Primates

, Volume 57, Issue 4, pp 541–547 | Cite as

Primate genotyping via high resolution melt analysis: rapid and reliable identification of color vision status in wild lemurs

  • Rachel L. Jacobs
  • Amanda N. Spriggs
  • Tammie S. MacFie
  • Andrea L. Baden
  • Mitchell T. Irwin
  • Patricia C. Wright
  • Edward E. LouisJr.
  • Richard R. Lawler
  • Nicholas I. Mundy
  • Brenda J. Bradley
Original Article

Abstract

Analyses of genetic polymorphisms can aid our understanding of intra- and interspecific variation in primate sociality, ecology, and behavior. Studies of primate opsin genes are prime examples of this, as single nucleotide variants (SNVs) in the X-linked opsin gene underlie variation in color vision. For primate species with polymorphic trichromacy, genotyping opsin SNVs can generally indicate whether individual primates are red-green color-blind (denoted homozygous M or homozygous L) or have full trichromatic color vision (heterozygous ML). Given the potential influence of color vision on behavior and fitness, characterizing the color vision status of study subjects is becoming commonplace for many primate field projects. Such studies traditionally involve a multi-step sequencing-based method that can be costly and time-consuming. Here we present a new reliable, rapid, and relatively inexpensive method for characterizing color vision in primate populations using high resolution melt analysis (HRMA). Using lemurs as a case study, we characterized variation at exons 3 and/or 5 of the X-linked opsin gene for 87 individuals representing nine species. We scored opsin genotypes and color vision status using both traditional sequencing-based methods as well as our novel melting-curve based HRMA protocol. For each species, the melting curves of varying genotypes (homozygous M, homozygous L, heterozygous ML) differed in melting temperature and/or shape. Melting curves for each sample were consistent across replicates, and genotype-specific melting curves were consistent across DNA sources (blood vs. feces). We show that opsin genotypes can be quickly and reliably scored using HRMA once lab-specific reference curves have been developed based on known genotypes. Although the protocol presented here focuses on genotyping lemur opsin loci, we also consider the larger potential for applying this approach to various types of genetic studies of primate populations.

Keywords

Opsin Strepsirrhines Sensory ecology Technique Single nucleotide variant genotyping 

