Fish Reproduction in the Middle and Lower Uruguay River as Detected by Molecular and Morphological Identification of Ichthyoplankton

The Uruguay River is one of two La Plata River Basin tributaries. The Salto Grande Dam limits the middle and lower sections of the river and impairs the upstream displacement of adult fish, but not the downstream passage of fish larvae. The presence of adult and larvae of migratory species up and downstream of the dam suggests they may reproduce in both river sections; however, the identification of their spawning areas warrants the use of molecular methods. This work used next generation sequencing DNA barcoding of mitochondrial cytochrome b from fish eggs and newly hatched larvae, as well as morphological identification of older larvae to detect migratory fish spawning from both river sections. All developmental stages of short‐distance migratory and resident fish accounted for most of the ichthyoplankton from both river sections. Eggs, newly hatched and older larvae of several long‐distance migratory fish were detected in the Middle Uruguay River; however, the absence of earliest developmental stages in the context of the potential larval passage through the dam, casts doubts on the occurrence or the magnitude of reproduction of these species in the Lower Uruguay River. The new impoundments proposed for the Middle Uruguay River will severely threaten the spawning areas of long‐distance migratory fish, which can lead to future conservation issues. Further research involving high spatial and temporal resolution sampling and molecular identification of fish eggs and newly hatched larvae is needed to identify the spawning areas of the most valued species in the Lower Uruguay River.