45 results on '"R. Paul Scofield"'
Search Results
2. A new extinct species of Polynesian sandpiper (Charadriiformes: Scolopacidae: Prosobonia) from Henderson Island, Pitcairn Group, and the phylogenetic relationships of Prosobonia
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Theresa L. Cole, Alice Cibois, Shaohong Feng, Jamie R. Wood, R. Paul Scofield, Vanesa L. De Pietri, Alan J. D. Tennyson, Graham M. Wragg, Wanjun Chen, Justin J. F. J. Jansen, Kieren J. Mitchell, Alan Cooper, and Trevor H. Worthy
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0106 biological sciences ,0303 health sciences ,Charadriiformes ,Extinction ,Sandpiper ,Phylogenetic tree ,Zoology ,Biology ,biology.organism_classification ,010603 evolutionary biology ,01 natural sciences ,03 medical and health sciences ,Prosobonia ,Molecular phylogenetics ,Paleoecology ,Animal Science and Zoology ,Molecular clock ,Ecology, Evolution, Behavior and Systematics ,030304 developmental biology - Abstract
We describe a new species of Polynesian sandpiper from Henderson Island, Prosobonia sauli sp. nov., based on multiple Holocene fossil bones collected during the Sir Peter Scott Commemorative Expedition to the Pitcairn Islands (1991–92). Prosobonia sauli is the only species of Prosobonia to be described from bone accumulations and extends the record of known extinct Polynesian sandpipers to four. It is readily differentiated from the extant Tuamotu Sandpiper P. parvirostris in several features of the legs and bill, implying ecological adaptations to different environments. The geographically nearest Prosobonia populations to Henderson Island were found on Mangareva, where it is now extinct. A previous record of a species of Prosobonia from Tubuai, Austral Islands, is here shown to belong to the Sanderling Calidris alba. Our analyses of newly sequenced genetic data, which include the mitochondrial genomes of P. parvirostris and the extinct Tahiti Sandpiper P. leucoptera, confidently resolve the position of Prosobonia as sister-taxon to turnstones and calidrine sandpipers. We present a hypothesis for the timing of divergence between species of Prosobonia and other scolopacid lineages. Our results further provide a framework to interpret the evolution of sedentary lineages within the normally highly migratory Scolopacidae.
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- 2020
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3. Comprehensive evidence for subspecies designations in Cook’s Petrel Pterodroma cookii with implications for conservation management
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Matt J. Rayner, Ilina Cubrinovska, Alan J. D. Tennyson, Ayla L. Van Loenen, Michael Bunce, R. Paul Scofield, Lara D. Shepherd, and Tammy E. Steeves
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0106 biological sciences ,0301 basic medicine ,Conservation genetics ,education.field_of_study ,Ecology ,biology ,Range (biology) ,Population ,Zoology ,Petrel ,Subspecies ,biology.organism_classification ,010603 evolutionary biology ,01 natural sciences ,03 medical and health sciences ,030104 developmental biology ,Geography ,Barrier island ,biology.animal ,Genetic structure ,Animal Science and Zoology ,Seabird ,education ,Nature and Landscape Conservation - Abstract
SummaryCook’s Petrel Pterodroma cookii is an endemic New Zealand seabird that has experienced a large range decline since the arrival of humans and now only breeds on two offshore islands (Te Hauturu-o-Toi/Little Barrier Island and Whenua Hou/Codfish Island) at the extreme ends of its former distribution. Morphological, behavioural, and mitochondrial cytochrome oxidase 1 (CO1) sequence data led a previous study to recognise the two extant populations as distinct conservation management units. Here, we further examine the genetic relationship between the extant populations using two nuclear introns (β-fibint7 and PAX). Using one mitochondrial locus (CO1), we also investigate the past distribution of a single nucleotide polymorphism (SNP) that differentiates the modern populations using bone and museum skins sourced from within its former range across New Zealand’s North and South Islands. We found significant population genetic structure between the two extant Cook’s Petrel populations for one of the two nuclear introns (β-fibint7). The mitochondrial DNA CO1 analysis indicated that the SNP variant found in the Codfish Island population was formerly widely distributed across both the North and South Islands, whereas the Little Barrier Island variant was detected only in North Island samples. We argue that these combined data support the recognition of the extant populations as different subspecies. Previous names for these taxa exist, thus Cook’s Petrel from Little Barrier Island becomes Pterodroma cookii cookii and Cook’s Petrel from Codfish Island becomes P. c. orientalis. Furthermore, we suggest that both genetic and non-genetic data should be taken into consideration when planning future mainland translocations. Namely, any translocations on the South Island should be sourced from Codfish Island and future translocations on the North Island should continue to be sourced from Little Barrier Island only.
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- 2020
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4. Mitogenomic evidence of close relationships between New Zealand’s extinct giant raptors and small-sized Australian sister-taxa
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M. Thomas P. Gilbert, James Haile, Ross Barnett, Sophia R. Cameron-Christie, Michael Knapp, Olga Kardailsky, R. Paul Scofield, Simon Y. W. Ho, Stefan Prost, Jessica E. Thomas, Nicolas Dussex, and Michael Bunce
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0106 biological sciences ,0301 basic medicine ,Eagle ,Early Pleistocene ,Biology ,Extinction, Biological ,010603 evolutionary biology ,01 natural sciences ,Predation ,03 medical and health sciences ,biology.animal ,Genetics ,Animals ,Body Size ,Molecular Biology ,Phylogeny ,Ecology, Evolution, Behavior and Systematics ,Base Sequence ,Raptors ,Ecology ,Island gigantism ,Harrier ,Bayes Theorem ,biology.organism_classification ,030104 developmental biology ,Ancient DNA ,Sister group ,Genome, Mitochondrial ,Hieraaetus ,New Zealand - Abstract
Prior to human arrival in the 13th century, two large birds of prey were the top predators in New Zealand. In the absence of non-volant mammals, the extinct Haast's eagle (Hieraaetus moorei), the largest eagle in the world, and the extinct Eyles' harrier (Circus teauteensis) the largest harrier in the world, had filled ecological niches that are on other landmasses occupied by animals such as large cats or canines. The evolutionary and biogeographic history of these island giants has long been a mystery. Here we reconstruct the origin and evolution of New Zealand’s giant raptors using complete mitochondrial genome data. We show that both Eyles’ harrier and Haast’s eagle diverged from much smaller, open land adapted Australasian relatives in the late Pliocene to early Pleistocene. These events coincided with the development of open habitat in the previously densely forested islands of New Zealand. Our study provides evidence of rapid evolution of island gigantism in New Zealand’s extinct birds of prey. Early Pleistocene climate and environmental changes were likely to have triggered the establishment of Australian raptors into New Zealand. Our results shed light on the evolution of two of the most impressive cases of island gigantism in the world.
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- 2019
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5. Global political responsibility for the conservation of albatrosses and large petrels
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Scott A. Shaffer, Steffen Oppel, April Hedd, Henri Weimerskirch, Benjamin Metzger, John P. Y. Arnould, Richard J. Cuthbert, Martin Beal, José Pedro Granadeiro, Christopher J. R. Robertson, José Manuel Reyes-González, Lorna Deppe, Paul M. Sagar, Valentina Colodro, William A. Montevecchi, Carolina Hazin, Matthieu Le Corre, Mark Carey, Flavio Quintana, Richard A. Phillips, Jill A. Awkerman, Michelle Antolos, José Manuel Arcos, Susan M. Waugh, Christopher A. Surman, Daniel Oro, Elizabeth J. Pearmain, Jaimie Cleeland, Leia Navarro-Herrero, Tim Reid, Karine Delord, Zuzana Zajková, Virginia Morera-Pujol, Manuela G. Forero, Vikash Tatayah, D. G. Nicholls, Takashi Yamamoto, Graeme A. Taylor, Peter Hodum, Audrey Jaeger, Ryan D. Carle, Herculano Andrade Dinis, Robert M. Suryan, David R. Thompson, Ridha Ouni, R. Paul Scofield, Kiyoaki Ozaki, Amanda N. D. Freeman, Elizabeth A. Bell, Ross M. Wanless, José Manuel Igual, Graham Robertson, Kim L. Stevens, Javier Arata, Todd J. Landers, Jonathan J. Felis, Josh Adams, Deon Nel, David J. Anderson, Ben J. Dilley, Paulo Catry, Fumio Sato, Teresa Militão, Michael A. Bell, Mohamed Salah Romdhane, Akinori Takahashi, Raül Ramos, Peter G. Ryan, Nirmal Shah, Kath Walker, Stefan Schoombie, Marta Cruz-Flores, Akira Fukuda, Thomas A. Clay, Fernanda De Felipe, Graeme Elliott, Jacob González-Solís, Laura Zango, Leigh G. Torres, Maria P. Dias, Azwianewi B. Makhado, Melinda G. Conners, European Commission, National Science Foundation (US), Universidad de Barcelona, Ministerio de Educación y Ciencia (España), Ministerio de Ciencia e Innovación (España), Ministerio de Economía y Competitividad (España), Generalitat de Catalunya, Marine and Environmental Sciences Centre [Portugal] (MARE), Instituto Universitário de Ciências Psicológicas, Sociais e da Vida = University Institute of Psychological, Social and Life Sciences (ISPA), BirdLife International, British Antarctic Survey (BAS), Natural Environment Research Council (NERC), The Royal Society for the Protection of Birds, Western Ecological Research Center, Wake Forest University, Oregon State University (OSU), SEO/BirdLife, Deakin University [Burwood], U.S. Environmental Protection Agency, Wildlife Management International Limited, La Trobe University, Oikonos Ecosysteme Knowledge [Chile], University of Liverpool, DST/NRF Centre of Excellence at the Percy FitzPatrick Institute of African Ornithology, Department of Biological Sciences, University of Cape Town, Oikonos Ecosystem Knowledge [Chile], University of California [Santa Cruz] (UC Santa Cruz), University of California (UC), Institut de Recerca de la Biodiversitat - Biodiversity Research Institute [Barcelona, Spain] (IRBio UB), Universitat de Barcelona (UB), World Land Trust, Centre d'Études Biologiques de Chizé - UMR 7372 (CEBC), La Rochelle Université (ULR)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), The Hutton’s Shearwater Charitable Trust, Associação Projecto Vitó, New Zealand Department of Conservation (DOC), DoC, CSIC, EBD, E-41080 Seville, Spain, Partenaires INRAE, Nature North, University of Shizuoka, Universidade de Lisboa = University of Lisbon (ULISBOA), Environment and Climate Change Canada, University of Puget Sound, Institut Mediterrani d'Estudis Avancats (IMEDEA), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC)-Universidad de las Islas Baleares (UIB), Ecologie marine tropicale dans les Océans Pacifique et Indien (ENTROPIE [Réunion]), Institut de Recherche pour le Développement (IRD)-Université de La Réunion (UR)-Centre National de la Recherche Scientifique (CNRS), University of Auckland [Auckland], Auckland Museum, Auckland Council, Department of Environment, Agriculture and Fisheries [South Africa] (Oceans and Coasts), BirdLife [Malta], Memorial University of Newfoundland = Université Memorial de Terre-Neuve [St. John's, Canada] (MUN), WWF-Netherlands, Chisholm Institute, Centre d'Estudis Avançats de Blanes (CEAB), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), Faculté des Sciences Mathématiques, Physiques et Naturelles de Tunis (FST), Université de Tunis El Manar (UTM), Yamashina Institute for Ornithology, Instituto de Biología de Organismos Marinos [Chubut] (IBIOMAR), Consejo Nacional de Investigaciones Científicas y Técnicas [Buenos Aires] (CONICET), University of Tasmania [Hobart, Australia] (UTAS), Wild Press, Institut National Agronomique de Tunisie, National Institute of Water and Atmospheric Research [Christchurch] (NIWA), Canterbury Museum, San Jose State University [San Jose] (SJSU), Nature Seychelles, Halfmoon Biosciences, National Institute of Polar Research [Tokyo] (NiPR), Mauritian Wildlife Foundation, National Institute of Water and Atmospheric Research [Wellington] (NIWA), National Taiwan Ocean University (NTOU), Office of the Parliamentary Commissioner for the Environment, Meiji Institute for Advanced Study of Mathematical Sciences (MIMS), Meiji University [Tokyo], Instituto Universitário de Ciências Psicológicas, Sociais e da Vida (ISPA), University of California [Santa Cruz] (UCSC), University of California, Université de La Rochelle (ULR)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Universidade de Lisboa (ULISBOA), Centre National de la Recherche Scientifique (CNRS)-Université de La Réunion (UR)-Institut de Recherche pour le Développement (IRD), Memorial University of Newfoundland [St. John's], San Jose State University [San José] (SJSU), and Meiji university
