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21 - Collection, storage and analysis of non-invasive genetic material in primate biology

Published online by Cambridge University Press:  05 June 2012

Joanna M. Setchell
Affiliation:
University of Durham
Deborah J. Curtis
Affiliation:
Oxford Brookes University
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Summary

WHY NON-INVASIVE?

Non-invasive genetic analysis using new, high-precision molecular tools has been an extremely important recent development in primatology, with the promise of pioneering studies in the early–mid 1990s (see, for example, Morin et al., 1994) now being realized at the level of large-scale population studies over broad spatial scales (see, for example, Constable et al., 2001; Anthony et al., 2007b). However, it remains technically demanding, time-consuming, expensive and prone to error. Here, we introduce the applications of non-invasive genetics in primatology, then cover protocols for the most common non-invasive sample types, including faeces, urine and hair, outlining the limitations, pitfalls, and methodologies required. We also describe storage protocols for other possible sources of DNA (deoxyribonucleic acid), including blood and tissue biopsy samples for occasions when animals are captured and handled (Chapters 7 and 8).

APPLICATIONS

Molecular phylogenetic studies continue to add to our knowledge of primate diversity, evolution and hence adaptation (see, for example, Burrell et al., 2009). Phylogenetic analysis can also be used below the species level to study the underlying biogeographical factors that have contributed to the diversity present in primate populations today. This approach has been used to highlight new, evolutionarily distinct populations within well-studied species and to pinpoint potentially important geographical barriers that may delimit genetic divergences across the range of species (see, for example, Gonder et al., 1997).

Type
Chapter
Information
Field and Laboratory Methods in Primatology
A Practical Guide
, pp. 371 - 386
Publisher: Cambridge University Press
Print publication year: 2011

