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Conventional versus real‐time quantitative PCR for rare species detection
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| Zeitschriftentitel: | Ecology and Evolution |
|---|---|
| Personen und Körperschaften: | , , , , , , |
| In: | Ecology and Evolution, 8, 2018, 23, S. 11799-11807 |
| Format: | E-Article |
| Sprache: | Englisch |
| veröffentlicht: |
Wiley
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| Schlagwörter: |
| author_facet |
Xia, Zhiqiang Johansson, Mattias L. Gao, Yangchun Zhang, Lei Haffner, Gordon Douglas MacIsaac, Hugh J. Zhan, Aibin Xia, Zhiqiang Johansson, Mattias L. Gao, Yangchun Zhang, Lei Haffner, Gordon Douglas MacIsaac, Hugh J. Zhan, Aibin |
|---|---|
| author |
Xia, Zhiqiang Johansson, Mattias L. Gao, Yangchun Zhang, Lei Haffner, Gordon Douglas MacIsaac, Hugh J. Zhan, Aibin |
| spellingShingle |
Xia, Zhiqiang Johansson, Mattias L. Gao, Yangchun Zhang, Lei Haffner, Gordon Douglas MacIsaac, Hugh J. Zhan, Aibin Ecology and Evolution Conventional versus real‐time quantitative PCR for rare species detection Nature and Landscape Conservation Ecology Ecology, Evolution, Behavior and Systematics |
| author_sort |
xia, zhiqiang |
| spelling |
Xia, Zhiqiang Johansson, Mattias L. Gao, Yangchun Zhang, Lei Haffner, Gordon Douglas MacIsaac, Hugh J. Zhan, Aibin 2045-7758 2045-7758 Wiley Nature and Landscape Conservation Ecology Ecology, Evolution, Behavior and Systematics http://dx.doi.org/10.1002/ece3.4636 <jats:title>Abstract</jats:title><jats:p>Detection of species in nature at very low abundance requires innovative methods. Conventional PCR (cPCR) and real‐time quantitative PCR (qPCR) are two widely used approaches employed in environmental DNA (eDNA) detection, though lack of a comprehensive comparison of them impedes method selection. Here we test detection capacity and false negative rate of both approaches using samples with different expected complexities. We compared cPCR and qPCR to detect invasive, biofouling golden mussels (<jats:italic>Limnoperna fortunei</jats:italic>), in samples from laboratory aquaria and irrigation channels where this mussel was known to occur in central China. Where applicable, the limit of detection (LoD), limit of quantification (LoQ), detection rate, and false negative rate of each PCR method were tested. Quantitative PCR achieved a lower LoD than cPCR (1 × 10<jats:sup>−7</jats:sup> vs. 10<jats:sup>−6</jats:sup> ng/μl) and had a higher detection rate for both laboratory (100% vs. 87.9%) and field (68.6% vs. 47.1%) samples. Field water samples could only be quantified at a higher concentration than laboratory aquaria and total genomic DNA, indicating inhibition with environmental samples. The false negative rate was inversely related to the number of sample replicates. Target eDNA concentration was negatively related to distance from sampling sites to the water (and animal) source. Detection capacity difference between cPCR and qPCR for genomic DNA and laboratory aquaria can be translated to field water samples, and the latter should be prioritized in rare species detection. Field environmental samples may involve more complexities—such as inhibitors—than laboratory aquaria samples, requiring more target DNA. Extensive sampling is critical in field applications using either approach to reduce false negatives.</jats:p> Conventional versus real‐time quantitative PCR for rare species detection Ecology and Evolution |
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| title |
Conventional versus real‐time quantitative PCR for rare species detection |
| title_unstemmed |
Conventional versus real‐time quantitative PCR for rare species detection |
| title_full |
Conventional versus real‐time quantitative PCR for rare species detection |
| title_fullStr |
Conventional versus real‐time quantitative PCR for rare species detection |
| title_full_unstemmed |
Conventional versus real‐time quantitative PCR for rare species detection |
| title_short |
Conventional versus real‐time quantitative PCR for rare species detection |
| title_sort |
conventional versus real‐time quantitative pcr for rare species detection |
| topic |
Nature and Landscape Conservation Ecology Ecology, Evolution, Behavior and Systematics |
| url |
http://dx.doi.org/10.1002/ece3.4636 |
| publishDate |
2018 |
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11799-11807 |
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<jats:title>Abstract</jats:title><jats:p>Detection of species in nature at very low abundance requires innovative methods. Conventional PCR (cPCR) and real‐time quantitative PCR (qPCR) are two widely used approaches employed in environmental DNA (eDNA) detection, though lack of a comprehensive comparison of them impedes method selection. Here we test detection capacity and false negative rate of both approaches using samples with different expected complexities. We compared cPCR and qPCR to detect invasive, biofouling golden mussels (<jats:italic>Limnoperna fortunei</jats:italic>), in samples from laboratory aquaria and irrigation channels where this mussel was known to occur in central China. Where applicable, the limit of detection (LoD), limit of quantification (LoQ), detection rate, and false negative rate of each PCR method were tested. Quantitative PCR achieved a lower LoD than cPCR (1 × 10<jats:sup>−7</jats:sup> vs. 10<jats:sup>−6</jats:sup> ng/μl) and had a higher detection rate for both laboratory (100% vs. 87.9%) and field (68.6% vs. 47.1%) samples. Field water samples could only be quantified at a higher concentration than laboratory aquaria and total genomic DNA, indicating inhibition with environmental samples. The false negative rate was inversely related to the number of sample replicates. Target eDNA concentration was negatively related to distance from sampling sites to the water (and animal) source. Detection capacity difference between cPCR and qPCR for genomic DNA and laboratory aquaria can be translated to field water samples, and the latter should be prioritized in rare species detection. Field environmental samples may involve more complexities—such as inhibitors—than laboratory aquaria samples, requiring more target DNA. Extensive sampling is critical in field applications using either approach to reduce false negatives.</jats:p> |