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0106 biological sciences ,seabird ,Environmental management ,Science Policy ,Population ,Fishing ,Biodiversity ,Biodiversity conservation ,010603 evolutionary biology ,01 natural sciences ,Politics ,tracking data ,Ocells marins ,14. Life underwater ,education ,Applied Ecology ,Research Articles ,education.field_of_study ,Multidisciplinary ,010604 marine biology & hydrobiology ,conservation ,SciAdv r-articles ,Gestió ambiental ,Sea birds ,15. Life on land ,[SDE.ES]Environmental Sciences/Environmental and Society ,Fishery ,Geography ,International waters ,Work (electrical) ,13. Climate action ,Threatened species ,high seas ,Conservació de la diversitat biològica ,Fisheries management ,ecology ,[SDE.BE]Environmental Sciences/Biodiversity and Ecology ,Research Article - Abstract
Migratory marine species cross political borders and enter the high seas, where the lack of an effective global management framework for biodiversity leaves them vulnerable to threats. Here, we combine 10,108 tracks from 5775 individual birds at 87 sites with data on breeding population sizes to estimate the relative year-round importance of national jurisdictions and high seas areas for 39 species of albatrosses and large petrels. Populations from every country made extensive use of the high seas, indicating the stake each country has in the management of biodiversity in international waters. We quantified the links among national populations of these threatened seabirds and the regional fisheries management organizations (RFMOs) which regulate fishing in the high seas. This work makes explicit the relative responsibilities that each country and RFMO has for the management of shared biodiversity, providing invaluable information for the conservation and management of migratory species in the marine realm., This project has received funding from the European Union’s Horizon 2020 Research and Innovation Programme under the Marie Skłodowska-Curie grant agreement no. 766417. Research made possible with the support, permissions, and funding granted by the following organizations, institutions, and grant agreements: Marine Conservation Program of DPIPWE Tasmania; American Bird Conservancy; Bureau of Ocean Energy Management; communities of Isla Mocha and Islas Juan Fernández; Corporación Nacional Forestal and Servicio Agrícola y Ganadería (Chile); Environment Canada; the National Fish and Wildlife Foundation; the National Geographic Society; ProDelphinus; and the Wallis Foundation; NSF grants DEB 9304579, DEB 9629539, DEB9806606, DEB0235818, and DEB 0842199 to D.J.A.; the National Geographic Society; the U.S. Fish and Wildlife Service; U.S. Geological Survey Ecosystems Mission Area, Wake Forest University; Max-Planck Society and State of Baden-Wuerttemberg Innovation funding; Colorado State University International Programs; Swiss Friends of Galapagos; the International Center for Tropical Ecology at University of Missouri-St. Louis; the Instituto Antartico Chileno (INACH) and the Australian Antarctic Division (AAD); LIFE “Marine IBAs IN Spain” (LIFE04NAT/ES/000049, 2004-2009) and LIFE+ INDEMARES (2009-2014); Sea World Research and Rescue Foundation Inc.; Holsworth Wildlife Research Endowment; and Winifred Violet Scott Trust; FCT-Portugal through projects (UIDB/04292/2020 and UIDP/04292/2020 and UIDP/50017/2020 and UIDB/50017/2020, granted to MARE and CESAM, respectively); the Falklands Islands Government; Natural Environmental Research Council (NERC) core funding to British Antarctic Survey Ecosystems Programme and Official Development Assistance Atlantic Islands project (NE/ R000 107/1); the New Zealand Department of Conservation; Ministry for Primary Industries; Ngāti Rehua Ngāti Wai ki Aotea; Falklands Island Conservation; University of Barcelona (APIF/2015, to M.C.-F.); the French Polar Institute (program IPEV n°109 to H.W.); Réserve Naturelle Nationale des Terres Australes Françaises; and the Zones Atelier Antarctique (LTSER France, CNRS-INEE); European funds through the European Commission Training and Mobility of Researchers Programme (ERBFMBICT983030); Spanish funds through the Ministerio de Ciencia y Tecnología (REN2002-01164/GLO), Ministerio de Educación y Ciencia (CGL2006-01315/BOS), Ministerio de Ciencia e Innovación (CGL2009-11278/BOS), and Ministerio de Economía y Competitividad (CGL2013-42585-P); Catalan funds through the Generalitat de Catalunya (2001SGR00091); and additional funding from SEO/BirdLife (programa Migra & proyecto LIFE+ Indemares), Fundación Banco Bilbao Vizcaya Argentaria (BIOCON04/099) and Fundación Biodiversidad (18PCA4328, 2012-2013); NSERC Discovery Grant and Government of Canada’s Program for International Polar Year to W.A.M.; and an ACAP AC Grant in 2013-14, predoctoral contract BES-2017-079874 of the Spanish Ministerio de Industria, Economía y Competitividad (to L.N.-H.); Spanish Foundation for Biodiversity and Spanish Ministry of Science grant ref. CGL2013-42203-R; the Pew Environment Group via the Pew Fellowship Award in Marine Conservation (to M.L.C.); National Research Foundation; South Africa and Oceans and Coasts; Department of Environment, Agriculture and Fisheries; Malta Seabird Project (LIFE10NAT/MT/090) co-funded by the LIFE program of the European Commission and the Maltese Ministry for the Environment, Sustainable Development and Climate Change, in partnership with the Royal Society for the Protection of Bird and the Portuguese Society for the Study of Birds; predoctoral contract BES-2014-068025 of the Spanish Ministerio de Industria, Economía y Competitividad (to V.M.-P.); Scientific Expert PIM initiative (Petites Iles de Méditerranée); the PIM initiative (Petites Iles de Méditerranée); the Tunisian Coastal Protection and Planning Agency (APAL); Ministry of the Environment, Japan; Funding by Fundación Ecocentro, Argentina; Wildlife Conservation Society, USA; and Ministerio de Ciencia, Tecnología e Innovación, Argentina; Centro Nacional Patagónico (CONICET), postdoctoral contracts by Beatriu de Pinós (2010-BP_A-00173), Juan de la Cierva (JCI-2009-05426), PLEAMAR (2017/2349), and Ramón y Cajal (RYC-2017-22055) programme (to R.R.); Seventh Framework Programme (Research Executive Agency of the European Commission, 618841, FP7-PEOPLE-2013-CIG); Fondation Total pour la Biodiversité (project: Trophic ecology and impacts of bycatch on the avifauna communities of Zembra archipelago); Agence de Protection et d’Aménagement du Littoral (APAL-Tunisia); Killam Postdoctoral fellowship from Dalhousie University; South African National Antarctic Programme; ACAP; Papahānaumokuākea Marine National Monument; NOAA; Japan Society for the Promotion of Science Kakenhi grant 19651100 and 15H02857; National Parks and Conservation Service (Mauritius) (to M.L.C.); IPEV Prog 109; and NASA. The use of trade, product, or firm names in this publication is for descriptive purposes only and does not imply endorsement by the U.S. government. The scientific results and conclusions, as well as any views or opinions expressed herein, are those of the authors and do not necessarily reflect those of the NOAA or the Department of Commerce. This communication reflects only the authors’ view, and the Research Executive Agency of the European Union is not responsible for any use that may be made of the information it contains. Z.Z. acknowledges funding from a predoctoral grant (APIF/2012) from the University of Barcelona. J.Ad. acknowledges funding from the U.S. Geological Survey Ecosystems Mission Area, U.S. Bureau of Ocean Energy Management, Pacific OCS Region.
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- 2021
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6. Factors (type, colour, density, and shape) determining the removal of marine plastic debris by seabirds from the South Pacific Ocean: Is there a pattern?
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Cristián G. Suazo, Guillermo Luna-Jorquera, Martin Thiel, Marcelo M. Rivadeneira, Christopher J. R. Robertson, Matías Portflitt-Toro, Valeria Hidalgo-Ruz, Diego Miranda-Urbina, Hanna Frick, Marcus Eriksen, Juan Serratosa, and R. Paul Scofield
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0106 biological sciences ,Abiotic component ,geography ,geography.geographical_feature_category ,Ecology ,biology ,Range (biology) ,010604 marine biology & hydrobiology ,Ocean current ,Environmental aspects ,Aquatic Science ,010603 evolutionary biology ,01 natural sciences ,Debris ,Oceanography ,Nest ,Ocean gyre ,biology.animal ,Environmental science ,Seabird ,Nature and Landscape Conservation ,South Pacific Gyre - Abstract
1. While floating near the sea surface plastic debris interacts with a number of external factors, including many different organisms. Seabirds have the most extensive documented history of interactions with plastics, through ingestion, entanglement, and nest construction. 2. In the present study, eight seabird species from the South Pacific Ocean were used as a proxy to determine potential patterns of removal of marine plastic debris, and three hypotheses were tested in relation to their feeding habits and nesting areas. 3. Plastics from abiotic compartments (Chilean continental coast, South Pacific Gyre, and Rapa Nui beaches) and biotic compartments (surface‐feeding seabirds, diving seabirds, and nesting areas) were compared, according to their type, colour, shape, and density. 4. Continental beaches had a relatively wide range of colours and shapes, with many non‐buoyant plastics. Samples from the South Pacific Gyre (SPG) and Rapa Nui (Easter Island) beaches comprised mainly hard, rounded, buoyant, and white/grey plastics. 5. These results indicate that the composition of floating plastics from terrestrial sources changes during transport with oceanic currents, reducing the proportion of prey‐like plastics present in the subtropical gyres. 6. The stomach contents of surface‐feeding and diving seabirds were dominated by hard, white/grey, and round plastic items, similar to plastics from the SPG, suggesting non‐selective (accidental or secondary) ingestion. 7. Nesting areas had a more variable composition of brightly coloured plastics, suggesting a pattern of selective removal of plastics by seabirds, probably from oceanic sources. 8. The present study reveals extensive interactions of seabirds with plastics on a broader scale, which is highly relevant given that the impacts of plastics on seabirds are increasing worldwide, compromising their efficient conservation.
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- 2021
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7. Ancient crested penguin constrains timing of recruitment into seabird hotspot
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Daniel B. Thomas, Alan J. D. Tennyson, Walker Pett, Daniel T. Ksepka, Tracy A. Heath, and R. Paul Scofield
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0106 biological sciences ,Neogene ,010603 evolutionary biology ,01 natural sciences ,General Biochemistry, Genetics and Molecular Biology ,03 medical and health sciences ,biology.animal ,Hotspot (geology) ,Animals ,Ecosystem ,Crested penguin ,Phylogeny ,030304 developmental biology ,General Environmental Science ,0303 health sciences ,General Immunology and Microbiology ,biology ,Ecology ,Fossils ,Bayes Theorem ,General Medicine ,biology.organism_classification ,Biological Evolution ,Spheniscidae ,Pygoscelis ,Beak ,Geography ,Palaeobiology ,Upwelling ,Seabird ,General Agricultural and Biological Sciences ,New Zealand - Abstract
New Zealand is a globally significant hotspot for seabird diversity, but the sparse fossil record for most seabird lineages has impeded our understanding of how and when this hotspot developed. Here, we describe multiple exceptionally well-preserved specimens of a new species of penguin from tightly dated (3.36–3.06 Ma) Pliocene deposits in New Zealand. Bayesian and parsimony analyses place Eudyptes atatu sp. nov. as the sister species to all extant and recently extinct members of the crested penguin genus Eudyptes . The new species has a markedly more slender upper beak and mandible compared with other Eudyptes penguins. Our combined evidence approach reveals that deep bills evolved in both crested and stiff-tailed penguins ( Pygoscelis ) during the Pliocene. That deep bills arose so late in the greater than 60 million year evolutionary history of penguins suggests that dietary shifts may have occurred as wind-driven Pliocene upwelling radically restructured southern ocean ecosystems. Ancestral area reconstructions using BioGeoBEARS identify New Zealand as the most likely ancestral area for total-group penguins, crown penguins and crested penguins. Our analyses provide a timeframe for recruitment of crown penguins into the New Zealand avifauna, indicating this process began in the late Neogene and was completed via multiple waves of colonizing lineages.
