Apogon_and_reference_opsins_alignment

All cardinalfish opsins identified here aligned with reference opsin sequences and Ccarpio ancestral opsin as outgroup

Apogon_genediversity_LWS

LWS opsin gene alignment for amino acid by amino acid assessment of sequence diversity

paml_rh1_alignment

Alignment of RH1 opsin sequences used for paml analysis

Data from: Cardinalfishes (Apogonidae) show visual system adaptations typical of nocturnally and diurnally active fish

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 (>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

Apogon_opsin_expression

R-script used to convert read numbers to relative gene expression

Apogon_and_reference_opsins_tree

Phylogenetic tree of cardinalfish and reference opsin gene sequences

paml_lws_alignment

Alignment of LWS opsin sequences used for paml analysis

paml_rh2a-1_alignment

Alignment of RH2A-1 opsin sequences used for paml analysis

Apogon_genediversity_RH2As

RH2A opsin gene alignments for amino acid by amino acid assessment of sequence diversity

paml_sws2ab_alignment

Alignment of SWS2Abeta opsin sequences used for paml analysis