Adaptive Gene Loss in Vertebrates: Photosensitivity as a Model Case


Current evolutionary thinking aims to amalgamate the conjectures first set out in Darwin's The Origin of Species with modern genetics to form a unified theory of phylogenetic change that explains the mechanisms mediating the diversity of life. With the advent of molecular biology, it has been shown that the mechanics of evolution fundamentally exert their effect at the molecular level and any genetic modification ultimately becomes fixed in the host genome if the resultant phenotype allows an organism to become better adapted to its ecology. The vertebrate colour visual sensory system, and the photopigment genes that form the first step in light detection, represents an ideal model to illustrate the influence of evolution at a molecular level, which through gene loss, duplication and genome rearrangement may allow an organism to adapt to an ever changing (and spectrally unique) environment.

Key Concepts:

  • Modern evolutionary thought seeks to amalgamate a multitude of scientific disciplines to produce a unified theory of phylogenesis.

  • Evolution fundamentally exerts its influence at the molecular level of genomes, genes, RNAs and proteins.

  • Evolutionary mechanic is a continuous process and specific genetic changes become selectively fixed if the resultant phenotype allows an organism to be better suited to a particular environment.

  • Adaptive evolution is the result of an ongoing interaction between an organism's physiology, its drive to survive and reproduce and its immediate ecology.

  • The mechanisms that mediate molecular adaptation have permitted the multiplicity of ecological niches to be colonised by a myriad of diverse life forms.

  • Sophisticated sensory systems ultimately form the interface that mediates the complex interactions between organisms and varied environments.

  • The vertebrate visual system is a model case for determining the mechanics of adaptive evolution.

  • In addition to gene duplication, genome rearrangement and genetic drift, gene loss is a major player in shaping the genetic substrate on which molecular adaptation may act.

Keywords: vertebrate; gene; opsin; adaptation; ecology; evolution

Figure 1.

Schematic (a) side view and (b) aerial view of an opsin, showing the presence of seven transmembrane domains (yellow) typical of the GPCR superfamily. Opsin residues involved in spectral tuning (coloured) and the retinal chromophore (orange) are shown.

Figure 2.

A phylogenetic tree of vertebrate opsin evolution, showing the presence of five main opsin classes in the pouched lamprey and those lost from the genome of the sea lamprey.

Figure 3.

A vertebrate lineage cladogram showing how the repertoire of opsins adapts through gene loss and duplication as a function of differential ecology. The presence of five opsins, which first evolved in the basal lampreys, is conserved at each major node (yellow star), except for the mammals where gene loss occurred early and throughout the mammalian lineage.



Amores A, Force A, Yan YL et al. (1998) Zebrafish hox clusters and vertebrate genome evolution. Science 282: 1711–1714.

Arrese CA, Hart NS, Thomas N et al. (2002) Trichromacy in Australian marsupials. Current Biology 12: 657–660.

Bailes HJ, Davies WL, Trezise AE et al. (2007) Visual pigments in a living fossil, the Australian lungfish Neoceratodus forsteri. BioMed Central Evolutionary Biology 7: 200.

Bowmaker JK (2008) Evolution of vertebrate visual pigments. Vision Research 48: 2022–2041.

Cappetta H, Duffin C and Zidek J (1993) The fossil record 2. In: Benton MJ (ed.) Chondrichthyes, pp. 593–609. London: Chapman and Hall.

Carvalho LS, Cowing JA, Wilkie SE et al. (2006) Shortwave visual sensitivity in tree and flying squirrels reflects changes in lifestyle. Current Biology 16: R81–R83.

Carvalho LS, Cowing JA, Wilkie SE et al. (2007) The molecular evolution of avian ultraviolet‐ and violet‐sensitive visual pigments. Molecular Biology and Evolution 24: 1843–1852.

Chinen A, Hamaoka T, Yamada Y et al. (2003) Gene duplication and spectral diversification of cone visual pigments of zebrafish. Genetics 163: 663–675.

Collin SP, Knight MA, Davies WL et al. (2003) Ancient colour vision: multiple opsin genes in the ancestral vertebrates. Current Biology 13: R864–R865.

Cowing JA, Arrese CA, Davies WL et al. (2008) Cone visual pigments in two marsupial species: the fat‐tailed dunnart (Sminthopsis crassicaudata) and the honey possum (Tarsipes rostratus). Proceedings of the Royal Society of London. Series B: Biological Sciences 275: 1491–1499.

