The diversity of opsins in Lake Baikal amphipods (Amphipoda: Gammaridae)

Abstract

Background Vision is a crucial sense for the evolutionary success of many animal groups. Here we explore the diversity of visual pigments (opsins) in the transcriptomes of amphipods (Crustacea: Amphipoda) and conclude that it is restricted to middle (MWS) and long wavelength-sensitive (LWS) opsins in the overwhelming majority of examined species. Results We evidenced (i) parallel loss of MWS opsin expression in multiple species (including two independently evolved lineages from the deep and ancient Lake Baikal) and (ii) LWS opsin amplification (up to five transcripts) in both Baikal lineages. The number of LWS opsins negatively correlated with habitat depth in Baikal amphipods. Some LWS opsins in Baikal amphipods contained MWS-like substitutions, suggesting that they might have undergone spectral tuning. Conclusions This repeating two-step evolutionary scenario suggests common triggers, possibly the lack of light during the periods when Baikal was permanently covered with thick ice and its subsequent melting. Overall, this observation demonstrates the possibility of revealing climate history by following the evolutionary changes in protein families.

Crustacean conundrums: a review of opsin diversity and evolution

“…Although ‘typical’ eye designs in some crustaceans express little opsin diversity (e.g. crayfish and brachyuran crabs [49,50], barnacles [51,52], some amphipods and cave isopods [30,53,54]), sparse literature suggests that in some species highly modified visual structures equate to exponentially increased opsin diversity (e.g. stomatopods [55,56]), while in others even relatively simple photoreceptor set-ups have revealed similarly high opsin diversity (e.g.…”

“…Amphipod visual systems generally consist of apposition compound eyes and range from no eyes in some deep sea species to large distributed retinas in the mesopelagic species Paraphronima gracilis [104]. Previous estimates indicate that amphipods typically have a low number of visual opsins (1-5), with most duplications occurring in the LWS clade [53]. Using transcriptomic data from nine species representing six families, we found one well-supported clade of LWS visual opsins in all species with an apparent duplication of this opsin evident in most species.…”

CrusTome: A transcriptome database resource for large-scale analyses across Crustacea

“…Despite this apparent overrepresentation, CrusTome includes representative of rare and obscure taxa that present intriguing opportunities for phylogenetics, systematics, and evolution, such as remipedes and bathynellaceans (Pérez-Moreno et al . 2016) and multiple deep-water malacostracans (DeLeo and Bracken-Grissom 2020; Drozdova et al . 2021).…”

“…The CrusTome mRNA and amino acid databases were created in two formats using default settings, as both BLAST and Diamond databases (Altschul et al 1990;Buchfink et al 2021; Figure 1F) for compatibility with existing annotation and analysis pipelines (e.g., see Das et al 2016;Pérez-Moreno et al 2018;Tang et al 2019;Drozdova et al 2021) and upcoming software. Diamond is an ultra-fast alignment software that achieves considerable sequence similarity search speeds orders of magnitude faster than BLAST, at a minimum sensitivity cost (Buchfink et al 2021), and as such would be appropriate for the high-throughput applications now available with CrusTome.…”

“…Presenting the database in this format also allows for simple and straight-forward incorporation into existing custom analysis pipelines, making it particularly suitable for scripting and high-throughput analyses (e.g., Pérez-Moreno et al . 2018; Drozdova et al . 2021).…”