3.2 The composition of fish communities at different taxonomic levels
The relative percentage of eDNA OTU richness showed that, at the order level (Fig. 3A), Cypriniformes, Cichliformes, Siluriformes, and Gobiiformes made up > 83% of the fish communities in the three rivers. At the family level (Fig. 3B), Cichlidae, Cultrinae, Cyprinidae, and Labeoninae made up > 56% of the fish communities in Zones II − VIII, whereas Cyprinidae, Oxudercidae, and Heteropteridae made up > 50% of the fish communities in Zone I. At the genus (Fig. 3C) and species levels (Fig. 3D), the composition of fish communities was dispersed and determined by different genera and species. Notably, except for zones I and II, where native Oryzias curvinotusand Hemiculter leucisculus had the highest OTU richness, respectively, exotic Coptodon zillii and Oreochromis aureus had the highest OTU richness in the other zones, indicating that the structure of fish communities in the middle and lower reaches was dominated by alien species. This result indicated that the eDNA metabarcoding protocol had advantages in discovering dominant species and exotic species.
The cluster analysis between the eight spatial zones showed that the order- and family-level grouping (Figs. 3A – 3B) was insufficient to distinguish the longitudinal differences in fish community composition from headwaters to the estuary. Compared with the order- and family-level grouping, the genus-level (Fig. 3C) grouping could more clearly distinguish the differences between upstream zones I − IV and downstream zones V − VIII. Moreover, the species-level grouping (Fig. 3D) was the most effective in distinguishing upstream zones I − III, midstream zones IV − V, and downstream zones VI – VIII. An interesting finding was that at the family level, upstream zone II and downstream zone VIII were clustered in the same group, which was caused by the widespread species of Cichlidae, Cultrinae, and Oxudercidae that could not be distinguished by family-level identification. In contrast, compared with the family level, the higher resolution at the genus and species levels could distinguish Coptodon and Oreochromis of Cichlidae as well as Hemiculter and Parabramis of Cultrinae, which were the key genera that distinguished fish distribution in the upper and lower reaches.