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- 2020
8. A framework for mapping the distribution of seabirds by integrating tracking, demography and phenology
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Elizabeth J. Pearmain, Leigh G. Torres, Azwianewi B. Makhado, Peter G. Ryan, Jaimie Cleeland, Jacob González-Solís, Paul M. Sagar, David Grémillet, Andrew Stanworth, Amanda N. D. Freeman, Yvan Richard, Lorna Deppe, David R. Thompson, Maria P. Dias, R. Paul Scofield, Todd J. Landers, Edward R. Abraham, Susan M. Waugh, Anne-Sophie Bonnet-Lebrun, Ross M. Wanless, Kath Walker, Richard A. Phillips, Leandro Bugoni, Philip N. Trathan, Kalinka Rexer-Huber, Henri Weimerskirch, Cleo Small, Letizia Campioni, Christopher J. R. Robertson, Paulo Catry, Deon Nel, Joel Rice, Jean-Claude Stahl, John P. Y. Arnould, Ana P. B. Carneiro, Ben J. Dilley, Thomas A. Clay, D. G. Nicholls, Kim L. Stevens, Javier Arata, Graeme Elliott, Tammy E. Davies, Elizabeth A. Bell, Steffen Oppel, Jonathan Handley, José Pedro Granadeiro, Faculdade de Ciências e Tecnologia (FCT NOVA), Universidade Nova de Lisboa (NOVA), Royal Society for the Protection of Birds, Université Panthéon-Sorbonne (UP1), British Antarctic Survey (BAS), Natural Environment Research Council (NERC), FitzPatrick Institute of African Ornithology, University of Cape Town-DST-NRF Centre of Excellence, Wake Forest University, DST/NRF Centre of Excellence at the Percy FitzPatrick Institute of African Ornithology, Department of Biological Sciences, University of Cape Town, BirdLife International, Instituto Antartico Chileno, School of Life and Environmental Sciences, Deakin University [Burwood], Faculty of Biomedical and Life Sciences, Graham Kerr Building, University of Glasgow, Marine and Environmental Sciences Centre [Portugal] (MARE), Instituto Universitário de Ciências Psicológicas, Sociais e da Vida (ISPA), MARE – Marine and Environmental Sciences Centre [Portugal], Instituto Universitário [Portugal], Xénobiotiques, Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, CESAM, Museu Nacional de Historia Natural, Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), Université Paul-Valéry - Montpellier 3 (UM3)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-École pratique des hautes études (EPHE)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Department of Zoology, University of Otago [Dunedin, Nouvelle-Zélande], School of Chemistry University of Birmingham, University of Birmingham [Birmingham], National Institute of Water and Atmospheric Research, National Institute of Water, Falklands Conservation, Royal Veterinary College [London], University of London [London], Natural Environment Research Council - British Antarctic Survey [Cambridge, UK], British Antarctic Survey NERC [UK], Department of Chemistry and Applied Science, College of William and Mary [Williamsburg] (WM), Centre d'études biologiques de Chizé (CEBC), Centre National de la Recherche Scientifique (CNRS), Faculdade de Ciências e Tecnologia = School of Science & Technology (FCT NOVA), Universidade Nova de Lisboa = NOVA University Lisbon (NOVA), Université Paris 1 Panthéon-Sorbonne (UP1), Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Recherche Agronomique (INRA), Centro de Estudos do Ambiente e do Mar (CESAM), Universidade de Lisboa (ULISBOA), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Université Paul-Valéry - Montpellier 3 (UPVM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut de Recherche pour le Développement (IRD [France-Sud]), National Institute of Water and Atmospheric Research [Wellington] (NIWA), Centre d'Études Biologiques de Chizé - UMR 7372 (CEBC), and Université de La Rochelle (ULR)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
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0106 biological sciences ,Megafauna ,Ecology (disciplines) ,Population ,distributions ,Distribution (economics) ,Conservation ,010603 evolutionary biology ,01 natural sciences ,petrels ,Longline fisheries ,Longline fishing ,megafauna ,At-sea threats ,biology.animal ,14. Life underwater ,education ,education.field_of_study ,Ecology ,biology ,business.industry ,010604 marine biology & hydrobiology ,Petrels ,albatrosses ,conservation ,Seabird density ,Fishery ,Bycatch ,seabird density ,Identification (information) ,Overexploitation ,Geography ,[SDE]Environmental Sciences ,Albatrosses ,Distributions ,Seabird ,business ,longline fisheries ,at‐sea threats - Abstract
1. The identification of geographic areas where the densities of animals are highest across their annual cycles is a crucial step in conservation planning. In marine environments, however, it can be particularly difficult to map the distribution of species, and the methods used are usually biased towards adults, neglecting the distribution of other life-history stages even though they can represent a substantial proportion of the total population. 2. Here we develop a methodological framework for estimating populationlevel density distributions of seabirds, integrating tracking data across the main life-history stages (adult breeders and non-breeders, juveniles and immatures). We incorporate demographic information (adult and juvenile/immature survival, breeding frequency and success, age at first breeding) and phenological data (average timing of breeding and migration) to weight distribution maps according to the proportion of the population represented by each life-history stage. 3. We demonstrate the utility of this framework by applying it to 22 species of albatrosses and petrels that are of conservation concern due to interactions with fisheries. Because juveniles, immatures and non-breeding adults account for 47%–81% of all individuals of the populations analysed, ignoring the distributions of birds in these stages leads to biased estimates of overlap with threats, and may misdirect management and conservation efforts. Population-level distribution maps using only adult distributions underestimated exposure to longline fishing effort by 18%–42%, compared with overlap scores based on data from all lifehistory stages. 4. Synthesis and applications. Our framework synthesizes and improves on previous approaches to estimate seabird densities at sea, is applicable for data-poor situations, and provides a standard and repeatable method that can be easily updated as new tracking and demographic data become available. We provide scripts in the R language and a Shiny app to facilitate future applications of our approach. We recommend that where sufficient tracking data are available, this framework be used to assess overlap of seabirds with at-sea threats such as overharvesting, fisheries bycatch, shipping, offshore industry and pollutants. Based on such an analysis, conservation interventions could be directed towards areas where they have the greatest impact on populations. Fundação para a Ciência e a Tecnologia - FCT; French Polar Institute IPEV; Falkland Islands Government info:eu-repo/semantics/publishedVersion
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- 2020
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9. Evidence for breeding of Megadyptes penguins in the North Island at the time of human arrival
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Theresa L. Cole, Alexander J. F. Verry, R. Paul Scofield, Alan J. D. Tennyson, and Nicolas J. Rawlence
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0106 biological sciences ,Extinction ,biology ,Ecology ,Biodiversity ,Yellow-eyed penguin ,biology.organism_classification ,Megadyptes ,010603 evolutionary biology ,01 natural sciences ,Archaeological evidence ,Waitaha penguin ,010601 ecology ,Prehistory ,Megadyptes antipodes ,Animal Science and Zoology - Abstract
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.
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- 2018
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10. Subsistence practices, past biodiversity, and anthropogenic impacts revealed by New Zealand-wide ancient DNA survey
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Lara D. Shepherd, Karen Greig, Frederik Valeur Seersholm, R. Paul Scofield, Michael Stat, Michael Knapp, Alicia Grealy, Richard Walter, Luke J. Easton, Anders J. Hansen, Theresa L. Cole, Michael Bunce, Alan J. D. Tennyson, and Nicolas J. Rawlence
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0106 biological sciences ,0301 basic medicine ,subsistence practices ,Fauna ,Biodiversity ,Social Sciences ,010603 evolutionary biology ,01 natural sciences ,paleoecology ,Bone and Bones ,03 medical and health sciences ,Animals ,Ecosystem ,14. Life underwater ,ancient DNA ,human impacts ,geography ,Multidisciplinary ,Subfossil ,geography.geographical_feature_category ,Ecology ,Fossils ,Subsistence agriculture ,DNA ,Gene Pool ,15. Life on land ,Biological Sciences ,bulk bone metabarcoding ,030104 developmental biology ,Ancient DNA ,Anthropology ,Archipelago ,Paleoecology ,New Zealand - Abstract
Significance The mode and tempo of extinctions and extirpations after the first contact phase of human settlements is a widely debated topic. As the last major landmass to be settled by humans, New Zealand offers a unique lens through which to study interactions of people and biota. By analyzing ancient DNA from more than 5,000 nondiagnostic and fragmented bones from 38 subfossil assemblages, we describe species and patterns that have been missed by morphological approaches. We report the identification of five species of whale from an archaeological context in New Zealand and describe the prehistoric kākāpō population structure. Taken together, this study demonstrates insights into subsistence practices and extinction processes and demonstrates the value of genetic analyses of fossil assemblages., New Zealand’s geographic isolation, lack of native terrestrial mammals, and Gondwanan origins make it an ideal location to study evolutionary processes. However, since the archipelago was first settled by humans 750 y ago, its unique biodiversity has been under pressure, and today an estimated 49% of the terrestrial avifauna is extinct. Current efforts to conserve the remaining fauna rely on a better understanding of the composition of past ecosystems, as well as the causes and timing of past extinctions. The exact temporal and spatial dynamics of New Zealand’s extinct fauna, however, can be difficult to interpret, as only a small proportion of animals are preserved as morphologically identifiable fossils. Here, we conduct a large-scale genetic survey of subfossil bone assemblages to elucidate the impact of humans on the environment in New Zealand. By genetically identifying more than 5,000 nondiagnostic bone fragments from archaeological and paleontological sites, we reconstruct a rich faunal record of 110 species of birds, fish, reptiles, amphibians, and marine mammals. We report evidence of five whale species rarely reported from New Zealand archaeological middens and characterize extinct lineages of leiopelmatid frog (Leiopelma sp.) and kākāpō (Strigops habroptilus) haplotypes lost from the gene pool. Taken together, this molecular audit of New Zealand’s subfossil record not only contributes to our understanding of past biodiversity and precontact Māori subsistence practices but also provides a more nuanced snapshot of anthropogenic impacts on native fauna after first human arrival.
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- 2018
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11. Flightless rails (Aves: Rallidae) from the early Miocene St Bathans Fauna, Otago, New Zealand
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Warren D. Handley, Vanesa L. De Pietri, Alan J. D. Tennyson, Michael Archer, Ellen K. Mather, Trevor H. Worthy, R. Paul Scofield, and Suzanne J. Hand
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0106 biological sciences ,Sexual dimorphism ,010506 paleontology ,Taxon ,Common species ,Osteology ,Fauna ,Paleontology ,Zoology ,Biology ,010603 evolutionary biology ,01 natural sciences ,0105 earth and related environmental sciences - Abstract
While known for over a decade to exist, fossil rails of the early Miocene (19–16 Ma) St Bathans Fauna, from the South Island of New Zealand, have not previously been described taxonomically or studied in detail. Here we use qualitative osteological features and analyse measurements from wing and leg bones to determine the number of taxa represented, their flight ability, and the presence and nature of sexual dimorphism within the identified taxa. We describe two new rail species in monospecific genera from the St Bathans Fauna: Priscaweka parvales gen. et sp. nov., which is extremely common, and Litorallus livezeyi gen. et sp. nov., a distinctly larger, uncommon species. Priscaweka parvales exhibited a significant degree of sexual dimorphism and was tiny, being the size of the extinct Chatham Island Rail Cabalus modestus. Both newly described species exhibit skeletal proportions and osteological features that indicate they had reduced wings and were flightless. These observations reveal that flightless ra...
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- 2018
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12. A new, large-bodied omnivorous bat (Noctilionoidea: Mystacinidae) reveals lost morphological and ecological diversity since the Miocene in New Zealand
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Gregg F. Gunnell, Steven W. Salisbury, Robin M. D. Beck, Michael Archer, Trevor H. Worthy, R. Paul Scofield, Nancy B. Simmons, Vanesa L. De Pietri, Suzanne J. Hand, and Alan J. D. Tennyson
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0106 biological sciences ,0301 basic medicine ,Fauna ,Biodiversity ,Zoology ,lcsh:Medicine ,010603 evolutionary biology ,01 natural sciences ,Article ,03 medical and health sciences ,Mystacinidae ,Genus ,Chiroptera ,Adaptive radiation ,Animals ,Ecosystem diversity ,lcsh:Science ,Southern Hemisphere ,Phylogeny ,Multidisciplinary ,Ecology ,biology ,Fossils ,Palaeontology ,lcsh:R ,Palaeoecology ,Bayes Theorem ,biology.organism_classification ,Biological Evolution ,Phenotype ,030104 developmental biology ,Taxon ,Geography ,lcsh:Q ,New Zealand - Abstract
Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/., A new genus and species of fossil bat is described from New Zealand’s only pre-Pleistocene Cenozoic terrestrial fauna, the early Miocene St Bathans Fauna of Central Otago, South Island. Bayesian total evidence phylogenetic analysis places this new Southern Hemisphere taxon among the burrowing bats (mystacinids) of New Zealand and Australia, although its lower dentition also resembles Africa’s endemic sucker-footed bats (myzopodids). As the first new bat genus to be added to New Zealand’s fauna in more than 150 years, it provides new insight into the original diversity of chiropterans in Australasia. It also underscores the significant decline in morphological diversity that has taken place in the highly distinctive, semi-terrestrial bat family Mystacinidae since the Miocene. This bat was relatively large, with an estimated body mass of ~40 g, and its dentition suggests it had an omnivorous diet. Its striking dental autapomorphies, including development of a large hypocone, signal a shift of diet compared with other mystacinids, and may provide evidence of an adaptive radiation in feeding strategy in this group of noctilionoid bats.
