R. Paul Scofield

The half-life of DNA in bone: measuring decay kinetics in 158 dated fossils

Claims of extreme survival of DNA have emphasized the need for reliable models of DNA degradation through time. By analysing mitochondrial DNA (mtDNA) from 158 radiocarbon-dated bones of the extinct New Zealand moa, we confirm empirically a long-hypothesized exponential decay relationship. The average DNA half-life within this geographically constrained fossil assemblage was estimated to be 521 years for a 242 bp mtDNA sequence, corresponding to a per nucleotide fragmentation rate (k) of 5.50 × 10–6 per year. With an effective burial temperature of 13.1°C, the rate is almost 400 times slower than predicted from published kinetic data of in vitro DNA depurination at pH 5. Although best described by an exponential model (R2 = 0.39), considerable sample-to-sample variance in DNA preservation could not be accounted for by geologic age. This variation likely derives from differences in taphonomy and bone diagenesis, which have confounded previous, less spatially constrained attempts to study DNA decay kinetics. Lastly, by calculating DNA fragmentation rates on Illumina HiSeq data, we show that nuclear DNA has degraded at least twice as fast as mtDNA. These results provide a baseline for predicting long-term DNA survival in bone.

Biogeographical and phylogenetic implications of an early Miocene wren (Aves: Passeriformes: Acanthisittidae) from New Zealand

ABSTRACT A new species and genus of acanthisittid wren (Aves: Passeriformes: Acanthisittidae) is described from the Early Miocene (19–16 Ma) St Bathans Fauna from Otago, New Zealand, based on four fossil bones. The first Tertiary fossil passerine to be described from New Zealand, it is similar in size to New Zealands smallest extant bird, the Rifleman Acanthisitta chloris. A phylogenetic analysis of 53 osteological characters and 24 terminal taxa, including four suboscines, basal corvoids (Menuridae, Atrichornithidae, Climacteridae, Ptilonorhynchidae, Maluridae, Dasyornithidae, Acanthizidae, Pardalotidae, Meliphagidae), and all seven Recent acanthisittid species, identifies it as the sister group to Acanthisitta. This, the first phylogenetic analysis of the basal passerine groups to use morphological characters, recovers a similar pattern of relationships of basal corvoid taxa to that obtained by recent molecular studies. The analysis also suggests that Acanthisitta chloris and the new species are the most deeply nested taxa within the family, suggesting that the radiation of Recent acanthisittids originated no later than the Early Miocene.

A Large Fruit Pigeon (Columbidae) from the Early Miocene of New Zealand

ABSTRACT. We describe a new genus and species of pigeon (Columbiformes) from a single coracoid from the St Bathans Fauna of New Zealand (16–19 mya). It is the first columbid species described from pre-Pliocene deposits in Australasia. Two apomorphies identify the fossil as belonging to the ptilinopine group of fruit pigeons, among which it is most similar to Hemiphaga, the large fruit pigeon currently endemic to the New Zealand biogeographic area. This reveals that the Hemiphaga lineage has been in New Zealand since the Early Miocene, which supports recent divergence-date estimates for Hemiphaga and its modern sister taxon (Lopholaimus) based on molecular data.

Fish Remains, Mostly Otoliths, from the Non-Marine Early Miocene of Otago, New Zealand

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.

Ancient mitochondrial genome reveals unsuspected taxonomic affinity of the extinct Chatham duck (Pachyanas chathamica) and resolves divergence times for New Zealand and sub-Antarctic brown teals.

The Chatham duck (Pachyanas chathamica) represented one of just three modern bird genera endemic to the Chatham archipelago (situated ~850 km east of New Zealand) but became extinct soon after humans first settled the islands (c. 13th-15th centuries AD). The taxonomic affinity of the Chatham duck remains largely unresolved; previous studies have tentatively suggested placements within both Tadornini (shelducks) and Anatini (dabbling ducks). Herein, we sequence a partial mitochondrial genome (excluding the D-loop) from the Chatham duck and discover that it was a phenotypically-divergent species within the genus Anas (Anatini). This conclusion is further supported by a re-examination of osteological characters. Our molecular analyses convincingly demonstrate that the Chatham duck is the most basal member of a sub-clade comprising the New Zealand and sub-Antarctic brown teals (the brown teal [A. chlorotis], Auckland Island teal [A. aucklandica] and Campbell Island teal [A. nesiotis]). Molecular clock calculations based on an ingroup fossil calibration support a divergence between the Chatham duck and its sister-taxa that is consistent with the estimated time of emergence of the Chatham Islands. Additionally, we find that mtDNA divergence between the two sub-Antarctic teal species (A. aucklandica and A. nesiotis) significantly pre-dates the last few glacial cycles, raising interesting questions about the timing of their dispersal to these islands, and the recent phylogeographic history of brown teal lineages in the region.

