Skip to main content
Log in

Noninvasive population genetics: a review of sample source, diet, fragment length and microsatellite motif effects on amplification success and genotyping error rates

  • Technical Note
  • Published:
Conservation Genetics Aims and scope Submit manuscript

Abstract

Noninvasive population genetics has found many applications in ecology and conservation biology. However, the technical difficulties inherent to the analysis of low quantities of DNA generally tend to limit the efficiency of this approach. The nature of samples and loci used in noninvasive population genetics are important factors that may help increasing the potential success of case studies. Here we reviewed the effects of the source of DNA (hair vs. faeces), the diet of focal species, the length of mitochondrial DNA fragments, and the length and repeat motif of nuclear microsatellite loci on genotyping success (amplification success and rate of allelic dropout). Locus-specific effects appeared to have the greatest impact, amplification success decreasing with both mitochondrial and microsatellite fragments’ length, while error rates increase with amplicons’ length. Dinucleotides showed best amplification success and lower error rates compared to longer repeat units. Genotyping success did not differ between hair- versus faeces-extracted DNA, and success in faeces-based analyses was not consistently influenced by the diet of focal species. While the great remaining variability among studies implies that other unidentified parameters are acting, results show that the careful choice of genetic markers may allow optimizing the success of noninvasive approaches.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Subscribe and save

Springer+ Basic
EUR 32.99 /Month
  • Get 10 units per month
  • Download Article/Chapter or Ebook
  • 1 Unit = 1 Article or 1 Chapter
  • Cancel anytime
Subscribe now

Buy Now

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Similar content being viewed by others

References

  • Adams JR, Kelly BT, Waits LP (2003) Using faecal DNA sampling and GIS to monitor hybridization between red wolves (Canis rufus) and coyotes (Canis latrans). Mol Ecol 12:2175–2186

    Article  PubMed  CAS  Google Scholar 

  • Alpers DL, Taylor AC, Bellman SA, Sherwin WB (2003) Pooling hair samples to increase DNA yield for PCR. Conserv Genet 4:779–788

    Article  CAS  Google Scholar 

  • Bayes MK, Smith KL, Alberts SC, Altmann J, Bruford MW (2000) Testing the reliability of microsatellite typing from faecal DNA in the savannah baboon. Conserv Genet 1:173–176

    Article  CAS  Google Scholar 

  • Bradley BJ, Vigilant L (2002) False alleles derived from microbial DNA pose a potential source of error in microsatellite genotyping of DNA from faeces. Mol Ecol Notes 2002:602–605

    Article  Google Scholar 

  • Bradley BJ, Boesch C, Vigilant L (2000) Identification and redesign of human microsatellite markers for genotyping wild chimpanzee (Pan troglodytes verus) and gorilla (Gorilla gorilla gorilla) DNA from feces. Conserv Genet 1:289–292

    Article  CAS  Google Scholar 

  • Broquet T, Petit E (2004) Quantifying genotyping errors in noninvasive population genetics. Mol Ecol 13:3601–3608

    Article  PubMed  CAS  Google Scholar 

  • Buchan JC, Archie EA, Van Horn RC, Moss CJ, Alberts SC (2005) Locus effects and sources of error in noninvasive genotyping. Mol Ecol Notes 5(3): 680–683

    Google Scholar 

  • Constable JL, Ashley MV, Goodall J, Pusey AE (2001) Noninvasive paternity assignment in Gombe chimpanzees. Mol Ecol 10:1279–1300

    Article  PubMed  CAS  Google Scholar 

  • Crawley MJ (2005) Statistical computing: an introduction to data analysis using S-Plus. John Wiley and sons Ltd, Chichester

    Google Scholar 

  • Fernando P, Vidya TNC, Rajapakse C, Dangolla A, Melnick DJ (2003) Reliable noninvasive genotyping: fantasy or reality? J␣Hered 94:115–123

    Article  PubMed  CAS  Google Scholar 

  • Flagstad Ø, Røed K, Stacy JE, Jakobsen KS (1999) Reliable noninvasive genotyping based on excremental PCR of nuclear DNA purified with a magnetic bead protocol. Mol Ecol 8:879–883