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- 2018
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13. Speciation, range contraction and extinction in the endemic New Zealand King Shag complex
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Matt J. Rayner, Martyn Kennedy, David S. Melville, Nicolas J. Rawlence, Jonathan M. Waters, Charlotte E. Till, Rob Schuckard, Hamish G. Spencer, Luke J. Easton, R. Paul Scofield, and Alan J. D. Tennyson
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0106 biological sciences ,0301 basic medicine ,common ,Population ,Biology ,Extinction, Biological ,010603 evolutionary biology ,01 natural sciences ,Bone and Bones ,Birds ,03 medical and health sciences ,Polynesians ,Genetics ,Animals ,education ,Molecular Biology ,Phylogeny ,Ecology, Evolution, Behavior and Systematics ,Holocene ,Principal Component Analysis ,education.field_of_study ,Extinction ,Osteology ,Fossils ,Ecology ,Discriminant Analysis ,DNA ,Sequence Analysis, DNA ,Cytochromes b ,Biodiversity hotspot ,030104 developmental biology ,Ancient DNA ,common.group ,Mainland ,New Zealand - Abstract
New Zealand’s endemic King Shag ( Leucocarbo carunculatus ) has occupied only a narrow portion of the northeastern South Island for at least the past 240 years. However, pre-human Holocene fossil and archaeological remains have suggested a far more widespread distribution of the three Leucocarbo species (King, Otago, Foveaux) on mainland New Zealand at the time of Polynesian settlement in the late 13th Century CE. We use modern and ancient DNA, and morphometric and osteological analyses, of modern King Shags and Holocene fossil Leucocarbo remains to assess the pre-human distribution and taxonomic status of the King Shag on mainland New Zealand, and the resultant conservation implications. Our analyses show that the King Shag was formerly widespread around southern coasts of the North Island and the northern parts of the South Island but experienced population and lineage extinctions, and range contraction, probably after Polynesian arrival. This history parallels range contractions of other New Zealand seabirds. Conservation management of the King Shag should take into account this species narrow distribution and probable reduced genetic diversity. Moreover, combined genetic, morphometric and osteological analyses of prehistoric material from mainland New Zealand suggest that the now extinct northern New Zealand Leucocarbo populations comprised a unique lineage. Although these distinctive populations were previously assigned to the King Shag (based on morphological similarities and geographic proximity to modern Leucocarbo populations), we herein describe them as a new species, the Kohatu Shag ( Leucocarbo septentrionalis ). The extinction of this species further highlights the dramatic impacts Polynesians and introduced predators had on New Zealand’s coastal and marine biodiversity. The prehistoric presence of at least four species of Leucocarbo shag on mainland NZ further highlights its status as a biodiversity hotspot for Phalacrocoracidae.
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- 2017
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14. Using super-high resolution satellite imagery to census threatened albatrosses
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R. Paul Scofield, Richard A. Phillips, and Peter T. Fretwell
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0106 biological sciences ,biology ,Aerial survey ,Ecology ,010604 marine biology & hydrobiology ,Royal albatross ,Wildlife ,Endangered species ,Albatross ,15. Life on land ,biology.organism_classification ,010603 evolutionary biology ,01 natural sciences ,Fishery ,Geography ,Wandering albatross ,Threatened species ,Animal Science and Zoology ,Satellite imagery ,Ecology, Evolution, Behavior and Systematics - Abstract
This study is the first to utilize 30-cm resolution imagery from the WorldView-3 (WV-3) satellite to count wildlife directly. We test the accuracy of the satellite method for directly counting individuals at a well-studied colony of Wandering Albatross Diomedea exulans at South Georgia, and then apply it to the closely related Northern Royal Albatross Diomedea sanfordi, which is near-endemic to the Chatham Islands and of unknown recent population status due to the remoteness and limited accessibility of the colonies. At South Georgia, satellite-based counts were comparable to ground-based counts of Wandering Albatross nests, with a slight over-estimation due to the presence of non-breeding birds. In the Chatham Islands, satellite-based counts of Northern Royal Albatross in the 2015/2016 season were similar to ground-based counts undertaken on the Forty-Fours islands in 2009/2010, but much lower than ground-based counts undertaken on The Sisters islands in 2009/2010, which is of major conservation concern for this endangered albatross species. We conclude that the ground-breaking resolution of the newly available WV-3 satellite will provide a step change in our ability to count albatrosses and other large birds directly from space without disturbance, at potentially lower cost and with minimal logistical effort.
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- 2017
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15. Multivariate skeletal analyses support a taxonomic distinction between New Zealand and Australian Eudyptula penguins (Sphenisciformes: Spheniscidae)
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R. Paul Scofield, Jonathan M. Waters, and Stefanie Grosser
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0106 biological sciences ,0301 basic medicine ,Morphometrics ,Osteology ,Ecology ,Spheniscidae ,Zoology ,Eudyptula ,Biology ,biology.organism_classification ,010603 evolutionary biology ,01 natural sciences ,Bergmann's rule ,03 medical and health sciences ,030104 developmental biology ,Plumage ,Animal Science and Zoology ,Conservation biology ,Sphenisciformes ,Ecology, Evolution, Behavior and Systematics ,Nature and Landscape Conservation - Abstract
Recent genetic analyses have revealed evidence for the existence of two distinct lineages of Little Penguin (genus Eudyptula), one endemic to New Zealand (E. minor), and the other widespread along the coasts of Australia and south-east New Zealand (E. novaehollandiae). Here we present the first comprehensive morphometric analysis of complete Eudyptula skeletons. We show that variability in Eudyptula body and bill size is associated with sea surface temperature gradients, suggesting that thermoregulatory processes underpin morphological variation in these seabirds. More importantly, we detect osteological differentiation between New Zealand and Australian specimens, providing further support for the taxonomic separation of these behaviourally and genetically distinct lineages. Broadly, our study shows the value of multivariate osteological analyses in helping to resolve the status of genetic lineages that appear morphologically ‘cryptic’ when considering external morphometrics and plumage features ...
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- 2017
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16. Recent advances in avian palaeobiology in New Zealand with implications for understanding New Zealand’s geological, climatic and evolutionary histories
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Trevor H. Worthy, R. Paul Scofield, and Vanesa L. De Pietri
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0106 biological sciences ,0301 basic medicine ,biology ,Ecology ,Paleobiology ,Vertebrate ,Zoology ,Biota ,15. Life on land ,010603 evolutionary biology ,01 natural sciences ,Indigenous ,03 medical and health sciences ,030104 developmental biology ,Taxon ,biology.animal ,Period (geology) ,Animal Science and Zoology ,Quaternary ,Holocene - Abstract
New Zealand, long recognised as a land where birds dominate the terrestrial vertebrate biota, lacked an informative fossil record for the non-marine pre-Pleistocene avifauna until the twenty-first century. Here we review recent research that alters the known diversity of the fossil Paleogene–Neogene birds and our understanding of the origin of New Zealand’s recent or modern biota. Since 2010, there has been a 50% increase in the number of described fossil bird species (now 45) for the pre-Quaternary period. Many represent higher taxa that are new or listed for New Zealand for the first time, including 12 genera (35 total), nine family-level taxa (18 total), and seven ordinal taxa. We also review recent multidisciplinary research integrating DNA and morphological analyses affecting the taxonomic diversity of the Quaternary avifauna and present revised diversity metrics. The Holocene avifauna contained 217 indigenous breeding species (67% endemic) of which 54 (25%) are extinct.
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- 2017
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17. The origin and phylogenetic relationships of the New Zealand ravens
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Kieren J. Mitchell, Scott Jarvie, Alan Cooper, Vanesa L. De Pietri, Jamie R. Wood, R. Paul Scofield, and Bastien Llamas
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0106 biological sciences ,0301 basic medicine ,Zoology ,Biology ,Subspecies ,010603 evolutionary biology ,01 natural sciences ,03 medical and health sciences ,Phylogenetics ,Genus ,Genetics ,Animals ,Clade ,Molecular Biology ,Phylogeny ,Ecology, Evolution, Behavior and Systematics ,Crows ,Phylogenetic tree ,Osteology ,Fossils ,Skull ,Australia ,DNA ,Sequence Analysis, DNA ,Cytochromes b ,Biological Evolution ,030104 developmental biology ,Taxon ,Ancient DNA ,Sequence Alignment ,New Zealand - Abstract
The relationships of the extinct New Zealand ravens (Corvus spp.) are poorly understood. We sequenced the mitogenomes of the two currently recognised species and found they were sister-taxa to a clade comprising the Australian raven, little raven, and forest raven (C.coronoides, C. mellori and C. tasmanicus respectively). The divergence between the New Zealand ravens and Australian raven clade occurred in the latest Pliocene, which coincides with the onset of glacial deforestation. We also found that the divergence between the two putative New Zealand species C. antipodum and C. moriorum probably occurred in the late Pleistocene making their separation as species untenable. Consequently, we consider Corax antipodum (Forbes, 1893) to be a subspecies of Corvus moriorum Forbes, 1892. We re-examine the osteological evidence that led 19th century researchers to assign the New Zealand taxa to a separate genus, and re-assess these features in light of our new phylogenetic hypotheses. Like previous researchers, we conclude that the morphology of the palate of C. moriorum is unique among the genus Corvus, and suggest this may be an adaptation for a specialist diet.
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- 2017
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18. Who, Where, What, Wren? Using Ancient DNA to Examine the Veracity of Museum Specimen Data: A Case Study of the New Zealand Rock Wren (Xenicus gilviventris)
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Bruce C. Robertson, Alan J. D. Tennyson, Lachie Scarsbrook, R. Paul Scofield, Kerry A. Weston, Nicolas J. Rawlence, and Alexander J. F. Verry
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0106 biological sciences ,0301 basic medicine ,Xenicus ,Population ,Species distribution ,Endangered species ,lcsh:Evolution ,translocation ,010603 evolutionary biology ,01 natural sciences ,museum skin ,03 medical and health sciences ,taxonomy ,lcsh:QH540-549.5 ,lcsh:QH359-425 ,education ,Endemism ,Ecology, Evolution, Behavior and Systematics ,education.field_of_study ,Ecology ,biology ,conservation ,biology.organism_classification ,Archaeology ,030104 developmental biology ,Geography ,Ancient DNA ,Type locality ,re-introduction ,lcsh:Ecology ,Xenicus gilviventris - Abstract
Museum specimens provide a record of past species distribution and are an increasingly important resource for conservation genetic research. The scientific value of these specimens depends upon the veracity of their associated data and can be compromised by inaccurate details; including taxonomic identity, collection locality, and collector. New Zealand contains many endemic species that have been driven to extinction or reduced to relict distributions following the arrival of humans and mammalian predators, including the Acanthisittid wrens (of which only two of the eight described species presently persist). One of these is the New Zealand rock wren (Xenicus gilviventris), currently classified as an endangered species and experiencing ongoing population declines. Here we analyze ancient DNA retrieved from New Zealand rock wren museum skins to establish the veracity of their recorded collection localities—New Zealand rock wrens exhibit strong north-south genetic structuring along the Southern Alps of New Zealand's South Island. We include the only specimen reportedly collected from New Zealand's North Island, outside the known range of New Zealand rock wrens, specimens collected by Henry Hamersley Travers, a collector known for poor record keeping and potentially fraudulent specimen data, and type specimens of proposed Xenicus taxa. Multiple instances of inaccurate collection locality were detected, including that of the New Zealand rock wren reportedly collected from the North Island, which matches individuals from the southern South Island. Syntypes of X. haasti, and a syntype of X. gilviventris clustered with individuals belonging to the northern New Zealand rock wren lineage. Our results suggest that New Zealand rock wrens have not been historically extirpated from New Zealand's North Island, and that caution must be taken when utilizing museum specimens to inform conservation management decisions. Additionally, we describe the type locality of both X. gilviventris and X. haasti, with genetic and historical evidence suggesting that the specimens used to describe these taxa were collected from the headwaters of the Rakaia River. This study demonstrates that ancient DNA analysis can add value to museum specimens by revealing incorrect specimen data and inform the conservation management and taxonomy of endangered species.
