Ground-truthing phylotype assignments for Antarctic invertebrates
Biodiversity information from Antarctic terrestrial habitats helps conservation efforts, but the distribution and diversity particularly of microinvertebrates remains poorly understood. Springtails, mites, tardigrades, nematodes and rotifers are difficult to identify using morphological features, he...
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Online Access: | https://eprints.utas.edu.au/24610/ https://eprints.utas.edu.au/24610/1/Czechowski%20et%20al%202016%20DNA%20Barcodes.pdf https://doi.org/10.1515/dna-2017-0001 |
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ftunivtasmania:oai:eprints.utas.edu.au:24610 2023-05-15T13:31:52+02:00 Ground-truthing phylotype assignments for Antarctic invertebrates Czechowski, P Clarke, LJ Cooper, A Stevens, M 2017 application/pdf https://eprints.utas.edu.au/24610/ https://eprints.utas.edu.au/24610/1/Czechowski%20et%20al%202016%20DNA%20Barcodes.pdf https://doi.org/10.1515/dna-2017-0001 en eng De Gruyter Open https://eprints.utas.edu.au/24610/1/Czechowski%20et%20al%202016%20DNA%20Barcodes.pdf Czechowski, P, Clarke, LJ orcid:0000-0002-0844-4453 , Cooper, A and Stevens, M 2017 , 'Ground-truthing phylotype assignments for Antarctic invertebrates' , DNA Barcodes, vol. 5, no. 1 , pp. 1-13 , doi:10.1515/dna-2017-0001 <http://dx.doi.org/10.1515/dna-2017-0001>. environmental DNA metataxonomic mitochondrial cytochrome c oxidase I COI 18S rDNA Illumina 454 biodiversity survey Article PeerReviewed 2017 ftunivtasmania https://doi.org/10.1515/dna-2017-0001 2021-09-06T22:17:30Z Biodiversity information from Antarctic terrestrial habitats helps conservation efforts, but the distribution and diversity particularly of microinvertebrates remains poorly understood. Springtails, mites, tardigrades, nematodes and rotifers are difficult to identify using morphological features, hence DNA-based metabarcoding methods are well suited for their study. We compared taxonomy assignments of a high throughput sequencing metabarcoding approach using one ribosomal DNA (18S rDNA) and one mitochondrial DNA (cytochrome c oxidase subunit I - COI) marker with morphological reference data. Specifically, we compared metabarcoding or morphological taxonomic assignments on multiple taxonomic levels in an artificial DNA blend containing Australian invertebrates, and in seven extracts of Antarctic soils containing known micro-faunal taxa. Avoiding arbitrary application of metabarcoding analysis parameters, we calibrated those parameters with metabarcoding data from non-Antarctic soils. Metabarcoding approaches employing 18S rDNA and COI markers enabled detection of small and cryptic Antarctic invertebrates, and on low taxonomic ranks 18S data outperformed COI data in this respect. Morphological taxonomy determination did not outperform metabarcoding approaches. Our study demonstrates how barcoding markers can be tested prior to their application to specific taxonomic groups, and that taxonomy fidelity of markers needs to be validated in relation to environment, taxa, and available reference information. Article in Journal/Newspaper Antarc* Antarctic University of Tasmania: UTas ePrints Antarctic DNA Barcodes 5 1 1 13 |
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Open Polar |
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University of Tasmania: UTas ePrints |
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ftunivtasmania |
language |
English |
topic |
environmental DNA metataxonomic mitochondrial cytochrome c oxidase I COI 18S rDNA Illumina 454 biodiversity survey |
spellingShingle |
environmental DNA metataxonomic mitochondrial cytochrome c oxidase I COI 18S rDNA Illumina 454 biodiversity survey Czechowski, P Clarke, LJ Cooper, A Stevens, M Ground-truthing phylotype assignments for Antarctic invertebrates |
topic_facet |
environmental DNA metataxonomic mitochondrial cytochrome c oxidase I COI 18S rDNA Illumina 454 biodiversity survey |
description |
Biodiversity information from Antarctic terrestrial habitats helps conservation efforts, but the distribution and diversity particularly of microinvertebrates remains poorly understood. Springtails, mites, tardigrades, nematodes and rotifers are difficult to identify using morphological features, hence DNA-based metabarcoding methods are well suited for their study. We compared taxonomy assignments of a high throughput sequencing metabarcoding approach using one ribosomal DNA (18S rDNA) and one mitochondrial DNA (cytochrome c oxidase subunit I - COI) marker with morphological reference data. Specifically, we compared metabarcoding or morphological taxonomic assignments on multiple taxonomic levels in an artificial DNA blend containing Australian invertebrates, and in seven extracts of Antarctic soils containing known micro-faunal taxa. Avoiding arbitrary application of metabarcoding analysis parameters, we calibrated those parameters with metabarcoding data from non-Antarctic soils. Metabarcoding approaches employing 18S rDNA and COI markers enabled detection of small and cryptic Antarctic invertebrates, and on low taxonomic ranks 18S data outperformed COI data in this respect. Morphological taxonomy determination did not outperform metabarcoding approaches. Our study demonstrates how barcoding markers can be tested prior to their application to specific taxonomic groups, and that taxonomy fidelity of markers needs to be validated in relation to environment, taxa, and available reference information. |
format |
Article in Journal/Newspaper |
author |
Czechowski, P Clarke, LJ Cooper, A Stevens, M |
author_facet |
Czechowski, P Clarke, LJ Cooper, A Stevens, M |
author_sort |
Czechowski, P |
title |
Ground-truthing phylotype assignments for Antarctic invertebrates |
title_short |
Ground-truthing phylotype assignments for Antarctic invertebrates |
title_full |
Ground-truthing phylotype assignments for Antarctic invertebrates |
title_fullStr |
Ground-truthing phylotype assignments for Antarctic invertebrates |
title_full_unstemmed |
Ground-truthing phylotype assignments for Antarctic invertebrates |
title_sort |
ground-truthing phylotype assignments for antarctic invertebrates |
publisher |
De Gruyter Open |
publishDate |
2017 |
url |
https://eprints.utas.edu.au/24610/ https://eprints.utas.edu.au/24610/1/Czechowski%20et%20al%202016%20DNA%20Barcodes.pdf https://doi.org/10.1515/dna-2017-0001 |
geographic |
Antarctic |
geographic_facet |
Antarctic |
genre |
Antarc* Antarctic |
genre_facet |
Antarc* Antarctic |
op_relation |
https://eprints.utas.edu.au/24610/1/Czechowski%20et%20al%202016%20DNA%20Barcodes.pdf Czechowski, P, Clarke, LJ orcid:0000-0002-0844-4453 , Cooper, A and Stevens, M 2017 , 'Ground-truthing phylotype assignments for Antarctic invertebrates' , DNA Barcodes, vol. 5, no. 1 , pp. 1-13 , doi:10.1515/dna-2017-0001 <http://dx.doi.org/10.1515/dna-2017-0001>. |
op_doi |
https://doi.org/10.1515/dna-2017-0001 |
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DNA Barcodes |
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1766021694665785344 |