A simple, economical protocol for DNA extraction and amplification where there is no lab
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Genetic analyses are well suited to address many research questions in the study of wild populations, yet species of interest often have distributions that are geographically distant from molecular laboratories, necessitating potentially lengthy transport of biological specimens. Performing basic genetic analyses on site would avoid the project delays and risks of sample quality decline associated with transport, as well as allow original specimens to remain in the country of origin. Further, diagnostic genetic assays performed in the field could provide real-time information allowing for more nimble adjustments to research plans and use of resources. To this end, we developed protocols for reliably performing front-end genetics bench work in the field, without the requirements of electricity or permanent shelter. We validated these protocols on buccal swabs collected during routine capturing of sifaka lemurs (Propithecus verreauxi) at Bezà Mahafaly Special Reserve in Southwest Madagascar and faecal samples collected from captive sifakas (P. coquereli) at the Duke Lemur Center. Our basic protocol pipeline involves a chelating resin based DNA extraction followed by whole genome amplification or polymerase chain reaction using reagents stored at ambient temperature and portable, compact equipment powered by a lightweight solar panel. We achieved a high success rate (>80%) in downstream procedures, demonstrating the promise of such protocols for performing basic genetic analyses in a broad range of field situations.
KeywordsPopulation genetics Genotyping Sex-typing Field methods Capacity building Madagascar
We thank Sibien Mahereza, Enafa, Elahavelo Efitroarane, Efitiria, Eduoard, Lydia Greene, Roshna Wunderlich, Chloe Chen-Kraus, and Erin Ehmke for helping with sample collection; Rachel Jacobs, Gary Aronsen, and Katie Grogan for lab assistance; Sebastian Kraves of miniPCR for technical support; Yale University, The George Washington University, and James Madison University for funding. We would also like to thank two anonymous reviewers for their helpful comments. All research conformed to institutional and national guidelines. The research conducted at Bezà Mahafaly Special Reserve falls under James Madison University IACUC number A03-14. Research at the Duke Lemur Center was conducted under Duke research number 0-2-16-3 and with Duke IACUC number A168-14-07. This is Duke Lemur Center Publication Number 1345.
Compliance with ethical standards
Conflict of interest
The authors have no conflicts of interest to declare.
- Allendorf FW, Luikart G (2009) Conservation and the genetics of populations. Wiley-Blackwell, OxfordGoogle Scholar
- Jacobs RL, MacFie TS, Spriggs AN, Baden AL, Morelli TL, Irwin MT, Lawler RR, Pastorini J, Mayor M, Lei R, Culligan R, Hawkins MTR, Kappeler PM, Wright PC, Louis EE, Mundy NI, Bradley BJ (2017) Novel opsin gene variation in large-bodied, diurnal lemurs. Biol Lett 13:20170050CrossRefPubMedPubMedCentralGoogle Scholar
- Sussman RW, Richard AF, Ratsirarson J, Sauther ML, Brockman DK, Gould L, Lawler R, Cuozzo FP (2012) Bezà Mahafaly Special Reserve: long-term research on lemurs in southwestern Madagascar. In: Kappeler PM, Watts DP (eds) Long-term field studies of primates. Springer, Berlin Heidelberg, pp 45–66CrossRefGoogle Scholar
- Wedrowicz F, Saxton T, Mosse J, Wright W, Hogan FE (2016) A non-invasive tool for assessing pathogen prevalence in koala (Phascolarctos cinereus) populations: detection of Chlamydia pecorum and koala retrovirus (KoRV) DNA in genetic material sourced from scats. Conserv Genet Resour 8:511–521CrossRefGoogle Scholar