10.5061/DRYAD.4MW6M90C7
Ricci, Virginie
0000-0001-6466-1930
University of Basel
Ronco, Fabrizia
0000-0003-1583-8108
University of Basel
Musilova, Zuzana
Charles University
Salzburger, Walter
University of Basel
Molecular evolution and depth-related adaptations of rhodopsin in the
adaptive radiation of cichlid fishes in Lake Tanganyika
Dryad
dataset
2022
Vision
Rod photoreceptors
Opsin
spectral tuning
Freshwater fish
photic environment
FOS: Natural sciences
European Research Council
https://ror.org/0472cxd90
617585
Swiss National Science Foundation
https://ror.org/00yjd3n13
176039
Swiss National Science Foundation
https://ror.org/00yjd3n13
166550
Czech Science Foundation
https://ror.org/01pv73b02
21-31712S
2022-04-02T00:00:00Z
2022-04-02T00:00:00Z
en
https://doi.org/10.1038/s41586-020-2930-4
https://doi.org/10.5281/zenodo.6407335
2261966 bytes
8
CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
The visual sensory system is essential for animals to perceive their
environment and is thus under strong selection. In aquatic environments,
light intensity and spectrum differ primarily along a depth gradient.
Rhodopsin (RH1) is the only opsin responsible for dim-light vision in
vertebrates and has been shown to evolve in response to the respective
light conditions, including along a water depth gradient in fishes. In
this study, we examined the diversity and sequence evolution of RH1 in the
virtually entire adaptive radiation of cichlid fishes in Lake Tanganyika,
focusing on adaptations to the achromatic environment with respect to
depth. We show that Tanganyikan cichlid genomes contain a single copy of
RH1. The 76 variable amino acid sites detected in RH1 across the radiation
were not uniformly distributed along the protein sequence, and 31 of these
variable sites show signals of positive selection. Moreover, the amino
acid substitutions at 15 positively selected sites appeared to be
depth-related, including three key tuning sites that directly mediate
shifts in the peak spectral sensitivity, one site involved in protein
stability, and 11 sites that may be functionally important on the basis of
their physicochemical properties. Among the strongest candidate sites for
deep-water adaptations are two known key tuning sites (positions 292 and
299) and three newly identified variable sites (37, 104 and 290). Our
study, which is th first compralehensive analysis of RH1 evolution in a
massive adaptive radiation of cichlid fishes, provides novel insights into
the evolution of RH1 in a freshwater environment.
For this study, we revisited the Illumina sequence data from our previous
work, in which we had produced whole genome sequences for a nearly
taxonomically complete sample of the cichlid fish fauna of LT (raw
sequencing data are available on NCBI under the BioProject accession
number PRJNA550295, https://www.ncbi.nlm.nih.gov/bioproject/; Ronco et
al., 2021). Making use of the available raw DNA reads, we (i) identified
and newly assembled the intron-less RH1 coding sequence; (ii) quantified
the diversity of both nucleotides and amino acid sequences of RH1; (iii)
tested if environmental pressures have shaped RH1 protein sequence
evolution; and (iv) screened for candidate amino acid substitutions that
are associated with water depth and hence potentially represent
depth-related adaptations.
A GitHub reposit is available for further information:
https://github.com/Ninet93/RH1_Ricci_et_al.git