Extraordinarily low evolutionary rates of short wavelength-sensitive opsin pseudogenes

• We cloned the SWS1 opsin pseudogene of the deep-sea fish pearleye.
• SWS1 genes in several vertebrate lineages have lost their abilities to make opsins.
• The pseudogenization events took place separately 15–140 × 106 years ago.
• Evolutionary rates of these pseudogenes ranged between 0.9 and 2.0 × 10− 9/site/year.

Aquatic organisms such as cichlids, coelacanths, seals, and cetaceans are active in UV–blue color environments, but many of them mysteriously lost their abilities to detect these colors. The loss of these functions is a consequence of the pseudogenization of their short wavelength-sensitive (SWS1) opsin genes without gene duplication. We show that the SWS1 gene (BdenS1ψ) of the deep-sea fish, pearleye (Benthalbella dentata), became a pseudogene in a similar fashion about 130 million years ago (Mya) yet it is still transcribed. The rates of nucleotide substitution (~ 1.4 × 10− 9/site/year) of the pseudogenes of these aquatic species as well as some prosimian and bat species are much smaller than the previous estimates for the globin and immunoglobulin pseudogenes.