DOI: 10.5061/dryad.s4mw6m97c
title: Community metabarcoding reveals the relative role of environmental filtering and spatial processes in metacommunity dynamics of soil microarthropods across a mosaic of montane forests

description: Disentangling the relative role of environmental filtering and spatial
 processes in driving metacommunity structure across mountainous regions
 remains challenging, as the way we quantify spatial connectivity in
 topographically and environmentally heterogeneous landscapes can influence
 our perception of which process predominates. More empirical datasets are
 required to account for taxon- and context-dependency but relevant
 research in understudied areas is often compromised by the taxonomic
 impediment. We here employed haplotype-level community DNA
 metabarcoding, enabled by stringent filtering of Amplicon Sequence
 Variants (ASVs), to characterize metacommunity structure of soil
 microarthropod assemblages across a mosaic of five forest habitats on the
 Troodos mountain range in Cyprus. We found
 similar β diversity patterns at ASV and species (OTU,
 Operational Taxonomic Unit) levels, which pointed to a primary role of
 habitat filtering resulting in the existence of largely distinct
 metacommunities linked to different forest types. Within-habitat turnover
 was correlated to topoclimatic heterogeneity, again emphasizing the role
 of environmental filtering. However, when integrating landscape matrix
 information for the highly fragmented Quercus
 alnifolia habitat, we also detected a major role of spatial
 isolation determined by patch connectivity, indicating that stochastic and
 niche-based processes synergistically govern community assembly. Alpha
 diversity patterns varied between ASV and OTU levels, with OTU richness
 decreasing with elevation and ASV richness following a longitudinal
 gradient, potentially reflecting a decline of genetic diversity eastwards
 due to historical pressures. Our study demonstrates the utility of
 haplotype-level community metabarcoding for characterising metacommunity
 structure of complex assemblages and improving our understanding of
 biodiversity dynamics across mountainous landscapes worldwide.
description: <strong>Raster layers</strong><br>  <br>
 This ZIP folder contains the TIF files corresponding to the digital
 elevation model (“01_DEM” subfolder), six WorldClim layers (“02_WorldClim”
 subfolder), four ENVIREM layers (“03_ENVIREM” subfolder) and the spatial
 distribution of <em>Quercus</em>
 <em>alnifolia</em> patches (“04_Quercus_alnifolia” subfolder).
 This latter subfolder also contains input files (ASCII format) for
 CIRCUITSCAPE corresponding to the isolation-by-resistance (IBR) scenarios
 defined by (i) the distribution of <em>Quercus</em>
 <em>alnifolia</em> forest patches assuming increasing
 resistance values (from 5 to 1,000,000) for
 non-<em>Quercus</em> cells, (ii) the topographic complexity as
 estimated by the terrain roughness index (TRI) and (iii) a “flat” scenario
 (NULL) whose cells have a fixed resistance (=1) value. Geographic
 coordinates of <em>Quercus</em> <em>alnifolia</em>
 sampling sites are also provided in the format required by CIRCUITSCAPE.
 The WorldClim and ENVIREM layers were processed and interpolated at 90
 meters resolution as detailed in Supplemental Information.
 File: <em>0A_Raster_layers.zip</em>
 <strong>Community tables</strong><br>
  <br> Filtered community tables (taxa in rows, sites in columns)
 used for downstream analyses, at both ASV and OTU levels. Sampling site
 codes as in Table S1 in Supplemental Information. File:
 <em>0B_Community_tables.zip</em>
  <br> <strong>DNA sequences</strong><br>
  <br> Files in FASTA format containing DNA sequences of (a)
 fully-filtered ASVs derived from metabarcoding data and (b) Sanger
 sequences of ‘voucher’ specimens. File:
 <em>0C_DNAsequences.zip</em>  <br>
 <strong>GLMM input file</strong><br>  <br> Input
 file for Generalized Linear Mixed Models (GLMM), which were used to
 analyse the relationship between ASV- and OTU-based richness (RICH) or
 local contribution to beta diversity (LCBD) per site and the topoclimatic
 variables (ENV<sub>PC1</sub> and
 ENV<sub>PC2</sub>) as predictors, with latitude and longitude
 as covariates and forest habitat type as a random effect. Sampling site
 codes as in Table S1 in Supplemental Information. File:
 <em>01_GLMM.zip</em>  <br>
 <strong>PCNM input files</strong><br>  <br> This
 ZIP folder contains the topographic weighted distance matrices
 (SPA<sub>TWD</sub>) used as input files in Principal
 Coordinates of Neighbour Matrices (PCNM) analyses to generate spatial
 predictors, at across-habitats and within-habitat scales. Sampling site
 codes as in Table S1 in Supplemental Information. File:
 <em>02_PCNM.zip</em> <br>
 <strong>dbRDA input files</strong><br>  <br> This
 ZIP folder contains the input files used to perform Distance-Based
 Redundancy Analysis (dbRDA), at both across-habitats and within-habitat
 scales, including (a) the community dissimilarity matrices based on the
 Simpson dissimilarity index calculated at both ASV and OTU level, and (b)
 tables of spatial (SPA<sub>PCNMi</sub>) and environmental
 predictors (habitat type, ENV<sub>PC1</sub> and
 ENV<sub>PC2</sub>). Sampling site codes as in Table S1 in
 Supplemental Information.<br>  <br> File:
 <em>03_dbRDA.zip</em>  <br>
 <strong>mvGLM input files</strong> This ZIP
 folder contains the input files used to perform Multivariate Generalized
 Linear Models (mvGLMs), at both across-habitats and within-habitat scales,
 including (a) community tables (presence/absence) for both ASV and OTU
 level, and (b) spatial (SPA<sub>PCNMi</sub>) and environmental
 predictors (habitat type, ENV<sub>PC1</sub> and
 ENV<sub>PC2</sub>). Sampling site codes as in Table S1 in
 Supplemental Information.<br>  <br> File:
 <em>04_mvGLM.zip</em>  <br>
 <strong>MMRR and distance decay input files</strong><br>
  <br> This ZIP folder contains the input files used to perform
 Multivariate Matrix Regression with Randomization (MMRR), including (a)
 community dissimilarity matrices based on the Simpson dissimilarity index
 calculated at both ASV and OTU level for <em>Quercus</em>
 <em>alnifolia</em> sampling sites, and (b) distance matrices
 based on (i) resistance due to habitat fragmentation
 (FRA<sub>IBR</sub>) assuming increasing resistance values
 (from 5 to 1,000,000) for non-<em>Quercus</em> cells, (ii)
 resistance due to topographic complexity (TRI<sub>IBR</sub>),
 (iii) resistance due to a “flat landscape”
 (NULL<sub>IBR</sub>), (iv) weighted topographic (SPATWD)
 distances and (v) topoclimatic (ENV<sub>PC1-2</sub>)
 distances. Sampling site codes as in Table S1 in Supplemental
 Information. File:
 <em>05_MMRR-DistanceDecay.zip</em>