Datasets

This .zip files contains two folders. The folder "Control" contains the 15 raw 454 sequence files generated from the "Test Pools" analysis detailed in Table 2 of the manuscript, and a file of 27 Sanger sequences listed in Table S1. The folder "Tenerife" contains the 6 raw 454 sequence files associated generated from the "Tenerife Forest Samples" analysis detailed in Table 3 of the manuscript

Primers, MIDs, sequence formats and consensus reference sequence used in this study.

<p>ColFol-for ColFol-rev are the Sanger primers. 454-ColFol-for and 454-Col307-rev are the primers for mass amplification. Adaptors A and B are used by the ‘454’ sequencer to attach individual DNA molecules to microscopic beads, for subsequent sequencing. MIDs (Multiplex Identifiers) are 7 bp sequences that allow different samples to be sequenced together on a single ‘454’ plate and then separated bioinformatically for downstream analysis. There is no MID with 454-Col307-rev because we only pyrosequenced from the forward direction. Row 5 is an example of a 454 read after demultiplexing with the Roche tools. The forward primer is underlined, and the reverse primer dashed underlined. The MID tag is removed during demultiplexing. Row 6 is an example of a sequence after processing of sequences to produce a file of unique sequences.</p

Denoising of mtDNA COI amplicons generated from community samples of Collembola from two forest sites on the island of Tenerife with the pipeline of Yu <i>et al.</i> (2012).

<p>Steps 1–3 represent reduction of unique sequence volume by denoising, while steps 4 and 5 further reduce unique sequence volume by the creation of summary clusters of sequences. See Yu <i>et al.</i> (2012) for a detailed explanation of each of the steps. Bracketed values in step 2 represent sequences inferred to be chimeras with the <i>de novo</i> chimera detection function UCHIME in USEARCH, all of which were removed in step 4 of PyroClean.</p

Neighbour joining tree of PyroCleaned sequences derived from two forest sampling sites in the island of Tenerife, and 21 taxonomically identified Sanger sequences samples from Tenerife (in bold).

<p>Sequence identifiers represent MID tag, the name of the sequence, and the frequency representation of the sequence. Sequences were assessed for taxonomic identity against the BOLD Identification Database, and we report closest matches for Collembola, and non-Collembola if matching is higher. Letters in bold represent sequence matches to Collembola of 99% or higher: <b>A</b> – <i>Tetrodontophora bielanensis</i> (88%), <i>Pelosia muscerda</i> (Lepidoptera, 91%), <b>B</b> – <i>Tetrodontophora bielanensis</i> (89%), <i>Myotis ikonnikova</i> (Chiroptera, 91%); <b>C</b> – <i>Tetrodontophora bielanensis</i> (89%), <i>Myotis ikonnikova</i> (Chiroptera, 91%); <b>D</b> – <i>Verhoeffiella sp.</i> (89%), <i>Stenopsyche</i> (Trichoptera, 92%), <b>E</b> – no significant match, <i>Stenopsyche</i> (Trichoptera, 94%), <b>F</b> – <i>Folsomia</i> (94%), <i>Ophiogomphus</i> (Odonata, 95%), <b>G</b> – <i>Protaphorura</i> (99%), <b>H</b> – <i>Protaphorura</i> (100%), <b>I</b> – <i>Xenylla humicola</i> (90%), <i>Carterocephalus silvicola</i> (Lepidoptera, 91%), <b>J</b> – <i>Bourletiella</i> (89%), <b>K</b> – <i>Lepidocyrtus violaceus</i> (88%), <i>Herona marathus</i> (Lepidoptera, 90%) <b>L</b> – <i>Tullbergia sp.</i> (99%), <b>M</b> – <i>Parisotoma notabilis</i> L3 (92%), <b>N</b> – <i>Folsomina yosii</i> (90%), <b>O</b> – <i>Isotomiella</i> (99%), <b>P</b> – <i>Parisotoma notabilis</i> (100%), <b>Q</b> - <i>Parisotoma notabilis</i> (100%), <b>R</b> – <i>Parisotoma notabilis</i> (100%), <b>S</b> – <i>Xenylla humicola</i> (90%), <i>Finlaya</i> (Culicidae, 91%), <b>T</b> – <i>Verhoeffiella</i> sp. (90%), <b>U</b> – <i>Entomobrya atrocincta</i> (100%), <b>V</b> - <i>Entomobrya atrocincta</i> (99%), <b>W</b> - <i>Entomobrya atrocincta</i> (100%), <b>X</b> – <i>Parisotoma notabilis</i> (94%), <i>Phasus</i> (Lepidoptera, 96%), <b>Y</b> – <i>Isotomurus</i> (92%), <b>Z</b> – <i>Desoria sp.</i> (91%), <i>Bathymunida nebulosa</i> (Decapoda, 95%), <b>AA</b> – Entomobryidae (90%), <i>Polytremis pellucida</i> (Lepidoptera, 93%), <b>AB</b> – <i>Isotoma sp.</i> (91%), <i>Neophylax rickeri</i> (Trichoptera, 92%), <b>AC</b> – <i>Isotomurus</i> (86%), Chordate (90%), <b>AD</b> – <i>Neanura muscorum</i> (100%), <b>AE</b> – <i>Ceratophysella sp.</i> (99%), <b>AF</b> – <i>Ceratophysella sp.</i> (100%). The five sequences with an asterisk are potential numts or pcr error that exceed the final filter threshold. The two sequences with a filled circle are left in as an example of probable numts.</p

Heat map of the percentage representation of the 27 Collembola genomes within each of the 5 genomic pools, and within each of the three MID tag pools derived from each of the 5 genomic pools.

<p>For visual clarity, percentage representation of 2% or more is presented as maximum representation. See Supplementary <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0057615#pone-0057615-t001" target="_blank">Table 1</a> to see the actual percentages of each sequence found, and species names.</p

Regression analyses of the percentage of collembolan mtDNA COI sequences within an MID tag pool (<i>y</i> axis) against the percentage of genomic template from which they are derived within an experimental genomic pool (<i>x</i> axis).

<p>Data come from <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0057615#pone.0057615.s003" target="_blank">Table S1</a>. The panels from top to bottom are MID1 against pool 1, MID4 against pool 2, and MID7 against pool 3.</p

Mitogenome assemblies

File 'UKbees_mitogenomes_of_48_species_20150529.gb' (GenBank format) contains the mitochondrial assemblies of the 48 bee species

Metabarcoding data

This dataset includes the post-denoising (BLUE) and post-merging (FLASH) sequence data, the map files for library splitting, the merged *.fna file for all sequences from all samples, the representative sequence of each OTU, and the command files

arthropods.txt

Example input file for the R script, containing species X site data

Ailaoshan dataset: all fna and qual files

see Readme file: dryad metadata.tx