15 research outputs found
Genotyping faecal samples of Bengal tiger Panthera tigris tigris for population estimation: A pilot study
BACKGROUND: Bengal tiger Panthera tigris tigris the National Animal of India, is an endangered species. Estimating populations for such species is the main objective for designing conservation measures and for evaluating those that are already in place. Due to the tiger's cryptic and secretive behaviour, it is not possible to enumerate and monitor its populations through direct observations; instead indirect methods have always been used for studying tigers in the wild. DNA methods based on non-invasive sampling have not been attempted so far for tiger population studies in India. We describe here a pilot study using DNA extracted from faecal samples of tigers for the purpose of population estimation. RESULTS: In this study, PCR primers were developed based on tiger-specific variations in the mitochondrial cytochrome b for reliably identifying tiger faecal samples from those of sympatric carnivores. Microsatellite markers were developed for the identification of individual tigers with a sibling Probability of Identity of 0.005 that can distinguish even closely related individuals with 99.9% certainty. The effectiveness of using field-collected tiger faecal samples for DNA analysis was evaluated by sampling, identification and subsequently genotyping samples from two protected areas in southern India. CONCLUSION: Our results demonstrate the feasibility of using tiger faecal matter as a potential source of DNA for population estimation of tigers in protected areas in India in addition to the methods currently in use
High efficiency protocol of DNA extraction from Micromys minutus mandibles from owl pellets: a tool for molecular research of cryptic mammal species
Microsatellite repeat motif and amplicon length affect amplification success of degraded faecal DNA
A methodological approach for non-invasive sampling for population size estimates in wild boars (Sus scrofa)
Conservation genetics of the giant otter (Pteronura brasiliensis (Zimmerman, 1780)) (Carnivora, Mustelidae)
Noninvasive Genotyping of the Red-Legged Partridge (Alectoris rufa, Phasianidae): Semi-Nested PCR of Mitochondrial DNA from Feces
Exposure to chemically-dispersed oil is more harmful to early developmental stages of the Northern shrimp Pandalus borealis than mechanically-dispersed oil
The influence of evolutionary distance between cross-species microsatellites and primer base-pair composition on allelic dropout rates
Allelic dropouts (ADO) are an important
source of genotyping error and because of their negative
impact on non-invasive sampling techniques, have become
the focus of considerable attention. Previous studies have
noted that ADO rates are greater with increasing allele size
and in tetranucleotides. It has also been suggested, but not
tested, that ADO rates may be higher in studies using crossspecies
microsatellites and that mutations may play a role
in ADO rates. Here we examine the relationship between
ADO rates and the relationship between evolutionary distance
since divergence time between species for which the
microsatellite was designed for and species on which it was
used (divergence times), and how this may interact with
median allele size. In addition, as the adenosine (A) and
thymine (T) content of the primer may increase mutation
rates, we also included total % AT content of the primer in
the analyses. Finally, we examined whether other commonly
associated causes of ADO (i.e. repeat motif length,
median allele size and allele number) co-varied. We found
that ADO rates were positively associated to divergence
time and median allele size. Repeat motif length, median
allele size and allele number positively covaried suggesting
a link between mutability and these parameters. Results
from previous studies that did not correct for co-variation
among these parameters may have been confounded. AT
content of the primer was positively associated with ADO
rates. The best linear regression model contained divergence
time, median allele size and total % AT content,
explaining 21% of the variation in ADO rates. The available
evidence suggests that mutations partly cause ADO
and that studies using cross-species microsatellites may be
at higher risk of ADO. Based on our results we highlight
some important considerations in the selection of microsatellites
for all conservation genetic studies