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A Practive Faeces Collection Protocol for Multidisciplinary Research in Wildlife Science


Affiliations
1 Wildlife Institute of India, Chandrabani, Dehradun 248 001, India
 

Faecal samples have become an important noninvasive source of information in wildlife biology and ecological research. Despite regular use of faeces, there is no universal protocol available for faeces collection and storage to answer various questions in wildlife biology. In this study we collected 1408 faeces from ten different species using a dry sampling approach, and achieved 77.49% and 75.25% success rate in mitochondrial and nuclear marker amplifications respectively. We suggest a universal framework to use the same samples to answer different questions. This protocol provides an easy, quick and cheap option to collect non-invasive samples from species living in different environmental conditions to answer multidisciplinary questions in wildlife biology.

Keywords

Non-invasive Wildlife Research, Species Biology, Dry Sampling, Variable Habitats, Field Logistics.
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  • Storr, G., Microscopic analysis of faeces, a technique for ascertaining the diet of herbivorous mammals. Aust. J. Biol. Sci., 1961, 14, 157–164.

  • O’Brien, S. J. and Johnson, W. E., Big cat genomics. Annu. Rev. Genomics Hum. Genet., 2005, 6, 407–429.

  • Broquet, T., Ray, N., Petit, E. and Fryxell, J. M., Genetic isolation by distance and landscape connectivity in the American marten (Martes americana). Landsc. Ecol., 2006, 21, 877–889.

  • Hebert, P. D. N., Penton, E. H., Burns, J. M., Janzen, D. H. and Hallwachs, W., Ten species in one : DNA barcoding reveals cryptic species in the neotropical skipper butterfly Astraptes fulgerator. Proc. Natl. Acad. Sci. USA, 2004, 101, 14812–14817.

  • Flagstad, O. et al., Two centuries of the Scandinavian wolf population: patterns of genetic variability and migration during an era of dramatic decline. Mol. Ecol., 2003, 12, 869–880.

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

  • Price, T. D. et al., Niche filling slows the diversification of Himalayan songbirds. Nature, 2014, 509, 222–225.

  • Wasser, S. K. et al., Genetic assignment of large seizures of elephant ivory reveals Africa's major poaching hotspots. Science, 2015, 349, 84–87.

  • Moreira, N. et al., Reproductive steroid hormones and ovarian activity in felids of the Leopardus genus. Zoo Biol., 2001, 20, 103–116.

  • Rolland, R. M., Hunt, K. E., Kraus, S. D. and Wasser, S. K., Assessing reproductive status of right whales (Eubalaena glacialis) using fecal hormone metabolites. Gen. Comp. Endocrinol., 2005, 142, 308–317.

  • Marathe, R. R., Goel, S. S., Ranade, S. P., Jog, M. M. and Watve, M. G., Patterns in abundance and diversity of faecally dispersed parasites of tiger in Tadoba National Park, central India. BMC Ecol., 2002, 2, 6.

  • Barutzki, D. and Schaper, R., Results of parasitological examinations of faecal samples from cats and dogs in Germany between 2003 and 2010. Parasitol. Res., 2011, 109, 45–60.

  • Batchelor, D. J., Tzannes, S., Graham, P. A., Wastling, J. M., Pinchbeck, G. L. and German, A. J., Detection of endoparasites with zoonotic potential in dogs with gastrointestinal disease in the UK. Transbound. Emerg. Dis., 2008, 55, 99–104.

  • Shehzad, W. et al., Carnivore diet analysis based on nextgeneration sequencing: application to the leopard cat (Prionailurus bengalensis) in Pakistan. Mol. Ecol., 2012, 21, 1951–1965.

  • Murphy, M. A., Waits, L. P. and Kendall, K. C., Quantitative evaluation of fecal drying methods for brown bear DNA analysis. Wildl. Soc. Bull., 2000, 28, 951–957.

  • Shores, C., Mondol, S. and Wasser, S. K., Comparison of DNA and hair-based approaches to dietary analysis of free-ranging wolves (Canis lupus). Conserv. Genet. Resour., 2015, 7, 871–878.

  • Murphy, M. A., Waits, L. P., Kendall, K. C., Wasser, S. K., Hibgee, J. A. and Bogden, R., An evaluation of long-term preservation methods for brown bear (Ursus arctos) faecal DNA samples. Wildl. Soc. Bull., 2002, 3, 435–440.

  • Wasser, S. K., Shedlock, A. M., Comstock, K., Ostrander, E. A, Mutayoba, B. and Stephens, M., Assigning African elephant DNA to geographic region of origin: applications to the ivory trade. Proc. Natl. Acad. Sci. USA, 2004, 101, 14847–14852.

  • Frantzen, M. A. J., Silk, J. B., Ferguson, J. W. H., Wayne, R. K., and Kohn, and M. H., Empirical evaluation of preservation methods for faecal DNA. Mol. Ecol., 1998, 7, 1423–1428.