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- 2019
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19. Archival DNA reveals cryptic biodiversity within the Spotted Shag (Phalacrocorax punctatus) from New Zealand
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Matt J. Rayner, R. Paul Scofield, Tim G. Lovegrove, Alan J. D. Tennyson, Debbie Stoddart, Luke J. Easton, Jonathan M. Waters, Martyn Kennedy, Melanie J. Vermeulen, Nicolas J. Rawlence, and Hamish G. Spencer
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0106 biological sciences ,0301 basic medicine ,Phalacrocorax punctatus ,biology ,Biodiversity ,Zoology ,biology.organism_classification ,010603 evolutionary biology ,01 natural sciences ,03 medical and health sciences ,030104 developmental biology ,Archival dna ,Animal Science and Zoology ,Ecology, Evolution, Behavior and Systematics - Abstract
Genetic data are increasingly being used to prioritize species conservation in a fiscally constrained age of seemingly boundless conservation crises. Such data can also reveal previously cryptic biodiversity requiring further revision of conservation management guidelines. Using a combination of mitochondrial (control region) and nuclear (beta fibrinogen intron 7) DNA, and morphology, we reveal that the endemic New Zealand Spotted Shag (Phalacrocorax punctatus) complex exhibits phylogenetic structure that is decoupled from previously recorded qualitative morphological variation. Crucially, the most genetically distinct populations within P. punctatus are from northern New Zealand; recent surveys show that these populations, which house important genetic diversity within Spotted Shags, are in danger of being extirpated. In contrast, we find the previously phenotypically differentiated nominate (P. punctatus punctatus) and Blue (P. punctatus oliveri) Shag subspecies show no genetic and morphological separation, and are of least conservation concern.
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- 2019
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20. Evidence for a giant parrot from the Early Miocene of New Zealand
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Suzanne J. Hand, Vanesa L. De Pietri, Michael Archer, Trevor H. Worthy, and R. Paul Scofield
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0106 biological sciences ,0303 health sciences ,Fossils ,Fauna ,Palaeontology ,Zoology ,Biology ,Habroptila ,010603 evolutionary biology ,01 natural sciences ,Agricultural and Biological Sciences (miscellaneous) ,Biological Evolution ,Corrections ,03 medical and health sciences ,Taxon ,Parrots ,Genus ,Animals ,Psittaciformes ,General Agricultural and Biological Sciences ,Phylogeny ,030304 developmental biology ,New Zealand - Abstract
Insular avifaunas have repeatedly spawned evolutionary novelties in the form of unusually large, often flightless species. We report fossils from the Early Miocene St Bathans Fauna of New Zealand that attests to the former existence of a giant psittaciform, which is described as a new genus and species. The fossils are two incomplete tibiotarsi from a bird with an estimated mass of 7 kg, double that of the heaviest known parrot, the kakapo Strigops habroptila . These psittaciform fossils show that parrots join the growing group of avian taxa prone to giantism in insular species, currently restricted to palaeognaths, anatids, sylviornithids, columbids, aptornithids, ciconiids, tytonids, falconids and accipitrids.
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- 2019
21. History Repeats: Large Scale Synchronous Biological Turnover in Avifauna From the Plio-Pleistocene and Late Holocene of New Zealand
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R. Paul Scofield, Matt S. McGlone, Nicolas J. Rawlence, and Michael Knapp
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glacial ,0106 biological sciences ,0301 basic medicine ,Pleistocene ,lcsh:Evolution ,Biodiversity ,010603 evolutionary biology ,01 natural sciences ,03 medical and health sciences ,Phylogenetics ,lcsh:QH540-549.5 ,lcsh:QH359-425 ,avifauna ,Glacial period ,Ecology, Evolution, Behavior and Systematics ,Holocene ,Ecology ,Australia ,Plio-Pleistocene ,Gondwana ,030104 developmental biology ,Geography ,birds ,Biological dispersal ,lcsh:Ecology ,New Zealand - Abstract
New Zealand’s unique biodiversity has long been considered both the product of a ‘Moa’s Ark’ isolationist experiment since the break-up of Gondwana and the result of millions of years of transoceanic migration. Increasingly, palaeontological and genetic evidence suggest that much of New Zealand avifauna results from dispersal from Australia. We synthesise a growing number of evolutionary genetic studies to show a previously unrecognised clustering of divergence times in Australian and New Zealand bird species pairs, across the avian phylogeny, around 2.5 million years ago at the beginning of the Pleistocene. The timing coincides with the dramatic environmental changes associated with the Plio-Pleistocene transition. Intriguingly, recent anthropogenic impacts and environmental modifications are replicating in some important ways conditions during the Pleistocene glacial periods, resulting in a new wave of avian ‘native invaders’ into New Zealand.
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- 2019
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22. DNA barcoding a unique avifauna: an important tool for evolution, systematics and conservation
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Jacqueline Tizard, Allan J. Baker, Tjard Bergmann, David M. Lambert, Craig D. Millar, John Waugh, R. Paul Scofield, Oliver Haddrath, Les Christidis, Janette A Norman, Erika Tavares, Selina Patel, and B. J. Gill
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0106 biological sciences ,0301 basic medicine ,Systematics ,Conservation of Natural Resources ,Entomology ,Evolution ,DNA barcodes ,Conservation ,Biology ,Subspecies ,010603 evolutionary biology ,01 natural sciences ,DNA barcoding ,Coalescent theory ,Birds ,Electron Transport Complex IV ,COI ,03 medical and health sciences ,Species Specificity ,QH359-425 ,Animals ,DNA Barcoding, Taxonomic ,Cytochrome c oxidase subunit I ,New Zealand birds ,Phylogeny ,Ecology, Evolution, Behavior and Systematics ,Islands ,Geography ,Phylogenetic tree ,15. Life on land ,Biological Evolution ,030104 developmental biology ,Evolutionary biology ,GenBank ,Specimen identification ,New Zealand ,Research Article - Abstract
Background DNA barcoding utilises a standardised region of the cytochrome c oxidase I (COI) gene to identify specimens to the species level. It has proven to be an effective tool for identification of avian samples. The unique island avifauna of New Zealand is taxonomically and evolutionarily distinct. We analysed COI sequence data in order to determine if DNA barcoding could accurately identify New Zealand birds. Results We sequenced 928 specimens from 180 species. Additional Genbank sequences expanded the dataset to 1416 sequences from 211 of the estimated 236 New Zealand species. Furthermore, to improve the assessment of genetic variation in non-endemic species, and to assess the overall accuracy of our approach, sequences from 404 specimens collected outside of New Zealand were also included in our analyses. Of the 191 species represented by multiple sequences, 88.5% could be successfully identified by their DNA barcodes. This is likely a conservative estimate of the power of DNA barcoding in New Zealand, given our extensive geographic sampling. The majority of the 13 groups that could not be distinguished contain recently diverged taxa, indicating incomplete lineage sorting and in some cases hybridisation. In contrast, 16 species showed evidence of distinct intra-species lineages, some of these corresponding to recognised subspecies. For species identification purposes a character-based method was more successful than distance and phylogenetic tree-based methods. Conclusions DNA barcodes accurately identify most New Zealand bird species. However, low levels of COI sequence divergence in some recently diverged taxa limit the identification power of DNA barcoding. A small number of currently recognised species would benefit from further systematic investigations. The reference database and analysis presented will provide valuable insights into the evolution, systematics and conservation of New Zealand birds. Electronic supplementary material The online version of this article (10.1186/s12862-019-1346-y) contains supplementary material, which is available to authorized users.
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- 2019
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23. Mitochondrial Genomes from New Zealand’s Extinct Adzebills (Aves: Aptornithidae: Aptornis) Support a Sister-Taxon Relationship with the Afro-Madagascan Sarothruridae
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Kieren J. Mitchell, R. Paul Scofield, Alan Cooper, Alexander P. Boast, Peter Houde, Brendan Chapman, Michael Bunce, Trevor H. Worthy, Alan J. D. Tennyson, and Michael B. Herrera
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0106 biological sciences ,Adzebill ,Zoology ,010603 evolutionary biology ,01 natural sciences ,03 medical and health sciences ,Phylogenetics ,Vicariance ,ancient DNA ,lcsh:QH301-705.5 ,030304 developmental biology ,Nature and Landscape Conservation ,0303 health sciences ,Subfossil ,Aptornis ,Ecology ,biology ,Ecological Modeling ,biology.organism_classification ,Agricultural and Biological Sciences (miscellaneous) ,phylogenetics ,Ancient DNA ,Sister group ,lcsh:Biology (General) ,Kiwi ,Biological dispersal ,New Zealand - Abstract
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&ndash, 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&rsquo, s near relatives were formerly more widespread. In addition, our estimate for the divergence time between the two Quaternary adzebill species (0.2&ndash, 2.3 Ma) coincides with the emergence of a land-bridge between the North and South islands of New Zealand (ca. 1.5&ndash, 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.
- Published
- 2019
24. Genetic and morphological evidence for two species ofLeucocarboshag (Aves, Pelecaniformes, Phalacrocoracidae) from southern South Island of New Zealand
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Alan J. D. Tennyson, Martyn Kennedy, Eric Pasquet, Jonathan M. Waters, Chris Lalas, Hamish G. Spencer, Cody Fraser, Luke J. Easton, R. Paul Scofield, Nicolas J. Rawlence, and Mark Adams
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0106 biological sciences ,0301 basic medicine ,Pelecaniformes ,Morphometrics ,biology ,Phylogenetic tree ,Osteology ,Zoology ,biology.organism_classification ,010603 evolutionary biology ,01 natural sciences ,03 medical and health sciences ,Paleontology ,030104 developmental biology ,Ancient DNA ,Sister group ,biology.animal ,Animal Science and Zoology ,Seabird ,Clade ,Ecology, Evolution, Behavior and Systematics - Abstract
Leucocarbo shags are a species-rich seabird clade exhibiting a southern circumpolar distribution. New Zealand's endemic Stewart Island shag, Leucocarbo chalconotus (G. R. Gray, 1845), comprises two regional groups (Otago and Foveaux Strait) that show consistent differences in relative frequencies between pied (black and white) and bronze (wholly dark) plumages, the extent and colour of facial carunculation, body size (based on postcranial morphometrics), and breeding season. Moreover, previous genetic research on modern and historical specimens utilizing mitochondrial DNA control-region sequences has also shown that the Otago and Foveaux lineages may not be sister taxa; instead, in several analyses the Otago lineage is sister to the endemic Chatham Island shag, Leucocarbo onslowi (Forbes, 1893). We present new ancient DNA analyses of the type specimens for the Otago and Foveaux Strait lineages of L. chalconotus, including a phylogenetic reanalysis of the available ancient, historical, and modern control-region sequence data for these lineages (including L. onslowi), and additional statistical analyses incorporating new morphometric characters. These analyses indicate that under the diagnosable species concept the two lineages of Stewart Island shag represent two separate species, which we now recognize as the Otago shag, L. chalconotus (G. R. Gray, 1845), and the Foveaux shag, Leucocarbo stewarti (Ogilvie-Grant, 1898).
- Published
- 2016
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25. First monk seal from the Southern Hemisphere rewrites the evolutionary history of true seals
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R. Paul Scofield, Alan J. D. Tennyson, Erich M. G. Fitzgerald, Alistair R. Evans, Justin W. Adams, James P. Rule, and Felix G. Marx
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0106 biological sciences ,Seal (emblem) ,0303 health sciences ,General Immunology and Microbiology ,Ecology ,Biogeography ,Equator ,General Medicine ,010603 evolutionary biology ,01 natural sciences ,General Biochemistry, Genetics and Molecular Biology ,03 medical and health sciences ,Geography ,Phylogenetics ,Tribe ,General Agricultural and Biological Sciences ,Southern Hemisphere ,030304 developmental biology ,General Environmental Science - Abstract
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.
- Published
- 2020
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26. First Complete Wing of a Stem Group Sphenisciform from the Paleocene of New Zealand Sheds Light on the Evolution of the Penguin Flipper
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Al A. Mannering, R. Paul Scofield, Leigh Love, Joseph J. Bevitt, Vanesa L. De Pietri, and Gerald Mayr
- Subjects
0106 biological sciences ,010506 paleontology ,Greensand ,Foraging ,Zoology ,muriwaimanu tuatahi ,010603 evolutionary biology ,01 natural sciences ,Predation ,Mandible (arthropod mouthpart) ,evolution ,Muriwaimanu tuatahi ,Sphenisciformes ,lcsh:QH301-705.5 ,wing-propelled diving ,0105 earth and related environmental sciences ,Nature and Landscape Conservation ,fossil birds ,Wing ,Ecology ,biology ,Ecological Modeling ,biology.organism_classification ,Agricultural and Biological Sciences (miscellaneous) ,lcsh:Biology (General) ,Feather ,visual_art ,visual_art.visual_art_medium ,Flipper ,Aves - Abstract
We describe a partial skeleton of a stem group penguin from the Waipara Greensand in New Zealand, which is tentatively assigned to Muriwaimanu tuatahi. The fossil includes the first complete wing of a Paleocene penguin and informs on previously unknown features of the mandible and tibiotarsus of small-sized Sphenisciformes from the Waipara Greensand. The wing is distinguished by important features from that of all geologically younger Sphenisciformes and documents an early stage in the evolution of wing-propelled diving in penguins. In particular, the wing of the new fossil exhibits a well-developed alular phalanx and the distal phalanges are not flattened. Because the wing phalanges resemble those of volant birds, we consider it likely that the wing feathers remained differentiated into functional categories and were not short and scale-like as they are in extant penguins. Even though the flippers of geologically younger penguins may favor survival in extremely cold climates, they are likely to have been shaped by hydrodynamic demands. Possible selective drivers include a diminished importance of the hindlimbs in subaquatic propulsion, new foraging strategies (the caudal end of the mandible of the new fossil distinctly differs from that of extant penguins), or increased predation by marine mammals.
