title: Evolutionary analysis of vision genes identifies potential drivers of visual differences between giraffe and okapi.
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 inCRYAAandOPN1LW. Significant selection divergence was identified inSAGwhile positive selection was detected inLUMwhen okapi is compared with ruminants and other mammals. Sequence analysis ofOPN1LWshowed that at least one of the sites known to affect spectral sensitivity of the red pigment is uniquely divergent between giraffe and other ruminants.
  
  
  CONCLUSIONS
  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.
authors.affiliation: 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.
authors.forename: Edson
authors.initials: E
authors.lastname: Ishengoma
authors.affiliation: The School of Life Sciences and Bio-Engineering, Nelson Mandela African Institution of Science and Technology , Arusha , Tanzania.
authors.forename: Morris
authors.initials: M
authors.lastname: Agaba
authors.affiliation: Department of Biology and the Huck Institute of Life Sciences, Pennsylvania State University , University Park , PA , United States.
authors.forename: Douglas R
authors.initials: DR
authors.lastname: Cavener
keywords: Adaptive evolution; Candidate vision genes; Giraffe; Okapi