Straube_et_al_Squaliform_phylogeny_data

These files contain data supporting results from Straube et al. 2015. Please see also Additional file 1 of the article

Rod photoreceptor spectral absorbance.

<p>Mean bleaching difference absorbance spectra (black symbols) with wavelength of maximum absorbance of the visual pigment (λ_max; top for (A) <i>S. aliae</i>; (B) <i>E. spinax</i>; and (C) <i>E. splendidus</i>. Data for A and C were obtained by spectrophotometry of visual pigment extracts, that of B by microspectrophotometery (MSP). Absorption spectra are best fitted with visual pigment templates of appropriate λ_max (grey line) according to <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0104213#pone.0104213-Govardovskii2" target="_blank">[86]</a>. For comparison purpose, dashed blue lines at bioluminescence peak (<i>B</i>_max) from <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0104213#pone.0104213-Claes7" target="_blank">[37]</a> were superimposed on absorbance curves.</p

Topographic maps of ganglion cell densities.

<p>Black arrows indicate retina orientation (N = nasal, V = ventral). For comparative purpose, <i>T. kabeyai</i> retina (which comes from a left eye contrary to the other retinas) was vertically mirrored. Isodensity lines were arbitrarily selected in order to highlight the specialisations. All the densities are ×10 cells mm⁻². Scale bars, 2 mm. mm.</p

Internal ocular features.

<p>(A) Ventral (left) and horizontal (right) choroidal tapeta (ta). Photographs were taken with (ventral tapetum) or without the retina (horizontal tapetum). Black arrows indicate retina/choroid orientation (N = nasal, V = ventral). o, optic nerve. Scale bars, 2 mm. (B) Retinal hexagonal photoreceptor mosaic (wholemount view). Scale bar, 2 µm. (C) Light micrographs of transverse section through the retina of two bioluminescent shark species showing variation in photoreceptor outer segment (OS) length and diameter. GCL, ganglion cell layer; INL, inner nuclear layer; IPL, inner plexiform layer; IS, photoreceptor inner segment; ONL, outer nuclear layer; OPL, outer plexiform layer. Scale bar, 20 µm. (D) Light micrographs of the Nissl stained GCL of <i>E. splendidus</i> (wholemount view; temporal area). ac, amacrine cell; gc, ganglion cell. Scale bar, 20 µm.</p

Visual performance parameters summary.

<p>*These values are calculated for the specimen used in the histological analysis of photoreceptors (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0104213#pone-0104213-t001" target="_blank">Table 1</a>). ∑, summation ratio; N, sensitivity to bioluminescent point sources; S, optical sensitivity; SPR, spatial resolving power.</p

Ganglion cell data summary from retina wholemounts.

<p>*The Schaeffer CE measures the accuracy of the counting; it should be <0.1 to be acceptable <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0104213#pone.0104213-Glaser1" target="_blank">[87]</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0104213#pone.0104213-Slomianka1" target="_blank">[88]</a>.</p>†<p>Numbers for sites and rod indicate the total number of sampling sites and total number of counted rods, respectively. F, female; L, left eye; M, male; R, right eye; TL, total length.</p

Topographic maps of photoreceptor densities.

<p>Black arrows indicate retina orientation (T = temporal, V = ventral). For comparative purpose, <i>T. kabeyai</i> retina (which comes from a left eye contrary to the other retinas) was vertically mirrored. Isodensity lines were arbitrarily selected in order to highlight the specialisations. All the densities are ×10³ cells mm⁻². Scale bars, 2 mm. mm.</p

Ocular measurements.

<p>*These data correspond to mean of 10 measurements from the central retina of a single specimen. F, female; INL, inner nuclear layer; IPL, inner plexiform layer; L, left eye; M, male; ONL, outer nuclear layer; OPL, outer plexiform layer; R, right eye; ROS, rod outer segment; RIS, rod inner segment; TL, total length.</p

External body and ocular features.

<p>(A) Phylogeny of sharks analysed in this study (from <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0104213#pone.0104213-Naylor1" target="_blank">[89]</a>). Lateral pictures of representative specimens indicate the position of the clade-specific bioluminescent lateral markings (la) and other bioluminescent areas probably involved in intraspecific behaviours (blue triangles). Scale bars, 5 cm. (B) Close-up of the eyes showing the position of aphakic gaps (white arrow) and translucent upper eyelid (te) or dorsal groove (dg) in some species. (C) Frontal (top left), ventral (middle left), dorsal (down left) and lateral (right) views of <i>E. spinax</i> head showing the part of the visual field subtended by the eyes. Note the presence of a pronounced frontal groove (fg) favouring frontal binocular vision. The dissected upper orbital region shows the translucent eyelid area (te) is delimited caudally and frontally by aggregations of photophores (pa) pointing towards the eye. (D) Head of <i>T. kabeyai</i> with protruded jaws (ja). Note how binocular vision is prevented frontally by an enlarged rostrum (ro) and facilitated ventrally (towards the end of the jaw) by a ventral groove (vg).</p

Comparative shark vision.

<p>Summary chart of statistical tests performed to compare the visual parameters of bioluminescent, deep living and shallow living sharks (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0104213#pone.0104213.s001" target="_blank">Dataset S1</a>). When a significant difference between groups was detected by ANOVA (*<i>P</i><0.05, **<i>P</i><0.01, ***<i>P</i><0.001), red colour was used to highlight the groups with statistically higher values (<i>P</i><0.05 with post-hoc Student's <i>t</i>-test). Mean parameter values for each group are indicated into the corresponding circles. Values into brackets correspond to the number of species encompassed by each group.</p