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Background. The capacity of species to respond and perceive visual signal is integral to their evolutionary success. Giraffe is closely related to okapi, but the two species have broad range of phenotypic differences including their visual capacities. Vision studies rank giraffe’s visual acuity higher than all other artiodactyls despite sharing similar vision ecological determinants with most of them. To what extent giraffe unique visual capacity and its difference with okapi is reflected by changes in their vision genes is not understood.
Methods. The recent availability of giraffe and okapi genome provided opportunity to identify giraffe and okapi vision genes. Multiple strategies were employed to identify thirty-six candidate mammalian vision genes in giraffe and okapi genomes. Quantification of selection pressure was performed by a combination of branch-site test of positive selection and clade models of selection divergence through comparing giraffe and okapi vision genes and their corresponding orthologous sequences from other mammals obtained from public gene banks.
Results. Signatures of selection was identified in key genes that could potentially underlie giraffe and okapi visual adaptations. Importantly, some genes that contribute to optical transparency of the eye and those that are critical in light signaling pathway were found to show signatures of adaptive evolution or selection divergence. Comparison between giraffe and other ruminants identifies significant selection divergence in CRYAA and OPN1LW in giraffe. Significant selection divergencewas identified in SAG while positive selection was detected in LUM when okapi is compared with ruminants and other mammals. Sequence analysis of OPN1LW showed that at least one of the sites known to affect spectral sensitivity of the red pigment is uniquely divergent between giraffe and other ruminants.
Discussion. By taking a systemic approach to gene function in vision, the results provide the first molecular clues associated with giraffe and okapi vision adaptation. At least some of the genes that exhibit signature of selection may reflect adaptive response to differences in giraffe and okapi habitat. Moreover, requirement for long distance vision associated with predation likely played an important role in the adaptive pressure on giraffe vision genes.
This is a submission to PeerJ for review.
Candidate vision genes in mammals and their actual/possible role in visio
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