References

  1. Bowmaker JK, Dartnall HJA, Mollon JD (1980) Micro-spectrophotometric demonstration of 4 classes of photoreceptor in an Old World primate, Macaca fascicularis. J Physiol Lond 298:131–143CrossRefPubMedPubMedCentralGoogle Scholar
  2. Bunce JA, Isbell LA, Neitz M, Bonci D, Surridge AK, Jacobs GH, Smith DG (2011) Characterization of opsin gene alleles affecting color vision in a wild population of titi monkeys (Callicebus brunneus). Am J Primatol 73:189–196CrossRefPubMedGoogle Scholar
  3. Cho MH, Ciulla D, Klanderman BJ, Raby BA, Silverman EK (2008) High resolution melting curve analysis of genomic and whole genome amplified DNA. Clin Chem 54:2055–2058CrossRefPubMedPubMedCentralGoogle Scholar
  4. Dacey DM (2000) Parallel pathways for spectral coding in primate retina. Annu Rev Neurosci 23:743–775CrossRefPubMedGoogle Scholar
  5. Doktycz MJ (2002) Nucleic acids: thermal stability and denaturation. Wiley, Chichester. http://www.els.net. doi:10.1038/npg.els.0003123
  6. Dulai KS, von Dornum M, Mollon JD, Hunt DM (1999) The evolution of trichromatic color vision by opsin gene duplication in New World and Old World primates. Genome Res 9:629–638PubMedGoogle Scholar
  7. Dwight Z, Palais R, Wittwer CT (2011) uMELT: prediction of high-resolution melting curves and dynamic melting profiles of PCR products in a rich web application. Bioinformatics 27:1019–1020CrossRefPubMedGoogle Scholar
  8. Fedigan L, Melin AD, Addicott J, Kawamura S (2014) The heterozygote superiority hypothesis for polymorphic color vision is not supported by long-term fitness data from wild Neotropical monkeys. PLoS One 9:e84872CrossRefPubMedPubMedCentralGoogle Scholar
  9. Hiramatsu C, Tsutsui T, Matsumoto Y, Aureli F, Fedigan LM, Kawamura S (2005) Color vision polymorphism in wild capuchins (Cebus capucinus) and spider monkeys (Ateles geoffroyi) in Costa Rica. Am J Primatol 67:447–461CrossRefPubMedGoogle Scholar
  10. Hiramatsu C, Melin AD, Aureli F, Schaffner CM, Vorobyev M, Matsumoto Y, Kawamura S (2008) Importance of achromatic contrast in short-range fruit foraging in primates. PLoS One 3:e3356CrossRefPubMedPubMedCentralGoogle Scholar
  11. Hiwatashi T, Okabe Y, Tsutsui T, Hiramatsu C, Melin AD, Oota H, Schaffner CM, Aureli F, Fedigan LM, Innan H, Kawamura S (2010) An explicit signature of balancing selection for color vision variation in New World monkeys. Mol Biol Evol 27:453–464CrossRefPubMedGoogle Scholar
  12. Jacobs GH (1984) Within species variations in visual capacity among squirrel monkeys (Saimiri sciureus) color vision. Vision Res 24:1267–1277CrossRefPubMedGoogle Scholar
  13. Jacobs GH (1993) The distribution and nature of color vision among the mammals. Biol Rev Camb Philos 68:413–471CrossRefGoogle Scholar
  14. Jacobs GH (1995) Variations in primate color vision: mechanisms and utility. Evol Anthropol 3:196–205CrossRefGoogle Scholar
  15. Jacobs GH (1998) A perspective on color vision in platyrrhine monkeys. Vis Res 38:3307–3313CrossRefPubMedGoogle Scholar
  16. Jacobs RL, Bradley BJ (2016) Considering the influence of nonadaptive evolution on primate color vision. PLoS One 11:e0149664. doi:10.1371/journal.pone.0149664 CrossRefPubMedPubMedCentralGoogle Scholar
  17. Jacobs GH, Deegan JF (2003) Photopigment polymorphism in prosimians and the origins of primate trichromacy. In: Mollon JD, Pokorny J, Knoblauch K (eds) Normal and defective colour vision. Oxford University Press, Oxford, pp 14–20CrossRefGoogle Scholar
  18. Leonhardt SD, Tung J, Camden JB, Leal M, Drea CM (2009) Seeing red: behavioral evidence of trichromatic color vision in strepsirrhine primates. Behav Ecol 20:1–12CrossRefGoogle Scholar
  19. Liew M, Pryor R, Palais R, Meadows C, Erali M, Lyon E, Wittwer C (2004) Genotyping of single-nucleotide polymorphisms by high-resolution melting of small amplicons. Clin Chem 50:1156–1164CrossRefPubMedGoogle Scholar
  20. McIntosh A, Bennett C, Dickson D, Anestis SF, Watts DP, Webster TH, Fontenot MB, Bradley BJ (2012) The apolipoprotein E (APOE) gene appears functionally monomorphic in chimpanzees (Pan troglodytes). PLoS One 7:e47760CrossRefPubMedPubMedCentralGoogle Scholar
  21. Melin AD, Fedigan LM, Hiramatsu C, Sendall CL, Kawamura S (2007) Effects of colour vision phenotype on insect capture by a free-ranging population of white-faced capuchins, Cebus capucinus. Anim Behav 73:205–214CrossRefGoogle Scholar
  22. Melin AD, Fedigan LM, Hiramatsu C, Kawamura S (2008) Polymorphic color vision in white-faced capuchins (Cebus capucinus): is there foraging niche divergence among phenotypes? Behav Ecol Sociobiol 62:659–670CrossRefGoogle Scholar
