Short Communication

Conservation Genetics

, Volume 8, Issue 6, pp 1465-1470

First online:

Rapid multiplex PCR based species identification of wild tigers using non-invasive samples

  • Nibedita MukherjeeAffiliated withNational Centre for Biological SciencesWildlife Conservation Society-India Program, Centre for Wildlife Studies
  • , Samrat MondolAffiliated withNational Centre for Biological Sciences
  • , Anish AndheriaAffiliated withWildlife Conservation Society-India Program, Centre for Wildlife Studies
  • , Uma RamakrishnanAffiliated withNational Centre for Biological SciencesWildlife Conservation Society-India Program Email author 

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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.


Fecal samples Molecular species identification Conservation Degraded DNA