Davies WL, Carvalho LS, Cowing JA et al. (2007b) Visual pigments of the platypus: a novel route to mammalian colour vision. Current Biology 17: R161–R163.

Davies WL, Carvalho LS, Tay BH et al. (2009b) Into the blue: gene duplication and loss underlie color vision adaptations in a deep‐sea chimaera, the elephant shark Callorhinchus milii. Genome Research 19: 415–426.

Davies WL, Collin SP and Hunt DM (2009a) Adaptive gene loss reflects differences in the visual ecology of basal vertebrates. Molecular Biology and Evolution 26: 1803–1809.

Davies WL, Cowing JA, Bowmaker JK et al. (2009c) Shedding light on serpent sight: the visual pigments of henophidian snakes. Journal of Neuroscience 29: 7519–7525.

Davies WL, Cowing JA, Carvalho LS et al. (2007a) Functional characterization, tuning, and regulation of visual pigment gene expression in an anadromous lamprey. FASEB Journal 21: 2713–2724.

Dulai KS, von Dornum M, Mollon JD et al. (1999) The evolution of trichromatic color vision by opsin gene duplication in New World and Old World primates. Genome Research 9: 629–638.

Fernholm B and Holmberg K (1975) The eyes in three genera of hagfish (Eptatretus, Paramyxine and Myxine) – a case of degenerative evolution. Vision Research 15: 253–259.

Froese R and Pauly D (eds) (2009) Fishbase (

Harosi F and Kleinschmidt J (1993) Visual pigments in the sea lamprey. Petromyzon marinus. Visual Neuroscience 10: 711–715.

Hart NS and Hunt DM (2007) Avian visual pigments: characteristics, spectral tuning, and evolution. American Naturalist 169: S7–26.

Hart NS, Lisney TJ, Marshall NJ et al. (2004) Multiple cone visual pigments and the potential for trichromatic colour vision in two species of elasmobranch. Journal of Experimental Biology 207: 4587–4594.

Hisatomi O, Takahashi Y, Taniguchi Y et al. (1999) Primary structure of a visual pigment in bullfrog green rods. FEBS Letters 447: 44–48.

Hunt DM, Dulai KS, Partridge JC et al. (2001) The molecular basis for spectral tuning of rod visual pigments in deep‐sea fish. Journal of Experimental Biology 204: 3333–3344.

Jaillon O, Aury JM, Brunet F et al. (2004) Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto‐karyotype. Nature 431: 946–957.

Jerlov NG (1976) Marine Optics. Amsterdam: Elsevier Scientific.

Last PR and Stevens JD (1994) Sharks and Ray of Australia: 513. Australia: CSIRO.

Lucas SG and Lou Z (1993) Adelobasileus from the upper Triassic of west Texas: the oldest mammal. Journal of Vertebrate Paleontology 13: 309–334.

Minamoto T and Shimizu I (2005) Molecular cloning of cone opsin genes and their expression in the retina of a smelt, Ayu (Plecoglossus altivelis, Teleostei). Comparative Biochemistry and Physiology – Part B: Biochemistry and Molecular Biology 140: 197–205.

Mohun SM, Davies WL, Bowmaker JK et al. (2010) Identification and characterization of visual pigments in caecilians (Amphibia: Gymnophiona), an order of limbless vertebrates with rudimentary eyes. Journal of Experimental Biology 213: 3586–3592.

Newman LA and Robinson PR (2005) Cone visual pigments of aquatic mammals. Visual Neuroscience 22: 873–879.

Owens GL, Windsor DJ, Mui J et al. (2009) A fish eye out of water: ten visual opsins in the four‐eyed fish, Anableps anableps. PLoS ONE 4: e5970.

O'Brien J, Ripps H and Al‐Ubaidi MR (1997) Molecular cloning of a rod opsin cDNA from the skate retina. Gene 193: 141–150.

Palacios AG, Bozinovic F, Vielma A et al. (2010) Retinal photoreceptor arrangement, SWS1 and LWS opsin sequence, and electroretinography in the South American marsupial Thylamys elegans (Waterhouse, 1839). Journal of Comparative Neurology 518: 1589–1602.

Parry JW, Carleton KL, Spady T et al. (2005) Mix and match color vision: tuning spectral sensitivity by differential opsin gene expression in Lake Malawi cichlids. Current Biology 15: 1734–1739.

