4.2 Appropriate threshold of taxonomic classification for
evaluating fish diversity
Compared with aquatic invertebrates, fish have more comprehensive DNA
information in the gene bank, and thus, using eDNA metabarcoding to
distinguish fish diversity has broad application prospects. Wang et al.
(2023) suggested that in complex habitats, such as fresh and brackish
converging lakes, analysing the invertebrate composition or diversity at
the phylum or class level (at least to family) is effective enough to
reflect the environmental properties. The great difference between eDNA
usefulness for fish and invertebrates is the structure of primary
taxonomic units, which is much simpler for fish than for invertebrates.
At the class or order level, different invertebrate assemblages had
totally different ecological properties (e.g., freshwater vs. brackish
or littoral vs. limnetic); however, for fishes, order-level
identification could not distinguish the habitat-specific ecological
properties. Thus, according to our results, we recommend that an
appropriate threshold for eDNA-based fish monitoring is at the genus or
species level, which could be further chosen according to the monitoring
or research targets. For example, if users focus on the influence of
environmental changes on fish community structure, genus-level
identification with eDNA is effective; if users focus on the fish
distribution, species-level identification might be favourable.