The boxplot distribution of sequence similarities for different 18S rRNA gene regions in the intra-species (S), inter-species but intra-genus (G), inter-genus but intra-family (F), inter-family but intra-order (O), and inter-order (I) categories.

<p>The central boxes represent the middle three quarters of the data. The total number of samples in each plot is listed at the bottom of each box.</p

Copepod 18S rRNA genes used in the statistical similarity analysis.

<p>Copepod 18S rRNA genes used in the statistical similarity analysis.</p

Taxonomic Resolutions Based on 18S rRNA Genes: A Case Study of Subclass Copepoda

<div><p>Biodiversity studies are commonly conducted using 18S rRNA genes. In this study, we compared the inter-species divergence of variable regions (V1–9) within the copepod 18S rRNA gene, and tested their taxonomic resolutions at different taxonomic levels. Our results indicate that the 18S rRNA gene is a good molecular marker for the study of copepod biodiversity, and our conclusions are as follows: 1) 18S rRNA genes are highly conserved intra-species (intra-species similarities are close to 100%); and could aid in species-level analyses, but with some limitations; 2) nearly-whole-length sequences and some partial regions (around V2, V4, and V9) of the 18S rRNA gene can be used to discriminate between samples at both the family and order levels (with a success rate of about 80%); 3) compared with other regions, V9 has a higher resolution at the genus level (with an identification success rate of about 80%); and 4) V7 is most divergent in length, and would be a good candidate marker for the phylogenetic study of <i>Acartia</i> species. This study also evaluated the correlation between similarity thresholds and the accuracy of using nuclear 18S rRNA genes for the classification of organisms in the subclass Copepoda. We suggest that sample identification accuracy should be considered when a molecular sequence divergence threshold is used for taxonomic identification, and that the lowest similarity threshold should be determined based on a pre-designated level of acceptable accuracy.</p></div

A comparison of the nucleotide divergences of the copepod 18S rRNA genes of different regions.

<p>184 18S rRNA genes representing 184 copepod species (excluding species in the genus <i>Acartia</i>) were used to calculate pairwise genetic distances using <i>p</i>-distance. Values are shown as means ± SD. Variable names are consist with <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0131498#pone.0131498.t001" target="_blank">Table 1</a>.</p

Sequence characteristics of the 18S rRNA gene from 8 species in the genus <i>Acartia</i>, and 184 other copepod species.

<p>18S, copepod 18S rRNA genes with the two ends trimmed (all the variable regions were intact); TCs, Total conserved region sequences in 18S; CVs, combination of all variable regions; V1-9, variable regions; GC, GC contents; Nt, total number of sites compared; Nc, total number of conserved sites; Nv, total number of variable sites; PI, parsimony-informative sites.</p><p>Sequence characteristics of the 18S rRNA gene from 8 species in the genus <i>Acartia</i>, and 184 other copepod species.</p

Entropy plot calculated based on site variability in an alignment of 184 copepod 18S rRNA genes, and the distribution of variable regions.

<p>A trend line represents the mean variability for successive windows of 20 positions.</p

Zebrafish intestinal volumes (nL) for different individuals sampled at different days post-fertilization (dpf).

<p>Individuals-A to D denote different replicate zebrafish individuals sampled at a specific dpf.</p>a<p>Female zebrafish, and</p>b<p>Male zebrafish.</p

Bacterial richness relationships with (A) habitat size (volume nL) and (B) time (days post-fertilization) plotted on log₁₀ scale axes.

<p>Given are the (A) species-volume relationship and (B) species-time relationship power law equations. For (A): <i>r</i>² = 0.25, <i>F</i>_1,28 = 9.16, <i>P</i><0.005; and (B) <i>r</i>² = 0.26, <i>F</i>_1,28 = 10.0, <i>P</i><0.004. Also given are the 95% confidence and prediction intervals (inner and outer dashed lines, respectively).</p

Summary statistics for Mantel and partial Mantel tests.

<p>The Mantel statistic <i>r</i>(<i>AB</i>) estimates the correlation between two proximity matrices, <i>A</i> and <i>B</i>. Whereas, the partial Mantel <i>r</i>(<i>AB</i>.<i>C</i>) statistic estimates the correlation between <i>A</i> and <i>B</i> whilst controlling for the effects of <i>C</i>. Also given is <i>P</i> to ascertain whether the Mantel and partial Mantel regression coefficients were significantly different from zero following 9,999 permutations. Given are bacterial community similarity <i>S</i> (Sørensen index) and also <i>V</i>, <i>T</i>, and <i>F</i>, which are differences in habitat size (volume, nL), temporal distance (days post-fertilization), and food diet, respectively.</p

Histological analyses of liver tissues. Liver tissues from 4 different diet treatments were formaldehyde-fixed, followed by staining with Hematoxylin and eosin.

<p>The results (75×) from transgenic fish are shown in the upper panels, and wild-type controls with corresponding diet treatments in the lower panels. Arrows in upper panels indicate lipid droplet (blue) and those in lower panels (green) show glycogen deposits.</p