2.4 Community diversity and composition
We used the eight taxonomic subsets (arthropod orders) of ASVs to
conduct analyses of community diversity and composition among sampling
sites, considering haplotypes (raw ASVs) and all CLs (0.5%, 1.5%, 3%,
5% and 7.5% lineages, plus that corresponding to the GMYC species
delimitation. We first estimated total accumulation richness curves for
multiple levels of genetic similarity (AVS, 3% and 5% CL) using the R
package betapart(Baselga & Orme,
2012). Then we tested for significant differences in alpha diversity
among communities by performing ANOVAs with post-hoc.kruskal (method
Bonferroni).
Total beta diversity (Sorensen index, βsor ),
additive turnover (Simpson index, βsim ; species
replacement, without the effect of variation in richness) and nestedness
(Sorensen–Simpson index, βsne ; pure richness
effect) components were then estimated based on community compositions
at different hierarchical levels. We used the R packagevegan (Oksanen
et al., 2019) and community composition matrices to perform
non-parametric multidimensional scaling ordination (NMDS) based on
Sorensen similarity. Plots were created with the ordispideroption to visualise the compositional ordination of the communities
among sites. We then compared arthropod communities composition between
sites with an analysis of similarity (ANOSIM) test for each taxonomic
group. ANOSIM is a non-parametric analogue for analyzing variance and
testing multivariate differences between groups, based on a resemblance
matrix and rank dissimilarity
(Clarke, 1993). Plots
were made in R using package ggplot2(Wickham et al.,
2020).