Table 2.
Taxonomic composition of OTUs for single sites compared with plant survey data
| Method | Level | Imperfect_matches | Recaptured species | Unregistered species | Redundant species | Lost species |
|---|---|---|---|---|---|---|
| CROP | 98% | 0.56 ± 0.16/0.50 ± 0.17 | 0.31 ± 0.13/0.34 ± 0.13 | 0.12 ± 0.11/0.13 ± 0.12 | 0.02 ± 0.05/0.02 ± 0.06 | 0.00 ± 0.01 |
| CROP | 97% | 0.80 ± 0.13/0.79 ± 0.13 | 0.13 ± 0.11/0.14 ± 0.11 | 0.06 ± 0.10/0.07 ± 0.10 | 0.00 ± 0.00/0.00 ± 0.00 | 0.00 ± 0.00 |
| CROP | 95% | 0.87 ± 0.09/0.86 ± 0.09 | 0.09 ± 0.09/0.10 ± 0.09 | 0.04 ± 0.09/0.04 ± 0.09 | 0.00 ± 0.00/0.00 ± 0.00 | 0.00 ± 0.00 |
| DADA2 | 100% | 0.66 ± 0.12/0.40 ± 0.14 | 0.22 ± 0.10/0.43 ± 0.16 | 0.08 ± 0.07/0.14 ± 0.11 | 0.03 ± 0.03/0.03 ± 0.05 | 0.02 ± 0.04 |
| DADA2( + VS) | 98.50% | 0.51 ± 0.15/0.29 ± 0.14 | 0.36 ± 0.14/0.54 ± 0.17 | 0.11 ± 0.08/0.16 ± 0.12 | 0.01 ± 0.03/0.02 ± 0.05 | 0.02 ± 0.09 |
| DADA2( + VS) | 98% | 0.48 ± 0.16/0.29 ± 0.14 | 0.38 ± 0.15/0.54 ± 0.15 | 0.12 ± 0.09/0.16 ± 0.12 | 0.01 ± 0.03/0.01 ± 0.03 | 0.02 ± 0.09 |
| DADA2( + VS) | 97% | 0.46 ± 0.16/0.29 ± 0.14 | 0.40 ± 0.14/0.53 ± 0.15 | 0.13 ± 0.09/0.16 ± 0.12 | 0.01 ± 0.03/0.02 ± 0.04 | 0.01 ± 0.03 |
| DADA2( + VS) | 96% | 0.42 ± 0.16/0.27 ± 0.14 | 0.43 ± 0.15/0.55 ± 0.16 | 0.13 ± 0.1/0.16 ± 0.12 | 0.01 ± 0.02/0.01 ± 0.03 | 0.01 ± 0.03 |
| DADA2( + VS) | 95% | 0.39 ± 0.16/0.25 ± 0.14 | 0.45 ± 0.17/0.56 ± 0.17 | 0.15 ± 0.1/0.19 ± 0.12 | 0.00 ± 0.02/0.00 ± 0.02 | 0.01 ± 0.03 |
| SWARM | 99% | 0.80 ± 0.15/0.32 ± 0.12 | 0.11 ± 0.10/0.46 ± 0.14 | 0.05 ± 0.05/0.19 ± 0.10 | 0.03 ± 0.03/0.03 ± 0.05 | 0.02 ± 0.05 |
| SWARM | 98.50% | 0.74 ± 0.16/0.29 ± 0.11 | 0.15 ± 0.11/0.48 ± 0.13 | 0.08 ± 0.07/0.22 ± 0.10 | 0.03 ± 0.04/0.01 ± 0.02 | 0.02 ± 0.05 |
| SWARM | 98% | 0.69 ± 0.17/0.26 ± 0.12 | 0.18 ± 0.11/0.49 ± 0.14 | 0.10 ± 0.08/0.24 ± 0.11 | 0.03 ± 0.03/0.01 ± 0.03 | 0.03 ± 0.05 |
| SWARM | 97% | 0.66 ± 0.17/0.25 ± 0.12 | 0.20 ± 0.11/0.48 ± 0.14 | 0.12 ± 0.09/0.27 ± 0.11 | 0.02 ± 0.03/0.00 ± 0.01 | 0.03 ± 0.05 |
| SWARM | 96% | 0.65 ± 0.17/0.25 ± 0.12 | 0.20 ± 0.11/0.49 ± 0.14 | 0.13 ± 0.09/0.27 ± 0.11 | 0.02 ± 0.03/0.00 ± 0.01 | 0.03 ± 0.05 |
| SWARM | 95% | 0.55 ± 0.17/0.24 ± 0.11 | 0.27 ± 0.13/0.48 ± 0.16 | 0.16 ± 0.10/0.28 ± 0.13 | 0.02 ± 0.04/0.00 ± 0.01 | 0.05 ± 0.08 |
| VSEARCH | 98.50% | 0.85 ± 0.09/0.43 ± 0.14 | 0.10 ± 0.07/0.42 ± 0.15 | 0.04 ± 0.03/0.14 ± 0.09 | 0.01 ± 0.02/0.01 ± 0.04 | 0.02 ± 0.05 |
| VSEARCH | 98% | 0.80 ± 0.12/0.41 ± 0.16 | 0.13 ± 0.09/0.44 ± 0.16 | 0.05 ± 0.05/0.15 ± 0.09 | 0.02 ± 0.02/0.01 ± 0.03 | 0.02 ± 0.05 |
| VSEARCH | 97% | 0.70 ± 0.14/0.39 ± 0.15 | 0.21 ± 0.11/0.45 ± 0.14 | 0.08 ± 0.06/0.15 ± 0.10 | 0.02 ± 0.03/0.01 ± 0.03 | 0.02 ± 0.04 |
| VSEARCH | 96% | 0.64 ± 0.14/0.36 ± 0.14 | 0.25 ± 0.11/0.47 ± 0.14 | 0.09 ± 0.07/0.16 ± 0.10 | 0.02 ± 0.03/0.01 ± 0.03 | 0.01 ± 0.03 |
| VSEARCH | 95% | 0.60 ± 0.14/0.36 ± 0.14 | 0.28 ± 0.11/0.47 ± 0.15 | 0.10 ± 0.07/0.16 ± 0.10 | 0.02 ± 0.03/0.00 ± 0.01 | 0.01 ± 0.03 |
Effect of curation on the taxonomic composition of single sites for OTU tables produced with different clustering methods at several levels. Values before the slash are values prior to curation with LULU. Values after the slash are post-curation values. Values are average proportions for single sites (given with standard deviations). Imperfect matches are calculated as the proportion of OTUs for each site that have a less than 100% reference database match. Recaptured species are calculated as the proportion of OTUs with a perfect reference database match and a unique taxonomic annotation corresponding to a plant species recorded for the site. Unregistered species are calculated as the proportion of OTUs with a perfect reference database match and a unique taxonomic annotation corresponding to a plant species not recorded for the site. Redundant species are calculated as the proportion of OTUs with a perfect reference database match and a redundant taxonomic annotation (i.e., already represented by a recaptured or unregistered species). Lost species is the proportion of the recaptured species lost during curation