Reliable microsatellite genotyping of the Eurasian badger (Meles meles) using faecal DNA

The potential link between badgers and bovine tuberculosis has made it vital to develop accurate techniques to census badgers. Here we investigate the potential of using genetic profiles obtained from faecal DNA as a basis for population size estimation. After trialling several methods we obtained a...

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Published in:Molecular ecology 2003-06, Vol.12 (6), p.1649-1661
Main Authors: Frantz, A. C., Pope, L. C., Carpenter, P. J., Roper, T. J., Wilson, G. J., Delahay, R. J., Burke, T.
Format: Article
Language:English
Subjects:
Alleles
Animals
bovine tuberculosis
Carnivora - genetics
Feces - chemistry
Genotype
Likelihood Functions
mark-recapture models
maximum-likelihood model
Microsatellite Repeats - genetics
molecular scatology
multiple-tubes approach
Population Density
population size estimation
Research Design
Specimen Handling - methods
United Kingdom
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cited_by cdi_FETCH-LOGICAL-c5398-b4c03085a0893b0ad467a199a94acbca4cce03db5050e17df06c59cf070923b13
cites cdi_FETCH-LOGICAL-c5398-b4c03085a0893b0ad467a199a94acbca4cce03db5050e17df06c59cf070923b13
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container_title Molecular ecology
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creator Frantz, A. C.
Pope, L. C.
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description The potential link between badgers and bovine tuberculosis has made it vital to develop accurate techniques to census badgers. Here we investigate the potential of using genetic profiles obtained from faecal DNA as a basis for population size estimation. After trialling several methods we obtained a high amplification success rate (89%) by storing faeces in 70% ethanol and using the guanidine thiocyanate/silica method for extraction. Using 70% ethanol as a storage agent had the advantage of it being an antiseptic. In order to obtain reliable genotypes with fewer amplification reactions than the standard multiple‐tubes approach, we devised a comparative approach in which genetic profiles were compared and replication directed at similar, but not identical, genotypes. This modified method achieved a reduction in polymerase chain reactions comparable with the maximum‐likelihood model when just using reliability criteria, and was slightly better when using reliability criteria with the additional proviso that alleles must be observed twice to be considered reliable. Our comparative approach would be best suited for studies that include multiple faeces from each individual. We utilized our approach in a well‐studied population of badgers from which individuals had been sampled and reliable genotypes obtained. In a study of 53 faeces sampled from three social groups over 10 days, we found that direct enumeration could not be used to estimate population size, but that the application of mark–recapture models has the potential to provide more accurate results.
doi_str_mv 10.1046/j.1365-294X.2003.01848.x
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source Wiley-Blackwell Journals
subjects Alleles
Animals
bovine tuberculosis
Carnivora - genetics
Feces - chemistry
Genotype
Likelihood Functions
mark-recapture models
maximum-likelihood model
Microsatellite Repeats - genetics
molecular scatology
multiple-tubes approach
Population Density
population size estimation
Research Design
Specimen Handling - methods
United Kingdom
title Reliable microsatellite genotyping of the Eurasian badger (Meles meles) using faecal DNA
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