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

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

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

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

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

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

A novel allele of ASY3 is associated with greater meiotic stability in autotetraploid Arabidopsis lyrata

In this study we performed a genotype-phenotype association analysis of meiotic stability in 10 autotetraploid Arabidopsis lyrata and A. lyrata/A. arenosa hybrid populations collected from the Wachau region and East Austrian Forealps. The aim was to determine the effect of eight meiosis genes under extreme selection upon adaptation to whole genome duplication. Individual plants were genotyped by high-throughput sequencing of the eight meiosis genes (ASY1, ASY3, PDS5b, PRD3, REC8, SMC3, ZYP1a/b) implicated in synaptonemal complex formation and phenotyped by assessing meiotic metaphase I chromosome configurations. Our results reveal that meiotic stability varied greatly (20–100%) between individual tetraploid plants and associated with segregation of a novel ASYNAPSIS3 (ASY3) allele derived from A. lyrata. The ASY3 allele that associates with meiotic stability possesses a putative in-frame tandem duplication (TD) of a serine-rich region upstream of the coiled-coil domain that appears to have arisen at sites of DNA microhomology. The frequency of multivalents observed in plants homozygous for the ASY3 TD haplotype was significantly lower than in plants heterozygous for ASY3 TD/ND (non-duplicated) haplotypes. The chiasma distribution was significantly altered in the stable plants compared to the unstable plants with a shift from proximal and interstitial to predominantly distal locations. The number of HEI10 foci at pachytene that mark class I crossovers was significantly reduced in a plant homozygous for ASY3 TD compared to a plant heterozygous for ASY3 ND/TD. Fifty-eight alleles of the 8 meiosis genes were identified from the 10 populations analysed, demonstrating dynamic population variability at these loci. Widespread chimerism between alleles originating from A. lyrata/A. arenosa and diploid/tetraploids indicates that this group of rapidly evolving genes may provide precise adaptive control over meiotic recombination in the tetraploids, the very process that gave rise to them