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| author | Xia, Zhiqiang, Johansson, Mattias L., Gao, Yangchun, Zhang, Lei, Haffner, Gordon Douglas, MacIsaac, Hugh J., Zhan, Aibin |
| author_facet | Xia, Zhiqiang, Johansson, Mattias L., Gao, Yangchun, Zhang, Lei, Haffner, Gordon Douglas, MacIsaac, Hugh J., Zhan, Aibin, Xia, Zhiqiang, Johansson, Mattias L., Gao, Yangchun, Zhang, Lei, Haffner, Gordon Douglas, MacIsaac, Hugh J., Zhan, Aibin |
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| description | <jats:title>Abstract</jats:title><jats:p>Detection of species in nature at very low abundance requires innovative methods. Conventional PCR (cPCR) and real‐time quantitative PCR (qPCR) are two widely used approaches employed in environmental DNA (eDNA) detection, though lack of a comprehensive comparison of them impedes method selection. Here we test detection capacity and false negative rate of both approaches using samples with different expected complexities. We compared cPCR and qPCR to detect invasive, biofouling golden mussels (<jats:italic>Limnoperna fortunei</jats:italic>), in samples from laboratory aquaria and irrigation channels where this mussel was known to occur in central China. Where applicable, the limit of detection (LoD), limit of quantification (LoQ), detection rate, and false negative rate of each PCR method were tested. Quantitative PCR achieved a lower LoD than cPCR (1 × 10<jats:sup>−7</jats:sup> vs. 10<jats:sup>−6</jats:sup> ng/μl) and had a higher detection rate for both laboratory (100% vs. 87.9%) and field (68.6% vs. 47.1%) samples. Field water samples could only be quantified at a higher concentration than laboratory aquaria and total genomic DNA, indicating inhibition with environmental samples. The false negative rate was inversely related to the number of sample replicates. Target eDNA concentration was negatively related to distance from sampling sites to the water (and animal) source. Detection capacity difference between cPCR and qPCR for genomic DNA and laboratory aquaria can be translated to field water samples, and the latter should be prioritized in rare species detection. Field environmental samples may involve more complexities—such as inhibitors—than laboratory aquaria samples, requiring more target DNA. Extensive sampling is critical in field applications using either approach to reduce false negatives.</jats:p> |
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| spelling | Xia, Zhiqiang Johansson, Mattias L. Gao, Yangchun Zhang, Lei Haffner, Gordon Douglas MacIsaac, Hugh J. Zhan, Aibin 2045-7758 2045-7758 Wiley Nature and Landscape Conservation Ecology Ecology, Evolution, Behavior and Systematics http://dx.doi.org/10.1002/ece3.4636 <jats:title>Abstract</jats:title><jats:p>Detection of species in nature at very low abundance requires innovative methods. Conventional PCR (cPCR) and real‐time quantitative PCR (qPCR) are two widely used approaches employed in environmental DNA (eDNA) detection, though lack of a comprehensive comparison of them impedes method selection. Here we test detection capacity and false negative rate of both approaches using samples with different expected complexities. We compared cPCR and qPCR to detect invasive, biofouling golden mussels (<jats:italic>Limnoperna fortunei</jats:italic>), in samples from laboratory aquaria and irrigation channels where this mussel was known to occur in central China. Where applicable, the limit of detection (LoD), limit of quantification (LoQ), detection rate, and false negative rate of each PCR method were tested. Quantitative PCR achieved a lower LoD than cPCR (1 × 10<jats:sup>−7</jats:sup> vs. 10<jats:sup>−6</jats:sup> ng/μl) and had a higher detection rate for both laboratory (100% vs. 87.9%) and field (68.6% vs. 47.1%) samples. Field water samples could only be quantified at a higher concentration than laboratory aquaria and total genomic DNA, indicating inhibition with environmental samples. The false negative rate was inversely related to the number of sample replicates. Target eDNA concentration was negatively related to distance from sampling sites to the water (and animal) source. Detection capacity difference between cPCR and qPCR for genomic DNA and laboratory aquaria can be translated to field water samples, and the latter should be prioritized in rare species detection. Field environmental samples may involve more complexities—such as inhibitors—than laboratory aquaria samples, requiring more target DNA. Extensive sampling is critical in field applications using either approach to reduce false negatives.</jats:p> Conventional versus real‐time quantitative PCR for rare species detection Ecology and Evolution |
| spellingShingle | Xia, Zhiqiang, Johansson, Mattias L., Gao, Yangchun, Zhang, Lei, Haffner, Gordon Douglas, MacIsaac, Hugh J., Zhan, Aibin, Ecology and Evolution, Conventional versus real‐time quantitative PCR for rare species detection, Nature and Landscape Conservation, Ecology, Ecology, Evolution, Behavior and Systematics |
| title | Conventional versus real‐time quantitative PCR for rare species detection |
| title_full | Conventional versus real‐time quantitative PCR for rare species detection |
| title_fullStr | Conventional versus real‐time quantitative PCR for rare species detection |
| title_full_unstemmed | Conventional versus real‐time quantitative PCR for rare species detection |
| title_short | Conventional versus real‐time quantitative PCR for rare species detection |
| title_sort | conventional versus real‐time quantitative pcr for rare species detection |
| title_unstemmed | Conventional versus real‐time quantitative PCR for rare species detection |
| topic | Nature and Landscape Conservation, Ecology, Ecology, Evolution, Behavior and Systematics |
| url | http://dx.doi.org/10.1002/ece3.4636 |