Abstract
Conservation and management of rare and elusive species requires accurate data on presence or absence. In such cases, molecular genetics based species identification approaches can prove invaluable, especially in conjuncture with non-invasive DNA sampling. However, non-invasive sources yield DNA in low concentration that is degraded, which could result in false negatives for species identification. In this paper, we developed a set of primers for PCR-based species identification of tigers. Our results reveal high rates (upto 90%) of species identification for both fresh (less than 48 h) and old (between 7 days and 3 months) fecal samples from the field. Experiments reveal that multiplex PCR (amplifying more than one genomic region) results in an increase in conclusive species identification (and a consequent decrease in the number of false negatives) from 55% to 89% for old fecal samples. We demonstrate that this increased success is because we experimentally overcome the problems of low DNA template quantity (using the multiplex PCR kit, increases species identification from 55% to 72%) and low template DNA quality (two sets of primers increase the species identification success from 72% to 89%). We recommend that multiplex PCR based methods be used (in conjuncture with species specific primers) for other rare and elusive species since such methods will potentially significantly decrease error in species identification.
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Acknowledgements
We thank Karnataka Forest Department, especially Mr. A. K. Varma, IFS, Chief Wildlife Warden, for permission to conduct this study. We thank The Rhino and Tiger Conservation Fund of the United States Fish and Wildlife Service, Wildlife Conservation Society, New York and Wildlife Conservation Society-India Program for funding the study. We thank the National Centre for Biological Science for laboratory facilities, funding and technical support. We thank the Centre for Wildlife Studies for field support. We thank Dr. K. Ullas Karanth for initiation of this project. Special thanks to Dr. S. Mukherjee, Mr. S. Kumar, Dr. J. Krishnaswamy, Mr. T. Shivanand, Mr. A. Purandare, Mr. J. James, Mr. Velumani, Ms. V. Ranganathan, Mr. D. Chakraborty, Mr. D. Jathanna, Ms. A. Das and Dr. G. Hyde for conceptual input and comments on earlier versions of this manuscript. Comments from an anonymous reviewer significantly improved this manuscript. We thank the field assistants for help with sample collection. We thank Ms. Sonia for sequencing assistance and Mr. Krishna Narain for logistic support.
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Nibetida Mukherjee and Samrat Mondol have contributed equally to this manuscript.
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Mukherjee, N., Mondol, S., Andheria, A. et al. Rapid multiplex PCR based species identification of wild tigers using non-invasive samples. Conserv Genet 8, 1465–1470 (2007). https://doi.org/10.1007/s10592-007-9289-z
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DOI: https://doi.org/10.1007/s10592-007-9289-z