Christchurch, New Zealand
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Holdaway R.N.,Palaecol Research Ltd. | Holdaway R.N.,University of Canterbury | Hawke D.J.,Christchurch Polytechnic Institute of Technology | Bunce M.,Murdoch University | And 2 more authors.
Notornis | Year: 2011

Stable isotopic (d 13C; d 15N) analysis of bone collagen and other refractory biological materials is a mainstay of palaeoecological research, but comparability between individuals depends on homogeneity within the sample specimens. Long bones of extinct New Zealand moa display lines of arrested growth that reflect prolonged development over several years, leading to potential systematic inhomogeneity in stable isotopic enrichment within the bone. We tested whether the isotopic content within a Euryapteryx curtus tibiotarsus is homogeneous by measuring d 15N and d 13C values in 6 adjacent 1cm-diameter cortical bone cores arranged along the bone axis from each of the proximal and distal ends. We then measured isotopic ratios in 5 radial slices of a core from the mid-shaft of a Pachyornis elephantopus tibiotarsus to see if there was any depth (ontogenetic) effect at a single sampling point. The d 13C value increased with distance from the proximal bone end, but neither d 13C nor d 15N values in samples from the distal end of the bone were correlated with position. Within mid-shaft cortical bone, the d 13C value decreased with depth but d 15N values were constant. Sampling the entire depth of cortical bone from the caudal surface at the distal end of the tibiotarsus, if feasible, therefore provides a spatially homogenous material, free of maturation effects on stable isotopic composition. If for any reason that position cannot be sampled, the outer (radial) layer at the mid-shaft can be substituted. © The Ornithological Society of New Zealand, Inc.


Horton T.W.,Geological science | Holdaway R.N.,Geological science | Holdaway R.N.,University of Canterbury | Holdaway R.N.,Palaecol Research Ltd | And 10 more authors.
Biology Letters | Year: 2011

Humpback whale seasonal migrations, spanning greater than 6500 km of open ocean, demonstrate remarkable navigational precision despite following spatially and temporally distinct migration routes. Satellite-monitored radio tag-derived humpback whale migration tracks in both the South Atlantic and South Pacific include constant course segments of greater than 200 km, each spanning several days of continuous movement. The whales studied here maintain these directed movements, often with better than 18 precision, despite the effects of variable seasurface currents. Such remarkable directional precision is difficult to explain by established models of directional orientation, suggesting that alternative compass mechanisms should be explored. © 2011 The Royal Society.


Steeves T.E.,University of Canterbury | Holdaway R.N.,University of Canterbury | Holdaway R.N.,Palaecol Research Ltd. | Hale M.L.,University of Canterbury | And 6 more authors.
Biology Letters | Year: 2010

Ancient DNA has revolutionized the way in which evolutionary biologists research both extinct and extant taxa, from the inference of evolutionary history to the resolution of taxonomy. Here, we present, to our knowledge, the first study to report the rediscovery of an 'extinct' avian taxon, the Tasman booby (Sula tasmani), using classical palaeontological data combined with ancient and modern DNA data. Contrary to earlier work, we show an overlap in size between fossil and modern birds in the North Tasman Sea (classified currently as S. tasmani and Sula dactylatra fullagari, respectively). In addition, we show that Holocene fossil birds have mitochondrial control region sequences that are identical to those found in modern birds. These results indicate that the Tasman booby is not an extinct taxon: S. dactylatra fullagari O'Brien & Davies, 1990 is therefore a junior synonym of Sula tasmani van Tets, Meredith, Fullagar & Davidson, 1988 and all North Tasman Sea boobies should be known as S. d. tasmani. In addition to reporting the rediscovery of an extinct avian taxon, our study highlights the need for researchers to be cognizant of multidisciplinary approaches to understanding taxonomy and past biodiversity. © 2009 The Royal Society.