- Published
- 2020
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27. Ancient DNA of crested penguins: Testing for temporal genetic shifts in the world's most diverse penguin clade
- Author
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Theresa L. Cole, R. Paul Scofield, Alan J. D. Tennyson, Jonathan M. Waters, Ursula Ellenberg, David R. Thompson, Jamie R. Wood, Kyle W. Morrison, Thomas Mattern, Nicolas J. Rawlence, Colin M. Miskelly, Nicolas Dussex, and David M. Houston
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0106 biological sciences ,0301 basic medicine ,Time Factors ,Demographic history ,Range (biology) ,Population Dynamics ,Biodiversity ,Zoology ,Biology ,010603 evolutionary biology ,01 natural sciences ,Coalescent theory ,Evolutionsbiologi ,Electron Transport Complex IV ,03 medical and health sciences ,Genetics ,Animals ,Humans ,Crested penguin ,DNA, Ancient ,Molecular Biology ,Ecology, Evolution, Behavior and Systematics ,Phylogeny ,Evolutionary Biology ,Genetic diversity ,geography ,geography.geographical_feature_category ,Pacific Ocean ,Fossils ,Genetic Variation ,Bayes Theorem ,biology.organism_classification ,Spheniscidae ,030104 developmental biology ,Ancient DNA ,Haplotypes ,Archipelago ,New Zealand - Abstract
Human impacts have substantially reduced avian biodiversity in many parts of the world, particularly on isolated islands of the Pacific Ocean. The New Zealand archipelago, including its five subantarctic island groups, holds breeding grounds for a third of the world's penguin species, including several representatives of the diverse crested penguin genus Eudyptes. While this species-rich genus has been little studied genetically, recent population estimates indicate that several Eudyptes taxa are experiencing demographic declines. Although crested penguins are currently limited to southern regions of the New Zealand archipelago, prehistoric fossil and archaeological deposits suggest a wider distribution during prehistoric times, with breeding ranges perhaps extending to the North Island. Here, we analyse ancient, historic and modern DNA sequences to explore two hypotheses regarding the recent history of Eudyptes in New Zealand, testing for (1) human-driven extinction of Eudyptes lineages; and (2) reduced genetic diversity in surviving lineages. From 83 prehistoric bone samples, each tentatively identified as 'Eudyptes spp.', we genetically identified six prehistoric penguin taxa from mainland New Zealand, including one previously undescribed genetic lineage. Moreover, our Bayesian coalescent analyses indicated that, while the range of Fiordland crested penguin (E. pachyrhynchus) may have contracted markedly over the last millennium, genetic DNA diversity within this lineage has remained relatively constant. This result contrasts with human-driven biodiversity reductions previously detected in several New Zealand coastal vertebrate taxa.
- Published
- 2018
28. On the taxonomic composition and phylogenetic affinities of the recently proposed clade Vegaviidae Agnolín et al., 2017 ‒ neornithine birds from the Upper Cretaceous of the Southern Hemisphere
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Gerald Mayr, Trevor H. Worthy, R. Paul Scofield, and Vanesa L. De Pietri
- Subjects
0106 biological sciences ,010506 paleontology ,biology ,Australornis ,Paleontology ,Zoology ,Crown group ,biology.organism_classification ,Polarornis ,010603 evolutionary biology ,01 natural sciences ,Cretaceous ,Gaviiformes ,Vegavis ,Taxon ,Fossil birds ,Taxonomy (biology) ,Aves ,Phylogeny ,0105 earth and related environmental sciences ,Mesozoic ,Taxonomy - Abstract
© 2018 Elsevier. This manuscript version is made available under the CC-BY-NC-ND 4.0 license: http://creativecommons.org/licenses/by-nc-nd/4.0/ This author accepted manuscript is made available following 24 month embargo from date of publication (Feb 2018) in accordance with the publisher’s archiving policy, Polarornis and Vegavis from the Upper Cretaceous of Antarctica are among the few Mesozoic birds from the Southern Hemisphere. In the original descriptions, they were assigned to two widely disparate avian clades, that is, Gaviiformes and crown group Anseriformes, respectively. In a recent publication, however, specimens referred to both taxa were classified into a new higher-level taxon, Vegaviidae, to which various other late Mesozoic and early Cenozoic avian taxa were also assigned. Here, we detail that classification into Vegaviidae is poorly supported for most of these latter fossils, which is particularly true for Australornis lovei and an unnamed phaethontiform fossil from the Waipara Greensand in New Zealand. Plesiomorphic traits of the pterygoid and the mandible clearly show that Vegavis is not a representative of crown group Anseriformes, and we furthermore point out that even anseriform or galloanserine affinities of Vegaviidae have not been firmly established.
- Published
- 2018
29. A new species of lapwing (Charadriidae: Vanellus) from the late Pliocene of central Australia
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Vanesa L. De Pietri, Trevor H. Worthy, Gavin J. Prideaux, and R. Paul Scofield
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0106 biological sciences ,010506 paleontology ,biology ,Plover ,Fauna ,Zoology ,Subspecies ,biology.organism_classification ,010603 evolutionary biology ,01 natural sciences ,Monophyly ,Vanellus ,Geography ,Animal Science and Zoology ,Ecology, Evolution, Behavior and Systematics ,Charadriidae ,Vanellus miles ,0105 earth and related environmental sciences ,Nature and Landscape Conservation ,Lapwing - Abstract
We describe a new species of lapwing plover from the late Pliocene Kanunka Local Fauna of South Australia (3.6–2.6 mya).Vanellus liffyae sp. nov. is based on an almost complete coracoid, which is most similar in morphology to that of the Masked Lapwing (Vanellus miles). Nevertheless, it differs from this species and from the Banded Lapwing (V. tricolor), the only other extant resident Australian species, in size and other morphological details. A monophyletic Australasian group including V. tricolor and the two subspecies of V. miles (i.e. miles and novaehollandiae) had been previously recovered from phenotypic data and is here supported by analyses of COI data. We conclude that, based on the material available for study, Vanellus liffyae sp. nov. is a member of the Australasian clade, which was present in Australia minimally by 3 mya. How Vanellus liffyae sp. nov. relates to the extant taxa within this clade, however, is still unclear. https://rn:lsid:zoobank.org:pub:55AE3295-F3D6-40FC-810C-8277A75696E0
- Published
- 2018
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30. A critical evaluation of how ancient DNA bulk bone metabarcoding complements traditional morphological analysis of fossil assemblages
- Author
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Dáithí C. Murray, Diana A. Fusco, James Haile, Alicia Grealy, Matthew C. McDowell, Gavin J. Prideaux, R. Paul Scofield, and Michael Bunce
- Subjects
0106 biological sciences ,0303 health sciences ,Archeology ,Global and Planetary Change ,Extinction ,Range (biology) ,Ecology ,Biodiversity ,Endangered species ,Sampling (statistics) ,Geology ,Biology ,010603 evolutionary biology ,01 natural sciences ,DNA sequencing ,03 medical and health sciences ,Ancient DNA ,Taxon ,Ecology, Evolution, Behavior and Systematics ,030304 developmental biology - Abstract
When pooled for extraction as a bulk sample, the DNA within morphologically unidentifiable fossil bones can, using next-generation sequencing, yield valuable taxonomic data. This method has been proposed as a means to rapidly and cost-effectively assess general ancient DNA preservation at a site, and to investigate temporal and spatial changes in biodiversity; however, several caveats have yet to be considered. We critically evaluated the bulk bone metabarcoding (BBM) method in terms of its: (i) repeatability, by quantifying sampling and technical variance through a nested experimental design containing sub-samples and replicates at several stages; (ii) accuracy, by comparing morphological and molecular family-level identifications; and (iii) overall utility, by applying the approach to two independent Holocene fossil deposits, Bat Cave (Kangaroo Island, Australia) and Finsch's Folly (Canterbury, New Zealand). For both sites, bone and bone powder sub-sampling were found to contribute significantly to variance in molecularly identified family assemblage, while the contribution of library preparation and sequencing was almost negligible. Nevertheless, total variance was small. Sampling over 80% fewer bones than was required to morphologically identify the taxonomic assemblages, we found that the families identified molecularly are a subset of the families identified morphologically and, for the most part, represent the most abundant families in the fossil record. In addition, we detected a range of extinct, extant and endangered taxa, including some that are rare in the fossil record. Given the relatively low sampling effort of the BBM approach compared with morphological approaches, these results suggest that BBM is largely consistent, accurate, sensitive, and therefore widely applicable. Furthermore, we assessed the overall benefits and caveats of the method, and suggest a workflow for palaeontologists, archaeologists, and geneticists that will help mitigate these caveats. Our results show that DNA analysis of bulk bone samples can be a universally useful tool for studying past biodiversity, when integrated with existing morphology-based approaches. Despite several limitations that remain, the BBM method offers a cost-effective and efficient way of studying fossil assemblages, offering complementary insights into evolution, extinction, and conservation.
- Published
- 2015
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31. Wading a lost southern connection: Miocene fossils from New Zealand reveal a new lineage of shorebirds (Charadriiformes) linking Gondwanan avifaunas
- Author
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R. Paul Scofield, Suzanne J. Hand, Trevor H. Worthy, Alan J. D. Tennyson, and Vanesa L. De Pietri
- Subjects
0106 biological sciences ,010506 paleontology ,Charadriiformes ,Lineage (genetic) ,biology ,Paleontology ,Postcrania ,Zoology ,biology.organism_classification ,010603 evolutionary biology ,01 natural sciences ,Taxon ,Sister group ,Vicariance ,Pedionomidae ,Clade ,0105 earth and related environmental sciences - Abstract
Author version made available following 12 month embargo from date of publication (12 October 2015) in accordance with Publisher copyright policy., An endemic and previously unknown lineage of shorebirds (Charadriiformes: Scolopaci) is described from early Miocene (19 16 Ma) deposits of New Zealand. Hakawai melvillei gen. et sp. nov. represents the first pre-Quaternary record of the clade in New Zealand and offers the earliest evidence of Australasian breeding for any member of the Scolopaci. Hakawai melvillei was a representative of the clade that comprises the South American seedsnipes (Thinocoridae) and the Australian Plains-wanderer (Pedionomidae), and presumed derived features of its postcranial skeleton indicate a sister taxon relationship to Australian pedionomids. Our findings reinforce that terrestrial adaptations in seedsnipes and the Plains-wanderer are convergent as previously proposed, and support an ancestral wading ecology for the clade. Although vicariance events may have contributed to the split between pedionomids and H. melvillei, the proposed sister taxon relationship between these taxa indicates that the split of this lineage from
- Published
- 2015
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32. A Paleocene penguin from New Zealand substantiates multiple origins of gigantism in fossil Sphenisciformes
- Author
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Alan J. D. Tennyson, Gerald Mayr, Vanesa L. De Pietri, and R. Paul Scofield
- Subjects
0106 biological sciences ,010506 paleontology ,Science ,General Physics and Astronomy ,Zoology ,Biology ,Body size ,010603 evolutionary biology ,01 natural sciences ,Article ,General Biochemistry, Genetics and Molecular Biology ,Extant taxon ,ddc:590 ,medicine ,Animals ,Body Size ,Sphenisciformes ,lcsh:Science ,Clade ,Phylogeny ,0105 earth and related environmental sciences ,Multidisciplinary ,Fossils ,Ecology ,General Chemistry ,medicine.disease ,Biological Evolution ,Spheniscidae ,Gigantism ,Taxon ,lcsh:Q ,Taxonomy (biology) ,Cenozoic ,New Zealand - Abstract
One of the notable features of penguin evolution is the occurrence of very large species in the early Cenozoic, whose body size greatly exceeded that of the largest extant penguins. Here we describe a new giant species from the late Paleocene of New Zealand that documents the very early evolution of large body size in penguins. Kumimanu biceae, n. gen. et sp. is larger than all other fossil penguins that have substantial skeletal portions preserved. Several plesiomorphic features place the new species outside a clade including all post-Paleocene giant penguins. It is phylogenetically separated from giant Eocene and Oligocene penguin species by various smaller taxa, which indicates multiple origins of giant size in penguin evolution. That a penguin rivaling the largest previously known species existed in the Paleocene suggests that gigantism in penguins arose shortly after these birds became flightless divers. Our study therefore strengthens previous suggestions that the absence of very large penguins today is likely due to the Oligo-Miocene radiation of marine mammals., The oldest known penguin fossils date to approximately 62 million years ago. Here, Mayr et al. describe Kumimanu biceae, an extinct penguin from approximately 55–60 million years ago, which represents an independent origin of giant size soon after the evolutionary transition from flight to diving.
