Estimates of α and β diversity at ASV and OTU levels
The resulting fully-filtered ASVs were clustered into operational
taxonomic units (OTUs) based on patristic pairwise distances, using a
threshold of 3% genetic divergence, which is commonly applied on
arthropod COI metabarcoding datasets (Dopheide et al., 2019; Yu et al.,
2012). Patristic distances were calculated based on a UPGMA tree,
reconstructed using F84 model-corrected pairwise distances and a
mafft FFT-NS-i alignment (Katoh & Standley, 2013). These
analyses were conducted using the adegenet (Jombart, 2008), phangorn (Schliep, 2011) and ape (Paradis & Schliep,
2019) packages in R (R Core Team, 2020).
Using the ASV and OTU datasets, we calculated α diversity for each soil
layer, sampling site and habitat type. We also calculated community
dissimilarity among sampling sites and between soil layers using the
Sørensen index (βSOR), which we decomposed in its
additive components (Simpson dissimilarity index or spatial turnover
without the effect of variation in richness, βSIM, and
nestedness, βSNE; Baselga, 2010). Then, we used these
community dissimilarity matrices to calculate the local contribution to
β diversity (LCBD), a comparative indicator of the uniqueness of each
sample in terms of community composition (Legendre & De Cáceres, 2013).
We calculated the above diversity metrics using the betapart (Baselga & Orme, 2012) and adespatial (Dray et al., 2020) R packages.