title: Extraordinarily low evolutionary rates of short wavelength-sensitive opsin pseudogenes.
abstract: 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.
authors.affiliation: Department of Biology, Emory University, Atlanta, GA 30322, USA. Electronic address: syokoya@emory.edu.
authors.forename: Shozo
authors.initials: S
authors.lastname: Yokoyama
authors.forename: William T
authors.initials: WT
authors.lastname: Starmer
authors.forename: Yang
authors.initials: Y
authors.lastname: Liu
authors.forename: Takashi
authors.initials: T
authors.lastname: Tada
authors.forename: Lyle
authors.initials: L
authors.lastname: Britt
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D001483:Base Sequence; D023681:Cichlids / Q000235:genetics; D019143:Evolution, Molecular; D029941:Fish Proteins / Q000235:genetics; D010802:Phylogeny; D011544:Pseudogenes; D012168:Retinal Pigments / Q000235:genetics; D017299:Rod Opsins / Q000235:genetics*; D017421:Sequence Analysis
chemical_list: D029941:Fish Proteins; D012168:Retinal Pigments; D017299:Rod Opsins; C095853:short-wavelength opsin
keywords: Aquatic animals; BEB; Bayes empirical Bayes; ENCODE; M/LWS; ML; Molecular evolution; Mya; NEB; NJ; RH1; RH1-like; RH2; SWS1; SWS1 pseudogenes; maximum likelihood; middle and long wavelength-sensitive; million years ago; naive empirical Bayes; neighbor-joining; rhodopsin; short wavelength-sensitive type 1; the encyclopedia of DNA elements