Spatial density dependence in bird predation of <i>Andricus</i> bud galls at Puttenham Common.

<p>Analysis summaries are presented at three spatial scales: 1. Among shoots (within branches within trees); 2. Among branches (within trees); 3. Among trees within sites. Analyses for 2 & 3 were carried out over the averages of gall densities and predation rates at the lower levels of nesting. Analyses were all generalised linear models with quasibinomial errors and a logit link. Significance levels are shown unadjusted. Significance at P<0.05 after Dunn-Šidàk adjustment of significance levels for 3 tests are indicated by an asterisk (*).The right hand column shows the proportion of slopes at the hierarchical level analysed showing positive density dependence.</p

Between-week pairwise Spearman Rank Correlation Coefficients (R²).

<p>Matrix values above the diagonal show rank correlations in gall density, while values below the diagonal show rank correlations in predation rates. All correlations had 10 degrees of freedom, and all except one (predation rates between week 1 & 2 p = 0.052) are significant at p<0.05. All correlations for gall densities are significant at p<0.01.</p

Geographic locations of the eight sampling sites in Britain.

<p>Geographic locations of the eight sampling sites in Britain.</p

Patterns of spatial density dependence through time.

<p>The figure shows patterns in density dependence among trees over five weeks starting with the last week of March 2006 at Puttenham Common (site 2, Fig. 1). Significance levels are indicated by superscripts as follows: ns non significant; * p<0.05, ** p<0.01, *** p<0.001. p = 0.05 is equivalent to p = 0.017 after Dunn-Šidàk adjustment (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0053959#pone-0053959-t003" target="_blank">Table 3</a>).</p

Patterns of spatial density dependence among trees at each site.

<p>Significance levels are indicated by superscripts as follows: ns non significant; * p<0.05, ** p<0.01, *** p<0.001. p = 0.05 is equivalent to p = 0.017 after Dunn-Šidàk adjustment (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0053959#pone-0053959-t002" target="_blank">Table 2</a>). Note that the scale of the y-axis is different in for Dunrobin (h).</p

Phylogenetic relationships of virus-like contigs from the dog whelk.

<p>Mid-point rooted maximum likelihood phylogenetic trees for each of the virus-like contigs associated with viRNAs in the dog whelk (<i>Nucella lapillus</i>). New virus-like contigs described here are marked in red, sequences marked ‘TSA’ are derived from public transcriptome assemblies of the species named, and the scale is given in amino acid substitutions per site. Panels are: (A) rhabdoviruses related to lyssaviruses, inferred using the protein sequence of the nucleoprotein (the only open reading frame available from this contig, which is likely an EVE); (B) orthomyxoviruses related to influenza and thogoto viruses, inferred using the protein sequence of PB1; (C) rhabdoviruses and chuviruses, inferred from the RNA polymerase. Support values and accession identifiers are presented in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1007533#pgen.1007533.s002" target="_blank">S2 Fig</a> and <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1007533#pgen.1007533.s019" target="_blank">S3 Data</a>, and alignments in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1007533#pgen.1007533.s018" target="_blank">S2 Data</a>. Given the high level of divergence, alignments and inferred trees should be treated as tentative.</p

Distribution of small RNA pathways across the Metazoa.