  23. Mundy NI, Morningstar NC, Baden AL, Fernandez-Duque E, Bradley BJ (2016) Can colour vision re-evolve? Variation in the X-linked opsin locus of cathemeral Azara’s owl monkeys (Aotus a. azarae). Front Zool 13:9. doi:10.1186/s12983-016-0139-z CrossRefPubMedPubMedCentralGoogle Scholar
  24. Nathans J (1999) The evolution and physiology of human color vision: insights from molecular genetic studies of visual pigments. Neuron 24:299–312CrossRefPubMedGoogle Scholar
  25. Nathans J, Thomas D, Hogness DS (1986) Molecular genetics of human color vision: the genes encoding blue, green, and red pigments. Science 232:193–202CrossRefPubMedGoogle Scholar
  26. Neitz M, Neitz J, Jacobs GH (1991) Spectral tuning of pigments underlying red-green color vision. Science 252:971–974CrossRefPubMedGoogle Scholar
  27. Parant JM, George SA, Pryor R, Wittwer CT, Yost HJ (2009) A rapid and efficient method of genotyping zebrafish mutants. Dev Dyn 238:3168–3174CrossRefPubMedPubMedCentralGoogle Scholar
  28. Payne MS, Tabone T, Kemp MW, Keelan JA, Spiller OB, Newnham JP (2014) High-resolution melt PCR analysis for genotyping of Ureaplasma parvum isolates directly from clinical samples. J Clin Microbiol 52:599–606CrossRefPubMedPubMedCentralGoogle Scholar
  29. Ramón-Laca A, Gleeson D, Yockney I, Perry M, Nugent G, Forsyth DM (2014) Reliable discrimination of 10 ungulate species using high resolution melting analysis of faecal DNA. PLoS One 9:e92043CrossRefPubMedPubMedCentralGoogle Scholar
  30. Shyue SK, Boissinot S, Schneider H, Sampaio I, Schneider MP, Abee CR, Williams L, Hewett-Emmett D, Sperling HG, Cowing JA, Dulai KS, Hunt DM, Li W-H (1998) Molecular genetics of spectral tuning in New World monkey color vision. J Mol Evol 46:697–702CrossRefPubMedGoogle Scholar
  31. Smith BL, Lu CP, Bremer JRA (2010) High-resolution melting analysis (HRMA): a highly sensitive inexpensive genotyping alternative for population studies. Mol Ecol Resour 10:193–196CrossRefPubMedGoogle Scholar
  32. Smith AC, Surridge AK, Prescott MJ, Osorio D, Mundy NI, Buchanan-Smith HM (2012) The effect of colour vision status on insect prey capture efficiency by captive and wild tamarins (Saguinus spp.). Anim Behav 83:479–486CrossRefGoogle Scholar
  33. Surridge AK, Osorio D, Mundy NI (2003) Evolution and selection of trichromatic vision in primates. Trends Ecol Evol 18:198–205CrossRefGoogle Scholar
  34. Surridge AK, Suárez SS, Buchanan-Smith HM, Mundy NI (2005) Non-random association of opsin alleles in wild groups of red-bellied tamarins (Saguinus labiatus) and maintenance of the colour vision polymorphism. Biol Lett 1:465–468CrossRefPubMedPubMedCentralGoogle Scholar
  35. Tan Y, Li WH (1999) Vision—trichromatic vision in prosimians. Nature 402:36CrossRefPubMedGoogle Scholar
  36. Thomsen N, Ali RG, Ahmed JN, Arkell RM (2012) High-resolution melt analysis (HRMA); a viable alternative to agarose gel electrophoresis for mouse genotyping. PLoS One 7:e45252CrossRefPubMedPubMedCentralGoogle Scholar
  37. Tovee MJ (1994) The molecular genetics and evolution of primate color vision. Trends Neurosci 17:30–37CrossRefPubMedGoogle Scholar
  38. Tung J, Primus A, Bouley AJ, Severson TF, Alberts SC, Wray GA (2009) Evolution of a malaria resistance gene in wild primates. Nature 460:388–391PubMedGoogle Scholar
  39. Valenta K, Edwards M, Rafaliarison RR, Johnson SE, Holmes SM, Brown KA, Dominy NJ, Lehman SM, Parra EJ, Melin AD (2015) Visual ecology of true lemurs suggests a cathemeral origin for the primate cone opsin polymorphism. Funct Ecol. doi:10.1111/1365-2435.12575 Google Scholar
  40. Veilleux CC, Bolnick DA (2009) Opsin gene polymorphism predicts trichromacy in a cathemeral lemur. Am J Primatol 71:86–90CrossRefPubMedGoogle Scholar
  41. Veilleux CC, Jacobs RL, Cummings ME, Louis EE, Bolnick DA (2014) Opsin genes and visual ecology in a nocturnal folivorous lemur. Int J Primatol 35:88–107CrossRefGoogle Scholar
  42. Vogel ER, Neitz M, Dominy NJ (2007) Effect of color vision phenotype on the foraging of wild white-faced capuchins, Cebus capucinus. Behav Ecol 18:292–297CrossRefGoogle Scholar
  43. Vossen RHAM, Aten E, Roos A, den Dunnen JT (2009) High-resolution melting analysis (HRMA): more than just sequence variant screening. Hum Mutat 30:860–2866CrossRefPubMedGoogle Scholar
  44. Wittwer CT, Reed GH, Gundry CN, Vandersteen JG, Pryor RJ (2003) High-resolution genotyping by amplicon melting analysis using LCGreen. Clin Chem 49:853–860CrossRefPubMedGoogle Scholar
  45. Wooding S, Bufe B, Grassi C, Howard MT, Stone AC, Vazquez M, Dunn DM, Meyerhof W, Weiss RB, Bamshad MJ (2006) Independent evolution of bitter-taste sensitivity in humans and chimpanzees. Nature 440:930–934CrossRefPubMedGoogle Scholar
  46. Yokoyama S, Radlwimmer FB (1998) The “five-sites” rule and the evolution of red and green color vision in mammals. Mol Biol Evol 15:560–567CrossRefPubMedGoogle Scholar

