Yangtze finless porpoise (Neophocaena asiaeorientalis) prey fish diversity based on environmental DNA metabarcoding

Abstract Knowledge of the feeding habits of the Critically Endangered Neophocaena asiaorientalis (Yangtze finless porpoise, YFP) is vital for the management and protection of this species. However, stringent protections implemented in 2020 dictate that only non‐invasive methods may be used to gain information. Therefore, environmental DNA (eDNA) metabarcoding was used to obtain YFP prey diversity and community structures from different environmental samples collected from YFP habitat in April 2021. Sampling strategies for using eDNA to monitor the YFP were explored. Of the 63 fish species detected, more species were detected in samples from surface water than in samples from deeper water and sediment, but the diversity and community structures of fish in the samples from surface water, deeper water, and sediment did not significantly differ. The number of YFP sequences in the main lake area of Poyang Lake was significantly higher than that in other sampling areas. The YFP sequence number, operational taxonomic unit (OTU) number, and OTU occurrence frequency in surface water samples were higher than those in deeper water samples. Eighteen previously verified species of YFP prey fishes were detected, with more species detected in water samples than in sediment samples. The sequence numbers of the YFP and their prey fishes Ctenopharyngodon idella , Pseudolaubuca engraulis , and Tachysurus argentivittatus were significantly positively correlated, indicating that YFP preferentially selected these three species. Surface water samples yielded good results for the convenient and non‐invasive eDNA metabarcoding method of monitoring the feeding habits of this flagship species and for identifying early signals of YFP responses to changes in prey fish communities. The creation of critical conservation areas, eDNA monitoring standards, and emergency rescue plans are vital for YFP conservation.