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 primerReport as inadecuate




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 - Download this document for free, or read online. Document in PDF available to download.

BMC Genetics

, 17:37

Animal population genetics

Abstract

BackgroundNon-invasive sampling has opened avenues for the genetic study of elusive species, which has contributed significantly to their conservation. Where field based identity of non-invasive sample is ambiguous e.g. carnivore scats, it is essential to establish identity of the species through molecular approaches. A cost effective procedure to ascertain species identity is to use species specific primers SSP for PCR amplification and subsequent resolution through agarose gel electrophoresis. However, SSPs if ill designed can often cross amplify non-target sympatric species. Herein we report the problem of cross amplification with currently published SSPs, which have been used in several recent scientific articles on tigers Panthera tigris and leopards Panthera pardus in India. Since these papers form pioneering research on which future work will be based, an early rectification is required so as to not propagate this error further.

ResultsWe conclusively show cross amplification of three of the four SSPs, in sympatric non-target species like tiger SSP amplifying leopard and striped hyena Hyaena hyaena, and leopard SSP amplifying tiger, lion Panthera leo persica and clouded leopard Neofelis nebulosa, with the same product size. We develop and test a non-cross-amplifying leopard specific primer pair within the mitochondrial cytochrome b region. We also standardize a duplex PCR method to screen tiger and leopard samples simultaneously in one PCR reaction to reduce cost and time.

ConclusionsThese findings suggest the importance of an often overlooked preliminary protocol of conclusive identification of species from non-invasive samples. The cross amplification of published primers in conspecifics suggests the need to revisit inferences drawn by earlier work.

KeywordsSpecies specific primers SSP Non-invasive genetic sampling Fecal DNA Duplex PCR AbbreviationsDNAdeoxyribonucleic acid

SSPspecies specific primers

PCRpolymerase chain reaction

mtDNAmitochondrial DNA

TSPtiger specific primer

LSPleopard specific primer

SNPssingle nucleotide polymorphisms

Taannealing temperature

NCBInational center for biotechnology information

BLASTbasic local alignment search tool

Electronic supplementary materialThe online version of this article doi:10.1186-s12863-016-0344-y contains supplementary material, which is available to authorized users.

An erratum to this article is available at http:-dx.doi.org-10.1186-s12863-016-0451-9.

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Author: Pranay Amruth Maroju - Sonu Yadav - Vishnupriya Kolipakam - Shweta Singh - Qamar Qureshi - Yadvendradev Jhala

Source: https://link.springer.com/







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