Noninvasive alternatives for DNA collection from threatened rodents


Many rodent species are currently under conservation threat. However, population monitoring and status assessment are extremely challenging because of small body size, low abundance and elusive behavior of rodents. Furthermore, invasive methods of capture and tissue collection commonly used to address such studies can induce an unacceptable amount of stress to sensitive species. As a result, noninvasive techniques have become more widely used, but relatively few studies have applied noninvasive techniques to rodents. Here we present two noninvasive alternatives for the collection of DNA from Franklin’s ground squirrels (Poliocitellus franklinii). We compared the quantity, purity and degradation of DNA extracted from plucked hair and fecal pellets to tail snip tissues. We recovered more DNA from tail snips than either plucked hair or fecal pellets. Both hair and fecal pellets recovered DNA with purity ratios similar to tail snips. As expected, DNA recovered from fecal pellets exhibited a high degree of degradation compared to hair and tail tissues. Careful planning of field and laboratory protocols is therefore necessary to compensate for challenges associated with noninvasive tissue types. While there is no tissue that can universally be applied to all research projects, both hair and feces are viable alternatives to traditional invasive procedures and can be applied to threatened and endangered rodent species.

Share and Cite:

Green, M. , Ting, T. , Manjerovic, M. and Mateus-Pinilla, N. (2013) Noninvasive alternatives for DNA collection from threatened rodents. Natural Science, 5, 18-26. doi: 10.4236/ns.2013.55A003.

Conflicts of Interest

The authors declare no conflicts of interest.


