Evolutionary analysis of vision genes identifies potential drivers of visual differences between giraffe and okapi

Edson Ishengoma; Morris Agaba; Douglas R Cavener

doi:10.7717/peerj.3145

Evolutionary analysis of vision genes identifies potential drivers of visual differences between giraffe and okapi

PeerJ. 2017 Apr 6:5:e3145. doi: 10.7717/peerj.3145. eCollection 2017.

Authors

Edson Ishengoma¹, Morris Agaba², Douglas R Cavener³

Affiliations

¹ The School of Life Sciences and Bio-Engineering, Nelson Mandela African Institution of Science and Technology, Arusha, Tanzania; Mkwawa University of College of Education, University of Dar-es-Salaam, Iringa, Tanzania.
² The School of Life Sciences and Bio-Engineering, Nelson Mandela African Institution of Science and Technology , Arusha , Tanzania.
³ Department of Biology and the Huck Institute of Life Sciences, Pennsylvania State University , University Park , PA , United States.

Abstract

Background: The capacity of visually oriented species to perceive and respond to visual signal is integral to their evolutionary success. Giraffes are 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 many of them. The extent to which the giraffe's 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 genomes 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 tests of positive selection and clade models of selection divergence through comparing giraffe and okapi vision genes and orthologous sequences from other mammals.

Results: Signatures of selection were 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. Significant selection divergence was 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 adaptations. At least some of the genes that exhibit signature of selection may reflect adaptive response to differences in giraffe and okapi habitat. We hypothesize that requirement for long distance vision associated with predation and communication with conspecifics likely played an important role in the adaptive pressure on giraffe vision genes.

Keywords: Adaptive evolution; Candidate vision genes; Giraffe; Okapi.

Grants and funding

This work received support from the Tanzania Commission of Science and Technology, Nelson Mandela African Institute of Science and Technology, Penn State University, Biosciences Eastern and Central Africa–International Livestock Research Institute, Nashville Zoo and White Oak Holding and SEZARC. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.