Summer Occurrence of Early-Life Fishes in the Midstream Xijiang River: A Post-Commissioning COI Barcoding Baseline

Accurate identification of early-life fishes (eggs and larvae) is important for understanding recruitment and supporting fisheries management in regulated rivers. We monitored early-life fish assemblages in the Xunjiang reach of the midstream Xijiang River during May–August in 2024 and 2025 after the Datengxia Water Conservancy Project began operating, collecting 97,934 specimens. Stratified cytochrome c oxidase subunit I (COI) DNA barcoding yielded 2960 high-quality sequences (98.27% success rate), resolving 69 taxonomic units across 52 genera and 14 families, with a representative sequence subset audited using maximum-likelihood and Bayesian inference phylogenies. Cyprinidae accounted for 92.30% of the analyzed barcodes, with Squaliobarbus curriculus frequently represented. The survey recorded all Four Major Chinese Carps, Elopichthys bambusa, Ochetobius elongatus, and rheophilic benthic fishes such as Garra orientalis and Sinogastromyzon wui. Early-life stages of Cirrhinus mrigala, Labeo gonius and tilapias were also detected. Volume-standardized generalized additive models of the 2025 field counts showed associations of egg and larval densities with discharge and pronounced nonlinear seasonality for larvae. These findings provide monitoring data for fishery resource management and ecological flow assessment in the midstream Xijiang River.