Allentoft M.E.,University of Canterbury | Allentoft M.E.,Murdoch University | Bunce M.,Murdoch University | Scofield R.P.,Canterbury Museum | And 3 more authors.
Quaternary Science Reviews | Year: 2010

Ancient DNA was isolated from the bones of 267 individuals of the extinct New Zealand moa (Aves: Dinornithiformes) from two late Holocene deposits [Pyramid Valley (PV) and Bell Hill Vineyard (BHV)] located 5.7 km apart in North Canterbury, South Island. The two sites' combined fossil record cover the last 3000 years of pre-human New Zealand and mitochondrial DNA confirmed that four species (Dinornis robustus, Euryapteryx curtus, Emeus crassus, and Pachyornis elephantopus) were sympatric in the region. However, the relative species compositions in the two deposits differed significantly with D. robustus and E. crassus being most abundant at PV while E. curtus outnumbered the other three moa taxa combined at BHV. A subsample of 227 individuals had sufficient nuclear DNA preservation to warrant the use of molecular sexing techniques, and the analyses uncovered a remarkable excess of females in both deposits with an overall male to female ratio of 1:5.1. Among juveniles of E. curtus, the only species which was represented by a substantial fraction of juveniles, the sex ratio was not skewed (10 ♂, 10 ♀), suggesting that the observed imbalance arose as a result of differential mortality during maturation. Surprisingly, sex ratios proved significantly different between sites with a 1:2.2 ratio at BHV (n = 90) and 1:14.2 at PV (n = 137). Given the mobility of large ratites, and the proximity of the two fossil assemblages in space and time, these differences in taxonomic and gender composition indicate that moa biology and the local environment have affected the fossil representation dramatically and several possible explanations are offered. Apart from adding to our understanding of moa biology, these discoveries reinforce the need for caution when basing interpretation of the fossil record on material from a single site. © 2009 Elsevier Ltd. All rights reserved.


Allentoft M.E.,Murdoch University | Allentoft M.E.,University of Canterbury | Allentoft M.E.,Copenhagen University | Collins M.,University of York | And 15 more authors.
Proceedings of the Royal Society B: Biological Sciences | Year: 2012

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. © The Royal Society 2012.


Allentoft M.E.,Murdoch University | Allentoft M.E.,University of Canterbury | Oskam C.,Murdoch University | Houston J.,Murdoch University | And 9 more authors.
PLoS ONE | Year: 2011

We present the first set of microsatellite markers developed exclusively for an extinct taxon. Microsatellite data have been analysed in thousands of genetic studies on extant species but the technology can be problematic when applied to low copy number (LCN) DNA. It is therefore rarely used on substrates more than a few decades old. Now, with the primers and protocols presented here, microsatellite markers are available to study the extinct New Zealand moa (Aves: Dinornithiformes) and, as with single nucleotide polymorphism (SNP) technology, the markers represent a means by which the field of ancient DNA can (preservation allowing) move on from its reliance on mitochondrial DNA. Candidate markers were identified using high throughput sequencing technology (GS-FLX) on DNA extracted from fossil moa bone and eggshell. From the 'shotgun' reads, >60 primer pairs were designed and tested on DNA from bones of the South Island giant moa (Dinornis robustus). Six polymorphic loci were characterised and used to assess measures of genetic diversity. Because of low template numbers, typical of ancient DNA, allelic dropout was observed in 36-70% of the PCR reactions at each microsatellite marker. However, a comprehensive survey of allelic dropout, combined with supporting quantitative PCR data, allowed us to establish a set of criteria that maximised data fidelity. Finally, we demonstrated the viability of the primers and the protocols, by compiling a full Dinornis microsatellite dataset representing fossils of c. 600-5000 years of age. A multi-locus genotype was obtained from 74 individuals (84% success rate), and the data showed no signs of being compromised by allelic dropout. The methodology presented here provides a framework by which to generate and evaluate microsatellite data from samples of much greater antiquity than attempted before, and opens new opportunities for ancient DNA research. © 2011 Allentoft et al.


Oskam C.L.,Murdoch University | Allentoft M.E.,Murdoch University | Allentoft M.E.,Palaecol Research Ltd | Allentoft M.E.,Center for GeoGenetics | And 8 more authors.
Quaternary Science Reviews | Year: 2012