    Article  PubMed  CAS  Google Scholar 

  • Frantz AC, Pope LC, Carpenter PJ, Roper TJ, Wilson GJ, Delahay RJ, Burke T (2003) Reliable microsatellite genotyping of the Eurasian badger (Meles meles) using faecal DNA. Mol Ecol 12:1649–1661

    Article  PubMed  CAS  Google Scholar 

  • Frantzen MAJ, Silk JB, Ferguson JWH, Wayne RK, Kohn MH (1998) Empirical evaluation of preservation methods for faecal DNA. Mol Ecol 7:1423–1428

    Article  PubMed  CAS  Google Scholar 

  • Gagneux P (1997) Furtive mating in female chimpanzees. Nature 387:358–359

    Article  PubMed  CAS  Google Scholar 

  • Gerloff U, Schlötterer C, Rassmann K, Rambold I, Hohmann G, Fruth B, Tautz D (1995) Amplification of hypervariable simple sequence repeats (microsatellites) from excremental DNA of wild living bonobos (Pan paniscus). Mol Ecol 4:515–518

    CAS  Google Scholar 

  • Goossens B, Chikhi L, Utami SS, Ruiter de J, Bruford MW (2000) A multi-samples, multi-extracts approach for microsatellite analysis of faecal samples in an arboreal ape. Conserv Genet 1:157–162

    Article  CAS  Google Scholar 

  • Goossens B, Waits LP, Taberlet P (1998) Plucked hair samples as a source of DNA: reliability of dinucleotide microsatellite genotyping. Mol Ecol 7:1237–1241

    Article  PubMed  CAS  Google Scholar 

  • Hoffman JI, Amos W (2005) Microsatellite genotyping errors: detection approaches, common sources and consequences for paternal exclusion. Mol Ecol 14:599–612

    Article  PubMed  CAS  Google Scholar 

  • Höss M, Kohn M, Pääbo S, Knauer F, Schröder W (1992) Excrement analysis by PCR. Nature 359:199

    Article  PubMed  Google Scholar 

  • Huber S, Bruns U, Arnold W (2003) Genotyping herbivore feces facilitating their further analyses. Wildlife Soc Bull 31: 692–697

    Google Scholar 

  • Idaghdour Y, Broderick D, Korrida A (2003) Faeces as a source of DNA for molecular studies in a threatened population of great bustards. Conserv Genet 4:789–792

    Article  CAS  Google Scholar 

  • Kohn M, Knauer F, Stoffella A, Schröder W, Pääbo S (1995) Conservation genetics of the European brown bear – a study using excremental PCR of nuclear and mitochondrial sequences. Mol Ecol 4:95–103

    PubMed  CAS  Google Scholar 

  • Kohn MH, York EC, Kamradt DA, Haught G, Sauvajot RM, Wayne RK (1999) Estimating population size by genotyping faeces. Proc R Soc London B 266:657–663

    Article  CAS  Google Scholar 

  • Kruglyak S, Durrett RT, Schug MD, Aquadro CF (1998) Equilibrium distributions of microsatellite repeat length resulting from a balance between slippage events and point mutations. Proc Natl Acad Sci USA 95:10774–10778

    Article  PubMed  CAS  Google Scholar 

  • Lathuillière M, Ménard N, Gautier-Hion A, Crouau-Roy B (2001) Testing the reliability of noninvasive genetic sampling by comparing analyses of blood and fecal samples in Barbary Macaques (Macaca sylvanus). Am J Primatol 55:151–158

    Article  PubMed  Google Scholar 

  • Launhardt K, Epplen C, Epplen JT, Winkler P (1998) Amplification of microsatellites adapted from human systems in faecal DNA of wild Hanuman langurs (Presbytis entellus). Electrophoresis 19: 1356–1461

    Article  PubMed  CAS  Google Scholar 

  • Lucchini V, Fabbri E, Marucco F, Ricci S, Boitani L, Randi E (2002) Noninvasive molecular tracking of colonizing wolf (Canis lupus) packs in the western Italian Alps. Mol Ecol 11:857–868

    Article  PubMed  CAS  Google Scholar 

  • Miller CR, Waits LP (2003) The history of effective population size and genetic diversity in the Yellowstone grizzly (Ursus arctos): implications for conservation. Proc Natl Acad Sci USA 100:4334–4339

