Characterization of six cross-species microsatellite markers suitable for estimating the population parameters of the black-backed jackal (Canis mesomelas) using a non-invasive genetic recovery protocol

Robert S. James, Phillip L. James, Dawn Scott, Andrew Overall

Research output: Contribution to journalArticleResearchpeer-review

Abstract

The black-backed jackal has proven difficult to study in the wild due to its elusive behaviour. As a rabies vector and predator of livestock, understanding dispersal patterns and population structure is of importance when considering the management of this species in South Africa's rural areas. We have characterised a suite of six cross-species microsatellite markers suitable for this purpose and present a method to isolate suitable quantities of host DNA from faeces in order to undertake endpoint PCR. Allelic dropout and null allele frequencies were shown to be negligible for all loci. No evidence of selection could be detected at any of the loci examined. The genotype frequencies of the total sampled population were tested for concordance with Hardy-einberg equilibrium. No significant deficit of heterozygote individuals was detected globally when tested by locus and marker set. An excess of heterozygosity was recorded at three loci within a single study site. The total inbreeding coefficient FST was calculated at 3% across the sampled population. The average DNA copy number recovered from faecal deposits was quantified using a qPCR-TacMan reporter probe method. The results of this study indicate that the quantity of DNA recovered from faeces was sufficient to undertake endpoint PCR.
Original languageEnglish
Pages (from-to)1-21
Number of pages21
JournalCogent Biology
Issue number1
DOIs
Publication statusPublished - 1 Nov 2015

Fingerprint

jackals
Canis
microsatellite repeats
loci
endpoints
heterozygosity
DNA
feces
null alleles
inbreeding coefficient
rabies
rural areas
gene frequency
population structure
South Africa
livestock
predators
genotype
methodology

Bibliographical note

© 2015 The Author(s). This open access article is distributed under a Creative Commons Attribution (CC-BY) 4.0 license.

Keywords

  • microsatellite
  • black-backed jackal
  • qPCR
  • faeces
  • non-invasive genetic sampling

Cite this

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title = "Characterization of six cross-species microsatellite markers suitable for estimating the population parameters of the black-backed jackal (Canis mesomelas) using a non-invasive genetic recovery protocol",
abstract = "The black-backed jackal has proven difficult to study in the wild due to its elusive behaviour. As a rabies vector and predator of livestock, understanding dispersal patterns and population structure is of importance when considering the management of this species in South Africa's rural areas. We have characterised a suite of six cross-species microsatellite markers suitable for this purpose and present a method to isolate suitable quantities of host DNA from faeces in order to undertake endpoint PCR. Allelic dropout and null allele frequencies were shown to be negligible for all loci. No evidence of selection could be detected at any of the loci examined. The genotype frequencies of the total sampled population were tested for concordance with Hardy-einberg equilibrium. No significant deficit of heterozygote individuals was detected globally when tested by locus and marker set. An excess of heterozygosity was recorded at three loci within a single study site. The total inbreeding coefficient FST was calculated at 3{\%} across the sampled population. The average DNA copy number recovered from faecal deposits was quantified using a qPCR-TacMan reporter probe method. The results of this study indicate that the quantity of DNA recovered from faeces was sufficient to undertake endpoint PCR.",
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Characterization of six cross-species microsatellite markers suitable for estimating the population parameters of the black-backed jackal (Canis mesomelas) using a non-invasive genetic recovery protocol. / James, Robert S.; James, Phillip L.; Scott, Dawn; Overall, Andrew.

In: Cogent Biology, No. 1, 01.11.2015, p. 1-21.

Research output: Contribution to journalArticleResearchpeer-review

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