Datasets supporting Leasi et al. Communications Biology

<div>This file includes 8 datasets used in Leasi et al. - Communications Biology. Title of the manuscript "Biodiversity estimates and ecological interpretations of meiofaunal communities are biased by the taxonomic approach".</div><div><br></div><div>We compare biodiversity assessments of a diverse meiofaunal community derived by applying multiple taxonomic methods based on comparative morphology, molecular phylogenetic analysis, DNA barcoding of individual specimens, and metabarcoding of environmental DNA. We show that biodiversity estimates are strongly biased across taxonomic methods and phyla. Such biases affect understanding of community structures and ecological interpretations. Samples were collected from 19 sites located in Panama.</div><div><br></div><div>Table S1. List of sampled locations and environmental parameters investigated. <br></div><div><br></div><div>Table S2. List of individuals and taxa collected and analyzed with the respective unique barcode voucher number. Each r18S sequence, entity revealed with GMYC, and OTU is associated to an ID code. Identical ID codes indicate identical r18S sequences, EEs, or OTUs. The same ID codes are shown in the phylogenetic trees. </div><div><br></div><div>Table S3. Operational taxonomic units of the seven focal phyla. Number of genetic reads is indicated for each sampled station. The phylogenetic trees are constructed considering the Sample-ID code. The last column indicates the percentage of blasting with the reference. The term “TREE” indicates that the taxonomy was obtained by reconstructed the phylogeny.</div><div><br></div><div>Table S4. Sequence variants of the seven focal phyla. Number of genetic reads is indicated for each sampled station. The phylogenetic trees are constructed considering the Sample-ID code. The last column indicates the percentage of blasting with the reference. The term “TREE” indicates that the taxonomy was obtained by reconstructed the phylogeny.</div><div><br></div><div>Table S5. Values of richness estimation obtained using Chao and Jackknife algorithms on morphotypes and sequence variants. </div><div><br></div><div>Table S6. Values of Jaccard dissimilarity based on incidence datasets measured within and between communities. </div><div><br></div><div>Table S7. Results obtained with PERMANOVA among all taxonomic methods and environmental parameters. </div><div><br></div><div>Table S8. Values of Phylogenetic Diversity (PD), Mean Phylogenetic Diversity (MPD), and Mean Nearest Taxon Distance (MNTD) measured for each phylum and sampled site. SR, species richness. </div

Supplemental Table 6

Values of Jaccard dissimilarity based on incidence datasets measured within and between communities. Identical = 0; completely dissimilar = 1. Abbreviations: MT, morphotypes; EE, evolutionary independent entities obtained with GMYC; OTU, operational taxonomic units obtained with single individuals; eOTU, operational taxonomic units obtained with environmental samples; SV, sequence variants. L, littoral; SL, sublittoral; O, offshore. Dissimilarity values were estimated using both the focal phyla (SV; eOTU) and whole meiofauna dataset (SV2; eOTU2)

Supplemental Table 8

Values of Phylogenetic Diversity (PD), Mean Phylogenetic Diversity (MPD), and Mean Nearest Taxon Distance (MNTD) measured for each phylum and sampled site. SR, species richness. <br

Supplemental Table 1

<div>List of sampled locations and environmental parameters investigated. Coordinates are indicated in decimal system. </div><div>Abbreviations: Lat, Latitude; Long, Longitude; MGS, mean grain size.</div

Supplemental Table 2

List of individuals and taxa collected and analyzed with the respective unique barcode voucher number. Each r18S sequence, entity revealed with GMYC, and OTU is associated to an ID code. Identical ID codes indicate identical r18S sequences, EEs, or OTUs. The same ID codes are shown in the phylogenetic trees. <br

Supplemental Table 4

Sequence variants of the seven focal phyla. Number of genetic reads is indicated for each sampled station. The phylogenetic trees are constructed considering the Sample-ID code. The last column indicates the percentage of blasting with the reference. The term “TREE” indicates that the taxonomy was obtained by reconstructed the phylogeny

Supplemental Table 5

Values of richness estimation (underlined) obtained using Chao and Jackknife algorithms on morphotypes (MT) and sequence variants (SV). The richness is estimated for each phylum and for the total sampled area. Actual richness identified with each method is shown for a direct comparison. Species were estimated using both the focal phyla (SV) and whole meiofauna dataset (SV2). “*” indicates phyla which richness estimated using metabarcoding is lower than number of actual morphotypes identified with morphological taxonomy.<br

Supplemental Table 3

Operational taxonomic units of the seven focal phyla. Number of genetic reads is indicated for each sampled station. The phylogenetic trees are constructed considering the Sample-ID code. The last column indicates the percentage of blasting with the reference. The term “TREE” indicates that the taxonomy was obtained by reconstructed the phylogeny

Supplemental Table 7

Results obtained with PERMANOVA among all taxonomic methods and environmental parameters. Community structures obtained with metabarcoding are analyzed on both a restricted dataset, namely the seven focal phyla (eOTU, SV) and totally (eOTU2, SV2). Significances among environmental parameters are underlined. *, significant correlation (p < 0.05); +, nearly significant correlation (0.05 < p < 0.1). Abbreviations: MT, morphotypes taxonomy; EE, evolutionary independent entities obtained with GMYC; OTU, operational taxonomic units obtained with single individuals; eOTU, operational taxonomic units obtained with metabarcoding; SV, sequence variants obtained with metabarcoding