[1] IUCN (2012) IUCN red list of threatened species. Version 2012.2.
[2] álvarez-Castaneda, S.T. and Ortega-Rubio, A. (2003) Current status of rodents on islands in the Gulf of California. Biological Conservation, 109, 157-163. doi:10.1016/S0006-3207(02)00121-0
[3] Alasaad, S., Soriguer, R.C., Jowers, M.J., Marchal, J.A., Romero, I. and Sánchez, A. (2011) Applicability of mitochondrial DNA for the identification of Arvicolid species from faecal samples: A case study from the threatened Cabrera’s vole. Molecular Ecology Resources, 11, 409414. doi:10.1111/j.1755-0998.2010.02939.x
[4] Moncrief, N.D., Van Den Bussche, R.A., Dueser, R.D., Loftis, D., Cockett, N.E. and Culver, M. (2008) Diagnostic genetic marker than differentiates Eastern fox squirrels from Eastern gray squirrels. The Journal of Wildlife Management, 72, 320-323. doi:10.2193/2006-149
[5] Moran, S., Turner, P.D. and O’Reilly, C. (2008) Noninvasive genetic identification of small mammal species using real-time polymerase chain reaction. Molecular Ecology Resources, 8, 1267-1269. doi:10.1111/j.1755-0998.2008.02324.x
[6] Kohn, M. and Wayne, R.K. (1997) Facts from feces revisited. Trends in Ecology and Evolution, 12, 223-227. doi:10.1016/S0169-5347(97)01050-1
[7] Piggott, M.P. and Taylor, A.C. (2003) Remote collection of animal DNA and its applications in conservation management and understanding the population biology of rare and cryptic species. Wildlife Research, 30, 1-13. doi:10.1071/WR02077
[8] Eggert, L.S., Eggert, J.A. and Woodruff, D.S. (2003) Estimating population sizes for elusive animals: The forest elephants of Kakum National Park, Ghana. Molecular Ecology, 12, 1389-1402. doi:10.1046/j.1365-294X.2003.01822.x
[9] Fernando, P., Pfrender, M.E., Encalada, S.E. and Lande, R. (2000) Mitochondrial DNA variation, phylogeography and population structure of the Asian elephant. Heredity, 84, 362-372. doi:10.1046/j.1365-2540.2000.00674.x
[10] Garnier, J.N., Bruford, M.W. and Goossens, B. (2001) Mating system and reproductive skew in the black rhinoceros. Molecular Ecology, 10, 2031-2041. doi:10.1046/j.0962-1083.2001.01338.x
[11] Hass, M., Kohn, M., Paabo, S., Knauer, F. and Schroder, W. (1992) Excrement analysis by PCR. Nature, 359, 199. doi:10.1038/359199a0
[12] Kohn, M., Knauer, F., Stoffella, A., Schroder, W. and Paabo, S. (1995) Conservation genetics of the European brown bear—A study using excremental PCR of nuclear and mitochondrial sequences. Molecular Ecology, 4, 95103. doi:10.1111/j.1365-294X.1995.tb00196.x
[13] Lucchini, V., Fabbri, E., Marucco, F., Ricci, S., Boitani, L. and Randi, E. (2002) Noninvasive molecular tracking of colonizing wolf (Canis lupus) packs in the western Italian Alps. Molecular Ecology, 11, 857-868. doi:10.1046/j.1365-294X.2002.01489.x
[14] Kohn, M.H., York, E.C., Kamradt, D.A., Haught, G., Sauvajot, R.M. and Wayne, R.K. (1999) Estimating population size by genotyping faeces. Proceedings of the Royal Society B, 266, 657-663. doi:10.1098/rspb.1999.0686
[15] Spriggs, D.R. (1987) Transgenic mice and the language of cells. The Journal of Infectious Diseases, 155, 596-597. doi:10.1093/infdis/155.3.596
[16] Wang, R., Painter, J.N. and Hanski, I. (2002) Amplification of DNA markers from scat samples of the least weasel Mustela nivalis nivalis. Acta Theriologica, 47, 425431. doi:10.1007/BF03192467
[17] Aars, J., Ims, R.A., Liu, H.-P., Mulvey, M. and Smith, M.H. (1998) Bank voles in linear habitats show restricted gene flow as revealed by mitochondrial DNA (mtDNA). Molecular Ecology, 7, 1383-1389. doi:10.1046/j.1365-294x.1998.00487.x
[18] Higuchi, R., von Beroldingen, C.H., Sensabaugh, G.F. and Erlich, H.A. (1988) DNA typing from single hairs. Nature, 332, 543-546. doi:10.1038/332543a0
[19] Broderick, D., Idaghdour, Y., Korrida, A. and Hellmich, J. (2003) Gene flow in great bustard populations across the Strait of Gibraltar as elucidated from excremental PCR and mtDNA sequencing. Conservation Genetics, 4, 793800. doi:10.1023/B:COGE.0000006111.65204.c9
[20] Ernest, H.B., Penedo, M.C.T., May, B.P., Syvanen, M. and Boyce, W.M. (2000) Molecular tracking of mountain lions in the Yosemite Valley region in California: Genetic analysis using microsatellites and faecal DNA. Molecular Ecology, 9, 433-441. doi:10.1046/j.1365-294x.2000.00890.x
[21] Palomares, F., Godoy, J.A., Piriz, A., O’Brien, J. and Johnson, W.E. (2002) Faecal genetic analysis to determine the presence and distribution of elusive carnivores: Design and feasibility for the Iberian lynx. Molecular Ecology, 11, 2171-2182. doi:10.1046/j.1365-294X.2002.01608.x
