLMs for species richness estimated from SDMs of each of the 15 most abundant families.
• Table S6. Families, genera, and number of species found exclusively west and east of the Purus Arch.

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