DNA barcoding a unique avifauna: an important tool for evolution, systematics and conservation View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2019-02-11

AUTHORS

Jacqueline Tizard, Selina Patel, John Waugh, Erika Tavares, Tjard Bergmann, Brian Gill, Janette Norman, Les Christidis, Paul Scofield, Oliver Haddrath, Allan Baker, David Lambert, Craig Millar

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. More... »

PAGES

52

Identifiers

URI

http://scigraph.springernature.com/pub.10.1186/s12862-019-1346-y

DOI

http://dx.doi.org/10.1186/s12862-019-1346-y

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1112063712

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/30744573


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25 schema:description 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.
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32 schema:keywords Additional Genbank sequences
33 COI sequence data
34 COI sequence divergence
35 DNA
36 DNA barcodes
37 DNA barcoding
38 GenBank sequences
39 I (COI) gene
40 New Zealand
41 New Zealand bird species
42 New Zealand birds
43 New Zealand species
44 Zealand
45 Zealand bird species
46 Zealand birds
47 Zealand species
48 accuracy
49 analysis
50 approach
51 assessment
52 avian samples
53 avifauna
54 barcodes
55 barcoding
56 bird species
57 birds
58 c oxidase I (COI) gene
59 cases hybridisation
60 character-based methods
61 conservation
62 conservative estimate
63 contrast
64 cytochrome c oxidase I (COI) gene
65 data
66 database
67 dataset
68 distance
69 distinct intra-species lineages
70 divergence
71 effective tool
72 estimates
73 evidence
74 evolution
75 extensive geographic sampling
76 further systematic investigation
77 genes
78 genetic variation
79 geographic sampling
80 group
81 hybridisation
82 identification
83 identification power
84 important tool
85 incomplete lineage sorting
86 insights
87 intra-species lineages
88 investigation
89 islands
90 levels
91 lineage sorting
92 lineages
93 low levels
94 majority
95 method
96 most New Zealand bird species
97 multiple sequences
98 non-endemic species
99 number
100 order
101 overall accuracy
102 oxidase I gene
103 phylogenetic tree-based methods
104 power
105 recognised subspecies
106 reference database
107 region
108 samples
109 sampling
110 sequence
111 sequence data
112 sequence divergence
113 small number
114 sorting
115 species
116 species identification
117 species level
118 specimens
119 standardised region
120 subspecies
121 systematic investigation
122 systematics
123 taxa
124 tool
125 tree-based methods
126 unique avifauna
127 unique island
128 valuable insights
129 variation
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