  • Nsubuga, A. M., Robbins, M. M., Roeder, A. D., Morin, P. A., Boesch, C. and Linda, V., Factors affecting the amount of genomic DNA extracted from ape faeces and the identification of an improved sample storage method. Mol. Ecol., 2004, 13, 2089– 2094.

  • Roeder, A. D., Archer, F. I., Poinar, H. N. and Morin, P. A., A novel method for collection and preservation of faeces for genetic studies. Mol. Ecol. Notes, 2004, 4, 761–764.

  • Reddy, P. A., Bhavanishankar, M., Bhagavatula, J., Harika, K., Mahla, R. S. and Shivaji, S., Improved methods of carnivore faecal sample preservation, DNA extraction and quantification for accurate genotyping of wild tigers. PLoS ONE, 2012, 7, 1–7.

  • Wasser, S. K., Houston, C. S., Koehler, G. M., Cadd, G. G. and Fain, S. R., Techniques for application of faecal DNA methods to field studies of Ursids. Mol. Ecol., 1997, 6, 1091–1097.

  • Hunt, K. E. and Wasser, S. K., Effect of long-term preservation methods on faecal glucocorticoid concentrations of grizzly bear and African elephant. Physiol. Biochem. Zool., 2003, 76, 918–928.

  • Ramón-Laca, A., Soriano, L., Gleeson, D. and Godoy, J. A., A simple and effective method for obtaining mammal DNA from faeces. Wildl. Biol., 2015, 21, 195–203.

  • Ball, M. C. et al., Characterization of target nuclear DNA from faeces reduces technical issues associated with the assumptions of low-quality and quantity template. Conserv. Genet., 2007, 8, 577– 586.

  • Wasser, S. K., Keim, J. L., Taper, M. L. and Lele, S. R., The influences of wolf predation, habitat loss, and human activity on caribou and moose in the Alberta oil sands. Front. Ecol. Environ., 2011, 9, 546–551.

  • Mondol, S., Ullas Karanth, K., Samba Kumar, N., Gopalaswamy, A. M., Andheria, A. and Ramakrishnan, U., Evaluation of noninvasive genetic sampling methods for estimating tiger population size. Biol. Conserv., 2009, 142, 2350–2360.

  • Broquet, T., Ménard, N. and 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., 2007, 8, 249–260.

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

  • Rutledge, L. Y., Holloway, J. J., Patterson, B. R. and White, B. N., An improved field method to obtain DNA for individual identification from wolf scat. J. Wildl. Manage., 2009, 73, 1430– 1435.

  • Cullingham, C. I., Curteanu, M., Ball, M. C. and Manseau, M., Feasibility and recommendations for swift fox faecal DNA profiling. J. Wildl. Manage., 2010, 74, 849–859.

  • Mukherjee, S., Goyal, S. P. and Chellam, R., Refined techniques for the analysis of Asiatic lion Panthera leo persica scats. Acta Theriol., 1994, 39, 425–430.

  • De, R., Joshi, B. D., Shukla, M., Pandey, P., Singh, R. and Goyal, S. P., Understanding predation behaviour of the tiger (Panthera tigris tigris) in Ranthambore tiger Reserve, Rajasthan, India: use of low-cost gel based molecular sexing of prey hairs from scats. Conserv. Genet. Resour., 2018, 97–104.

  • Wasser, S. K., Bevis, K., Gina, K. and Hanson, E., Noninvasive physiological measures of disturbance in the northern spotted owl. Conserv. Biol., 1997, 11, 1019–1022.

  • Palme, R., Rettenbacher, S., Touma, C., El-bahr, S. M. and Mostl, E., Stress hormones in mammals and birds: comparative aspects regarding metabolism, excretion, and noninvasive measurement in faecal samples. Ann. NY Acad. Sci., 2005, 1040, 162–171.

  • Schwarzenberger, F., Möstl, E., Palme, R. and Bamberg, E., Faecal steroid analysis for non-invasive monitoring of reproductive status in farm, wild and zoo animals. Anim. Reprod. Sci., 1996, 42, 515–526.

  • Creel, S., Social dominance and stress hormones. Trends Ecol. Evol., 2001, 16, 491–497.

  • Frantz, A. C. et al., Reliable microsatellite genotyping of the Eurasian badger (Meles meles) using faecal DNA. Mol. Ecol., 2003, 12, 1649–1661.

  • Vlčková, K., Mrázek, J., Kopečný, J. and Petrželková, K. J., Evaluation of different storage methods to characterize the fecal bacterial communities of captive western lowland gorillas (Gorilla gorilla gorilla). J. Microbiol. Meth., 2012, 91, 45–51.

  • Crawley, J. A. H., Chapman, S. N., Lummaa, V. and Lynsdale, C. L., Testing storage methods of faecal samples for subsequent measurement of helminth egg numbers in the domestic horse. Vet. Parasitol., 2016, 221, 130–133.

