Volume 36 Issue 2
Mar.  2015
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Alice LAGUARDIA, Jun WANG, Fang-Lei SHI, Kun SHI, Philip RIORDAN. Species identification refined by molecular scatology in a community of sympatric carnivores in Xinjiang, China. Zoological Research, 2015, 36(2): 72-78.
Citation: Alice LAGUARDIA, Jun WANG, Fang-Lei SHI, Kun SHI, Philip RIORDAN. Species identification refined by molecular scatology in a community of sympatric carnivores in Xinjiang, China. Zoological Research, 2015, 36(2): 72-78.

Species identification refined by molecular scatology in a community of sympatric carnivores in Xinjiang, China

Funds:  This study was supported by the Second National Survey of Terrestrial Wildlife in China, State Forestry Administration of China; the Darwin Inititive; and the Robertson Foundation.
 Appendix
Appendix 1&2
 
More Information
  • Corresponding author: Kun SHI
  • Received Date: 2014-05-19
  • Rev Recd Date: 2014-11-20
  • Publish Date: 2015-03-08
  • Many ecological studies and conservation management plans employ noninvasive scat sampling based on the assumption that species' scats can be correctly identified in the field. However, in habitats with sympatric similarly sized carnivores, misidentification of scats is frequent and can lead to bias in research results. To address the scat identification dilemma, molecular scatology techniques have been developed to extract DNA from the donor cells present on the outer lining of the scat samples. A total of 100 samples were collected in the winter of 2009 and 2011 in Taxkorgan region of Xinjiang, China. DNA was extracted successfully from 88% of samples and genetic species identification showed that more than half the scats identified in the field as snow leopard (Panthera uncia) actually belonged to fox (Vulpes vulpes). Correlation between scat characteristics and species were investigated, showing that diameter and dry weight of the scat were significantly different between the species. However it was not possible to define a precise range of values for each species because of extensive overlap between the morphological values. This preliminary study confirms that identification of snow leopard feces in the field is misleading. Research that relies upon scat samples to assess distribution or diet of the snow leopard should therefore employ molecular scatology techniques. These methods are financially accessible and employ relatively simple laboratory procedures that can give an indisputable response to species identification from scats.
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  • [1] 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). Molecular Ecology, 12(8): 2175-2186.
    [2] Ale SB, Yonzon P, Thapa K. 2007. Recovery of snow leopard Uncia uncia in Sagarmatha (Mount Everest) National Park, Nepal. Oryx, 41(1): 89-92.
    [3] Anwar MB, Jackson R, Nadeem MS, Jane?ka JE, Hussain S, Beg MA, Muhammad G, Qayyum M. 2011. Food habits of the snow leopard Panthera uncia (Schreber, 1775) in Baltistan, Northern Pakistan. European Journal of Wildlife Research, 57(5): 1077-1083.
    [4] Bagchi S, Mishra C. 2006. Living with large carnivores: predation on livestock by the snow leopard (Uncia uncia). Journal of Zoology, 268(3): 217-224.
    [5] Conradi M. 2006. Non-invasive sampling of snow leopards (Uncia uncia) in Phu valley, Nepal. Master thesis. Available at http: //urn.nb.no/URN: NBN: no-19945.
    [6] Cossíos D, Angers B. 2006. Identification of andean felid feces using PCR-RFLP. Mastozool Neotrop, 13(2): 239-244.
    [7] Danner D, Dodd N. 1982. Comparison of coyote and gray fox scat diameters. Journal of Wildlife Management, 46(1): 240-241.
    [8] Davison A, Birks JDS, Brookes RC, Braithwaite TC, Messenger JE. 2002. On the origin of faeces: morphological versus molecular methods for surveying rare carnivores from their scats. Journal of Zoology, 257(2): 141-143.
    [9] DeMatteo KE, Rinas MA, Argüelles CF, Zurano JP, Selleski N, Bitetti MSD, Eggert LS. 2014. Noninvasive techniques provide novel insights for the elusive bush dog (Speothos venaticus). Wildlife Society Bulletin, doi:  10.1002/wsb.474.