    Article  PubMed  CAS  Google Scholar 

  • Miller CR, Joyce P, Waits LP (2002) Assessing allelic dropout and genotype reliability using maximum likelihood. Genetics 160:357–266

    PubMed  Google Scholar 

  • Monteiro L, Bonnemaison D, Vekris A, Petry KG, Bonnet J, Vidal R, Cabrita J, Mégraud F (1997) Complex polysaccharides as PCR inhibitors in feces: Helicobacter pylori model. J Clin Microbiol 35:995–998

    PubMed  CAS  Google Scholar 

  • Morin PA, Chambers KE, 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 10:1835–1844

    Article  PubMed  CAS  Google Scholar 

  • Mowat G, Strobeck C (2000) Estimating population size of grizzly bears using hair capture, DNA profiling, and mark-recapture analysis. J Wildlife Manage 64:183–193

    Google Scholar 

  • Murphy MA, Waits LP, Kendall KC (2000) Quantitative evaluation of fecal drying methods for brown bear DNA analysis. Wildlife Soc Bull 28:951–957

    Google Scholar 

  • Murphy MA, Waits LP, Kendall KC, Wasser SK, Higbee JA, Bogden R (2002) An evaluation of long-term preservation methods for brown bear (Ursus arctos) faecal DNA samples. Conserv Genet 3:435–440

    Article  CAS  Google Scholar 

  • Murphy MA, Waits LP, Kendall KC (2003) The influence of diet on faecal DNA amplification and sex identification in brown bears (Ursus arctos). Mol Ecol 12:2261–2265

    Article  PubMed  CAS  Google Scholar 

  • Nievergelt CM, Mutschler T, Feistner ATC, Woodruff DS (2002) Social system of the Alaotran Gentle Lemur (Hapalemur griseus alaotrensis): genetic characterization of group composition and mating system. Am J Primatol 57:157–176

    Google Scholar 

  • Paetkau D (2003) An empirical exploration of data quality in DNA-based population inventories. Mol Ecol 12:1375–1387

    Article  PubMed  CAS  Google Scholar 

  • Palomares F, Godoy JA, Piriz A, O’Brien SJ, Johnson WE (2002) Faecal genetic analysis to determine the presence and distribution of elusive carnivores: design and feasibility for the Iberian lynx. Mol Ecol 11:2171–2182

    Article  PubMed  CAS  Google Scholar 

  • Paradis E, Claude J (2002) Analysis of comparative data using generalized estimating equations. J Theor Biol, 218:175–185

    Article  PubMed  Google Scholar 

  • Paradis E, Strimmer K, Claude J, Gangolf J, Opgen-Rhein R, Dutheil J, Noel Y, Bolker B (2005) ape: Analyses of Phylogenetics and Evolution. R package version 1.8

  • Parsons KM (2001) Reliable microsatellite genotyping of dolphin DNA from faeces. Mol Ecol 1:341–344

    CAS  Google Scholar 

  • Piggott MP, Taylor AC (2003) Remote collection of animal DNA and its applications in conservation management and understanding the population biology of rare and cryptic species. Wildlife Res 30:1–13

    Article  Google Scholar 

  • Reed JZ, Tollit DJ, Thompson PM, Amos W (1997) Molecular scatology: the use of molecular genetic analysis to assign species, sex and individual identity to seal faeces. Mol Ecol 6:225–234

    Article  PubMed  CAS  Google Scholar 

  • Roon DA, Waits LP, Kendall KC (2003) A quantitative evaluation of two methods for preserving hair samples. Mol Ecol Notes 3:163–166

    Article  CAS  Google Scholar 

  • Sefc KM, Payne RB, Sorenson MD (2003) Microsatellite amplification from museum feather samples: effects of fragment size and template concentration on genotyping errors. Auk 120:982–989

    Article  Google Scholar 

  • Sloane MA, Sunnucks P, Alpers D, Beheregaray LB, Taylor AC (2000) Highly reliable genetic identification of individual northern hairy-nosed wombats from single remotely collected hairs: a feasible censusing method. Mol Ecol 9:1233–1240

    Article  PubMed  CAS  Google Scholar 

  • Smith KL, Alberts SC, Bayes MK, Bruford MW, Altmann J, Ober C (2000) Cross-species amplification, non-invasive genotyping, and non-mendelian inheritance of human STRPs in savannah baboons. Am J Primatol 51:219–227

