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Citation for Study 18713

Citation title: "A framework for developing and validating taxon-specific primers for specimen identification from environmental DNA".

Study name: "A framework for developing and validating taxon-specific primers for specimen identification from environmental DNA".

This study is part of submission 18713 (Status: Published).

Citation

Macdonald A.J., & Sarre S.D. 2016. A framework for developing and validating taxon-specific primers for specimen identification from environmental DNA. Molecular Ecology Resources, .

Authors

• Macdonald A.J. (submitter)
• Sarre S.D.

Abstract

Taxon-specific DNA tests are applied to many ecological and management questions, increasingly using environmental DNA (eDNA). eDNA facilitates non-invasive ecological studies, but introduces additional risks of bias and error. For effective application, PCR primers must be developed for each taxon and validated in each system. We outline a nine step framework for the development and validation of taxon-specific primers for eDNA analysis in ecological studies, involving reference database construction, phylogenetic evaluation of the target gene, primer design, primer evaluation in silico, and laboratory evaluation of primer specificity, sensitivity, and utility. Our framework makes possible a rigorous evaluation of likely sources of error. The first five steps can be conducted relatively rapidly and (where reference DNA sequences are available) require minimal laboratory resources, enabling assessment of primer suitability before investing in further work. Steps six to eight require more costly laboratory analyses, but are essential to evaluate risks of false positive and false negative results, while step 9 relates to field implementation. As an example, we have developed and evaluated primers to specifically amplify part of the mitochondrial ND2 gene from Australian bandicoots. If adopted during the early stages of primer development, our framework will facilitate large-scale implementation of well-designed DNA tests to detect specific wildlife from eDNA samples. This will provide researchers and managers with an understanding of the strengths and limitations of their data and the conclusions that can be drawn from them.

Keywords

Bandicoot; DNA detection; eDNA; marsupial; mitochondrial DNA; ND2 gene; Peramelemorphia; predation; trace DNA

External links

About this resource

• Canonical resource URI: http://purl.org/phylo/treebase/phylows/study/TB2:S18713
• Other versions: Nexus NeXML
• Show BibTeX reference

  		@ARTICLE{TreeBASE2Ref25445,
  	 author = {Anna J MacDonald and Stephen D Sarre},
  	 title = {A framework for developing and validating taxon-specific primers for specimen identification from environmental DNA},
  	 year = {2016},
  	 keywords = {Bandicoot; DNA detection; eDNA; marsupial; mitochondrial DNA; ND2 gene; Peramelemorphia; predation; trace DNA},
  	 doi = {},
  	 url = {http://},
  	 pmid = {},
  	 journal = {Molecular Ecology Resources},
  	 volume = {},
  	 number = {},
  	 pages = {},
  	 abstract = {Taxon-specific DNA tests are applied to many ecological and management questions, increasingly using environmental DNA (eDNA). eDNA facilitates non-invasive ecological studies, but introduces additional risks of bias and error. For effective application, PCR primers must be developed for each taxon and validated in each system. We outline a nine step framework for the development and validation of taxon-specific primers for eDNA analysis in ecological studies, involving reference database construction, phylogenetic evaluation of the target gene, primer design, primer evaluation in silico, and laboratory evaluation of primer specificity, sensitivity, and utility. Our framework makes possible a rigorous evaluation of likely sources of error. The first five steps can be conducted relatively rapidly and (where reference DNA sequences are available) require minimal laboratory resources, enabling assessment of primer suitability before investing in further work. Steps six to eight require more costly laboratory analyses, but are essential to evaluate risks of false positive and false negative results, while step 9 relates to field implementation. As an example, we have developed and evaluated primers to specifically amplify part of the mitochondrial ND2 gene from Australian bandicoots. If adopted during the early stages of primer development, our framework will facilitate large-scale implementation of well-designed DNA tests to detect specific wildlife from eDNA samples. This will provide researchers and managers with an understanding of the strengths and limitations of their data and the conclusions that can be drawn from them.}
  }
  		

• Show RIS reference

  		TY  - JOUR
  ID  - 25445
  AU  - MacDonald,Anna J
  AU  - Sarre,Stephen D
  T1  - A framework for developing and validating taxon-specific primers for specimen identification from environmental DNA
  PY  - 2016
  KW  - Bandicoot; DNA detection; eDNA; marsupial; mitochondrial DNA; ND2 gene; Peramelemorphia; predation; trace DNA
  UR  - http://dx.doi.org/
  N2  - Taxon-specific DNA tests are applied to many ecological and management questions, increasingly using environmental DNA (eDNA). eDNA facilitates non-invasive ecological studies, but introduces additional risks of bias and error. For effective application, PCR primers must be developed for each taxon and validated in each system. We outline a nine step framework for the development and validation of taxon-specific primers for eDNA analysis in ecological studies, involving reference database construction, phylogenetic evaluation of the target gene, primer design, primer evaluation in silico, and laboratory evaluation of primer specificity, sensitivity, and utility. Our framework makes possible a rigorous evaluation of likely sources of error. The first five steps can be conducted relatively rapidly and (where reference DNA sequences are available) require minimal laboratory resources, enabling assessment of primer suitability before investing in further work. Steps six to eight require more costly laboratory analyses, but are essential to evaluate risks of false positive and false negative results, while step 9 relates to field implementation. As an example, we have developed and evaluated primers to specifically amplify part of the mitochondrial ND2 gene from Australian bandicoots. If adopted during the early stages of primer development, our framework will facilitate large-scale implementation of well-designed DNA tests to detect specific wildlife from eDNA samples. This will provide researchers and managers with an understanding of the strengths and limitations of their data and the conclusions that can be drawn from them.
  L3  - 
  JF  - Molecular Ecology Resources
  VL  - 
  IS  - 
  ER  -