[22] Paxinos, E., McIntosh, C., Ralls, K. and Fleischer, R. (1997) A noninvasive method for distinguishing among canid species: Amplification and enzyme restriction of DNA from dung. Molecular Ecology, 6, 483-486. doi:10.1046/j.1365-294X.1997.00206.x
[23] Taberlet, P., Camarra, J.-J., Griffin, S., Uhrès, E., Hanotte, O., Waits, L.P., Dubois-Paganon, C., Burke, T. and Bouvet, J. (1997) Noninvasive genetic tracking of the endangered Pyrenean brown bear population. Molecular Ecology, 6, 869-876. doi:10.1111/j.1365-294X.1997.tb00141.x
[24] Gerloff, U., Schlotterer, C., Rassmann, K., Rambold, I., Hohmann, G., Fruth, B. and Tautz, D. (1995) Amplification of hypervariable simple sequence repeats (microsatellites) from excremental DNA of wild living bonobos (Pan paniscus). Molecular Ecology, 4, 515-518. doi:10.1111/j.1365-294X.1995.tb00247.x
[25] Dallas, J.F., Coxon, K.E., Sykes, T., Chanin, P.R.F., Marshall, F., Carss, D.N., Bacon, P.J., Piertney, S.B. and Racey, P.A. (2003) Similar estimates of population genetic composition and sex ratio derived from carcasses and faeces of Eurasian otter Lutra lutra. Molecular Ecology, 12, 275-282. doi:10.1046/j.1365-294X.2003.01712.x
[26] Green, M.L., Herzing, D.L. and Baldwin, J.D. (2007) Noninvasive methodology for the sampling and extraction of DNA from free-ranging Atlantic spotted dolphins (Stenella frontalis). Molecular Ecology Notes, 7, 12871292. doi:10.1111/j.1471-8286.2007.01858.x
[27] Parsons, K.M., Dallas, J.F., Claridge, D.E., Durban, J.W., Balcomb III, K.C., Thompson, P.M. and Noble, L.R. (1999) Amplifying dolphin mitochondrial DNA from faecal plumes. Molecular Ecology, 8, 1766-1768. doi:10.1046/j.1365-294x.1999.00723-8.x
[28] Reed, J.Z., Tollit, D.J., Thompson, P.M. and Amos, W. (1997) Molecular scatology: The use of molecular genetic analysis to assign species, sex and individual identity to seal faeces. Molecular Ecology, 6, 225-234. doi:10.1046/j.1365-294X.1997.00175.x
[29] Tikel, D., Blair, D. and Marsh, H.D. (1996) Marine mammal faeces as a source of DNA. Molecular Ecology, 5, 456-457.
[30] Barbosa, S., Pauperio, J., Searle, J.B. and Alves, P.C. (2013) Genetic identification of Iberian rodent species using both mitochondrial and nuclear loci: Application to noninvasive sampling. Molecular Ecology Resources, 13, 43-56. doi:10.1111/1755-0998.12024
[31] Taberlet, P. and Luikart, G. (1999) Non-invasive genetic sampling and individual identification. Biological Journal of the Linnean Society, 68, 41-55. doi:10.1111/j.1095-8312.1999.tb01157.x
[32] Helgen, K.M., Cole, F.R., Helgen, L.E. and Wilson, D.E. (2009) Generic revision in the holarctic ground squirrel genus Spermophilus. Journal of Mammalogy, 90, 270305. doi:10.1644/07-MAMM-A-309.1
[33] Lewis, T. and Rongstad, O. (1992) The distribution of Franklin’s ground squirrel in Wisconsin and Illinois. Wisconsin Academy of Sciences, Arts and Letters, 80, 57-62.
[34] Ostroff, A.C. and Finck, E.J. (2003) Spermophilus franklinii. Mammalian Species, 724, 1-5. doi:10.1644/724
[35] Thorington, R.W., Koprowski, J.L., Steele, M.A. and Whatton, J.F. (2012) Squirrels of the world. Johns Hopkins University Press, Baltimore.
[36] Illinois Endangered Species Board (2011) Checklist of endangered and threatened animals and plants of Illinois.
[37] Indiana Department of Natural Resources (2012) Indiana’s State endangered species.
[38] Iowa Department of Natural Resources (2012) Iowa wildlife action plan.
[39] Missouri Department of Conservation (2013) Missouri species and communities of conservation concern checklist.
[40] Wisconsin Department of Natural Resources (2013) Franklin’s ground squirrel (Spermophilus franklinii).
[41] Piggott, M.P. (2004) Effect of sample age and season of collection on the reliability of microsatellite genotyping of faecal DNA. Wildlife Research, 31, 485-493. doi:10.1071/WR03096
[42] Maudet, C., Luikart, G., Dubray, D., Von Hardenberg, A. and Taberlet, P. (2004) Low genotyping error rates in wild ungulate faeces sampled in winter. Molecular Ecology Notes, 4, 772-775. doi:10.1111/j.1471-8286.2004.00787.x
[43] Sikes, R.S. and Gannon, W.L. (2011) Guidelines of the American Society of Mammalogists for the use of wild mammals in research. Journal of Mammalogy, 92, 235253. doi:10.1644/10-MAMM-F-355.1