<p>Phylogeny of selected metazoan (animal) phyla (topology follows [<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1007533#pgen.1007533.ref180" target="_blank">180</a>]) with a table recording the reported range of modal lengths for miRNAs, piRNAs, and viRNAs detectable by bulk sequencing from wild-type organisms (miRNA modes taken from miRbase). Entries marked ‘No’ have been reported to be absent, and those marked ‘?’ are untested. Focal taxa in this study are marked in colour, and the target table entries are outlined. Vertebrate viRNAs are marked ‘(×)’ as mammalian virus-derived small RNAs are only detectable in tissues and experimental systems lacking viral suppressors of RNAi and/or an interferon response [<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1007533#pgen.1007533.ref031" target="_blank">31</a>–<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1007533#pgen.1007533.ref035" target="_blank">35</a>]. Note that piRNAs are absent from some, but not all, nematodes [<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1007533#pgen.1007533.ref057" target="_blank">57</a>]. The column ‘dsRNA KD’ records whether dsRNA knockdown of gene expression using long dsRNA (i.e. a Dicer substrate) has been reported, as this may suggest the presence of an RNAi pathway capable of producing viRNAs from replicating viruses. The ‘Dcrs’ and ‘Agos’ columns record the inferred number of Dicers and (non-Piwi) Argonautes ancestrally present in each phylum, although the number of Dicers in Platyhelminthes is contentious as the putative second Dicer lacks the majority of expected Dicer domains. Broadly speaking, there are two competing hypotheses for the histories of Dicers and (non-Piwi) Argonautes in animals [<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1007533#pgen.1007533.ref047" target="_blank">47</a>,<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1007533#pgen.1007533.ref050" target="_blank">50</a>,<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1007533#pgen.1007533.ref181" target="_blank">181</a>]. The first (labelled H₁), posits that an early duplication in Dicer and/or Argonaute (marked D⁺ and A⁺ in dark green on the phylogeny) gave rise to at least two very divergent homologues of each gene in the lineage leading to the Metazoa, followed by subsequent losses (D^- and A^- in dark red). The second (H₂), suggests that divergent homologues are the result of more recent duplications (D⁺ and A⁺ in pale green), and where homologs have high divergence it is as a result of rapid evolution. Note that these hypotheses are independent for Argonautes and Dicers, and one may be ancient but the other recent. For Dicers, at least, the ‘ancient’ duplication is arguably better supported [<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1007533#pgen.1007533.ref047" target="_blank">47</a>], although it remains extremely difficult to determine orthology between the duplicates. In addition, Dicers and Argonautes have unambiguously diversified within some phyla (important examples marked A⁺ and D⁺ in grey)—as seen for the large nematode-specific WAGO clade of Argonautes (reviewed in [<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1007533#pgen.1007533.ref141" target="_blank">141</a>]), and the multiple Argonautes in vertebrates.</p

Small RNAs from TE-like contigs.

<p>The threecolumns show (left to right): the distribution of 20-30nt small RNAs along the length of a TE-like contig; the size distribution of small RNA reads (U red, G yellow, C blue, A green); and the sequence ‘logo’ of unique sequences for the dominant sequence length. Read counts above the x-axis represent reads mapping to the positive sense (coding) sequence, and counts below the x-axis represent reads mapping to the complementary sequence. For the sequence logos, the upper and lower plots show positive and negative sense reads respectively, and the y-axis of each measures relative information content in bits. Where available, reads from the oxidised library are shown (A-F), but other libraries display similar distributions (<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1007533#pgen.1007533.s008" target="_blank">S8 Fig</a>). These examples from sponge (A), sea anemone (B), starfish (C), earthworm (D), dog whelk (E-F) and brown alga (G) were chosen to best illustrate the presence of the ‘ping pong’ signature, but other examples are shown in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1007533#pgen.1007533.s008" target="_blank">S8 Fig</a>. Note that the size distribution of TE-derived small RNAs varies substantially among species, and that the dog whelk (E and F) displays at least two distinct patterns, one (F) reminiscent of that seen for some RNA virus contigs (<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1007533#pgen.1007533.g003" target="_blank">Fig 3C</a>). The data required to plot these figures is provided in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1007533#pgen.1007533.s014" target="_blank">S5 Table</a>.</p

Small RNAs from RNA virus-like contigs.

<p>Panels to the left show the distribution of 20-30nt small RNAs along the length of the virus-like contig, and panels to the right show the size distribution small RNA reads coloured by the 5' base (U red, G yellow, C blue, A green). Read counts above the x-axis represent reads mapping to the positive sense (coding) sequence and counts below the x-axis represent reads mapping to the complementary sequence. For the dog whelk (A-D), only reads from the oxidised library are shown. Other dog whelk libraries display similar distributions and the small-RNA ‘hotspot’ pattern along the contig is highly repeatable (<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1007533#pgen.1007533.s006" target="_blank">S6 Fig</a>). Small RNAs from the two segments of the orthomyxovirus (A and B) show strong strand bias to the negative strand and no 5' base composition bias. Those from the first rhabdo-like virus (C) display little strand bias and no base composition bias, and those from the second rhabdo virus-like contig, which is a probable EVE (D), derive only from the negative strand and display a very strong 5' U bias. There were insufficient reads from the positive strand of this virus to detect a ping-pong signature. Small RNAs from the four dog whelk contigs all display 28nt peaks. Small RNAs from the bunya/phlebo-like virus identified in the brown alga (E) derive from both strands, and show a strong 5' U bias with a peak size of 21nt. The data required to plot the size distributions are provided in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1007533#pgen.1007533.s014" target="_blank">S5 Table</a>.</p

Bpal.BLAST_and_Coverage_filtered_noINDELS_2609.vcf

VCF file for Biorhiza pallida ingroup individuals created using samtools. Contaminant and high coverage sequences have been removed from this file. The VCF_haploif_parser.pl script was run on this file