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

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

doi:10.1186/s12862-019-1346-y

Abstract

BackgroundDNA 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.ResultsWe 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.ConclusionsDNA 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.

Highlights

DNA barcoding utilises a standardised region of the cytochrome c oxidase I (COI) gene to identify specimens to the species level
Where DNA barcodes have highlighted inconsistences with established taxonomy, more detailed studies using a range of approaches have been undertaken and in many cases have been able to inform the processes of molecular evolution, biogeography and speciation
The present study aims to: 1) develop a working DNA barcoding database for the birds of New Zealand; 2) determine the percentage of currently recognized species that can be discriminated by DNA barcoding; 3) test the potential of DNA barcodes to correctly assign specimens to their nominal species; 4) identify taxa that could benefit from further investigation

Summary

Introduction

DNA barcoding utilises a standardised region of the cytochrome c oxidase I (COI) gene to identify specimens to the species level. We analysed COI sequence data in order to determine if DNA barcoding could accurately identify New Zealand birds. In the case of animals, the ‘barcode’ is a 648 bp region of the 5′ end of the cytochrome c oxidase I (COI) gene. DNA barcoding has become a Tizard et al BMC Evolutionary Biology (2019) 19:52 specimens within taxonomically well-resolved groups, DNA barcoding has proven to be a very useful tool [7, 8]. Traditional taxonomic identification requires increasingly rare expert knowledge and is often difficult or impossible for degraded specimens or incomplete remains. Where DNA barcodes have highlighted inconsistences with established taxonomy, more detailed studies using a range of approaches have been undertaken and in many cases have been able to inform the processes of molecular evolution, biogeography and speciation (reviewed in Barreira et al, [20])

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Conclusion