- Published
- 2017
33. A new species of extinct Late Quaternary giant tortoise from Hispaniola
- Author
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Samuel T. Turvey, Jorge L. Brocca, Juan Almonte, Sandra D. Chapman, R. Paul Scofield, and James P. Hansford
- Subjects
0106 biological sciences ,0301 basic medicine ,Tortoise ,Biodiversity ,Biology ,010603 evolutionary biology ,01 natural sciences ,03 medical and health sciences ,Cave ,Refugium (population biology) ,Megafauna ,Animals ,Ecology, Evolution, Behavior and Systematics ,Ecosystem ,geography ,geography.geographical_feature_category ,Subfossil ,Ecology ,Fossils ,Dominican Republic ,biology.organism_classification ,Biological Evolution ,Turtles ,030104 developmental biology ,Chelonoidis ,Animal Science and Zoology ,Quaternary - Abstract
Insular giant tortoise diversity has been depleted by Late Quaternary extinctions, but the taxonomic status of many extinct populations remains poorly understood due to limited available fossil or subfossil material, hindering our ability to reconstruct Quaternary island biotas and environments. Giant tortoises are absent from current-day insular Caribbean ecosystems, but tortoise remains from Quaternary deposits indicate the former widespread occurrence of these animals across the northern Caribbean. We report new Quaternary giant tortoise material from several cave sites in Pedernales Province, southern Dominican Republic, Hispaniola, representing at least seven individuals, which we describe as Chelonoidis marcanoi sp. nov. Although giant tortoise material was first reported from the Quaternary record of Hispaniola almost 35 years ago, tortoises are absent from most Quaternary deposits on the island, which has been studied extensively over the past century. The surprising abundance of giant tortoise remains in both vertical and horizontal caves in Hispaniola’s semi-arid ecoregion may indicate that this species was adapted to open dry habitats and became restricted to a habitat refugium in southeastern Hispaniola following climatic-driven environmental change at the Pleistocene-Holocene boundary. Hispaniola’s dry forest ecosystem may therefore have been shaped by giant tortoises for much of its evolutionary history.
- Published
- 2017
34. Ancient DNA and morphometric analysis reveal extinction and replacement of New Zealand's unique black swans
- Author
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Alan J. D. Tennyson, Luke J. Easton, Jonathan M. Waters, Afroditi Kardamaki, Nicolas J. Rawlence, and R. Paul Scofield
- Subjects
0106 biological sciences ,0301 basic medicine ,Species complex ,Evolution ,Lineage (evolution) ,Biology ,Extinction, Biological ,010603 evolutionary biology ,01 natural sciences ,Black swan theory ,General Biochemistry, Genetics and Molecular Biology ,03 medical and health sciences ,Cygnus atratus ,Megafauna ,Anseriformes ,symbols.heraldic_charge ,Animals ,Humans ,DNA, Ancient ,General Environmental Science ,Islands ,Extinction ,General Immunology and Microbiology ,Osteology ,Ecology ,Australia ,General Medicine ,030104 developmental biology ,Ancient DNA ,symbols ,General Agricultural and Biological Sciences ,New Zealand - Abstract
Prehistoric human impacts on megafaunal populations have dramatically reshaped ecosystems worldwide. However, the effects of human exploitation on smaller species, such as anatids (ducks, geese, and swans) are less clear. In this study we apply ancient DNA and osteological approaches to reassess the history of Australasia's iconic black swans ( Cygnus atratus ) including the palaeo-behaviour of prehistoric populations. Our study shows that at the time of human colonization, New Zealand housed a genetically, morphologically, and potentially ecologically distinct swan lineage ( C. sumnerensis , Poūwa), divergent from modern (Australian) C. atratus . Morphological analyses indicate C. sumnerensis exhibited classic signs of the ‘island rule’ effect, being larger, and likely flight-reduced compared to C. atratus . Our research reveals sudden extinction and replacement events within this anatid species complex, coinciding with recent human colonization of New Zealand. This research highlights the role of anthropogenic processes in rapidly reshaping island ecosystems and raises new questions for avian conservation, ecosystem re-wilding, and de-extinction.
- Published
- 2017
35. Bone histology, phylogeny, and palaeognathous birds (Aves: Palaeognathae)
- Author
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Jorge Cubo, Hayat Lamrous, Lucas J. Legendre, Armand de Ricqlès, Alan J. D. Tennyson, Estelle Bourdon, and R. Paul Scofield
- Subjects
0106 biological sciences ,Palaeognathae ,0303 health sciences ,Phylogenetic tree ,Zoology ,Histology ,Biology ,biology.organism_classification ,010603 evolutionary biology ,01 natural sciences ,Signal on ,03 medical and health sciences ,Sample size determination ,Phylogenetics ,Transect ,Ecology, Evolution, Behavior and Systematics ,030304 developmental biology - Abstract
The presence of a phylogenetic signal in the variation of osteohistological features has been recently debated in the literature. Previous studies have found a significant signal for some features, but these results were obtained on a small amount of characters and a reduced sample. Here we perform a comprehensive study in which we quantify the phylogenetic signal on 62 osteohistological features in an exhaustive sample of palaeognathous birds. We used four different estimators to measure phylogenetic signal – Pagel's λ, Abouheif's Cmean, Blomberg's K, and Diniz-Filho's phylogenetic eigenvector regressions PVR – and four topologies taken from the literature. Bone size and bone vascular density exhibit a strong phylogenetic signal, whereas all but four of the remaining features measured at the histological level – cellular size in caudal and medial transects of femora, and proportion of oblique vascular canals in rostral and caudal transects of tibiotarsi – exhibit a weaker signal. We also found that the impact of the topologies used in the analyses is very low compared with that of sample size. We conclude that the analysis of a comprehensive sample is crucial to obtain reliable quantifications of the phylogenetic signal. © 2014 The Linnean Society of London, Biological Journal of the Linnean Society, 2014, 112, 688–700.
- Published
- 2014
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36. A new fossil from the mid-Paleocene of New Zealand reveals an unexpected diversity of world's oldest penguins
- Author
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Gerald Mayr, R. Paul Scofield, and Vanesa L. De Pietri
- Subjects
0106 biological sciences ,010506 paleontology ,Greensand ,Zoology ,Tarsometatarsus ,010603 evolutionary biology ,01 natural sciences ,Animals ,Body Size ,Leg Bones ,Sphenisciformes ,Ecology, Evolution, Behavior and Systematics ,Phylogeny ,0105 earth and related environmental sciences ,Crossvallia ,biology ,Ecology ,Fossils ,General Medicine ,Biodiversity ,biology.organism_classification ,Spheniscidae ,Cretaceous ,Waimanu ,Anthropornis ,Type locality ,New Zealand - Abstract
We describe leg bones of a giant penguin from the mid-Paleocene Waipara Greensand of New Zealand. The specimens were found at the type locality of Waimanu manneringi and together with this species they constitute the oldest penguin fossils known to date. Tarsometatarsus dimensions indicate a species that reached the size of Anthropornis nordenskjoeldi, one of the largest known penguin species. Stem group penguins therefore attained a giant size very early in their evolution, with this gigantism existing for more than 30 million years. The new fossils are from a species that is phylogenetically more derived than Waimanu, and the unexpected coexistence of Waimanu with more derived stem group Sphenisciformes documents a previously unknown diversity amongst the world’s oldest penguins. The characteristic tarsometatarsus shape of penguins evolved early on, and the significant morphological disparity between Waimanu and the new fossil conflicts with recent Paleocene divergence estimates for penguins, suggesting an older, Late Cretaceous, origin.
- Published
- 2016
37. Phylogenetic relationships and terrestrial adaptations of the extinct laughing owl,Sceloglaux albifacies(Aves: Strigidae)
- Author
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Vanesa L. De Pietri, Nicolas J. Rawlence, Jamie R. Wood, Kieren J. Mitchell, Alan Cooper, and R. Paul Scofield
- Subjects
0106 biological sciences ,0301 basic medicine ,biology ,Osteology ,Sceloglaux albifacies ,Zoology ,biology.organism_classification ,010603 evolutionary biology ,01 natural sciences ,Predation ,Ninox rudolfi ,03 medical and health sciences ,030104 developmental biology ,Sister group ,Animal Science and Zoology ,Taxonomy (biology) ,Ninox ,Ecology, Evolution, Behavior and Systematics ,Ninox novaeseelandiae - Abstract
The taxonomic affinities of the monotypic owl genus Sceloglaux Kaup, 1848 have been widely debated. Here, we present a high-coverage mitogenome for the sole member of the genus, New Zealand's extinct laughing owl (Sceloglaux albifacies Gray, 1845), and assess its phylogenetic relationships. Our results provide strong support for Sceloglaux being nested within Ninox Hodgson, 1837, as sister taxon to the clade containing the barking owl (Ninox connivens Latham, 1801), Sumba boobook (Ninox rudolfi Meyer, 1882), and morepork (Ninox novaeseelandiae Gmelin, 1788). Accordingly, we synonymize Sceloglaux with Ninox, and recommend that the laughing owl hereafter be referred to as Ninox albifacies. Osteological analyses and a comparison of the wing and leg proportions of the laughing owl with those of other owls supports Gould's (1865) contention that it was largely a terrestrial owl, and predominantly caught prey on the ground. This is further supported by the relatively high abundance of terrestrial prey remains preserved in sediment deposits at former laughing owl nest sites.
- Published
- 2016
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38. Morphological, behavioural, and genetic evidence supports reinstatement of full species status for the grey-faced petrel,Pterodroma macroptera gouldi(Procellariiformes: Procellariidae)
- Author
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Hayley A. Lawrence, Dianne Gleeson, Graeme A. Taylor, Jamie R. Wood, Phil O'b. Lyver, and R. Paul Scofield
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0106 biological sciences ,0301 basic medicine ,biology ,Cytochrome b ,Zoology ,Petrel ,Procellariidae ,Subspecies ,Pterodroma lessonii ,biology.organism_classification ,010603 evolutionary biology ,01 natural sciences ,03 medical and health sciences ,030104 developmental biology ,Procellariiformes ,biology.animal ,Animal Science and Zoology ,Seabird ,Pterodroma macroptera ,Ecology, Evolution, Behavior and Systematics - Abstract
Although described as a distinct species in 1869, for more than a century now New Zealand's grey-faced petrel (Pterodroma macroptera gouldi Hutton, 1869) has been regarded as a subspecies of the great-winged petrel (P. macroptera A. Smith, 1840). However, several authors have recently questioned whether the taxon once again deserves full species status. Here, we demonstrate that the grey-faced petrel is sufficiently distinct in multiple facets of its biology (including mitochondrial DNA, plumage variation, morphometrics, osteology, vocalizations, external parasites, and feeding and breeding biology) to warrant reinstatement of full species status under the morphological, phylogenetic, and potentially biological species concepts. Moreover, we present new evidence from mitochondrial DNA (cytochrome c oxidase subunit 1 and cytochrome b) that suggests the great-winged petrel is actually more closely related to the white-headed petrel (Pterodroma lessonii Garnot, 1826) than to the grey-faced petrel. The reclassification of grey-faced petrel to full species status raises the degree of seabird endemism in New Zealand to 43%, emphasising the status of the archipelago as a hotspot for seabird diversity.
