DOI: 10.5061/dryad.z08kprrcv
title: COI Leray fragment of adult and juvenile spiders

description: Biodiversity loss is a major problem at the global scale, so
 bioinventories and monitoring samplings are essential to identify and
 tackle threats to biodiversity. Arthropods are usually misrepresented in
 these inventories, despite being the largest component of animal
 diversity. This is mainly due to the difficulty of identification in some
 arthropod groups, such as spiders, which can only be morphologically
 identified to species level at adult stages. Thus, juvenile spiders are
 usually discarded during sorting despite representing around half of the
 specimens, but the impact this has on community-level diversity estimates
 is still unknown. Here, we use a metabarcoding approach to assess the
 contribution that juvenile stages of spiders collected across the Iberian
 Peninsula have on diversity estimates, and their effect on diversity
 patterns across communities. We also compare the proportion of reads and
 the abundance of each family in the samples to assess the quantitative
 power of metabarcoding. The total number of species obtained as adults and
 juveniles was 363 and 331, respectively, with species found exclusively as
 juveniles representing an increase of 35% with respect to those found as
 adults. We observed that the differences in community composition between
 spider communities, especially the differences between communities at
 different latitudes, are greatly reduced when information about immature
 stages is taken into account. The proportion of reads obtained from
 metabarcoding for certain spider families was positively related to their
 proportion in weight and abundance in the sample, although the intensity
 of this relation was not constant across families. This suggests that
 metabarcoding data are to a certain extent quantitative. These findings do
 not question the information provided by adult-based inventories, but add
 a novel yet relevant layer of knowledge previously overlooked that may
 influence some of the interpretations derived from biological inventories.
description: For adult spiders: Legs of spiders were used
 for DNA extraction (more information about the specimens in Crespo et al,
 2018). Total genomic DNA was extracted using the REDExtract-N-Amp™ Tissue
 PCR Kit Protocol from Sigma-Aldrich, following the manufacturer’s protocol
 and performed in 96 well-plates. We amplified the mitochondrial cytochrome
 c oxidase (COI). The LCOI1490/ HCO2198 was the preferred combination of
 primers, while Nancy was used as a replacement for HCOI2198 and Ron as
 replacement for LCOI1490 (in that order). For problematic amplifications,
 we used the internal primers mlCOIintF/jgHCOI2198. The polymerase chain
 reaction (PCR) was performed in 96-well plates using 8 µl
 REDExtract-N-Amp™ PCR ReadyMix from Sigma-Aldrich, primers forward and
 reverse, 4 µl of diluted DNA and ultrapure, distilled water up to a total
 reaction volume of 20 µl. PCR products were cycle-sequenced in both
 directions at Macrogen Inc. (Seoul, South Korea). We trimmed the sequences
 to keep only the Leray 313 bp fragment. For juvenile
 spiders: We homogenised all the collected immature
 spiders with the help of liquid nitrogen. We obtained two extraction
 replicates from each homogenised plot sample, and we extracted a fraction
 of 0.3 g from each replicate using a PowerSoil DNA Isolation Kit (QIAGEN,
 Valencia, CA, USA). We used Leray-XT primers to amplify the Leray 313 bp
 fragment of mitochondrial cytochrome c oxidase (COI) and sequenced it in
 an Illumina Miseq V3 2x250 bp. OBITools were used for paired-end assembly,
 demultiplexing and quality control. Chimeras were removed with
 uchime_denovo in VSearch. Swarm 2.0 with d=13 was used for clustering
 MOTUs. Ecotag was used for taxonomic assignment using custom reference
 databases for the COI Leray region. LULU was used for removing
 supernumerary MOTUs arising from pseudogenes. Singleton MOTUs were
 removed.
description: # COI Leray fragment of adult and juvenile spiders
 [https://doi.org/10.5061/dryad.z08kprrcv](https://doi.org/10.5061/dryad.z08kprrcv) The dataset includes two fasta files, "Adults.fasta" and "Juveniles.fasta". The file "Adults.fasta" contains all the Cytochrome c Oxidase 1 (COI) sequences obtained from adult specimens, which were obtained by Sanger sequencing a variable number of legs. The "Juveniles.fasta" file contains all COI sequences obtained from metabarcoding analyses applied to bulk samples of juvenile specimens. All the reads obtained were clustered into MOTU's, which were taxonomically assigned to the deepest possible level. ## Description of the data and file structure Both files are in fasta format. The headers of the Adults.fasta file include the individual code of the specimen (MD-); the number of reads that were artificially included in the analyses of each sequence (count=50000); the taxonomy identifier (taxid) of each species in NCBI; the order name and associated numeric code; and the species name. The headers of the Juveniles.fasta file include the code of each MOTU (progressive numbers starting with the code MDOM); the samples were the MOTU was found and the number of reads in each; the total number of reads; and a progressive rank number (seq_rank). ## Sharing/Access information The original article associated to this data can be found here: https://onlinelibrary.wiley.com/doi/full/10.1111/1755-0998.13625