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The New Zealand endemic bat family Mystacinidae comprises just two Recent species referred to a single genus, Mystacina. The family was once more diverse and widespread, with an additional six extinct taxa recorded from Australia and New Zealand. Here, a new mystacinid is described from the early Miocene (19-16 Ma) St Bathans Fauna of Central Otago, South Island, New Zealand. It is the first pre-Pleistocene record of the modern genus and it extends the evolutionary history of Mystacina back at least 16 million years. Extant Mystacina species occupy old-growth rainforest and are semi-terrestrial with an exceptionally broad omnivorous diet. The majority of the plants inhabited, pollinated, dispersed or eaten by modern Mystacina were well-established in southern New Zealand in the early Miocene, based on the fossil record from sites at or near where the bat fossils are found. Similarly, many of the arthropod prey of living Mystacina are recorded as fossils in the same area. Although none of the Miocene plant and arthropod species is extant, most are closely related to modern taxa, demonstrating potentially long-standing ecological associations with Mystacina.

New Zealand's endemic Stewart Island Shag (Leucocarbo chalconotus) comprises two regional groups (Otago and Foveaux Strait) that show consistent differentiation in relative frequencies of pied versus dark-bronze morphotypes, the extent of facial carunculation, body size and breeding time. We used modern and ancient DNA (mitochondrial DNA control region one), and morphometric approaches to investigate the phylogeography and taxonomy of L. chalconotus and its closely related sister species, the endemic Chatham Island Shag (L. onslowi). Our analysis shows Leucocarbo shags in southern New Zealand comprise two well-supported clades, each containing both pied and dark-bronze morphs. However, the combined monophyly of these populations is not supported, with the L. chalconotus Otago lineage sister to L. onslowi. Morphometric analysis indicates that Leucocarbo shags from Otago are larger on average than those from Foveaux Strait. Principal co-ordinate analysis of morphometric data showed substantial morphological differentiation between the Otago and Foveaux Strait clades, and L. onslowi. The phylogeographic partitioning detected within L. chalconotus is marked, and such strong structure is rare for phalacrocoracid species. Our phylogenetic results, together with consistent differences in relative proportions of plumage morphs and facial carunculation, and concordant differentiation in body size and breeding time, suggest several alternative evolutionary hypotheses that require further investigation to determine the level of taxonomic distinctiveness that best represents the L. chalconotus Otago and Foveaux Strait clades.

The little spotted kiwi (Apteryx owenii) is a flightless ratite formerly found throughout New Zealand but now greatly reduced in distribution. Previous phylogeographic studies of the related brown kiwi (A. mantelli, A. rowi and A. australis), with which little spotted kiwi was once sympatric, revealed extremely high levels of genetic structuring, with mitochondrial DNA haplotypes often restricted to populations. We surveyed genetic variation throughout the present and pre-human range of little spotted kiwi by obtaining mitochondrial DNA sequences from contemporary and ancient samples. Little spotted kiwi and great spotted kiwi (A. haastii) formed a monophyletic clade sister to brown kiwi. Ancient samples of little spotted kiwi from the northern North Island, where it is now extinct, formed a lineage that was distinct from remaining little spotted kiwi and great spotted kiwi lineages, potentially indicating unrecognized taxonomic diversity. Overall, little spotted kiwi exhibited much lower levels of genetic diversity and structuring than brown kiwi, particularly through the South Island. Our results also indicate that little spotted kiwi (or at least hybrids involving this species) survived on the South Island mainland until more recently than previously thought.