Vision using multiple distinct rod opsins in deep-sea fishes

Abstract

31Vertebrate vision is accomplished through a set of light-sensitive photopigments, which 32 are located in the photoreceptors of the retina and consist of a visual opsin protein bound 33 to a chromophore. In dim-light, vertebrates generally rely upon a single rod opsin (RH1) 34 for obtaining visual information. By inspecting 101 fish genomes, we found that three 35 deep-sea teleost lineages have independently expanded their RH1 gene repertoires. 36 Amongst these, the silver spinyfin (Diretmus argenteus Johnson 1863) stands out as having 37 the highest number of visual opsins known for animals to date (2 cone and 38 rod opsins). 38 Spinyfins simultaneously express up to 14 RH1s encoding for photopigments with 39 different peak spectral sensitivities (λmax=448-513 nm) that cover the range of the residual 40 daylight, as well as the bioluminescence spectrum present in the deep-sea. Our findings 41 present novel molecular and functional evidence for the recurrent evolution of multiple 42 rod opsin-based vision in vertebrates. 43 44 SHORT ABSTRACT: Contrary to the single rod opsin used by most vertebrates, some fishes 45 use multiple rod opsins for vision in the dimly lit deep-sea. 46 Animals use vision for a variety of fundamental tasks including navigation, food acquisition, 47

Stable species boundaries despite ten million years of hybridization in tropical eels

“…However, since fossils do not directly constrain maximum ages, the upper boundary of 55 Ma was arbitrarily specified by Jacobsen et al (2014), and the divergence times estimated in their study would likely be underestimated if Anguillidae in fact originated earlier than 55 Ma. Nevertheless, we consider the timeline proposed by Jacobsen et al (2014) plausible for the following reasons: (i) According to this timeline, European and American anguillid species (A. anguilla and A. rostrata) diverged from Indo-Pacific members of the genus around 10.8 Ma, which is consistent with the Messinian age (7.2-5.3 Ma) of the earliest fossils of the genus, known from the Gessoso Solififera Formation in Northern Italy (Dela Pierre et al 2011); (ii) the timeline is consistent with those of two other recent studies based on genome-wide data (Musilova et al 2019) and a massive taxon set (Rabosky et al 2018), as the most recent common ancestor of A. anguilla and A. japonica (the only species pair included in all three studies) was estimated at 13.8 Ma in Jacobsen et al (2014), at 12.4 Ma in Musilova et al (2019), and at 12.9 Ma in Rabosky et al (2018).…”

“…Additionally, we compiled a multi-locus phylogenetic dataset based on genome assemblies of the five species A. anguilla, A. japonica, A. marmorata, A. obscura, and A. megastoma to estimate divergence times among Anguilla species independently of the timeline of Jacobsen et al (2014). Of these five species, genome assemblies of A. anguilla (NCBI accession GCA 000695075; Henkel et al 2012a) and A. japonica (NCBI accession GCA 000470695; Henkel et al 2012b) were included in the large-scale phylogenomic analysis of Musilova et al (2019), in which their divergence was estimated at around 12.37 Ma. We thus extracted ortholog sequences, corresponding to the loci used in Musilova et al (2019), from the three new genome assemblies of A. marmorata, A. obscura, and A. megastoma ( Supplementary Table 5), and aligned these jointly with those of A. anguilla and A. japonica.…”

Colours and colour vision in reef fishes: Past, present and future research directions

“…As previously mentioned, modelling predicts long-wavelength sensitive photoreceptors in reef fishes (Lythgoe, 1979;Marshall et al, 2003b). The recent rise of next-generation sequencing technologies has made it possible to survey the visual systems of a much larger number of reef fishes in a lot more detail than before (e.g., Cortesi et al 2015a,b;Musilova et al, 2018) It is important to realize that a snapshot of the genes does not necessarily tell us the time at which the genes are active, either in evolutionary or lifetime timescales. Extensive work on cichlids (Cichlidae) and other freshwater fishes suggests that for some species at least, the genomic opsin repertoire can be used in a pick-and mix way, allowing the animal the best combination possible for the environment in which it finds itself (Carleton et al, 2005;Bowmaker & Loew, 2007;Bowmaker, 2008).…”

“…These range from extant species with a single remaining opsin gene to species with up to 40 opsin gene copies in their genomes (Cortesi et al, 2015;Hofmann and Carleton, 2009;Musilova et al, 2018).…”

“…Musilova and colleagues compared the gene expression in 36 representative species distributed across teleost phylogeny, including reef fishes, and found that, consistent with anatomical measurements and predictive models of colour vision, many species express up to four cone opsin genes within their retina. However, they also found a considerable number of species that had more than four cone opsin transcripts at what appeared to be functionally relevant levels, within their retina(Musilova et al, 2018). Since two, three or at most four differently tuned photoreceptors suffice to solve colour related tasks under water, the question of why fishes have, and also express, so many different opsin genes in the first place remains interesting.…”