We present an annotated working list of the bird species breeding in New Zealand during the late Pleistocene and Holocene, up to the time of human contact. New Zealand is defined as including the three main islands and the surrounding smaller islands, plus outlying island groups from Norfolk Island in the northwest, the Kermadec, Chatham, Bounty, Antipodes, Campbell, Auckland, Snares, to Macquarie Islands, but excluding islands south of Macquarie Island and the Ross Dependency. Inclusions or exclusions of species from the list were based on specified criteria. We include only species with a breeding population and not vagrants that occur in New Zealand but which breed elsewhere. Species with validly published names were included if there was fossil evidence for a breeding population before human contact. Species with a breeding population at the time of European contact were included unless contrary evidence from the fossil record indicates that they actually colonised after human settlement. Species without a fossil record were included if a breeding population exists on a relatively undisturbed island within the New Zealand archipelago as defined above. Species now present on the main islands were excluded if they are absent from all well‐documented fossil faunas. Species were excluded from the breeding fauna and treated as vagrants where sustained breeding has not been demonstrated. The phylogenetic species concept is applied both to fossil and to living taxa. The late Quaternary fossil record of birds in New Zealand is excellent, and the contribution of extinct taxa to the total list is understood at least as well as that of the surviving taxa. Many taxa presently recognised at subspecific level are treated here as full species. Twelve extinct species whose former presence is known from fossil evidence, but for which no description has been published, are listed under informal species designations. Taxonomic considerations limited the extent to which the main list could reflect present understanding of the diversity of the avifauna; some undescribed species are at present subsumed under one species name. Where previous taxonomic publications provide precedence, available names at the species‐level have been used. A supplementary hypothetical species list includes all nomenclatural changes signalled in extensive annotations to the main list. In this list we accept 245 species in 110 genera representing 46 families; 176 species were endemic to the archipelago. Preliminary biogeographic analyses based on the composition of the supplementary list show that there were four separate regional faunas: a northern subtropical fauna (Norfolk, Kermadecs); the major fauna of the main islands (North, South, Stewart, and offshore islands); a Chathams fauna (Chatham Islands only); and a subantarctic fauna on the southern islands. Species with wider distributions formed link groups. The origin and compositions of the regional avifaunas and their endemic species differ with their geographic position, climate, and proximity to source faunas. Instances of speciation in groups such as the Coenocoiypha snipe and Petroica flycatchers, and adaptive radiations in groups including moa and acanthisittid wrens, show that there are many avenues for research on the rate of evolution in island and mainland populations of New Zealand birds and that there are large gaps in knowledge of even common taxa. A brief case study demonstrates the inadequacies of using species lists that do not include Holocene fossil species. Species‐area curves based on the total fauna differ substantially from those developed in previous studies based on incomplete, or biased, lists. Pleistocene glaciations caused the pattern of distribution of species on the main islands to change in concert with vegetation changes. Other possible effects include the elimination of warm climate species early in the cooling phase more than 1 million years ago, the speciation in groups including waders and parrots as new habitats (e.g., braided riverbeds and alpine areas) appeared, and the appearance regularly during the Pleistocene of islands that were potential staging points for colonisation of the Chatham Islands. For at least the past 100 000 years, until 2000 years ago, the fauna appears to have been very stable in composition, despite strong cyclic fluctuations in climate and vegetation. The effects of extinctions within the past 2000 years on the composition of the present fauna include the elimination of most of the endemic taxa from all but the subantarctic faunas. Only 169 species of the original late Holocene breeding fauna survive. The extinctions have resulted in a strong bias towards marine and coastal taxa in the present avifauna, in contrast to the balanced representation of terrestrial and marine species in the Pleistocene and Holocene fauna. The importance of systematic studies and the determination of the status of island populations to conservation and basic ornithological research is emphasised. The systematic status of many New Zealand birds is poorly known at present.

Living true seals (phocids) are the most widely dispersed semi-aquatic marine mammals, and comprise geographically separate northern (phocine) and southern (monachine) groups. Both are thought to have evolved in the North Atlantic, with only two monachine lineages—elephant seals and lobodontins—subsequently crossing the equator. The third and most basal monachine tribe, the monk seals, have hitherto been interpreted as exclusively northern and (sub)tropical throughout their entire history. Here, we describe a new species of extinct monk seal from the Pliocene of New Zealand, the first of its kind from the Southern Hemisphere, based on one of the best-preserved and richest samples of seal fossils worldwide. This unanticipated discovery reveals that all three monachine tribes once coexisted south of the equator, and forces a profound revision of their evolutionary history: rather than primarily diversifying in the North Atlantic, monachines largely evolved in the Southern Hemisphere, and from this southern cradle later reinvaded the north. Our results suggest that true seals crossed the equator over eight times in their history. Overall, they more than double the age of the north–south dichotomy characterizing living true seals and confirms a surprisingly recent major change in southern phocid diversity.

