DNA barcoding a relict avifauna: an important tool for systematics and conservation management
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Other Title
Authors
Tizard, J.
Patel, S.
Waugh, John
Tavares, E.
Bergmann, T.
Gill, B.
Norman, J.
Christidis, L.
Scofield, P.
Haddrath, O.
Baker, A.
Lambert, D.
Millar, C. D.
Patel, S.
Waugh, John
Tavares, E.
Bergmann, T.
Gill, B.
Norman, J.
Christidis, L.
Scofield, P.
Haddrath, O.
Baker, A.
Lambert, D.
Millar, C. D.
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Degree
Grantor
Date
2019-02-11
Supervisors
Type
Journal Article
Ngā Upoko Tukutuku (Māori subject headings)
Keyword
New Zealand birds
cytochrome c oxidase subunit I (COI)
COI gene
specimen identification
conservation
DNA barcodes
cytochrome c oxidase subunit I (COI)
COI gene
specimen identification
conservation
DNA barcodes
ANZSRC Field of Research Code (2020)
Citation
Tizard, J., Patel, S., Waugh, J., Tavares, E., Bergmann, T., Gill, B., Norman, J., Christidis, L., Scofield, P., Haddrath, O., Baker, A., Lambert, D., & Millar, C. D. (2018). DNA barcoding a relict avifauna: an important tool for systematics and conservation management. BMC Evolutionary Biology, 19 (52), X. doi:10.1186/s12862-019-1346-y
Abstract
BACKGROUND:
DNA barcoding utilises a standardised region of the cytochrome c oxidase I (COI) gene to identify specimens to the species level. It has proven to be an effective tool for identification of avian samples. The unique island avifauna of New Zealand is taxonomically and evolutionarily distinct. We analysed COI sequence data in order to determine if DNA barcoding could accurately identify New Zealand birds.
RESULTS:
We sequenced 928 specimens from 180 species. Additional Genbank sequences expanded the dataset to 1416 sequences from 211 of the estimated 236 New Zealand species. Furthermore, to improve the assessment of genetic variation in non-endemic species, and to assess the overall accuracy of our approach, sequences from 404 specimens collected outside of New Zealand were also included in our analyses. Of the 191 species represented by multiple sequences, 88.5% could be successfully identified by their DNA barcodes. This is likely a conservative estimate of the power of DNA barcoding in New Zealand, given our extensive geographic sampling. The majority of the 13 groups that could not be distinguished contain recently diverged taxa, indicating incomplete lineage sorting and in some cases hybridisation. In contrast, 16 species showed evidence of distinct intra-species lineages, some of these corresponding to recognised subspecies. For species identification purposes a character-based method was more successful than distance and phylogenetic tree-based methods.
CONCLUSIONS:
DNA barcodes accurately identify most New Zealand bird species. However, low levels of COI sequence divergence in some recently diverged taxa limit the identification power of DNA barcoding. A small number of currently recognised species would benefit from further systematic investigations. The reference database and analysis presented will provide valuable insights into the evolution, systematics and conservation of New Zealand birds.
Publisher
BMC (Biomedical Centre), part of Springer Nature
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Link to ePress publication
DOI
https://doi.org/10.1186/s12862-019-1346-y
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Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.