School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, 1142, New Zealand.
Unitec Institute of Technology, Auckland, New Zealand.
BMC Evol Biol. 2019 Feb 11;19(1):52. doi: 10.1186/s12862-019-1346-y.
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.
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.
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.
DNA 条形码利用细胞色素 c 氧化酶 I（COI）基因的标准化区域将标本鉴定到种的水平。它已被证明是鉴定鸟类样本的有效工具。新西兰独特的岛屿鸟类在分类学和进化上是不同的。我们分析了 COI 序列数据，以确定 DNA 条形码是否可以准确识别新西兰鸟类。
我们对 180 个物种的 928 个样本进行了测序。额外的 Genbank 序列将数据集扩展到 1416 个序列，来自估计的 236 个新西兰物种中的 211 个。此外，为了提高对非特有物种遗传变异的评估，并评估我们方法的整体准确性，我们还将来自新西兰以外的 404 个标本的序列纳入我们的分析中。在有多个序列代表的 191 个物种中，88.5%可以通过它们的 DNA 条形码成功识别。鉴于我们广泛的地理采样，这可能是 DNA 条形码在新西兰的保守估计。大多数无法区分的 13 个组包含最近分化的分类群，表明不完全谱系分选，在某些情况下还存在杂交。相比之下，16 个物种表现出明显的种内谱系证据，其中一些与公认的亚种相对应。对于物种鉴定目的，基于字符的方法比距离和基于系统发育树的方法更成功。
DNA 条形码可以准确识别大多数新西兰鸟类物种。然而，一些最近分化的分类群中 COI 序列的低差异限制了 DNA 条形码的鉴定能力。少数目前被认可的物种将受益于进一步的系统研究。本研究提供的参考数据库和分析结果将为新西兰鸟类的进化、系统学和保护提供有价值的见解。