Copyright information

© Japan Monkey Centre and Springer Japan 2016

Authors and Affiliations

  • Rachel L. Jacobs
    • 1
    • 2
    • 3
  • Amanda N. Spriggs
    • 1
    • 4
  • Tammie S. MacFie
    • 5
  • Andrea L. Baden
    • 3
    • 6
    • 7
    • 8
  • Mitchell T. Irwin
    • 9
  • Patricia C. Wright
    • 3
    • 10
  • Edward E. LouisJr.
    • 11
  • Richard R. Lawler
    • 12
  • Nicholas I. Mundy
    • 5
  • Brenda J. Bradley
    • 1
  1. 1.Department of Anthropology, Center for the Advanced Study of Human PaleobiologyThe George Washington UniversityWashingtonUSA
  2. 2.Interdepartmental Doctoral Program in Anthropological SciencesStony Brook UniversityStony BrookUSA
  3. 3.Centre ValBio Research Station, RanomafanaFianarantsoaMadagascar
  4. 4.Department of AnthropologyUniversity at Albany-SUNYAlbanyUSA
  5. 5.Department of ZoologyUniversity of CambridgeCambridgeUK
  6. 6.Department of AnthropologyHunter College of City University of New YorkNew YorkUSA
  7. 7.Departments of Anthropology and BiologyThe Graduate Center of City University of New YorkNew YorkUSA
  8. 8.The New York Consortium in Evolutionary PrimatologyNew YorkUSA
  9. 9.Department of AnthropologyNorthern Illinois UniversityDeKalbUSA
  10. 10.Department of AnthropologyStony Brook UniversityStony BrookUSA
  11. 11.Conservation Genetics DepartmentOmaha’s Henry Doorly Zoo and AquariumOmahaUSA
  12. 12.Department of Sociology and AnthropologyJames Madison UniversityHarrisonburgUSA

Personalised recommendations