Improved Methods of Carnivore Faecal Sample Preservation, DNA Extraction and Quantification for Accurate Genotyping of Wild Tigers

Reddy, P. Anuradha; Bhavanishankar, Maradani; Bhagavatula, Jyotsna; Harika, Katakam; Mahla, Ranjeet Singh; Shivaji, Sisinthy

doi:10.1371/journal.pone.0046732

Cited by 30 publications

(32 citation statements)

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“…Two buffers (GUS lysis buffer and RNAlater) worked well in the few studies that tested them however; this needs to be investigated further. Reddy et al (2012) found that the amount of amplifiable DNA in faeces declined with time. This is probably because environmental conditions (e.g.…”

Section: Discussionmentioning

confidence: 99%

“…Each of the twenty-three samples were preserved in the three different media (n=69); 95% ethanol, ASL buffer (Qiagen) and Two-step storage (ethanol and silica beads; e.g. Wasser et al, 1997;Reddy et al, 2012). Wherever a sample was encountered a small portion from the outer part of the faeces (c.f.…”

Section: Faecal Samplingmentioning

confidence: 99%

“…Afterwards the ethanol was carefully poured off and the dry solid faecal sample was transferred into the tube containing silica beads (c.f. Roeder et al, 2004;Reddy et al, 2012). The top of the tube containing the dry silica gel and faecal sample was then carefully stuffed with cotton wool to make it air tight.…”

Section: Faecal Samplingmentioning

confidence: 99%

“…These studies span an array of mammal species (Appendix 1) including several species of carnivores (e.g. Wasser et al, 1997;Murphy et al, 2002;Santini et al, 2007;Panasci et al, 2011;Reddy et al, 2012). A few studies comparing storage methods in tropical environments have been conducted mostly on primates (Gerloff et al, 1995;Frantzen et al, 1998;Bayes et al, 2000;Nsubuga et al, 2004;Vallet et al, 2007).…”

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Evaluating preservation medium for the storage of DNA in African lion Panthera leo faecal samples

Tende

Hansson

Ottosson³

et al. 2014

Current Zoology

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Lion faecal samples, collected in the field between 1 hour to 1 week after defecation were preserved in three different media (ethanol, ASL buffer and Two-step storage). The aim was to determine which faecal DNA field preservation method best enhances PCR amplification success. Samples stored in ethanol showed a significantly higher amplification success of microsatellite loci than samples stored in the other two media. In contrast, amplification success of a mitochondrial locus was similar among the samples stored in the three types of media. We reviewed twelve previous studies that employed different media for the storage of faeces, although patterns of success were not fully consistent among different media, ethanol storage was scored highest in the majority of these tests [Current Zoology 60 (3): 351-358, 2014].Keywords Amplification success, Faecal sample DNA, Lion Panthera leo, PCR, Preservation medium For small and elusive wildlife populations, noninvasive DNA sampling from faecal samples is a feasible method for obtaining genetic data (Kohn and Wayne, 1997). Several studies have employed this method to estimate and monitor wildlife (Kohn et al., 1999;Ernest et al., 2000;Banks et al., 2002, Flagstad et al., 2004, Bensch et al., 2006Perez et al., 2006;Zhang et al., 2009). For elusive carnivores such as lions Panthera leo non-invasive sampling is especially suitable because faecal samples are easily encountered and recovered along trails where they defecate to mark territory boundaries (Macdonald, 1980). However, studies that employ non-invasive sampling are confronted with pitfalls such as low quantity and quality DNA which can result in low genotyping success and frequent genotyping errors (Taberlet et al., 1997).The amount and quality of DNA initially present in faeces samples at the time of collection may change during the period of storage and will determine the amount and quality of DNA that can be extracted and used in downstream analyses. It is therefore important to transfer samples into a storage condition that best preserves the DNA prior to the laboratory analysis. The choice of a good preservation medium should be of prime importance for every genetic study, especially when collected samples cannot be processed immediately at the collection site. The identification of effective preservation methods can enhance PCR amplification success rate, increase genotyping accuracy and increase the feasibility of using faecal DNA for genetic studies.Faecal DNA has so far mainly been used in studies of mammals and less often for studies of birds (Idaghdour et al., 2003;Regnaut et al., 2006). In mammals, DNA has been recovered from faeces that were preserved dried (Höss et al., 1992;Kohn et al., 1995;Foran et al., 1997;Taberlet et al., 1997), in 70% ethanol (Höss, 1992;Kohn et al., 1995), in 99%-100% ethanol (Gerloff et al., 1995) and frozen at -20°C (Reed et al., 1997).Several studies have evaluated the relative genotyping success from two or more preservation media (Wasser et al., 1997;Frantzen et...

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Section: Discussionmentioning

confidence: 99%

Section: Faecal Samplingmentioning

confidence: 99%

Section: Faecal Samplingmentioning

confidence: 99%

mentioning

confidence: 99%

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Evaluating preservation medium for the storage of DNA in African lion Panthera leo faecal samples

Tende

Hansson

Ottosson³

et al. 2014

Current Zoology

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“…Oliveira e Duarte (2013) reportam um sucesso de amplificação de 45%, mas nenhuma amostra, de um total de 52, foi identificada. Michalski et al (2011) (REDDY et al, 2012;DEMAY et al, 2014 ) Vários fatores influenciam no sucesso de amplificação, sendo a degradação do DNA e a inibição por PCR os principais empecilhos ao lidar com amostras não invasivas (BEJA-PEREIRA et al, 2009). Condições climáticas favoráveis e o correto armazenamento, aparentemente, melhoram os resultados pela menor degradação ocorrida nessas situações (NSUBUGA et al, 2004;BRINKMAN et al, 2010).…”

Section: Discussionunclassified

Uso do espaço pelo veado-catingueiro (Mazama gouazoubira; Fisher, 1814): uma comparação entre colares GPS e DNA fecal

Peres¹

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Non‐invasive genetic censusing and monitoring of primate populations

Arandjelovic

Vigilant

2018

American J Primatol

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Knowing the density or abundance of primate populations is essential for their conservation management and contextualizing socio-demographic and behavioral observations. When direct counts of animals are not possible, genetic analysis of non-invasive samples collected from wildlife populations allows estimates of population size with higher accuracy and precision than is possible using indirect signs. Furthermore, in contrast to traditional indirect survey methods, prolonged or periodic genetic sampling across months or years enables inference of group membership, movement, dynamics, and some kin relationships. Data may also be used to estimate sex ratios, sex differences in dispersal distances, and detect gene flow among locations. Recent advances in capture-recapture models have further improved the precision of population estimates derived from non-invasive samples. Simulations using these methods have shown that the confidence interval of point estimates includes the true population size when assumptions of the models are met, and therefore this range of population size minima and maxima should be emphasized in population monitoring studies. Innovations such as the use of sniffer dogs or anti-poaching patrols for sample collection are important to ensure adequate sampling, and the expected development of efficient and cost-effective genotyping by sequencing methods for DNAs derived from non-invasive samples will automate and speed analyses.

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Improved Methods of Carnivore Faecal Sample Preservation, DNA Extraction and Quantification for Accurate Genotyping of Wild Tigers

Cited by 30 publications

References 19 publications

Evaluating preservation medium for the storage of DNA in African lion Panthera leo faecal samples

Evaluating preservation medium for the storage of DNA in African lion Panthera leo faecal samples

Uso do espaço pelo veado-catingueiro (Mazama gouazoubira; Fisher, 1814): uma comparação entre colares GPS e DNA fecal

Non‐invasive genetic censusing and monitoring of primate populations

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