The human colonisation of New Zealand in the late thirteenth century ad led to catastrophic impacts on the local biota and is among the most compelling examples of human over-exploitation of native fauna, including megafauna. Nearly half of the species in New Zealand' s pre-human avifauna are now extinct, including all nine species of large, flightless moa (Aves: Dinornithiformes). The abundance of moa in early archaeological sites demonstrates the significance of these megaherbivores in the diet of the first New Zealanders. Combining moa assemblage data, based on DNA identification of eggshell and bone, with morphological identification of bone (literature and museum catalogued specimens), we present the most comprehensive audit of moa to date from several significant 13th-15th century ad archaeological deposits across the east coast of the South Island. Mitochondrial DNA (mtDNA) was amplified from 251 of 323 (78%) eggshell fragments and 22 of 27 (88%) bone samples, and the analyses revealed the presence of four moa species: Anomalopteryx didiformis; Dinornis robustus; Emeus crassus and Euryapteryx curtus. The mtDNA, along with polymorphic microsatellite markers, enabled an estimate of the minimum number of individual eggs consumed at each site. Remarkably, in one deposit over 50 individual eggs were identified - a number that likely represents a considerable proportion of the total reproductive output of moa in the area and emphasises that human predation of all life stages of moa was intense. Molecular sexing was conducted on bones (n = 11). Contrary to previous ancient DNA studies from natural sites that consistently report an excess of female moa, we observed an excess of males (2.7:1), suggestive that males were preferential targets. This could be related to different behaviour between the two highly size-dimorphic sexes in moa. Lastly, we investigated the moa species from recovered skeletal and eggshell remains from seven Wairau Bar burials, and identified the presence of only the larger species of moa, E. curtus and D. robustus. © 2012 Elsevier Ltd.


Holdaway R.N.,Palaecol Research Ltd. | Holdaway R.N.,University of Canterbury | Allentoft M.E.,University of Canterbury | Allentoft M.E.,Copenhagen University | And 4 more authors.
Nature Communications | Year: 2014

New Zealand moa (Aves: Dinornithiformes) are the only late Quaternary megafauna whose extinction was clearly caused by humans. New Zealand offers the best opportunity to estimate the number of people involved in a megafaunal extinction event because, uniquely, both the Polynesian settlement of New Zealand and moa extinction are recent enough to be dated with a high degree of precision. In addition, the founding human population can be estimated from genetic evidence. Here we show that the Polynesian population of New Zealand would not have exceeded 2,000 individuals before extinction of moa populations in the habitable areas of the eastern South Island. During a brief (<150 years) period and at population densities that never exceeded ~0.01 km-2, Polynesians exterminated viable populations of moa by hunting and removal of habitat. High human population densities are not required in models of megafaunal extinction. © 2014 Macmillan Publishers Limited.


Allentoft M.E.,Copenhagen University | Heller R.,Copenhagen University | Holdaway R.N.,Palaecol Research Ltd | Holdaway R.N.,University of Canterbury | Bunce M.,Curtin University Australia
Heredity | Year: 2015

By analysing ancient DNA (aDNA) from 74 14 C-dated individuals of the extinct South Island giant moa (Dinornis robustus) of New Zealand, we identified four dyads of closely related adult females. Although our total sample included bones from four fossil deposits located within a 10 km radius, these eight individuals had all been excavated from the same locality. Indications of kinship were based on high pairwise genetic relatedness (r XY) in six microsatellite markers genotyped from aDNA, coupled with overlapping radiocarbon ages. The observed r XY values in the four dyads exceeded a conservative cutoff value for potential relatives obtained from simulated data. In three of the four dyads, the kinship was further supported by observing shared and rare mitochondrial haplotypes. Simulations demonstrated that the proportion of observed dyads above the cutoff value was at least 20 times higher than expected in a randomly mating population with temporal sampling, also when introducing population structure in the simulations. We conclude that the results must reflect social structure in the moa population and we discuss the implications for future aDNA research. © 2015 Macmillan Publishers Limited.


PubMed | Palaecol Research Ltd, Curtin University Australia and Copenhagen University
Type: Journal Article | Journal: Heredity | Year: 2015

By analysing ancient DNA (aDNA) from 74 (14)C-dated individuals of the extinct South Island giant moa (Dinornis robustus) of New Zealand, we identified four dyads of closely related adult females. Although our total sample included bones from four fossil deposits located within a 10 km radius, these eight individuals had all been excavated from the same locality. Indications of kinship were based on high pairwise genetic relatedness (rXY) in six microsatellite markers genotyped from aDNA, coupled with overlapping radiocarbon ages. The observed rXY values in the four dyads exceeded a conservative cutoff value for potential relatives obtained from simulated data. In three of the four dyads, the kinship was further supported by observing shared and rare mitochondrial haplotypes. Simulations demonstrated that the proportion of observed dyads above the cutoff value was at least 20 times higher than expected in a randomly mating population with temporal sampling, also when introducing population structure in the simulations. We conclude that the results must reflect social structure in the moa population and we discuss the implications for future aDNA research.

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