Pointer MA, Carvalho LS, Cowing JA et al. (2007) The visual pigments of a deep‐sea teleost, the pearl eye Scopelarchus analis. Journal of Experimental Biology 210: 2829–2835.

Potter I, Prince P and Croxall J (1979) Data on the adult marine and migratory phases in the life cycle of the southern hemisphere lamprey Geotria australis. Environmental Biology of Fishes 4: 65–69.

Reitner A, Sharpe LT and Zrenner E (1991) Is colour vision possible with only rods and blue‐sensitive cones? Nature 352: 798–800.

Sansom IJ, Smith MP and Smith MM (1996) Scales of thelodont and shark‐like fishes from the Ordovician. Nature 379: 628–630.

Shand J, Davies WL, Thomas N et al. (2008) The influence of ontogeny and light environment on the expression of visual pigment opsins in the retina of the black bream, Acanthopagrus butcheri. Journal of Experimental Biology 211: 1495–1503.

Shu D, Morris S, Han J et al. (2003) Head and backbone of the early Cambrian vertebrate Haikouichthys. Nature 421: 526–529.

Spady TC, Seehausen O, Loew ER et al. (2005) Adaptive molecular evolution in the opsin genes of rapidly speciating cichlid species. Molecular Biology and Evolution 22: 1412–1422.

Theiss SM, Lisney TJ, Collin SP et al. (2007) Colour vision and visual ecology of the blue‐spotted maskray, Dasyatis kuhlii (Muller and Henle, 1814). Journal of Comparative Physiology A 193: 67–79.

Tudge C (2000) The Variety of Life. Oxford: Oxford University Press.

Wakefield MJ, Anderson M, Chang E et al. (2008) Cone visual pigments of monotremes: filling the phylogenetic gap. Visual Neuroscience 25: 257–264.

Ward MN, Churcher AM, Dick KJ et al. (2008) The molecular basis of color vision in colorful fish: four long wave‐sensitive (LWS) opsins in guppies (Poecilia reticulata) are defined by amino acid substitutions at key functional sites. BioMed Central Evolutionary Biology 8: 210.

Weadick CJ and Chang BS (2007) Long‐wavelength sensitive visual pigments of the guppy (Poecilia reticulata): six opsins expressed in a single individual. BioMed Central Evolutionary Biology 7: S11.

Whitmore AV and Bowmaker JK (1989) Seasonal variation in cone sensitivity and short‐wave absorbing visual pigments in the rudd Scadinius erythrophythalmus. Journal of Comparative Physiology A 166: 103–115.

Yokoyama S (2000) Molecular evolution of vertebrate visual pigments. Progress in Retinal and Eye Research 19: 385–419.

Yokoyama S, Zhang H, Radlwimmer FB et al. (1999) Adaptive evolution of color vision of the Comoran coelacanth (Latimeria chalumnae). Proceedings of the National Academy of Sciences of the USA 96: 6279–6284.

Young JZ (1981) Chapter 19: the origin of mammals. In: Nixon M (ed.) The Life of Vertebrates, 3rd edn. Oxford: Oxford University Press.

Further Reading

Alberts B, Johnson A, Lewis J et al. (2008) Molecular Biology of the Cell, 5th edn. New York: Garland Science.

Bateson W (1909) Mendel's Principles of Heredity. Cambridge: Cambridge University Press.

Darwin CR (2006) On the Origin of Species, 1st edn. London: The Folio Society.

Dawkins R (2004) The Ancestor's Tale: A Pilgrimage to the Dawn of Life. London: Phoenix.

Fisher RA (1930) The Genetical Theory of Natural Selection. Oxford: Oxford University Press.

Gould SJ (1989) Wonderful Life: The Burgess Shale and the Nature of History. London: Hutchinson.

Haldane JBS (1932) The Causes of Evolution. London: Longmans Green and Co.

Page RDM and Holmes E (1998) Molecular Evolution: A Phylogenetic Approach. Oxford: Blackwell Science.

Pough FH, Janis CM and Heiser JB (2008) Vertebrate Life, 8th edn. San Francisco: Pearson Education.

Watson JD (1997) The Double Helix: A Personal Account of the Discovery of the Structure of DNA. London: Weidenfeld and Nicolson.

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Davies, Wayne L(Jan 2011) Adaptive Gene Loss in Vertebrates: Photosensitivity as a Model Case. In: eLS. John Wiley & Sons Ltd, Chichester. [doi: 10.1002/9780470015902.a0022890]