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New Zealand passerines : a contribution to passerine phylogeny : a thesis presented in partial fulfilment of the requirements for the degree of Master of Science (M.Sc.) in Genetics, Massey University, Palmerston North, New Zealand
The passerines are the largest avian order, with over 6000 species. There is strong evidence to suggest that this group arose in Australasia, with most deep lineages located in Australia, New Zealand and Papua New Guinea. The deepest lineage is the New Zealand wrens, which diverged from the main passerine lineage, possibly around 80 mya. The second split between the suboscines (mainly new world distribution) and oscines (Australasian origin) is well established. Within the oscines there are a number of small basal lineages, all located within Australasia, then around 45 mya the large division into the Passerida and the Core Corvoidea occurred. The Core Corvoidea have undergone many rapid radiations early on in their history, which has made resolving the relationships within the group complicated. The Passerida are classified into three main superfamilies, but the relationships of these three are unresolved, and the monophyly of each has been questioned.
Next generation Illumina sequencing was used to sequence the mitochondrial genomes of six native passerine species. We report a sequenced mitochondrial genome from a representative of each New Zealand passerine family, apparently a first for any country. For four new species (the fernbird, tomtit, pipit and waxeye) the mitochondrial genomes have been fully sequenced while there is partial mitochondrial genome sequence for two other species (the browncreeper and bellbird). These have been combined with the mitochondrial genome sequences of another 72 passerines including seven previously unpublished genomes. Phylogenetic trees have been produced using both maximum likelihood and Bayesian analyses, and these have been used to address a number of questions surrounding the phylogeny of the passerines.
The placements of the native New Zealand species are highlighted, and in many cases it confirms the results of earlier studies. The results suggest consideration needs to be given for formally classifying the Petroicidae, Callaeidae and Notiomystidae as basal Passerida, but whether these three families form a separate monophyletic group is still unresolved. Part of the polytomy at the base of the Core Corvoidea has been resolved. The monophyly of each of the three Passerida superfamilies have been confirmed, but it is still unclear which of the three superfamilies branched off first, and there is no support for the suggestion that the Paridae are their own fourth superfamily. A need for
the formation of an extensive collection of tissue/DNA samples from New Zealand‘s vertebrates has been identified, and a number of suggestions for the use of mitochondrial genome sequence when studying passerine phylogeny have been made.