DOI: 10.5061/dryad.t0p2f2c
title: Data from: Cardinalfishes (Apogonidae) show visual system adaptations typical of nocturnally and diurnally active fish

description: Animal visual systems adapt to environmental light on various timescales.
 In scotopic conditions, evolutionary time-scale adaptations include
 spectral tuning to a narrower light spectrum, loss (or inactivation) of
 visual genes, and pure-rod or rod-dominated retinas. Some fishes
 inhabiting shallow coral reefs may show activity during the day and at
 night. It is unclear whether these fishes show adaptations typical of
 exclusively nocturnal or deep-sea fishes, or of diurnally active
 shallow-water species. Here, we investigated visual pigment diversity in
 cardinalfishes (Apogonidae). Most cardinalfishes are nocturnal foragers,
 yet they aggregate in multispecies groups in and around coral heads during
 the day, engaging in social and predator avoidance behaviours. We
 sequenced retinal transcriptomes of 28 species found on the Great Barrier
 Reef, assessed the diversity of expressed opsin genes and predicted the
 spectral sensitivities of resulting photopigments using sequence
 information. Predictions were combined with microspectrophotometry (MSP)
 measurements in seven cardinalfish species. Retinal opsin expression was
 rod opsin (RH1) dominated (&gt;87%), suggesting the importance of
 scotopic vision. However, all species retained expression of multiple cone
 opsins also, presumably for colour vision. We found five distinct
 quantitative expression patterns among cardinalfishes, ranging from
 short-wavelength-shifted to long-wavelength-shifted. These results
 indicate that cardinalfishes are both well adapted to dim-light conditions
 and have retained a sophisticated colour vision sense. Other reef fish
 families also show both nocturnal and diurnal activity while most are
 strictly one or the other. It will be interesting to compare these
 behavioural differences across different phylogenetic groups using the
 criteria and methods developed here.
description: Apogon_and_reference_opsins_alignmentAll cardinalfish opsins identified here aligned with reference opsin sequences and Ccarpio ancestral opsin as outgroup.Apogon_and_reference_opsins_treePhylogenetic tree of cardinalfish and reference opsin gene sequences.Apogon_genediversity_LWSLWS opsin gene alignment for amino acid by amino acid assessment of sequence diversity.Apogon_genediversity_RH1RH1 opsin gene alignment for amino acid by amino acid assessment of sequence diversity.Apogon_genediversity_RH2AsRH2A opsin gene alignments for amino acid by amino acid assessment of sequence diversity.Apogon_genediversity_RH2BsRH2B opsin gene alignments for amino acid by amino acid assessment of sequence diversity.Apogon_genediversity_SWS2AsSWS2A opsin gene alignments for amino acid by amino acid assessment of sequence diversity.apogon_retinal_transcriptome_raw_readsTotal numbers of raw reads that mapped to the species specific opsin gene sequences for all used samples.Apogon_opsin_expressionR-script used to convert read numbers to relative gene expression.paml_lws_alignmentAlignment of LWS opsin sequences used for paml analysis.paml_rh1_alignmentAlignment of RH1 opsin sequences used for paml analysis.paml_rh2a-1_alignmentAlignment of RH2A-1 opsin sequences used for paml analysis.paml_rh2b-1_alignmentAlignment of RH2B-1 opsin sequences used for paml analysis.paml_sws2aa_alignmentAlignment of SWS2Aalpha opsin sequences used for paml analysis.paml_sws2ab_alignmentAlignment of SWS2Abeta opsin sequences used for paml analysis.