Primates

, Volume 57, Issue 4, pp 541–547

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

DOI: 10.1007/s10329-016-0546-y

Cite this article as:
Jacobs, R.L., Spriggs, A.N., MacFie, T.S. et al. Primates (2016) 57: 541. doi:10.1007/s10329-016-0546-y

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 

Funding information

Funder NameGrant NumberFunding Note
Yale University
    Natural Environment Research Council
      George Washington University
        National Science Foundation
        • 1227143

        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

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