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Many avian species endemic to Aotearoa New Zealand were driven to extinction or reduced to relict populations following successive waves of human arrival, due to hunting, habitat destruction and the introduction of mammalian predators. Among the affected species were the large flightless South Island takahē (Porphyrio hochstetteri) and the moho (North Island takahē; P. mantelli), with the latter rendered extinct and the former reduced to a single relictual population. Little is known about the evolutionary history of these species prior to their decline and/or extinction. Here we sequenced mitochondrial genomes from takahē and moho subfossils (12 takahē and 4 moho) and retrieved comparable sequence data from takahē museum skins (n = 5) and contemporary individuals (n = 17) to examine the phylogeny and recent evolutionary history of these species. Our analyses suggest that prehistoric takahē populations lacked deep phylogeographic structure, in contrast to moho, which exhibited significant spatial genetic structure, albeit based on limited sample sizes (n = 4). Temporal genetic comparisons show that takahē have lost much of their mitochondrial genetic diversity, likely due to a sudden demographic decline soon after human arrival (~750 years ago). Time‐calibrated phylogenetic analyses strongly support a sister species relationship between takahē and moho, suggesting these flightless taxa diverged around 1.5 million years ago, following a single colonisation of New Zealand by a flighted Porphyrio ancestor approximately 4 million years ago. This study highlights the utility of palaeogenetic approaches for informing the conservation and systematic understanding of endangered species whose ranges have been severely restricted by anthropogenic impacts. [ABSTRACT FROM AUTHOR]

Methodological and technological improvements are continually revolutionizing the field of ancient DNA. Most ancient DNA extraction methods require the partial (or complete) destruction of finite museum specimens, which disproportionately impacts small or fragmentary subfossil remains, and future analyses. We present a minimally destructive ancient DNA extraction method optimized for small vertebrate remains. We applied this method to detect lost mainland genetic diversity in the large New Zealand diplodactylid gecko genus Hoplodactylus, which is presently restricted to predator‐free island and mainland sanctuaries. We present the first mitochondrial genomes for New Zealand diplodactylid geckos, recovered from 19 modern, six historical/archival (1898–2011) and 16 Holocene Hoplodactylus duvaucelii sensu latu specimens, and one modern Woodworthia sp. specimen. No obvious damage was observed in post‐extraction micro‐computed tomography reconstructions. All "large gecko" specimens examined from extinct populations were found to be conspecific with extant Hoplodactylus species, suggesting their large relative size evolved only once in the New Zealand diplodactylid radiation. Phylogenetic analyses of Hoplodactylus samples recovered two genetically (and morphologically) distinct North and South Island clades, probably corresponding to distinct species. Finer phylogeographical structuring within Hoplodactylus spp. highlighted the impacts of Late Cenozoic biogeographical barriers, including the opening and closure of Pliocene marine straits, fluctuations in the size and suitability of glacial refugia, and eustatic sea‐level change. Recent mainland extinction obscured these signals from the modern tissue‐derived data. These results highlight the utility of minimally destructive DNA extraction in genomic analyses of less well studied small vertebrate taxa, and the conservation of natural history collections. see also the Perspective by Michael Bunce [ABSTRACT FROM AUTHOR]

Natural history collections worldwide contain a plethora of mollusc shells. Recent studies have detailed the sequencing of DNA extracted from shells up to thousands of years old and from various taphonomic and preservational contexts. However, previous approaches have largely addressed methodological rather than evolutionary research questions. Here, we report the generation of DNA sequence data from mollusc shells using such techniques, applied to Haliotis virginea Gmelin, 1791, a New Zealand abalone, in which morphological variation has led to the recognition of several forms and subspecies. We successfully recovered near‐complete mitogenomes from 22 specimens including 12 dry‐preserved shells up to 60 years old. We used a combination of palaeogenetic techniques that have not previously been applied to shell, including DNA extraction optimized for ultra‐short fragments and hybridization‐capture of single‐stranded DNA libraries. Phylogenetic analyses revealed three major, well‐supported clades comprising samples from: (1) The Three Kings Islands; (2) the Auckland, Chatham and Antipodes Islands; and (3) mainland New Zealand and Campbell Island. This phylogeographic structure does not correspond to the currently recognized forms. Critically, our nonreliance on freshly collected or ethanol‐preserved samples enabled inclusion of topotypes of all recognized subspecies as well as additional difficult‐to‐sample populations. Broader application of these comparatively cost‐effective and reliable methods to modern, historical, archaeological and palaeontological shell samples has the potential to revolutionize invertebrate genetic research. [ABSTRACT FROM AUTHOR]

The arrival of humans in New Zealand around 750 years ago resulted in widespread faunal extinctions including the endemic Waitaha penguin (Megadyptes waitaha). Previously thought to have only bred on coastal South Island and Stewart Island, recent genetic reanalysis of prehistoric large penguin bones from the lower North Island indicates that the Waitaha penguin may have been a common resident. Here we synthesise previous studies and present new palaeontological and archaeological evidence to suggest that the Waitaha penguin was probably breeding in the lower North Island at the time of human arrival, and did not represent vagrant individuals from more southerly breeding colonies. The elimination of breeding Megadyptes from the North Island would add to the already significant avifaunal losses from New Zealand, of which the North Island suffered the greatest biodiversity loss after the arrival of humans. [ABSTRACT FROM AUTHOR]

Cominella maculosa and C. virgata are common whelk species that inhabit rocky shores around much of the North Island of New Zealand, the northern South Island and, for C. maculosa, the Chatham Islands. This study used DNA sequences from the mitochondrial gene CO1 to examine the phylogeographical structure of populations of both species in areas that have not previously been sampled. Collections of both species were made from sites in the Cook Strait region, C. maculosa from the Chatham Islands and C. virgata from the northern North Island. Both species were found to have a considerable degree of genetic differentiation, but genetic diversity and phylogeographical patterns differed greatly between regions. South Island populations of C. virgata may have originated, or been supplemented, by human-mediated translocations. Phylogenetic analyses were conducted using the mitochondrial genes CO1 and 16S rRNA, and the nuclear gene 18S rRNA. The northern subspecies C. virgata brookesi did not form a monophyletic lineage and is synonymized with C. virgata. A lectotype is designated for Buccinum lineolatum Quoy & Gaimard, 1833, of which C. virgata is a replacement name. [ABSTRACT FROM AUTHOR]