  • Mukherjee, N., Mondol, S., Andheria, A. and Ramakrishnan, U., Rapid multiplex PCR based species identification of wild tigers using non-invasive samples. Conserv. Genet., 2007, 8, 1465–1470.

  • Mondol, S., Kumar, N. S., Gopalaswamy, A., Sunagar, K., Karanth, K. U. and Ramakrishnan, U., Identifying species, sex and individual tigers and leopards in the Malenad–Mysore Tiger Landscape, Western Ghats, India. Conserv. Genet. Resour., 2015, 7, 353–361.

  • Maroju, P. A., Yadav, S., Kolipakam, V., Singh, S., Qureshi, Q. and Jhala, Y., Schrodinger’s scat: a critical review of the currently available tiger (Panthera tigris) and leopard (Panthera pardus) specific primers in India, and a novel leopard specific primer. BMC Genet., 2016, 17, 37.

  • Modi, S., Mondol, S., Ghaskadbi, P., Hussain, Z., Nigam, P. and Habib, B., Non-invasive DNA-based species and sex identification of Asiatic wild dog (Cuon alpinus). J. Genet., 2018, 97, 1457–1461.

  • Farrell, L. E., Roman, J. and Sunquist, M. E., Dietary separation of sympatric carnivores identified by molecular analysis of scats. Mol. Ecol., 2000, 9, 1583–1590.

  • Gupta, S. K., Kumar, A. and Hussain, S. A., Novel primers for sequencing of the complete mitochondrial cytochrome b gene of ungulates using non-invasive and degraded biological samples. Conserv. Genet. Resour., 2014, 6, 499–501.

  • Mondol, S., Thatte, P., Yadav, P. and Ramakrishnan, U., A set of miniSTRs for population genetic analyses of tigers (Panthera tigris) with cross-species amplification for seven other Felidae. Conserv. Genet. Resour., 2012, 4, 63–66.

  • Ostrander, E. A., Sprague, G. F. and Rine, J., Identification and characterization of dinucleotide repeat (CA)n markers for genetic mapping in dog. Genomics, 1993, 16, 207–213.

  • Ostrander, E. A, Mapa, F. A, Yee, M. and Rine, J., One hundred and one new simple sequence repeat-based markers for the canine genome. Mammal Genome, 1995, 6, 192–195.

  • Kongrit, C., Siripunkaw, C., Brockelman, W. Y., Akkarapatumwong, V., Wright, T. F. and Eggert, L. S., Isolation and characterization of dinucleotide microsatellite loci in the Asian elephant (Elephas maximus). Mol. Ecol. Resour., 2008, 8, 175– 177.

  • Queirós, J., Godinho, R., Lopes, S., Gortazar, C., de la Fuente, J. and Alves, P. C., Effect of microsatellite selection on individual and population genetic inferences: an empirical study using crossspecific and species-specific amplifications. Mol. Ecol. Resour., 2015, 15, 747–760.


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  • A Practive Faeces Collection Protocol for Multidisciplinary Research in Wildlife Science

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Authors

Suvankar Biswas
Wildlife Institute of India, Chandrabani, Dehradun 248 001, India
Supriya Bhatt
Wildlife Institute of India, Chandrabani, Dehradun 248 001, India
Shrutarshi Paul
Wildlife Institute of India, Chandrabani, Dehradun 248 001, India
Shrushti Modi
Wildlife Institute of India, Chandrabani, Dehradun 248 001, India
Tista Ghosh
Wildlife Institute of India, Chandrabani, Dehradun 248 001, India
Bilal Habib
Wildlife Institute of India, Chandrabani, Dehradun 248 001, India
Parag Nigam
Wildlife Institute of India, Chandrabani, Dehradun 248 001, India
Gautam Talukdar
Wildlife Institute of India, Chandrabani, Dehradun 248 001, India
Bivash Pandav
Wildlife Institute of India, Chandrabani, Dehradun 248 001, India
Samrat Mondol
Wildlife Institute of India, Chandrabani, Dehradun 248 001, India

Abstract


Faecal samples have become an important noninvasive source of information in wildlife biology and ecological research. Despite regular use of faeces, there is no universal protocol available for faeces collection and storage to answer various questions in wildlife biology. In this study we collected 1408 faeces from ten different species using a dry sampling approach, and achieved 77.49% and 75.25% success rate in mitochondrial and nuclear marker amplifications respectively. We suggest a universal framework to use the same samples to answer different questions. This protocol provides an easy, quick and cheap option to collect non-invasive samples from species living in different environmental conditions to answer multidisciplinary questions in wildlife biology.

Keywords


Non-invasive Wildlife Research, Species Biology, Dry Sampling, Variable Habitats, Field Logistics.

References





DOI: https://doi.org/10.18520/cs%2Fv116%2Fi11%2F1878-1885