Statistical analyses
Statistical analyses were performed based on the results of the OTU
clustering and species composition analyses. Sequences with an OTU
threshold < 10 were discarded. OTUs with an identity value of
≥ 99% and an E-value of ≥ 10−5 were screened and the
OTUs from the same species were combined. If an OTU could not be
compared at the species level, statistics were created at the next
level, such as genus or family. Microsoft Excel was used to determine
the proportion of valid sequences for each fish sample.
The Shannon-Wiener diversity index (H), Pielou uniformity index (J),
richness index, and Simpson Dominance Index (D) were used to assess
community diversity. To explore the differences or similarities in
community composition between different groups of samples, the number of
OTUs was used to calculate the Bray-Curtis distance measure matrix for
nonmetric multidimensional scaling (NMDS), permutational multivariate
analysis of variance (PerMANOVA), and analysis of similarities (ANOSIM).
Additionally, the relationship between environmental factors and
community composition was investigated using canonical correspondence
analysis (CCA). Pearson correlation analyses were used to investigate
the influence of environmental and human factors on the species richness
index.
All analyses were conducted using R v2.5.6, with the vegan package used
for NMDS, PerMANOVA, ANOSIM, and diversity index calculations. The
Pacman package was used for the Pearson correlation analysis of
environmental factors, whereas diversity index boxplots were generated
using the Amplicon package. ANOVA was performed using Perim (v9.1.0)
software. The GAMs were implemented using the function “gam” with the
default settings in the R package “mgcv.”