DOI: 10.5061/dryad.cz8w9gjds
title: Bioluminescence and environmental light drive the visual evolution of deep-sea shrimp (Oplophoroidea)

description: Light functions as the universal language in the deep sea (&gt; 200
 m). Both bioluminescent emissions and downwelling light sources dimly
 illuminate the water column and can drive sensory system evolution. In
 pelagic environments, vertically migrating animals can experience drastic
 changes to their lighting environment across depth, subjecting them to
 unique selective pressures, possibly to distinguish between changes in
 ambient light and bioluminescent sources. Here we show that visual opsin
 diversity across a group of variable vertical migrators- bioluminescent
 deep-sea shrimp belonging to the Superfamily Oplophoroidea- is higher
 among species who migrate to shallower waters with more variable light
 conditions. Further, we provide evidence for adaptive visual evolution
 among species who have evolved an additional mode of bioluminescence
 (photophores), including positive selection for a putative mid-wavelength
 sensitive opsin that may facilitate light source discrimination.
 Diversification of this opsin appears to play an important role in the
 visual ecologies of photophore-bearing shrimp with its diversification in
 Oplophoroidea likely playing a critical role in the fitness and
 evolutionary success of this group.
description: Specimens were collected from the Gulf of Mexico and Florida
 Straits aboard the <em>RV </em>Point Sur<em>
 </em>(2015-2018), <em>RV</em> Sonne and<em> RV
 </em>Walton Smith (2016, 2017), respectively. Collections were done
 by a 9-meter<sup>2</sup> Tucker trawl fitted with a
 light-tight, thermally insulated cod-end MOC-10 system. All animals were
 sorted shipboard under dim red light and preserved and frozen in RNAlater.
 Eye tissues were dissected in RNAlater from three biological replicates
 for a majority of the shrimp species, except for <em>Systellaspis
 braueri</em> where only two replicates preserved for RNA work were
 available and the outgroup species <em>N. ensifer </em>(n=1).
 Total RNA was discretely extracted from tissues using Trizol/Chloroform
 reagents and rDNase (Macherey-Nagel) treated. RNAseq libraries were
 constructed from high-quality RNA using the
 NEBNext<sup>®</sup> Ultra<sup>TM</sup> II
 Directional library prep kit for Illumina<sup>®</sup> using
 the manufacturer’s protocol for use with the NEBNext Poly(A) mRNA Magnetic
 Isolation Module (NEB #E7490). Libraries had a target amplicon size of 330
 bp and contained NEBNext Multiplex Oligos for Illumina<sup>®
 </sup>dual index adaptors. Libraries were pooled and sequenced on an
 Illumina HiSeq4000 to obtain 150 bp paired-end reads at the
 GENEWIZ<sup>®</sup><sup> </sup>Core Facility
 (South Plainfield, NJ). Raw Illumina data was quality
 assessed (FastQC) prior to trimming with Trimmomatic
 v0.36 (<em>adapter.clip</em> 4:30:10,
  <em>min.read.length </em>30). Reads were then error-corrected
 (Rcorrector) and tissue-specific (eye) reference transcriptomes were
 assembled <em>de novo </em>for each species with Trinity
 v2.8.5
 (using <em>in silico </em>read normalization, a
 minimum contig length of 200 bp and a k-mer size of 23). Contamination was
 removed from each assembly (default parameters and the bacteria, archaea
 and viral database Minikraken2, v2). Duplicate transcripts and rRNA were
 removed using BBduk and dedupe (BBTools suite, available at: http://sourceforge.net/projects/bbmap). 