Climate shifts are key drivers of ecosystem change. Despite the critical importance of Antarctica and the Southern Ocean for global climate, the extent of climate-driven ecological change in this region remains controversial. In particular, the biological effects of changing sea ice conditions are poorly understood. We hypothesize that rapid postglacial reductions in sea ice drove biological shifts across multiple widespread Southern Ocean species. We test for demographic shifts driven by climate events over recent millennia by analyzing population genomic datasets spanning 3 penguin genera ( Eudyptes , Pygoscelis , and Aptenodytes ). Demographic analyses for multiple species (macaroni/royal, eastern rockhopper, Adélie, gentoo, king, and emperor) currently inhabiting southern coastlines affected by heavy sea ice conditions during the Last Glacial Maximum (LGM) yielded genetic signatures of near-simultaneous population expansions associated with postglacial warming. Populations of the ice-adapted emperor penguin are inferred to have expanded slightly earlier than those of species requiring ice-free terrain. These concerted high-latitude expansion events contrast with relatively stable or declining demographic histories inferred for 4 penguin species (northern rockhopper, western rockhopper, Fiordland crested, and Snares crested) that apparently persisted throughout the LGM in ice-free habitats. Limited genetic structure detected in all ice-affected species across the vast Southern Ocean may reflect both rapid postglacial colonization of subantarctic and Antarctic shores, in addition to recent genetic exchange among populations. Together, these analyses highlight dramatic, ecosystem-wide responses to past Southern Ocean climate change and suggest potential for further shifts as warming continues.

Fish remains described from the early Miocene lacustrine Bannockburn Formation of Central Otago, New Zealand, consist of several thousand otoliths and one skeleton plus another disintegrated skull. One species, Mataichthys bictenatus Schwarzhans, Scofield, Tennyson, and T. Worthy gen. et sp. nov., an eleotrid, is established on a skeleton with otoliths in situ. The soft embedding rock and delicate, three−dimensionally preserved fish bones were studied by CT−scanning technology rather than physical preparation, except where needed to extract the otolith. Fourteen species of fishes are described, 12 new to science and two in open nomenclature, representing the families Galaxiidae (Galaxias angustiventris, G. bobmcdowalli, G. brevicauda, G. papilionis, G. parvirostris, G. tabidus), Retropinnidae (Prototroctes modestus, P. vertex), and Eleotridae (Mataichthys bictenatus, M. procerus, M. rhinoceros, M. taurinus). These findings prove that most of the current endemic New Zealand/southern Australia freshwater fish fauna was firmly established in New Zealand as early as 19–16 Ma ago. Most fish species indicate the presence of large fishes, in some cases larger than Recent species of related taxa, for instance in the eleotrid genus Mataichthys when compared to the extant Gobiomorphus. The finding of a few otoliths from marine fishes corroborates the age determination of the Bannockburn Formation as the Altonian stage of the New Zealand marine Tertiary stratigraphy.Werner Schwarzhans, R. Paul Scofield, Alan J.D. Tennyson, Jennifer P. Worthy, and Trevor H. Worth

New Zealand's lesser short-tailed bat Mystacina tuberculata is one of only two of c.1100 extant bat species to use a true walking gait when manoeuvring on the ground (the other being the American common vampire bat Desmodus rotundus). Mystacina tuberculata is also the last surviving member of Mystacinidae, the only mammalian family endemic to New Zealand (NZ) and a member of the Gondwanan bat superfamily Noctilionoidea. The capacity for true quadrupedal terrestrial locomotion in Mystacina is a secondarily derived condition, reflected in numerous skeletal and muscular specializations absent in other extant bats. The lack of ground-based predatory native NZ mammals has been assumed to have facilitated the evolution of terrestrial locomotion and the unique burrowing behaviour of Mystacina, just as flightlessness has arisen independently many times in island birds. New postcranial remains of an early Miocene mystacinid from continental Australia, Icarops aenae, offer an opportunity to test this hypothesis.

The recently extinct New Zealand adzebills (Aptornithidae, Aptornis spp.) were an enigmatic group of large flightless birds that have long eluded precise taxonomic assignment as they do not closely resemble any extant birds. Adzebills were nearly wingless, weighed approximately 16–19 kg, and possessed massive adze-like reinforced bills whose function remains unknown. Using hybridisation enrichment and high-throughput sequencing of DNA extracted from subfossil bone and eggshell, near-complete mitochondrial genomes were successfully assembled from the two Quaternary adzebill species: the North Island Adzebill (Aptornis otidiformis) and South Island Adzebill (A. defossor). Molecular phylogenetic analyses confirm that adzebills are members of the Ralloidea (rails and allies) and are sister-taxon to the Sarothruridae, which our results suggest comprises the Madagascan wood rails (Mentocrex, two likely sp.) in addition to the tiny (<50 gram) rail-like Afro-Madagascan flufftails (Sarothrura, 9 spp.). Node age estimates indicate that the split between adzebills and Sarothruridae occurred ~39.6 Ma, suggesting that the ancestors of the adzebills arrived in New Zealand by long-distance dispersal rather than continental vicariance. This newly identified biogeographic link between physically distant New Zealand and Afro-Madagascar, echoed by the relationship between the New Zealand kiwi (Apterygiformes) and Madagascan elephant-birds (Aepyornithiformes), suggests that the adzebill’s near relatives were formerly more widespread. In addition, our estimate for the divergence time between the two Quaternary adzebill species (0.2–2.3 Ma) coincides with the emergence of a land-bridge between the North and South islands of New Zealand (ca. 1.5–2 Ma). This relatively recent divergence suggests that North Island adzebills are the result of a relatively recent dispersal from the South Island, from which the earliest (Miocene) adzebill fossil has been described.