Mean waveforms throughout the experiments.

<p>Top panel: comparison of the first consensus waveforms drawn for rhythmic crabs at 13.5°C. Lower panel: comparison of the consensus waveforms drawn for rhythmic crabs at 17.5°C. Data are replotted from <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0175403#pone.0175403.g001" target="_blank">Fig 1</a>. Each point represents mean ± SEM.</p

Individual actograms at 17°C and 13°C.

<p>Individual double-plotted actograms at 17°C (A) and 13°C (B) for 3 representative crabs for each experiment, kept first under a 12:12 LD cycle (10 and 8 days respectively) and then transferred to LL conditions (12 days for both). To the right of each actogram, periodograms display the period of the oscillation that significantly (<i>p</i> ≤ 0.05) explains most of the variance in the analysis, indicated in minutes. For each actogram, there are two periodograms corresponding to the activity under LD and LL, respectively. Crabs were collected in summer and tested in free-running either at 13 or 17°C. Crabs depicted under 13°C are not the same individuals depicted under 17°C.</p

Gene ontology annotation of the two transcriptomes (NEP-L and NEP-D).

<p>Gene ontology (GO) annotation of the assembled transcriptomes. <b>A:</b> The percentage distribution of functional categories between the two transcriptomes together with the proportion on no hits. <b>B:</b> The percentage of sequences distributed among 62 different functional groups of both samples (black columns: photophase; grey columns: scotophase).</p

Similarities between contigs and cloned fragments.

<p>Similarities observed during the alignment between the cloned sequences and the corresponding assembled contigs (<i>period</i>, <i>timeless</i>, <i>clock</i> and <i>bmal1</i>). For <i>α-act</i> the alignment was between the cloned sequence and the sequence retrieved from <i>H</i>. <i>americanus</i>.</p

Canonical clock genes expression (RT-qPCR).

<p>Canonical clock genes expression in <i>Nephrops</i> eyestalk. Measurements (n = 3 each time point) were normalized to <i>α-act</i> and <i>18S</i> and expressed as fold change respect to a control time point (7:30). Vertical bars represent the confidence limits. Black and white bars represent darkness and light hours, respectively. <i>Timeless</i> shows a significant pattern of expression (ANOVA, P < 0.05). Letters indicate the output of the Tukey’s post hoc test (a>b).</p

Waveform analysis.

<p>Waveform (24 h) analysis throughout the 10 days of experiment for a representative lobster (<b>A</b>) and averaged for the 14 lobsters used during the study (<b>B</b>). Activity is reported as displacement (cm) out of the burrow. Black and white bars represent darkness and light hours, respectively. Shadowed areas represent scotophase. Vertical lines represent the standard error of the mean and the horizontal line represents the MESOR. Arrows in <b>B</b> stay for the sampling points at which eyestalk were dissected for the RT-qPCR experiment.</p

Illumina sequencing.

<p>Descriptive statistics for the Illumina sequencing run and the assembly of the <i>de novo</i> transcriptomes.</p

Species distribution of annotated transcripts of the merged transcriptome (NEP-comb).

<p>The species distribution of the annotated hits of transcripts against the NCBI non-redundant protein sequence database (E-value cutoff to 10⁻⁶). Horizontal bars depict the number of hits for each one of the species. Only 30 species in order of number of annotated hits were presented, while the hits of all the other species are summed into the bar “<i>others”</i>.</p

Fold change and abundance levels of transcripts.

<p>Different expression values of the two lobsters NEP-L and NEP-D. The black dots represent the equally expressed transcripts, while the red ones the differently expressed. The x-axis represents the Log₂ of transcripts abundances. The y-axis represents the fold changes in abundances. In the upper part of the graph are plotted the transcripts of NEP-L and in the bottom part NEP-D.</p

DataSheet_1_Increasing trammel mesh size reduces biomass removal, mitigates discards and increases economic revenue in artisanal fisheries.docx

Small-scale fishing plays a major role in regional economies worldwide and, with a large number of small vessels involved, it provides employment and livelihood to coastal communities. Generally recognized as more selective than other fishing practices, small-scale fishery can nevertheless be subjected to high rates of discards of both non-target species and small-sized individuals, which in turn could lead to both decreased incomes for fishers and increased depletion of fish stocks. However, if the relationship between fish size and price has long been assessed, the effect of enhanced size-selectivity of fishing gears and consequent economic gains has been little investigated. This study, set in the Porto Cesareo Marine Protected Area (Italy, Ionian Sea), aimed at testing effective strategies to improve trammel net selectivity, reducing discards and maximizing the income for fishers. Different mesh sizes (20, 22 and 24 mm) trammel nets were employed. The study consisted in 72 fishing days from July 2012 to September 2013 and each day involved experimental fishing with the three mesh sizes. A total of 16008 specimens (103 species) were collected but the analysis focused on the 18 most common species in the area for a total of 12782 individuals. Mesh size trammel nets of 20 mm and 22 mm yielded most of the biomass, 324.8 and 321.5 kg respectively, while the 24 mm mesh yielded 280.7 kg. The 24 mm mesh, even if accounted for lower income compared to the 22 mm mesh (2383.9 € vs 2590.5 €, respectively), provided significant 50% reduction of discards compared to the 20 and 22 mm mesh. The use of 24 mm mesh size was found to be an effective strategy to reduce the number of discarded organisms and, consequently, the pressure exerted on local fish stocks with associated higher revenue for fishers. The results of this study demonstrated that trammel net selectivity can improve and support conservation measures and concurrently increase profitability of local fishery.</p