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- 2016
- Full Text
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39. Human-mediated extirpation of the unique Chatham Islands sea lion and implications for the conservation management of remaining New Zealand sea lion populations
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Justin J. Maxwell, Michael Knapp, Bruce C. Robertson, Catherine J. Collins, Alan J. D. Tennyson, Katherine Ann Horsburgh, Jo-Ann L. Stanton, Jonathan M. Waters, Christian N. Anderson, Nicolas J. Rawlence, Elizabeth Matisoo-Smith, Ian F. C. Smith, and R. Paul Scofield
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0106 biological sciences ,0301 basic medicine ,Conservation of Natural Resources ,Population ,Biodiversity ,Fisheries ,Biology ,Extinction, Biological ,010603 evolutionary biology ,01 natural sciences ,DNA, Mitochondrial ,03 medical and health sciences ,Megafauna ,Genetics ,Animals ,Humans ,Human Activities ,DNA, Ancient ,education ,Ecology, Evolution, Behavior and Systematics ,Phocarctos hookeri ,Islands ,education.field_of_study ,Ecology ,biology.organism_classification ,Sea Lions ,Bycatch ,Population decline ,030104 developmental biology ,Ancient DNA ,Mainland ,New Zealand - Abstract
While terrestrial megafaunal extinctions have been well characterized worldwide, our understanding of declines in marine megafauna remains limited. Here, we use ancient DNA analyses of prehistoric (
- Published
- 2016
40. Moa diet fits the bill: virtual reconstruction incorporating mummified remains and prediction of biomechanical performance in avian giants
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R. Paul Scofield, William C. H. Parr, Marie R. G. Attard, Peter Johnston, Trevor H. Worthy, Stephen Wroe, and Laura A. B. Wilson
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0106 biological sciences ,0301 basic medicine ,Range (biology) ,Introduced species ,Extinction, Biological ,010603 evolutionary biology ,01 natural sciences ,General Biochemistry, Genetics and Molecular Biology ,Birds ,03 medical and health sciences ,Imaging, Three-Dimensional ,Species Specificity ,Animals ,Herbivory ,Research Articles ,General Environmental Science ,Extinction ,General Immunology and Microbiology ,biology ,Ecology ,Fossils ,Skull ,Niche differentiation ,symbols.heraldic_supporter ,General Medicine ,15. Life on land ,biology.organism_classification ,Biomechanical Phenomena ,030104 developmental biology ,Habitat ,Evolutionary biology ,symbols ,Dromaius novaehollandiae ,General Agricultural and Biological Sciences ,Upland moa ,Ratite ,New Zealand - Abstract
The moa (Dinornithiformes) are large to gigantic extinct terrestrial birds of New Zealand. Knowledge about niche partitioning, feeding mode and preference among moa species is limited, hampering palaeoecological reconstruction and evaluation of the impacts of their extinction on remnant native biota, or the viability of exotic species as proposed ecological ‘surrogates'. Here we apply three-dimensional finite-element analysis to compare the biomechanical performance of skulls from five of the six moa genera, and two extant ratites, to predict the range of moa feeding behaviours relative to each other and to living relatives. Mechanical performance during biting was compared using simulations of the birds clipping twigs based on muscle reconstruction of mummified moa remains. Other simulated food acquisition strategies included lateral shaking, pullback and dorsoventral movement of the skull. We found evidence for limited overlap in biomechanical performance between the extant emu (Dromaius novaehollandiae) and extinct upland moa (Megalapteryx didinus) based on similarities in mandibular stress distribution in two loading cases, but overall our findings suggest that moa species exploited their habitats in different ways, relative to both each other and extant ratites. The broad range of feeding strategies used by moa, as inferred from interspecific differences in biomechanical performance of the skull, provides insight into mechanisms that facilitated high diversities of these avian herbivores in prehistoric New Zealand.
- Published
- 2016
41. The unexpected survival of an ancient lineage of anseriform birds into the Neogene of Australia: the youngest record of Presbyornithidae
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Vanesa L. De Pietri, Nikita V. Zelenkov, R. Paul Scofield, Walter E. Boles, and Trevor H. Worthy
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0106 biological sciences ,010506 paleontology ,Charadriiformes ,food.ingredient ,Zoology ,Tarsometatarsus ,Context (language use) ,010603 evolutionary biology ,01 natural sciences ,wilaru tedfordi ,Wilaru ,food ,miocene ,Waterfowl ,Earth Science ,lcsh:Science ,0105 earth and related environmental sciences ,fossil birds ,Multidisciplinary ,biology ,biology.organism_classification ,Anseriformes ,Presbyornithidae ,gondwana ,palaeobiogeography ,lcsh:Q ,Teviornis ,Research Article - Abstract
Published by the Royal Society under the terms of the Creative Commons Attribution License http://creativecommons.org/licenses/by/4.0/, which permits unrestricted use, provided the original author and source are credited., Presbyornithids were the dominant birds in Palaeogene lacustrine assemblages, especially in the Northern Hemisphere, but are thought to have disappeared worldwide by the mid-Eocene. Now classified within Anseriformes (screamers, ducks, swans and geese), their relationships have long been obscured by their strange wader-like skeletal morphology. Reassessment of the late Oligocene South Australian material attributed to Wilaru tedfordi, long considered to be of a stone-curlew (Burhinidae, Charadriiformes), reveals that this taxon represents the first record of a presbyornithid in Australia. We also describe the larger Wilaru prideauxi sp. nov. from the early Miocene of South Australia, showing that presbyornithids survived in Australia at least until ca 22 Ma. Unlike on other continents, where presbyornithids were replaced by aquatic crown-group anatids (ducks, swans and geese), species of Wilaru lived alongside these waterfowl in Australia. The morphology of the tarsometatarsus of these species indicates that, contrary to other presbyornithids, they were predominantly terrestrial birds, which probably contributed to their long-term survival in Australia. The morphological similarity between species of Wilaru and the Eocene South American presbyornithid Telmabates antiquus supports our hypothesis of a Gondwanan radiation during the evolutionary history of the Presbyornithidae. Teviornis gobiensis from the Late Cretaceous of Mongolia is here also reassessed and confirmed as a presbyornithid. These findings underscore the temporal continuance of Australia’s vertebrates and provide a new context in which the phylogeny and evolutionary history of presbyornithids can be examined.
- Published
- 2016
42. Bone growth marks reveal protracted growth in New Zealand kiwi (Aves, Apterygidae)
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Jorge Cubo, Armand de Ricqlès, Estelle Bourdon, Hayat Lamrous, R. Paul Scofield, Alan J. D. Tennyson, Jacques Castanet, Dept Ornithol, AMNH, Institut des Sciences de la Terre de Paris (iSTeP), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), CMC, and NMNZ
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0106 biological sciences ,Palaeognathae ,Dinornithidae ,Time Factors ,[SDU.STU]Sciences of the Universe [physics]/Earth Sciences ,010603 evolutionary biology ,01 natural sciences ,Predation ,03 medical and health sciences ,medicine ,Animals ,Skeletochronology ,ComputingMilieux_MISCELLANEOUS ,030304 developmental biology ,Bone growth ,Evolutionary Biology ,0303 health sciences ,Bone Development ,biology ,Ecology ,biology.organism_classification ,Agricultural and Biological Sciences (miscellaneous) ,Amazona amazonica ,medicine.anatomical_structure ,Kiwi ,Cortical bone ,Diaphyses ,General Agricultural and Biological Sciences ,New Zealand - Abstract
The presence of bone growth marks reflecting annual rhythms in the cortical bone of non-avian tetrapods is now established as a general phenomenon. In contrast, ornithurines (the theropod group including modern birds and their closest relatives) usually grow rapidly in less than a year, such that no annual rhythms are expressed in bone cortices, except scarce growth marks restricted to the outer cortical layer. So far, cyclical growth in modern birds has been restricted to the EoceneDiatryma, the extant parrotAmazona amazonicaand the extinct New Zealand (NZ) moa (Dinornithidae). Here we show the presence of lines of arrested growth in the long bones of the living NZ kiwi (Apteryxspp., Apterygidae). Kiwis take 5–6 years to reach full adult body size, which indicates a delayed maturity and a slow reproductive cycle. Protracted growth probably evolved convergently in moa and kiwi sometime since the Middle Miocene, owing to the severe climatic cooling in the southwest Pacific and the absence of mammalian predators.
- Published
- 2009
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43. Efficient profile-likelihood confidence intervals for capture-recapture models
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R. Paul Scofield, David Fletcher, Laurent Lamor, Roger Pradel, Jean-Dominique Lebreton, Olivier Gimenez, Rémi Choquet, Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), Institut de Recherche pour le Développement (IRD [France-Sud])-Centre National de la Recherche Scientifique (CNRS)-École pratique des hautes études (EPHE)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université Paul-Valéry - Montpellier 3 (UM3), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Université Paul-Valéry - Montpellier 3 (UPVM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut de Recherche pour le Développement (IRD [France-Sud])
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0106 biological sciences ,Statistics and Probability ,Overdisper- sion ,Population ,Profile-likelihood interval ,Nominal coverage level ,Boundary estimate ,01 natural sciences ,Robust confidence intervals ,010104 statistics & probability ,Overdispersion ,Statistics ,Econometrics ,Statistics::Methodology ,0101 mathematics ,[STAT.CO]Statistics [stat]/Computation [stat.CO] ,education ,CDF-based nonparametric confidence interval ,General Environmental Science ,Mathematics ,education.field_of_study ,Venzon and Moolgavkar's algorithm ,Applied Mathematics ,Multi-state model ,Agricultural and Biological Sciences (miscellaneous) ,Confidence interval ,[STAT]Statistics [stat] ,010601 ecology ,Sample size determination ,Confidence distribution ,Statistics, Probability and Uncertainty ,Binomial proportion confidence interval ,General Agricultural and Biological Sciences - Abstract
International audience; In a capture-recapture analysis, uncertainty in the parameter estimates is usually expressed by presenting classical Wald-type confidence intervals. This approach involves (1) the assumption that the maximum likelihood estimates are asymptotically normal and (2) numerical computation of the variance-covariance matrix of these estimates. When the sample size is small or when the estimates are on the boundary of their domain, a Wald confidence interval often performs badly. A natural alternative is to use profile-likelihood confidence intervals. In general, these intervals require a greater amount of computation. We propose a new implementation of this approach that is efficient, both in reducing the amount of computation and in coping with boundary estimates. We also show how profile-likelihood confidence intervals can be adjusted for overdispersion. Simulations were used to check whether nominal coverage levels were attained, and allowed us to compare this approach with the classical Wald procedure. We illustrate this work by considering a multi-state model for a sooty shearwater (Puffinus griseus) population.
- Published
- 2005
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44. A well-preserved new mid-paleocene penguin (Aves, Sphenisciformes) from the Waipara Greensand in New Zealand
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Leigh Love, R. Paul Scofield, Vanesa L. De Pietri, Gerald Mayr, and Al A. Mannering
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0106 biological sciences ,010506 paleontology ,biology ,Greensand ,Paleontology ,Zoology ,Tarsometatarsus ,Morphology (biology) ,biology.organism_classification ,010603 evolutionary biology ,01 natural sciences ,Waimanu ,Type species ,Taxon ,Apex (mollusc) ,Sphenisciformes ,0105 earth and related environmental sciences - Abstract
We describe a partial skeleton of a new stem group representative of the Sphenisciformes from the mid-Paleocene Waipara Greensand in New Zealand, which represents the best-preserved and most complete Paleocene penguin found so far. Sequiwaimanu rosieae, n. gen. et sp., is the fourth penguin species from the Waipara Greensand, which previously yielded two species that were assigned to the taxon Waimanu, in addition to leg bones of an unnamed giant penguin. Among other features, the new species is characterized by an articular facet for the furcula on the apex carinae of the sternum, which is unknown from other sphenisciforms. We perform detailed comparisons with the species assigned to Waimanu and show that the type species Waimanu manneringi differs in tarsometatarsus morphology from its putative congener ‘W.’ tuatahi, which is here assigned to the new taxon Muriwaimanu. Sequiwaimanu rosieae exhibits a more derived morphology than Muriwaimanu tuatahi, but its exact affinities to W. manneringi are ...
- Published
- 2017
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45. Population Estimate of Breeding Northern Giant Petrels Macronectes halli on Campbell Island, New Zealand
- Author
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R. Paul Scofield and Alan Wiltshire
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0106 biological sciences ,education.field_of_study ,biology ,Ecology ,Population ,Northern giant petrel ,biology.organism_classification ,010603 evolutionary biology ,01 natural sciences ,010605 ornithology ,Population estimate ,Animal Science and Zoology ,Conservation biology ,Nest site ,education ,Ornithology ,Southern Hemisphere ,Ecology, Evolution, Behavior and Systematics ,Nature and Landscape Conservation - Abstract
An extensive survey of the breeding population of the Northern Giant Petrel Macronectes halli on Campbell Island was conducted during the 1996—97 season. The number of breeding pairs was estimated to be at least 234. Globally, Northern Giant Petrel populations are thought to be increasing at some locations and decreasing at others. Comparison of the 1996—97 Campbell Island population estimate with historic records is unreliable as past surveys were often limited in the areas searched or were based on anecdotal evidence of breeding occurences. Northern Giant Petrels often move their nest site from year to year and so representative surveys of a restricted area are not appropriate for this species. Long-term monitoring of the whole population is required in order to detect true population trends.
- Published
- 2000
- Full Text
- View/download PDF
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