Overview of data

More than one third of all known bird species have had at least one (mean 6.2) DNA barcode(s) recorded on the Barcode of Life Data Systems (BOLD) database.[1] The All Birds Barcoding Initiative (ABBI)[2] is one of several initiatives overseen by the Consortium for the Barcode of Life,[3] each aimed at a particular component of the world’s biota such as Lepidoptera,[4] invasive pest species,[5] polar species[6] or fish.[7] As part of its aim to establish a public archive of DNA barcodes for the approximately 10000 species of birds in the world, ABBI has divided the world into eight regions: Palaearctic (including Europe, North Africa, The Middle East, Russia and North-East Asia), Afrotropical (Central and Southern Africa), Indomalayan (India and South-East Asia), Nearctic (North America), Neotropical (South and Central America), Oceania (Pacific Ocean and its islands) Antarctic and Australasia.[2] The first region to have a DNA barcode database of its avifauna published was the Nearctic[8, 9] then Korea,[10, 11] where 154 of 450 species have had DNA barcodes recovered and recorded. In addition, large projects of 500 of the Neotropical birds of Argentina and 296 Palearctic birds of Scandinavia have also been recently published.[12, 13]

One of the regions that is absent from this group of published databases is Australasia, comprising Australia, New Zealand and a number of offshore islands. With its widely scattered landmasses and vast areas of ocean from equatorial regions to the sub-Antarctic, spanning more than 70 degrees of longitude, Australasia has a large and diverse avifauna. New Zealand, the region’s most isolated major landmass 2000km to the South-East of Australia, hosts about 3% of the bird species of the world.[14] _{These species are characterised by a high level of}

endemism and include a large group of Southern pelagic species as well as the world’s greatest concentration of both living and extinct ratite species. These

unique features make this an important fauna to examine and characterise using DNA barcodes. Furthermore, many species found in this region are quite distinct from those in other published projects,[8-13] having undergone a very long period of isolation or because they belong to the southern circumpolar avifauna that has not been examined in this way before. Thus, they sometimes require different approaches to the isolation and amplification of appropriate sequences of DNA (Chapter 3).

Sequences of the barcode region of the mitochondrial COI gene came from several sources. Some were obtained from samples provided by a variety of institutions and people to the author of this thesis (31%), Selina Patel at the University of Auckland (49%) and Allan Baker and his team at the Royal Ontario Museum (20%), others came from existing files in GenBank (see Appendix D for accession numbers; see Appendix E for a complete list of all specimens in the Barcoding New Zealand Birds project with a breakdown of contributing sources). All barcodes along with specimen and sequence details have been lodged with the Barcode of Life Data Systems (BOLD)[1] _{and, with the exception of those already}

lodged with GenBank, can be found in the project named “Barcoding New Zealand Birds” on this site.

Fresh tissue samples for DNA barcoding were provided by Auckland War Memorial Museum and Otago Museum in New Zealand as well as Victoria Museum in Australia. In addition, fresh samples were provided by Wellington Zoo, Whakatane Bird Rescue and Sylvia Durrant Bird Rescue in Rothesay Bay, Auckland as well as from the collections of David Lambert and Craig Millar. Historical museum samples (see Chapter 3) were provided by Paul Scofield of Canterbury Museum, Christchurch.

While the overall number of bird species found in the greater New Zealand region is approximately 328, this number includes Antarctic species, species that have been introduced by human agency, stragglers (irregular visitors), rare vagrants (transitory and unexpected), migratory birds that spend some part of their lives in

New Zealand but do not breed here, as well as extinct and probably extinct species. Of the remainder, 71 species are endemic to New Zealand (breed only in New Zealand) and a further 79 are native species (naturally occurring and breeding in New Zealand and elsewhere).[15] These last two groups form the main taxa presented in these data (Table 4.2), but additional species, which have been introduced or which fall into some of the other categories have also had their DNA barcodes sequenced and are included in these data.

According to Fleming (1976), offshore islands such as the Chatham Islands, Auckland and Campbell islands, the Snares and the Kermadecs tend to have their own representatives of many taxa due to allopatric divergence.[16] Molecular data that exists, however, do not always support this conclusion,[17] and the divergence in nucleotides observed in these birds is generally less than that normally indicative of congeneric species. In addition, the collection and sequencing of a large group such as the birds of New Zealand is subject to the law of diminishing returns. Obtaining samples for the last few species is very much more time consuming than for the first samples. For these reasons, some species, particularly those of offshore island variants of mainland species do not appear in this study but will, with time, be added to the project.

Nonetheless, for these data to be useful for the identification of New Zealand birds, they should include all species, both common and uncommon, native, endemic or other found within this region. However, all the introduced species and many of the vagrants, stragglers and migratory species have already had DNA barcodes recovered elsewhere and these are publicly available through the BOLD website and GenBank. Thus, less emphasis has been placed on these groups and many have not been comprehensively sequenced for the Barcoding New Zealand Birds project. To date, 833 DNA barcode sequences from 215 bird species (77% of the total NZ avifauna) have been lodged in the Barcoding New Zealand Birds database with BOLD. Of these, 628 sequences from 126 species are native or endemic to New Zealand representing 84% of this group.