    [10] Farrell LE, Roman J, Sunquist ME. 2000. Dietary separation of sympatric carnivores identified by molecular analysis of scats. Molecular Ecology, 9(10): 1583-1590.
    [11] Fernandes CA, Ginja C, Pereira I, Tenreiro R, Bruford MW, Santos-Reis M. 2008. Species-specific mitochondrial DNA markers for identification of non-invasive samples from sympatric carnivores in the Iberian Peninsula. Conservation Genetics, 9(3): 681-690.
    [12] Foran DR, Crooks KR, Minta SC. 1997. Species identification from scat: an unambiguous genetic method. Wildlife Society Bulletin, 25(4): 835-839.
    [13] Fox JL, Sinha SP, Chundawat RS, Das PK. 1991. Status of the snow leopard Panthera uncia in Northwest India. Biological Conservation, 55(3): 283-298.
    [14] Gibbs JP. 2000. Monitoring populations. In: Boitani L, Fuller TK. Research Techniques in Animal Ecology, Controversies and Consequences. New York: Columbia University Press, 422.
    [15] Green J, Flinders J. 1981. Diameter and pH comparisons of coyote and red fox scats. Journal of Wildlife Management, 45(3): 765-767.
    [16] Harrington LA, Harrington AL, Hughes J, Stirling D, Macdonald DW. 2009. The accuracy of scat identification in distribution surveys: American mink, Neovison vison, in the northern highlands of Scotland. European Journal of Wildlife Research, 56(3): 377-384.
    [17] Höss M, Kohn M, Pääbo S. 1992. Excrement analysis by PCR. Nature, 359(6392): 199.
    [18] Hussain S. 2003. The status of the snow leopard in Pakistan and its conflict with local farmers. Oryx, 37(1): 26-33.
    [19] Jackson R, Ahlborn G. 1988. Observations on the ecology of snow leopard in west Nepal. In: Freeman H. Proceedings of the 5th International Snow Leopard Symposium. 65-87.
    [20] Jackson RM, Hunter DO. 1996. Snow Leopard Survey and Conservation Handbook. International Snow Leopard Trust, and US Geological Survey Biological Resources Division, Seattle, USA.
    [21] Jane?ka J, Munkhtsog B, Jackson R, Naranbaatar G, Mallon D, Murphy W. 2011. Comparison of noninvasive genetic and camera-trapping techniques for surveying snow leopards. Journal of Mammalogy, 92(4): 771-783.
    [22] Jane?ka J, Jackson R, Yuquang Z, Diqiang L, Munkhtsog B, Buckley-Beason V, Murphy W. 2008. Population monitoring of snow leopards using noninvasive collection of scat samples: a pilot study. Animal Conservation, 11(5): 401-411.
    [23] Karmacharya D, Thapa, K, Shrestha R, Dhakal M, Janecka JE. 2011. Noninvasive genetic population survey of snow leopards (Panthera uncia) in Kangchenjunga conservation area, Shey Phoksundo National Park and surrounding buffer zones of Nepal. BMC Research Notes, 4(1): 516.
    [24] Keehner JR. 2009. Using DNA sequence analysis of hair and feces to detect and identify carnivore species in National Parks of the Southwest. McNair Research Journal, 1: 32.
    [25] Kimura M. 1980. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. Journal of Molecular Evolution, 16(2): 111-120.
    [26] 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. Molecular Ecology, 4(1): 95-104.
    [27] Liu CG, Zheng SW, Ren JR. 2003. Research foods and foods source about snow Leopard(Panthera uncia). Journal of Shaanxi Normal University(Natural Science Edition), 31: 154-159.
    [28] Long RA, MacKay P, Ray J, Zielinski W. 2008. Noninvasive Survey Methods for Carnivores. 2nd ed. Washington, D.C.: Island Press.
    [29] Long RA, Donovan TM, Mackay P, Zielinski WJ, Buzas JS. 2007a. Effectiveness of scat detection dogs for detecting forest carnivores. Journal of Wildlife Management, 71: 2007-2017.
    [30] Long RA, Donovan TM, Mackay P, Zielinski WJ, Buzas JS. 2007b. Comparing scat detection dogs, cameras, and hair snares for surveying carnivores. Journal of Wildlife Management, 71(6): 2018-2025.
    [31] Lovari S, Ventimiglia M, Minder I. 2013. Food habits of two leopard species, competition, climate change and upper treeline: a way to the decrease of an endangered species? Ethology Ecology & Evolution, 25(4): 305-318.
    [32] Ma M, Munkhtsog B, Xu F, Mardan T, Yin SJ, Wei SD. 2005. Markings as indicator of snow leopard in field survey, in Xinjiang. Chinese Journal of Zoology, 40(4): 34-39.