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References

Allen, M., Engstrom, A. S., Meyers, S.et al. (1998). Mitochondrial DNA sequencing of shed hairs and saliva on robbery caps: Sensitivity and matching probabilities. J. Forensic Sci. 43, 453–64.CrossRefGoogle ScholarPubMed
Amos, W., Hoffman, J. I., Frodsham, A.et al. (2007). Automated binning of microsatellite alleles: problems and solutions. Mol. Ecol. Notes 7, 10–14.CrossRefGoogle Scholar
Andrés, O., Rönn, A.-C., Bonhomme, M.et al. (2008). A microarray system for Y chromosomal and mitochondrial single nucleotide polymorphism analysis in chimpanzee populations. Mol. Ecol. Res. 8, 529–39.CrossRefGoogle Scholar
Anthony, N. M., Clifford, S. L., Bawe-Johnson, M.et al. (2007a). Distinguishing mitochondrial sequences from nuclear integrations and PCR recombinants: guidelines for their diagnosis in complex sequence databases. Mol. Phylogenet. Evol. 43, 553–66.CrossRefGoogle ScholarPubMed
Anthony, N. M., Johnson-Bawe, M., Jeffery, K.et al. (2007b). The role of Pleistocene refugia and rivers in shaping gorilla genetic diversity in central Africa. Proc. Natl. Acad. Sci. USA 104, 20432–6.CrossRefGoogle ScholarPubMed
Boom, R., Sol, C. J. A., Salimans, M. M. M.et al. (1990). Rapid and simple method for purification of nucleic acids. J. Clin. Microbiol. 28, 495–603.Google ScholarPubMed
Bruford, M. W., Hanotte, O. & Burke, T. (1998). Single and multilocus DNA fingerprinting. In Molecular Genetic Analysis of Populations: A Practical Approach, ed. Hoelzel, A. R. (2nd edn), pp. 225–69. Oxford: Oxford University Press.Google Scholar
Burrell, A. S., Jolly, C. J., Tosi, A. J. & Disotell, T. R. (2009). Mitochondrial evidence for the hybrid origin of the kipunji, Rungwecebus kipunji (Primates: Papionini). Mol. Phyl. Evol 51, 340–8.CrossRefGoogle Scholar
Chikhi, L. & Bruford, M. W. (2005). Mammalian population genetics and genomics. In Mammalian Genomics, ed. Ruvinsky, A. & Marshall-Graves, J., pp. 539–83. Oxford: CABI Publishing.CrossRefGoogle Scholar
Chu, J.-H., Wu, H.-Y., Yang, Y.-J., Takenaka, O. & Lin, Y.-S. (1999). Polymorphic microsatellite loci and low invasive DNA sampling in Macaca cyclopis. Primates 40, 573–80.CrossRefGoogle Scholar
Constable, J. L., Ashley, M. V., Goodall, J. & Pusey, A. E. (2001). Noninvasive paternity assignment in Gombe chimpanzees. Mol. Ecol. 10, 1279–300.CrossRefGoogle ScholarPubMed
Coote, T. & Bruford, M. W. (1996). A set of human microsatellites amplify polymorphic markers in Old World apes and monkeys. J. Hered. 87, 406–10.CrossRefGoogle Scholar
Di Fiore, A. (2003). Molecular genetic approaches to the study of primate behavior, social organization, and reproduction. Yb. Phys. Anthropol. 46, 62–99.CrossRefGoogle Scholar
Flagstad, Ø., Røed, K., Stacy, J. & Jakobsen, K. S. (1999). Reliable non-invasive genotyping based on excremental PCR of nuclear DNA purified with a magnetic bead protocol. Mol. Ecol. 8, 879–83.CrossRefGoogle Scholar
Frankham, R., Ballou, J. D. & Briscoe, D. A. (2002). Introduction to Conservation Genetics. Cambridge: Cambridge University Press.CrossRefGoogle Scholar
Gerloff, U., Schlötterer, C., Rassmann, I.et al. (1995). Amplification of hypervariable simple sequence repeats (Microsatellites) from excremental DNA of wild living Bonobos (Pan paniscus). Molec. Ecol. 4, 515–18.CrossRefGoogle Scholar
Gonder, M. K., Oates, J. F., Disotell, T. R.et al. (1997). A new west African chimpanzee subspecies? Nature 388, 337.CrossRefGoogle ScholarPubMed
Goossens, B., Chikhi, L., Utami, S. S., Ruiter, J. R. & Bruford, M. W. (2000). A multi-samples, multi-extracts approach for microsatellite analysis of faecal samples in an arboreal ape. Cons. Gen. 1, 157–62.CrossRefGoogle Scholar
Hashimoto, C., Furuichi, T. & Takenaka, O. (1996). Matrilineal kin relationship and social behaviour of wild bonobos (Pan paniscus): sequencing the D-loop region of mitochondrial DNA. Primates 37, 305–18.CrossRefGoogle Scholar
Hayakawa, S. & Takenaka, O. (1999). Urine as another potential source for template DNA in polymerase chain reaction (PCR). Am. J. Primatol. 48, 299–304.3.0.CO;2-G>CrossRefGoogle Scholar
Hedmark, E., Flagstad, O., Segerström, P.et al. (2004). DNA-based individual and sex identification from wolverine (Gulo gulo) faeces and urine. Cons. Gen. 5, 405–10.CrossRefGoogle Scholar
Jeffery, K. J., Abernethy, K. A., Tutin, C. E. G. & Bruford, M. W. (2007). Biological and environmental degradation of gorilla hair and microsatellite amplification success. Biol. J. Linn. Soc. 91, 281–94.CrossRefGoogle Scholar
Jensen-Seaman, M. I., Sarmiento, E. E., Deinard, A. S. & Kidd, K. K. (2004). Nuclear integrations of mitochondrial DNA in gorillas. Am. J. Primatol. 63, 139–47.CrossRefGoogle ScholarPubMed
Linch, C. A., Smith, S. L. & Prahlow, J. A. (1998). Evaluation of the human hair root for DNA typing subsequent to microscopic comparison. J. Forensic Sci. 43, 305–14.CrossRefGoogle ScholarPubMed