description: # Bioluminescence and environmental light drive the visual evolution of
 deep-sea shrimp (Oplophoroidea)
 [https://doi.org/10.5061/dryad.cz8w9gjds](https://doi.org/10.5061/dryad.cz8w9gjds) ## Description of the data and file structure ## Bioluminescent shrimp eye transcriptomes Tissue-specific (eye) reference transcriptomes were assembled de novo for the 10 deep-sea shrimp species (Trinity v2.8.5), belonging to two families of bioluminescent shrimp- Oplophoridae (1-2 modes of bioluminescence) and Acanthephyridae (1 mode)- and one outgroup species (*N. ensifer)*. After contaminant removal, the final reference assemblies were used in downstream analyses, including ortholog identification to build a species tree for the Superfamily Oplophoroidea and the identification and characterization of putative visual opsins (r-opsins) to test whether there was evidence of positive selection. The resulting tree was used for Ancestral State Reconstruction (ASR) of opsin type (presence/absence of expression) and for the ASR of lighting environment for Oplophoroidea. Members of this superfamily migrate vertically in the water column, but some remain in deep waters where light is limited (&gt; 400meters) or can no longer penetrate (&gt;1000). For ASR species were categorized based on the shallowest depth of their known species range (=highest light presence or lowest light attenuation), as either 1) epipelagic &lt; 200m, 2) upper mesopelagic 200-400m, 3) mesopelagic 400-700m or 4) lower mesopelagic &gt; 700m.   ### Files and variables #### File: Astylo\_final.fasta **Description:** Eye transcriptome of *Acanthephyra stylorostratis* #### File: Apurp\_final.fasta **Description:** Eye transcriptome of *Acanthephyra purpurea* #### File: Eombango\_final.fasta **Description:** Eye transcriptome of *Ephyrina ombango* #### File: Hgracil\_final.fasta **Description:** Eye transcriptome of *Hymenodora gracilis* #### File: Mmollis\_final.fasta **Description:** Eye transcriptome of *Meningodora mollis* #### File: Nelegans\_final.fasta **Description:** Eye transcriptome of *Notostomus elegans* #### File: Nensi.trinity.fasta **Description:** Eye transcriptome of *Nematocarcinus ensifer* #### File: Ogracil\_final.fasta **Description:** Eye transcriptome of *Oplophorus gracilirostris* #### File: Sbraueri\_final.fasta **Description:** Eye transcriptome of *Systellaspis braueri* #### File: Scrist\_final.fasta **Description:** Eye transcriptome of *Systellaspis cristata* #### File: FinalOpsinTree.treefile **Description:** Arthropod opsin gene tree used to characterize opsins in this study, based on clade grouping with opsins with known wavelength sensitivities (lambda max).  #### File: PROMALS\_LWSaligned\_curated.fasta **Description:** Alignment of long-wavelength sensitive (LWS) opsins recovered from the shrimp eye transcriptomes.  #### File: oplophoroidea\_orthologs\_newtree.rooted.pruned.treefile **Description:** Species tree for the Superfamily Oplophoroidea based on 622 orthologous genes, with the outgroup removed after rooting for Ancestral State Reconstruction analyses.    #### File: PROMALS\_MWSaligned\_curated\_mws1.fasta **Description:** Alignment of mid-wavelength sensitive (MWS1) opsins (clade1) recovered from the shrimp eye transcriptomes.  #### File: PROMALS\_MWSaligned\_curated\_mws2.fasta **Description:** Alignment of mid-wavelength sensitive (MWS2) opsins (clade2) recovered from the shrimp eye transcriptomes.  #### File: PROMALSalignment\_OplophoroideaOpsins\_final.fasta **Description:** Alignment of Oplophoroidea opsins recovered from the shrimp eye transcriptomes.  #### File: oplophoridae\_lightingEnv.csv **Description:** Ancestral State Reconstruction coding for the lighting environment, based on the shallowest depth each species migrates to (=highest light presence or lowest light attenuation): epipelagic &lt; 200m, upper mesopelagic 200-400m, mesopelagic 400-700m or lower mesopelagic &gt; 700m ##### Variables * Assembly: Transcriptome assembly  * LE: Lighting environment category #### File: oplophoridae\_opsins\_binary.csv **Description:** Ancestral State Reconstruction coding for the presence/absence of expression of each opsin type in the shrimp eye transcriptomes. Opsin clade corresponds to clade identified with the opsin gene tree (FinalOpsinTree.treefile).  ##### Variables * Assembly: Transcriptome assembly  * S1: short wavelength sensitive opsin (SWS1) * S2: short wavelength sensitive opsin (SWS2) * SM: short/mid wavelength sensitive opsin (SWS/MWS) * M1: mid wavelength sensitive opsin (MWS1) * M2: mid wavelength sensitive opsin (MWS2) * L: long wavelength sensitive opsin (LWS2) ## Code/software ## Assembly files Transcriptomes can be viewed using a text editor (e.g. Sublime) or through command-line tools (e.g. nano) ## Alignment files Text editors (e.g. Sublime) can be used to view the alignments, or free software programs like AliView to view in more detail. ## Tree files Tree viewing software like FigTree can be used to view the tree files.  ## ASR coding files (.csv) The .csv files can be viewed with a text editors (e.g. Sublime) or using excel.