Ancestral duplications and highly dynamic opsin gene evolution in percomorph fishes

Abstract

Single-gene and whole-genome duplications are important evolutionary mechanisms that contribute to biological diversification by launching new genetic raw material. For example, the evolution of animal vision is tightly linked to the expansion of the opsin gene family encoding light-absorbing visual pigments. In teleost fishes, the most species-rich vertebrate group, opsins are particularly diverse and key to the successful colonization of habitats ranging from the bioluminescence-biased but basically dark deep sea to clear mountain streams. In this study, we report a previously unnoticed duplication of the violet-blue short wavelength-sensitive 2 (SWS2) opsin, which coincides with the radiation of highly diverse percomorph fishes, permitting us to reinterpret the evolution of this gene family. The inspection of close to 100 fish genomes revealed that, triggered by frequent gene conversion between duplicates, the evolutionary history of SWS2 is rather complex and difficult to predict. Coincidentally, we also report potential cases of gene resurrection in vertebrate opsins, whereby pseudogenized genes were found to convert with their functional paralogs. We then identify multiple novel amino acid substitutions that are likely to have contributed to the adaptive differentiation between SWS2 copies. Finally, using the dusky dottyback Pseudochromis fuscus, we show that the newly discovered SWS2A duplicates can contribute to visual adaptation in two ways: by gaining sensitivities to different wavelengths of light and by being differentially expressed between ontogenetic stages. Thus, our study highlights the importance of comparative approaches in gaining a comprehensive view of the dynamics underlying gene family evolution and ultimately, animal diversification.

Keywords: Percomorpha; SWS2; gene conversion; gene duplication; gene resurrection.

Fig. 1.

Evolutionary history of SWS2 in teleost fishes. A first ancestral duplication of SWS2 into SWS2A and SWS2B happened at the base of the Neoteleostei (orange), which was followed by a second percomorph-specific duplication of SWS2A into SWS2Aα and SWS2Aβ (yellow). A lineage-specific SWS2B duplication was further discerned in lizardfishes (Aulopiformes). SWS2 gene synteny is schematically shown by blue polygons pointing out the direction of transcription, and the highly conserved HCFC1 upstream and LWS or GNL3L (in case of LWS loss) downstream genes are shown in gray; missing polygons equal gene loss. A dotted line with a question mark indicates a lineage for which genomic data of the target region could not be obtained. Gene conversion is depicted on an exon by exon basis in orange. Phylogenetic reconstruction, including age estimation, is based on the consensus of the most recent global fish phylogenies (19, 27). Fig. S1 shows the SWS2 gene phylogeny.

Fig. 2.

Schematic of the evolutionary dynamics affecting SWS2 in teleosts. The orange box indicates lineages affected by the initial Neoteleostei-specific duplication of SWS2 (SWS2A and SWS2B); the yellow box shows the lineages additionally affected by the Percomorpha-specific duplication of SWS2A (SWS2Aα and SWS2Aβ). Note that gene loss and pseudogenization happened repeatedly and independently between fish lineages (examples shown in parentheses), causing various stages of SWS2 retention in extant taxa. The missing genomic target region for flatfishes is marked with a question mark. Interestingly, no complete gene loss of SWS2 has been found within percomorphs.

Fig. 3.

Integrative approach to study opsin gene evolution exemplified in the dusky dottyback P. fuscus. (A–C) Gene conversion approach. (A) Single-exon phylogenies show distinct phylogenetic placements of SWS2 copies when exon 1, 4, or 5 is used, whereas SWS2A copies are resolved as sister groups when exons 2 and 3 are analyzed. Letters α, β, and B mark the position of the corresponding dottyback gene in the trees. (B) Sliding window analysis. Pairwise dS rate between SWS2 copies calculated with a window of 30 and a step size of 1. The red arrow depicts low dS rates between SWS2A copies in exons 2 and 3 and part of exon 1, corresponding to gene conversion. (C) Amino acid alignment of known key tuning (yellow) (17) and retinal binding pocket sites, showing all variable positions across dottyback SWS2s. Additional putative key substitutions that were identified across fish families are highlighted in gray. The red asterisk marks the substitution A269T in SWS2Aβ, which is known to cause a positive shift in visual sensitivity of 6 nm (17). (D) MSP of adult and larval dottybacks. Orange shows spectral absorbance curves for adult and larval single cones at 457 nm λ_max (n = 4), and blue shows spectral absorbance curves for adult-specific single cones at 448 nm λ_max (n = 11). (E) Relative SWS gene expression measured by qRT-PCR in adult (n = 12) and larval (n = 10) dottybacks. Note that larvae almost exclusively express SWS2Aβ, whereas adults predominantly express SWS2Aα. **P < 0.01; ***P < 0.001.