An Early Miocene Diversity of Parrots (Aves, Strigopidae, Nestorinae) from New Zealand

ABSTRACT A new genus and three species of parrot (Psittaciformes, Strigopidae, Nestorinae) are described from the early Miocene (19–16 Ma) St Bathans Fauna of Otago, New Zealand, based on 85 fossils as follows: Nelepsittacus minimus (17), N. donmertoni (60), and N. daphneleeae (6), with two additional fossils representing a fourth unnamed taxon. These taxa range from small parrots approximately the size of Cyanoramphus species to one as large as the living Nestor notabilis. Apomorphies in the coracoid, humerus, tibiotarsus, and tarsometatarsus ally Nelepsittacus with Nestor and exclude a close relationship with Strigops, the other endemic genus assumed to have had a long history in New Zealand. With only nestorine parrots represented, the St Bathans Fauna has nothing in common with the Australian psittaciform fauna, in which cacatuids and a diversity of psittacid genera exist. These data add to the growing body of evidence that the New Zealand terrestrial vertebrate fauna, at a time minimally 3 Ma after the maximal marine inundation of Zealandia in the late Oligocene, was highly endemic, with no close relationship to the closest faunas in Australia. This high degree of endemism strongly suggests that the Zealandian terrestrial biota persisted, at least in part, through the Oligocene highstand in sea level.

A new species of the diving duck Manuherikia and evidence for geese (Aves: Anatidae: Anserinae) in the St Bathans Fauna (Early Miocene), New Zealand

Abstract A new species of the diving duck Manuherikia, larger than its two congeners, is described based on a humerus and several referred ulnae from the St Bathans Fauna, lower Bannockburn Formation, Manuherikia Group, of Early Miocene (19–16 Ma) age, in New Zealand. Evidence for anserines in the St Bathans Fauna is evaluated. Two coracoid fragments, a scapula and a proximal radius reveal a goose most similar to Cereopsis and Cnemiornis, so indicating the presence of the Cnemiornis lineage in New Zealand in the Early Miocene. Two more coracoids are provisionally interpreted as a small unusual anserine perhaps close to Cereopsis. These records extend the diversity of waterfowl described from the St Bathans Fauna to six named species in four genera, plus an additional two unnamed anserines, globally the richest Miocene waterfowl fauna known.

Terrestrial Turtle Fossils from New Zealand Refloat Moa's Ark

Two fossils from the diverse St Bathans Fauna from Early Miocene sediments in New Zealand are described and identified as from a large, probably terrestrial turtle. They are the first freshwater or terrestrial turtles to have been reported from the Cenozoic of New Zealand. Recent authors have used the absence of turtles and species they considered unlikely to raft to New Zealand to debunk the long held theory that an element of the New Zealand fauna was ancient and vicariant and had evolved on what David Bellamy called Moas Ark. The discovery that large non-marine turtles were once present in New Zealand adds to a growing and diverse list of terrestrial taxa known from Zealandia shortly after its maximum inundation in the Late Oligocene. Many of these taxa, including a diverse herpetofaunal component, represent lineages endemic to New Zealand and had poor dispersal capabilities, supporting the long held view that a part of the Zealandian fauna was vicariant in origin.

Lost in translation or deliberate falsification? Genetic analyses reveal erroneous museum data for historic penguin specimens.

Historic museum specimens are increasingly used to answer a wide variety of questions in scientific research. Nevertheless, the scientific value of these specimens depends on the authenticity of the data associated with them. Here we use individual-based genetic analyses to demonstrate erroneous locality information for archive specimens from the late nineteenth century. Specifically, using 10 microsatellite markers, we analysed 350 contemporary and 43 historic yellow-eyed penguin (Megadyptes antipodes) specimens from New Zealands South Island and sub-Antarctic regions. Factorial correspondence analysis and an assignment test strongly suggest that eight of the historic specimens purportedly of sub-Antarctic origin were in fact collected from the South Island. Interestingly, all eight specimens were obtained by the same collector, and all are currently held in the same museum collection. Further inspection of the specimen labels and evaluation of sub-Antarctic voyages did not reveal whether the erroneous data are caused by incorrect labelling or whether deliberate falsification was at play. This study highlights a promising extension to the well-known applications of assignment tests in molecular ecology, which can complement methods that are currently being applied for error detection in specimen data. Our results also serve as a warning to all who use archive specimens to invest time in the verification of collection information.

Ancient DNA Analyses Reveal Contrasting Phylogeographic Patterns amongst Kiwi (Apteryx spp.) and a Recently Extinct Lineage of Spotted Kiwi

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.