Degeneration of olfactory receptor gene repertories in primates: No direct link to full trichromatic vision

Molecular Biology and Evolution

Volumn 27, Issue 5, 2010, Pages 1192-1200

  Matsui, Atsushi ^a   Go, Yasuhiro ^a   Niimura, Yoshihito ^b  

^a KYOTO UNIVERSITY   (Japan)

^b TOKYO MEDICAL AND DENTAL UNIVERSITY   (Japan)

Author keywords

Color vision; Gene loss; Multigene family; Olfactory receptor; Primate evolution; Smell sense

Indexed keywords

ARTICLE; CERCOPITHECIDAE; CHIMPANZEE; COLOR VISION; GENE LOSS; GENE SEQUENCE; GENOME; HUMAN; MACACA; MARMOSET; MULTIGENE FAMILY; NONHUMAN; OLFACTORY RECEPTOR; ORANG UTAN; ORTHOLOGY; PLATYRRHINI; PRIMATE; PROSIMIAN; RECEPTOR GENE; SCANDENTIA; SEQUENCE ANALYSIS; SMELLING;

ANIMALS; CERCOPITHECIDAE; COLOR VISION; EVOLUTION, MOLECULAR; HUMANS; MULTIGENE FAMILY; PLATYRRHINI; PRIMATES; RECEPTORS, ODORANT; SEQUENCE HOMOLOGY, NUCLEIC ACID;

CERCOPITHECIDAE; HOMO; MACACA; MAMMALIA; PLATYRRHINI; PRIMATES; STREPSIRHINI; TUPAIIDAE;

EID: 77951529170     PISSN: 07374038     EISSN: 15371719     Source Type: Journal    
DOI: 10.1093/molbev/msq003     Document Type: Article

References (55)

1. Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. 1997. Gapped Blast and PSI-Blast: a new generation of protein database search programs. Nucleic Acids Res. 25:3389-3402.
2. Barton RA. 2006. Olfactory evolution and behavioral ecology in primates. Am J Primatol. 68:545-558.
3. Buck L, Axel R. 1991. A novel multigene family may encode odorant receptors: a molecular basis for odor recognition. Cell 65:175-187.
4. Caine NG, Mundy NI. 2000. Demonstration of a foraging advantage for trichromatic marmosets (Callithrix geoffroyi) dependent on food colour. Proc R Soc Lond B. 267:439-444.
5. Caine NG, Osorio D, Mundy NI. Forthcoming. 2009. A foraging advantage for dichromatic marmosets (Callithrix geoffroyi) at low light intensity. Biol Lett. 6:36-38.
6. Chimpanzee Sequencing and Analysis Consortium. 2005. Initial sequence of the chimpanzee genome and comparison with the human genome. Nature 437:69-87.
7. Deeb SS. 2006. Genetics of variation in human color vision and the retinal cone mosaic. Curr Opin Genet Dev. 16:301-307.
8. Dominy NJ, Lucas PW. 2001. Ecological importance of trichromatic vision to primates. Nature 410:363-366.
9. Farris JS. 1977. Phylogenetic analysis under Dollo's law. Syst Zool. 26:77-88.
10. Genome 10K Community of Scientists. 2009. Genome 10K: a proposal to obtain whole-genome sequence for 10,000 vertebrate species. J Hered. 100:659-674.
11. Gilad Y, Man O, Glusman G. 2005. A comparison of the human and chimpanzee olfactory receptor gene repertoires. Genome Res. 15:224-230.
12. Gilad Y, Man O, Pääbo S, Lancet D. 2003. Human specific loss of olfactory receptor genes. Proc Natl Acad Sci USA. 100: 3324-3327.
13. Gilad Y, Przeworski M, Lancet D. 2004. Loss of olfactory receptor genes coincides with the acquisition of full trichromatic vision in primates. PLoS Biol. 2:e5.
14. Gilad Y, Wiebe V, Przeworski M, Lancet D, Pääbo S. 2007. Correction: loss of olfactory receptor genes coincides with the acquisition of full trichromatic vision in primates. PLoS Biol. 5:e148.
15. Glusman G, Yanai I, Rubin I, Lancet D. 2001. The complete human olfactory subgenome. Genome Res. 11:685-702.
16. Go Y, Niimura Y. 2008. Similar numbers but different repertoires of olfactory receptor genes in humans and chimpanzees. Mol Biol Evol. 25:1897-1907.
17. Hasin-Brumshtein Y, Lancet D, Olender T. 2009. Human olfaction: from genomic variation to phenotypic diversity. Trends Genet. 25:178-184.
18. Hedges SB, Dudley J, Kumar S. 2006. TimeTree: a public knowledge-base of divergence times among organisms. Bioinformatics 22:2971-2972.
19. Hiramatsu C, Melin AD, Aureli F, Schaffner CM, Vorobyev M, Kawamura S. 2009. Interplay of olfaction and vision in fruit foraging of spider monkeys. Anim Behav. 77:1421-1426.
20. Hiramatsu C, Melin AD, Aureli F, Schaffner CM, Vorobyev M, Matsumoto Y, Kawamura S. 2008. Importance of achromatic contrast in short-range fruit foraging of primates. PLoS ONE. 3:e3356
21. International Human Genome Sequencing Consortium. 2001. Initial sequencing and analysis of the human genome. Nature 409:860-921.
22. Jacobs GH. 1996. Primate photopigments and primate color vision. Proc Natl Acad Sci USA. 93:577-581.
23. Jacobs GH. 2007. New World monkeys and color. Int J Primatol. 28:729-759.
24. Jacobs GH, Neitz M, Deegan JF, Neitz J. 1996. Trichromatic colour vision in New World monkeys. Nature 382:156-158.
25. Kawamura S, Hirai M, Takenaka O, Radlwimmer FB, Yokoyama S. 2001. Genomic and spectral analyses of long to middle wavelength-sensitive visual pigments of common marmoset (Callithrix jacchus). Gene 269:45-51.
26. Laska M, Freist P, Krause S. 2007. Which senses play a role in nonhuman primate food selection? A comparison between squirrel monkeys and spider monkeys. Am J Primatol. 69:282-294.
27. Laska M, Seibt A, Weber A. 2000. 'Microsmatic' primates revisited: olfactory sensitivity in the squirrel monkey. Chem Senses. 25:47-53.
28. Le Quesne WJ. 1974. The uniquely evolved character concept and its cladistic application. Syst Zool. 23:513-517.
29. Martin RD. 1990. Primate origins and evolution: a phylogenetic reconstruction. London: Chapman Hall. p. 327-329
30. Matsui A, Rakotondraparany F, Munechika I, Hasegawa M, Horai S. 2009. Molecular phylogeny and evolution of prosimians based on complete sequences of mitochondrial DNAs. Gene 441:53-66.
31. Melin AD, Fedigan LM, Hiramatsu C, Hiwatashi T, Parr N, Kawamura S. 2009. Fig foraging by dichromatic and trichromatic Cebus capucinus in a tropical dry forest. Int J Primatol. 30:753-775.
32. Melin AD, Fedigan LM, Hiramatsu C, Sendall C, Kawamura S. 2007. Effects of colour vision phenotype on insect capture by a free-ranging population of white-faced capuchins, Cebus capucinus. Anim Behav. 73:205-214.
33. Mombaerts P. 2004. Genes and ligands for odorant, vomeronasal and taste receptors. Nat Rev Neurosci. 5:263-278. (Pubitemid 38478654)
34. Müller S, Wienberg J. 2001. "Bar-coding" primate chromosomes: molecular cytogenetic screening for the ancestral hominoid karyotype. Hum Genet. 109:85-94.
35. Murphy WJ, Pringle TH, Crider TA, Springer MS, Miller W. 2007. Using genomic data to unravel the root of the placental mammal phylogeny. Genome Res. 17:413-421.
36. Nei M, Gojobori T. 1986. Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Mol Biol Evol. 3:418-426.
37. Nei M, Niimura Y, Nozawa M. 2008. The evolution of animal chemosensory receptor gene repertoires: roles of chance and necessity. Nat Rev Genet. 9:951-963.
38. Newman T, Trask BJ. 2003. Complex evolution of 7E olfactory receptor genes in segmental duplications. Genome Res. 13: 781-793.
39. Niimura Y. 2009. On the origin and evolution of vertebrate olfactory receptor genes: comparative genome analysis among 23 chordate species. Genome Biol Evol. 1:34-44.
40. Niimura Y, Nei M. 2003. Evolution of olfactory receptor genes in the human genome. Proc Natl Acad Sci USA. 100:12235-12240.
41. Niimura Y, Nei M. 2005a. Comparative evolutionary analysis of olfactory receptor gene clusters between humans and mice. Gene 346:13-21.
42. Niimura Y, Nei M. 2005b. Evolutionary dynamics of olfactory receptor genes in fishes and tetrapods. Proc Natl Acad Sci USA. 102:6039-6044.
43. Niimura Y, Nei M. 2006. Evolutionary dynamics of olfactory and other chemosensory receptor genes in vertebrates. J Hum Genet. 51:505-517.
44. Niimura Y, Nei M. 2007. Extensive gains and losses of olfactory receptor genes in mammalian evolution. PLoS ONE. 2:e708.
45. Onishi A, Koike S, Ida M, et al. (13 co-authors). 1999. Dichromatism in macaque monkeys. Nature 402:139-140.
46. Perry GH, Martin RD, Verrelli BC. 2007. Signatures of functional constraint at aye-aye opsin genes: the potential of adaptive color vision in a nocturnal primate. Mol Biol Evol. 24:1963-1970.
47. Rhesus Macaque Genome Sequencing and Analysis Consortium. 2007. Evolutionary and biomedical insights from the rhesus macaque genome. Science 316:222-234.
48. Saito A, Mikami A, Kawamura S, et al. (13 co-authors). 2005. Advantage of dichromats over trichromats in discrimination of color-camouflaged stimuli in nonhuman primates. Am J Primatol. 67:425-436.
49. Saito H, Chi Q, Zhuang H, Matsunami H, Mainland JD. 2009. Odor coding by a mammalian receptor repertoire. Sci Signal. 2:ra9.
50. Schmitz J, Ohme M, Zischler H. 2001. SINE insertions in cladistic analyses and the phylogenetic affiliations of Tarsius bancanus to other primates. Genetics 157:777-784.
51. Smith AC, Buchanan-Smith HM, Surridge AK, Osorio D, Mundy NI. 2003. The effect of colour vision status on the detection and selection of fruits by tamarins (Saguinus spp.). J Exp Biol. 206:3159-3165.
52. Terao K, Mikami A, Saito A, et al. (15 co-authors). 2005. Identification of a protanomalous chimpanzee by molecular genetic and electroretinogram analyses. Vision Res. 45:1225-1235.
53. Thompson JD, Higgins DG, Gibson TJ. 1994. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignments through sequence weighting, position specific gap penalties and weight matrix choice. Nucleic Acids Res. 22:4673-4680.
54. Zhang X, Firestein S. 2002. The olfactory receptor gene superfamily of the mouse. Nat Neurosci. 5:124-133.
55. Zozulya S, Echeverri F, Nguyen T. 2001. The human olfactory receptor repertoire. Genome Biol. 2:research0018.1-researc0018.12.