Conservation Genetics Resources

, Volume 10, Issue 1, pp 119–125 | Cite as

A simple, economical protocol for DNA extraction and amplification where there is no lab

  • Elaine E. GuevaraEmail author
  • David C. Frankel
  • Jeannin Ranaivonasy
  • Alison F. Richard
  • Joelisoa Ratsirarson
  • Richard R. Lawler
  • Brenda J. Bradley
Methods and Resources Article


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.


Population 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.

Supplementary material

12686_2017_758_MOESM1_ESM.docx (6.9 mb)
Supplementary material 1—protocol sheet (DOCX 7100 KB)


  1. Alberts SC, Buchan JC, Altmann J (2006) Sexual selection in wild baboons: from mating opportunities to paternity success. Anim Behav 72:1177–1196CrossRefGoogle Scholar
  2. Allendorf FW, Luikart G (2009) Conservation and the genetics of populations. Wiley-Blackwell, OxfordGoogle Scholar
  3. Bergl RA, Vigilant L (2008) Genetic analysis reveals population structure and recent migration within the highly fragmented range of the Cross River gorilla (Gorilla gorilla diehli). Mol Ecol 16:501–516CrossRefGoogle Scholar
  4. Bradley BJ, Robbins MM, Williamson EA, Steklis HD, Steklis NG, Eckhardt N, Boesch C, Vigilant L (2005) Mountain gorilla tug-of-war: Silverbacks have limited control over reproduction in multimale groups. Proc Natl Acad Sci USA 102:9418–9423CrossRefPubMedPubMedCentralGoogle Scholar
  5. Bunting S, Burnett E, Hunter RB, Field R, Hunter KL (2014) Incorporating molecular genetics into remote expedition fieldwork. Trop Conserv Sci 7:270–281CrossRefGoogle Scholar
  6. Caragiulo A, Pickles RS, Smith JA, Smith O, Goodrich J, Amato G (2015) Tiger (Panthera tigris) scent DNA: a valuable conservation tool for individual identification and population monitoring. Conserv Genet Resour 7:681–683CrossRefGoogle Scholar
  7. Castro I, Mason KM, Armstrong DP, Lambert DM (2004) Effect of extra-pair paternity on effective population size in a reintroduced population of the endangered hihi, and potential for behavioural management. Conserv Genet 5:381–393CrossRefGoogle Scholar
  8. Goossens B, Chikhi L, Jalil MF, Ancrenaz M, Lackman-Ancrenaz I, Mohamed M, Andau P, Bruford MW (2005) Patterns of genetic diversity and migration in increasingly fragmented and declining orangutan (Pongo pygmaeus) populations from Sabah, Malaysia. Mol Ecol 14:441–456CrossRefPubMedGoogle Scholar
  9. Gray TN, Vidya TN, Potdar S, Bharti DK, Sovanna P (2014) Population size estimation of an Asian elephant population in eastern Cambodia through non-invasive mark-recapture sampling. Conserv Genet 15:803–810CrossRefGoogle Scholar
  10. Griffin AS, Pemberton JM, Brotherton PN, McIlrath G, Gaynor D, Kansky R, O’Riain J, Clutton-Brock TH (2003) A genetic analysis of breeding success in the cooperative meerkat (Suricata suricatta). Behav Ecol 14:472–480CrossRefGoogle Scholar
  11. 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
  12. Kalinowski ST, Taper ML, Marshall TC (2007) Revising how the computer program CERVUS accommodates genotyping error increases success in paternity assignment. Mol Ecol 16:1099–1106CrossRefPubMedGoogle Scholar
  13. Kohn MH, Murphy WJ, Ostrander EA, Wayne RK (2006) Genomics and conservation genetics. Trends Ecol Evol 21:629–637CrossRefPubMedGoogle Scholar
  14. Lawler RR, Richard AF, Riley MA (2001) Characterization and screening of microsatellite loci in a wild lemur population (Propithecus verreauxi verreauxi). Am J Primatol 55:253–259CrossRefPubMedGoogle Scholar
  15. Marx V (2015) PCR heads into the field. Nat Methods 12:393–397CrossRefPubMedGoogle Scholar
  16. Pallen MJ (2014) Diagnostic metagenomics: potential applications to bacterial, viral and parasitic infections. Parasitology 141:1856–1862CrossRefPubMedPubMedCentralGoogle Scholar
  17. Quéméré E, Crouau-Roy BR, Rabarivola C, Louis EE Jr, Chikhi L (2010) Landscape genetics of an endangered lemur (Propithecus tattersalli) within its entire fragmented range. Mol Ecol 19:1606–1621CrossRefPubMedGoogle Scholar
  18. Richard AF, Dewar RE, Schwartz M, Ratsirarson J (2002) Life in the slow lane? Demography and life histories of male and female sifaka (Propithecus verreauxi verreauxi). J Zool 256:421–436CrossRefGoogle Scholar
  19. Ruegg K, Rosenbaum HC, Anderson EC, Engel M, Rothschild A, Baker CS, Palumbi SR (2013) Long-term population size of the North Atlantic humpback whale within the context of worldwide population structure. Conserv Genet 14:103–114CrossRefGoogle Scholar
  20. Schwensow N, Eberle M, Sommer S (2008) Compatibility counts: MHC-associated mate choice in a wild promiscuous primate. Proc R Soc Lond B 275:555–564CrossRefGoogle Scholar
  21. 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
  22. Taberlet P, Camarra JJ, Griffin S, Uhres E, Hanotte O, Waits LP, Dubois-Paganon C, Burke T, Bouvet J (1997) Noninvasive genetic tracking of the endangered Pyrenean brown bear population. Mol Ecol 6:869–876CrossRefPubMedGoogle Scholar
  23. Thalmann O, Wegmann D, Spitzner M, Arandjelovic M, Guschanski K, Leuenberger C, Bergl RA, Vigilant L (2011) Historical sampling reveals dramatic demographic changes in western gorilla populations. BMC Evol Biol 11:85. doi: 10.1186/1471-2148-11-85 CrossRefPubMedPubMedCentralGoogle Scholar
  24. Villesen P, Fredsted T (2006) Fast and non-invasive PCR sexing of primates: apes, old world monkeys, new world monkeys and Strepsirrhines. BMC Ecol 6:8. doi: 10.1186/1472-6785-6-8 CrossRefPubMedPubMedCentralGoogle Scholar
  25. 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
  26. Zehr SM, Roach RG, Haring D, Taylor J, Cameron FH, Yoder AD (2014) Life history profiles for 27 strepsirrhine primate taxa generated using captive data from the Duke Lemur Center. Sci Data 1:140019. doi: 10.1038/sdata.2014.19.CrossRefPubMedPubMedCentralGoogle Scholar

Copyright information

© Springer Science+Business Media Dordrecht 2017

Authors and Affiliations

  1. 1.Department of Anthropology, Center for the Advanced Study of Human PaleobiologyThe George Washington University, Science & Engineering HallWashington, DCUSA
  2. 2.Department of AnthropologyYale UniversityNew HavenUSA
  3. 3.Département des Eaux et ForêtsUniversity of AntananarivoAntananarivoMadagascar
  4. 4.Department of Sociology and AnthropologyJames Madison UniversityHarrisonburgUSA

Personalised recommendations