    [33] Ma M, Xu F, Munkhtsog B, Wu YQ, McCarthy T, McCarthy K. 2011. Monitoring of population density of snow leopard in Xinjiang. Journal of Ecology and Rural Environment, 27(1): 79-83. (in Chinese)
    [34] Madden T. 2002. The BLAST Sequence Analysis Tool. In: McEntyre J, Ostell J. The NCBI Handbook. Bethesda (MD): National Center for Biotechnology Information (US).
    [35] McCarthy K, Fuller T, Ming M, McCarthy T, Waits L, Jumabaev K. 2008. Assessing estimators of snow leopard abundance. Journal of Wildlife Management, 72(8): 1826-1833.
    [36] Mills LS, Pilgrim KL, Schwartz MK, Mckelvey K. 2001. Identifying lynx and other North American felids based on MtDNA analysis. Conservation Genetics, 1(3): 285-288.
    [37] Mukherjee S, Ashalakshmi CN, Home C, Ramakrishnan U. 2010. An evaluation of the PCR-RFLP technique to aid molecular-based monitoring of felids and canids in India. BMC Research Notes, 3: 159.
    [38] Naidu A, Smythe LA, Thompson RW, Culver M. 2011. Genetic Analysis of Scats Reveals Minimum Number and Sex of Recently Documented Mountain Lions. Journal of Fish and Wildlife Management, 2(1): 106-111.
    [39] Oli MK. 1993. A key for the identification of the hair of mammals of a snow leopard (Panthera uncia) habitat in Nepal. Journal of Zoology, 231(1): 71-93.
    [40] Peres-Neto PR, Jackson DA, Somers KM. 2003. Giving meaningful interpretation to ordination axes: assessing loading significance in principal component analysis. Ecology, 84(9): 2347-2363.
    [41] Prugh LR, Ritland CE. 2005. Molecular testing of observer identification of carnivore feces in the field. Wildlife Society Bulletin, 33(1): 189-194.
    [42] R Development Core Team. 2013. R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria.
    [43] Rodgers TW, Jane?ka JE. 2012. Applications and techniques for non-invasive faecal genetics research in felid conservation. European Journal of Wildlife Research, 59(1): 1-16.
    [44] Rozhnov VV, Zvychainaya EY, Kuksin AN, Poyarkov AD. 2011. Noninvasive molecular genetic analysis in studying the ecology of the snow leopard: Problems and prospects. Russian Journal of Ecology, 42(6): 439-444.
    [45] Santini A, Lucchini V, Fabbri E, Randi E. 2007. Ageing and environmental factors affect PCR success in wolf (Canis lupus) excremental DNA samples. Molecular Ecology Notes, 7(6): 955-961.
    [46] Shehzad W, Mccarthy TM, Pompanon F, Purevjav L, Coissac E, Riaz T, Taberlet P. 2012. Prey Preference of Snow Leopard (Panthera uncia) in South Gobi, Mongolia. PloS One, 7(2): e32104.
    [47] Stenglein JL, De Barba M, Ausband DE, Waits LP. 2010. Impacts of sampling location within a faeces on DNA quality in two carnivore species. Molecular Ecology Resources, 10(1): 109-114.
    [48] Sunquist ME, Sunquist F. 2002. Wild Cats of the World. Chicago, IL: University of Chicago Press.
    [49] Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. 2013. MEGA6: molecular evolutionary genetics analysis version 6. 0. Molecular Biology and Evolution, 30(12): 2725-2729.
    [50] Wang J, Laguardia A, Damerell PJ, Riordan P, Shi K. 2014. Dietary overlap of snow leopard and other carnivores in the Pamirs of Northwestern China. Chinese Science Bulletin, 59(25): 3162-3168.
    [51] Wei FW, Rao G, Li M, Fang SG, Feng ZJ. 2001. Molecular scatology and its application--Reliability, limitation and prospect. Acta Theriologica Sinica, 21(2): 143-152. (in Chinese)
    [52] Xu F, Ma M, Yin SJ, Mardan T. 2005. Snow leopard survey in Tumor Nature Reserve, Xinjiang. Sichuan Journal of Zoology, 24(4): 608-610. (in Chinese)
    [53] Zhang Y, He L, Duo H, Li D, Jin K. 2009. A preliminary study on the population genetic structure of snow leopard (Unica unica) in Qinghai Province utilizing fecal DNA. Acta Theriologica Sinica, 29(3): 310-315. (in Chinese)
    [54] Zhang Z, Schwartz S, Wagner L, Miller W. 2000. A greedy algorithm for aligning DNA sequences. Journal of Computational Biology, 7(1-2): 203-214.
    [55] Zuercher GL, Gipson PS, Stewart GC. 2003. Identification of carnivore feces by local peoples and molecular analyses. WIldlife Society Bulletin, 31(4): 961-970.
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Species identification refined by molecular scatology in a community of sympatric carnivores in Xinjiang, China

