Sequencing results
We retrieved DNA barcodes of 368 out of the 376 species represented as
adults in the sampling plots. After the cleaning, filtering, and
chimaera removal process, the sequencing of juvenile pool samples
generated a total of 15,805,993 sequence reads and 3,839,513 unique
sequences. After manually adding the sequences of the adults, the Swarm
algorithm grouped all sequences in 4,668 non-singleton MOTUs, of which
140 contained exclusively adult artificial sequences. After the curation
process (retaining only Araneae, removing non-iberian taxa, and removing
artificially added adult sequences), the final dataset for juveniles
consisted of 9,956,432 reads distributed in 1,343 MOTUs. The process of
removing pseudogenes eliminated 455 MOTUs and left 888 final juvenile
MOTUs (final dataset in Table S2, Supporting information). The
sequencing of three of the four replicates of plot PM1 was unsuccessful
so we omitted these samples from subsequent analyses.
The steps involved in refining the taxonomic assignment of these MOTUs
(merging the species that were found to be indistinguishable by the
LERAY COI fragment, checking online genetic databases and the COI tree
to improve taxonomic assignments, and assigning the remaining unassigned
MOTUs to their best match in the reference library) assigned the 888
MOTUs to 524 different species. Filtering out MOTUs with less than 5
reads left 411 MOTUS that, when collapsed by their taxonomic assignment,
corresponded to 350 different species. Finally, considering only MOTUs
with at least 5 replicates in a plot and presence in at least 2 of its
replicates as present in that plot left 331 different species.
Rarefaction curves (Fig. S1, Supporting information) showed that almost
every plot reached a plateau in all or some of its replicates. The
exceptions were the only remaining replicate of PM1 and two of the
replicates of PS2, all of which yielded very low numbers of reads.