    Article  PubMed  CAS  Google Scholar 

  • Taberlet P, Luikart G (1999) Non-invasive genetic sampling and individual identification. Biol J Linnean Soc 68:41–55

    Article  Google Scholar 

  • Taberlet P, Waits LP, Luikart G (1999) Noninvasive genetic sampling: look before you leap. Trends Ecol Evol 14:323–327

    Article  PubMed  Google Scholar 

  • Valière N, Taberlet P (2000) Urine collected in the field as a source of DNA for species and individual identification. Mol Ecol 9:2150–2152

    PubMed  Google Scholar 

  • Valière N, Berthier P, Mouchiroud D, Pontier D (2002) GEMINI: software for testing the effects of genotyping errors and multitubes approach for individual identification. Mol Ecol Notes 2:83–86

    Google Scholar 

  • Valière N, Fumagalli L, Gielly L, Miquel C, Lequette B, Poulle M-L, Weber J-M, Arlettaz R, Taberlet P (2003) Long-distance wolf recolonization of France and Switzerland inferred from non-invasive genetic sampling over a period of 10 years. Anim Conserv 6:83–92

    Article  Google Scholar 

  • Vege S, McCracken GF (2001) Microsatellite genotypes of big brown bats (Eptesicus fuscus: Vespertilionidae, Chiroptera) obtained from their feces. Acta Chiropterol 3:237–244

    Google Scholar 

  • Vigilant L (1999) An evaluation of techniques for the extraction and amplification of DNA from naturally shed hairs. Biol Chem 380: 1329–1331

    Article  PubMed  CAS  Google Scholar 

  • Vigilant L (2002) Technical challenges in the microastellite genotyping of a wild chimpanzee population. Evol Anthropol Suppl 1:162–165

    Article  Google Scholar 

  • Vigilant L, Hofreiter M, Siedel H, Boesch C (2001) Paternity and relatedness in wild chimpanzee communities. Proc Natl Acad Sci USA 98:12890–12895

    Article  PubMed  CAS  Google Scholar 

  • Walsh PS, Metzger DA, Higuchi R (1991) Chelex 100 as a medium for simple extraction of DNA for PCR based typing from forensic material. Biotechniques 10:506–513

    PubMed  CAS  Google Scholar 

  • Wasser SK, Houston CS, Koehler GM, Cadd GG, Fain SR (1997) Techniques for application of faecal DNA methods to field studies of Ursids. Mol Ecol 6:1091–1097

    Article  PubMed  CAS  Google Scholar 

  • Wattier R, Engel CR, Saumitou-Laprade P, Valero M (1998) Short allele dominance as a source of heterozygote deficiency at microsatellite loci: experimental evidence at the dinucleotide locus Gv1CT in Gracilaria gracilis (Rhodophyta). Mol Ecol 7: 1569–1573

    Article  CAS  Google Scholar 

  • Whittier CA, Dhar AK, Stem C, Goodall J, Alcivar-Warren A (1999) Comparison of DNA extraction methods for PCR amplification of mitochondrial cytochrome c oxidase subunit II (COII) DNA from primate fecal samples. Biotechnol Techniq 13:771–779

    Article  CAS  Google Scholar 

  • Woods JG, Paetkau D, Lewis B, McLellan B, Proctor M, Strobeck C (1999) Genetic tagging of free-ranging black and brown bears. Wildlife Soc Bull 27:616–627

    Google Scholar 

Download references

Acknowledgements

We are grateful to E. Paradis, J.-S. Pierre, N.␣Salamin and J. Yearsley for answering our questions on generalized linear models and generalized estimating equations. We thank authors of the papers reviewed that gave us some details on their respective studies. We thank also J. Jaquiéry and two anonymous reviewers for comments on a previous draft.

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Thomas Broquet.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Broquet, T., Ménard, N. & Petit, E. Noninvasive population genetics: a review of sample source, diet, fragment length and microsatellite motif effects on amplification success and genotyping error rates. Conserv Genet 8, 249–260 (2007). https://doi.org/10.1007/s10592-006-9146-5

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10592-006-9146-5

Keywords

Navigation