Funds:  This study was supported by the Second National Survey of Terrestrial Wildlife in China, State Forestry Administration of China; the Darwin Inititive; and the Robertson Foundation.
 Appendix
Appendix 1&2
 
    Corresponding author: Kun SHI

Abstract: Many ecological studies and conservation management plans employ noninvasive scat sampling based on the assumption that species' scats can be correctly identified in the field. However, in habitats with sympatric similarly sized carnivores, misidentification of scats is frequent and can lead to bias in research results. To address the scat identification dilemma, molecular scatology techniques have been developed to extract DNA from the donor cells present on the outer lining of the scat samples. A total of 100 samples were collected in the winter of 2009 and 2011 in Taxkorgan region of Xinjiang, China. DNA was extracted successfully from 88% of samples and genetic species identification showed that more than half the scats identified in the field as snow leopard (Panthera uncia) actually belonged to fox (Vulpes vulpes). Correlation between scat characteristics and species were investigated, showing that diameter and dry weight of the scat were significantly different between the species. However it was not possible to define a precise range of values for each species because of extensive overlap between the morphological values. This preliminary study confirms that identification of snow leopard feces in the field is misleading. Research that relies upon scat samples to assess distribution or diet of the snow leopard should therefore employ molecular scatology techniques. These methods are financially accessible and employ relatively simple laboratory procedures that can give an indisputable response to species identification from scats.

Alice LAGUARDIA, Jun WANG, Fang-Lei SHI, Kun SHI, Philip RIORDAN. Species identification refined by molecular scatology in a community of sympatric carnivores in Xinjiang, China. Zoological Research, 2015, 36(2): 72-78.
Citation: Alice LAGUARDIA, Jun WANG, Fang-Lei SHI, Kun SHI, Philip RIORDAN. Species identification refined by molecular scatology in a community of sympatric carnivores in Xinjiang, China. Zoological Research, 2015, 36(2): 72-78.
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