Sample collection
The São Francisco River Basin harbors at least 205 fish species (Alves et al., 2007), making it an excellent challenge for testing the sensibility and resolution of different markers within such complex Neotropical ichthyofauna. Thirty ichthyoplankton samples were used, denoted SF01 to SF30, 22 composed of eggs and eight composed of larvae. The larvae samples were assembled with similar-sized fragments of all specimens to minimize bias due to larvae size and relative read abundance estimative of input DNA from each pool.