[44] Brinkman, T.J., Person, D.K., Schwartz, M.K., Pilgrim, K.L., Colson, K.E. and Hundertmark, K.J. (2010) Individual identification of Sitka black-tailed deer (Odocoileus hemionus sitkensis) using DNA from fecal pellets. Conservation Genetics Resources, 2, 115-118. doi:10.1007/s12686-010-9176-7
[45] Goossens, B., Waits, L.P. and Taberlet, P. (1998) Plucked hair samples as a source of DNA: Reliability of dinucleotide microsatellite genotyping. Molecular Ecology, 7, 1237-1241. doi:10.1046/j.1365-294x.1998.00407.x
[46] Frantzen, M.A.J., Silk, J.B., Ferguson, J.W.H., Wayne, R.K. and Kohn, M.H. (1998) Empirical evaluation of preservation methods for faecal DNA. Molecular Ecology, 7, 1423-1428. doi:10.1046/j.1365-294x.1998.00449.x
[47] Taberlet, P., Waits, L.P. and Luikart, G. (1999) Noninvasive genetic sampling: Look before you leap. Trends in Ecology and Evolution, 14, 323-327. doi:10.1016/S0169-5347(99)01637-7
[48] Green, M.L., Herzing, D.L. and Baldwin, J.D. (2011) Reproductive success of male Atlantic spotted dolphins (Stenella frontalis) revealed by noninvasive genetic analysis of paternity. Canadian Journal of Zoology, 89, 239253. doi:10.1139/Z10-111
[49] Bonin, A., Bellemain, E., Bronken Eidesen, P., Pompanon, F., Brochmann, C. and Taberlet, P. (2004) How to track and assess genotyping errors in population genetics studies. Molecular Ecology, 13, 3261-3273. doi:10.1111/j.1365-294X.2004.02346.x
[50] Ruibal, M., Peakall, R., Claridge, A., Murray, A. and Firestone, K. (2010) Advancement to hair-sampling surveys of a medium-sized mammal: DNA-based individual identification and population estimation of a rare Australian marsupial, the spotted-tailed quoll (Dasyurus maculatus). Wildlife Research, 37, 27-38. doi:10.1071/WR09087
[51] Gagneux, P., Boesch, C. and Woodruff, D.S. (1997) Microsatellite scoring errors associated with noninvasive genotyping based on nuclear DNA amplified from shed hair. Molecular Ecology, 6, 861-868. doi:10.1111/j.1365-294X.1997.tb00140.x
[52] Mowat, G. and Strobeck, C. (2000) Estimating population size of grizzly bears using hair capture, DNA profiling, and mark-recapture analysis. The Journal of Wildlife Management, 64, 183-193. doi:10.2307/3802989
[53] Woods, J.G., Paetkau, D., Lewis, D., McLellan, B.N., Proctor, M. and Strobeck, C. (1999) Genetic tagging of free-ranging black and brown bears. Wildlife Society Bulletin, 27, 616-627.
[54] Brinkman, T.J., Schwartz, M.K., Person, D.K., Pilgrim, K.L. and Hundertmark, K.J. (2010) Effects of time and rainfall on PCR success using DNA extracted from deer fecal pellets. Conservation Genetics, 11, 1547-1552. doi:10.1007/s10592-009-9928-7
[55] Navidi, W., Arnheim, N. and Waterman, M.S. (1992) A multiple-tubes approach for accurate genotyping of very small DNA samples using PCR: Statistical considerations. American Journal of Human Genetics, 50, 347-359.
[56] Taberlet, P., Griffin, S., Goossens, B., Questiau, S., Manceau, V., Escaravage, N., Waits, L.P. and Bouvet, J. (1996) Reliable genotyping of samples with very low DNA quantities using PCR. Nucleic Acids Research, 24, 31893194. doi:10.1093/nar/24.16.3189
[57] Matsuda, H., Imaizumi, K., Kubota, S., Miyasaka, S., Yoshina, M. and Seta, S. (1997) Technical investigation of DNA extraction from single hair shaft. Reports of the National Research Institute of Police Science, 50, 23-28.
[58] Hellmann, A., Rohleder, U., Schmitter, H. and Wittig, M. (2001) STR typing of human telogen hairs—A new approach. International Journal of Legal Medicine, 114, 269-273. doi:10.1007/s004140000175
[59] Sanecki, G.M. and Green, K. (2005) A technique for using hair tubes beneath the snowpack to detect winter-active small mammals in the subnivean space. European Journal of Wildlife Research, 51, 41-47. doi:10.1007/s10344-004-0069-5
[60] Scotts, D.J. and Craig, S.A. (1988) Improved hair-sampling tube for the detection of rare mammals. Australian Wildlife Research, 15, 469-472. doi:10.1071/WR9880469
[61] Suckling, G.C. (1978) A hair sampling tube for the detection of small mammals in trees. Australian Wildlife Research, 5, 249-252. doi:10.1071/WR9780249
[62] Foran, D.R., Minta, S.C. and Heinemeyer, K.S. (1997) DNA-based analysis of hair to identify species and individuals for population research and monitoring. Wildlife Society Bulletin, 25, 840-847.

Copyright © 2022 by authors and Scientific Research Publishing Inc.

Creative Commons License

This work and the related PDF file are licensed under a Creative Commons Attribution 4.0 International License.