Linch, C. A., Whiting, D. A., & Holland, M. M. (2001). Human hair histogenesis for the mitochondrial DNA forensic scientist. J. Forensic Sci. 46, 844–53.CrossRefGoogle ScholarPubMed
Morin, P. A., Moore, J. J., Chakraborthy, R.et al. (1994). Kin selection, social structure, gene flow, and the evolution of chimpanzees. Science 265, 1193–201.CrossRefGoogle ScholarPubMed
Morin, P. A., Chambers, K. E., Boesch, C. & Vigilant, L. (2001). Quantitative polymerase chain reaction analysis of DNA from noninvasive samples for accurate microsatellite genotyping of wild chimpanzees (Pan troglodytes verus). Mol. Ecol. 10, 1835–44.CrossRefGoogle Scholar
Morin, P. A., Martien, K. & Taylor, B. L. (2009). Assessing statistical power of SNPs for population structure and conservation studies. Mol. Ecol. Res. 9, 66–73.CrossRefGoogle ScholarPubMed
Murphy, M. A., Waits, L. P. & Kendall, K. P. (2000). Quantitative evaluation of fecal drying methods for brown bear DNA analysis. Wildl. Soc. Bull. 28, 951–7.Google Scholar
Murphy, M. A., Kendall, K. C., Robinsom, A. & Waits, L. P. (2007). The impact of time and field conditions on brown bear (Ursus arctos) faecal DNA amplification. Conserv. Genet. 8, 1219–24.CrossRefGoogle Scholar
Pompanon, F., Bonin, A., Bellemain, E. & Taberlet, P. (2005). Genotyping errors: causes, consequences and solutions. Nature Rev. Genet. 6, 847–59.CrossRefGoogle ScholarPubMed
Roeder, A. D., Archer, F. I., Poinar, H. N. & Morin, P. A. (2004). A novel method for collection and preservation of faeces for genetic studies. Mol. Ecol. Notes 4, 761–4.CrossRefGoogle Scholar
Roeder, A. D., Bonhomme, M., Heijmans, C.et al. (2009). A large panel of microsatellites for genetic studies in the infra-order Catarrhini. Folia Primatol. 80, 63–9.CrossRefGoogle ScholarPubMed
Rönn, A.-C., Andrés, O., Bruford, M. W.et al. (2006). Multiple displacement amplification for generating an unlimited source of DNA for genotyping in nonhuman primate species. Int. J. Primatol. 27, 1145–69.CrossRefGoogle Scholar
Sastre, N., Francino, O., Lampreave, G.et al. (2009). Sex identification of wolf (Canis lupus) using non-invasive samples. Conserv. Genet. 10, 555–8.CrossRefGoogle Scholar
Smith, S., Aitken, N., Schwarz, C. & Morin, P. A. (2004). Characterization of 15 SNP markers for chimpanzees (Pan troglodytes). Mol. Ecol. Notes 4, 348–51.CrossRefGoogle Scholar
Soto-Calderon, I. D., Ntie, S., Mickala, P.et al. (2009). Effects of storage type and time on DNA amplification success in tropical ungulate faeces. Mol. Ecol. Res. 9, 471–9.CrossRefGoogle ScholarPubMed
Sugiyama, Y., Kawamoto, S., Takenaka, O., Kumizaki, K. & Norikatsu, W. (1993). Paternity discrimination and inter-group relationships of chimpanzees at Bossou. Primates 34, 545–52.CrossRefGoogle Scholar
Sunnucks, P. (2000). Efficient genetic markers for population biology. Trends Ecol. Evol. 15, 199–203.CrossRefGoogle ScholarPubMed
Symondson, W. O. C. (2002). Molecular identification of prey in predator diets. Mol. Ecol. 11, 627–41.CrossRefGoogle ScholarPubMed
Taberlet, P., Griffin, S., Goossens, B.et al. (1996). Reliable genotyping of samples with very low DNA quantities using PCR. Nucleic Acids Res. 24, 3189–94.CrossRefGoogle ScholarPubMed
Takenaka, O., Takashi, H., Kawamoto, S., Arakawa, M. & Takenaka, A. (1993). Polymorphic microsatellite DNA amplification customised for chimpanzee paternity testing. Primates 34, 27–35.CrossRefGoogle Scholar
Thalmann, O., Hebler, J., Poinar, H. N., Pääbo, S. & Vigilant, L. (2004). Unreliable mtDNA data due to nuclear insertions: a cautionary tale from analysis of humans and other great apes. Mol. Ecol. 13, 321–35.CrossRefGoogle ScholarPubMed
Valderrama, X., Karesh, W. B., Wildman, D. E & Melnick, D. J. (1999). Non-invasive methods for collecting fresh hair tissue. Mol. Ecol. 8, 1749–52.CrossRefGoogle Scholar
Valière, N. & Taberlet, P. (2000). Urine collected in the field as a source of DNA for species and individual identification. Mol. Ecol. 9, 2149–54.CrossRefGoogle Scholar
Heuverswyn, F., Li, Y. Y., Neel, C.et al. (2006). Human immunodeficiency viruses – SIV infection in wild gorillas. Nature 444, 164.CrossRefGoogle ScholarPubMed
Vigilant, L. (1999). An evaluation of techniques for the extraction and amplification of DNA from naturally shed hairs. Biol. Chem, 380, 1329–31.CrossRefGoogle ScholarPubMed
Walsh, P. S., Metzger, D. A., & Higuchi, R. (1991). Chelex-100 as a medium for simple extraction of DNA for PCR-based typing from forensic material. Biotechniques 10, 506–13.Google ScholarPubMed
Waits, L. P. & Paetkau, D. (2005). Non-invasive genetic sampling tools for wildlife biologists: a review of applications and recommendations for accurate data collection. J. Wildl. Mgt. 69, 1419–33.CrossRefGoogle Scholar
Wasser, S. K., Houston, C. S., Koehler, G. M., Cadd, G. G. & Fain, S. R. (1997). Techniques for application of faecal DNA methods to field studies of Ursids. Mol. Ecol. 6, 1091–7.CrossRefGoogle ScholarPubMed
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