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Garg KM, Gwee CY, Chattopadhyay B, Ng NS, Prawiradilaga DM, David G, Fuchs J, Hung Le Manh, Martinez J, Olsson U, Vuong Tan Tu, Chhin S, Alström P, Lei F, Rheindt FE. When colors mislead: Genomics and bioacoustics prompt re-classification of Asian flycatcher radiation (Aves: Niltavinae). Mol Phylogenet Evol 2024; 193:107999. [PMID: 38160993 DOI: 10.1016/j.ympev.2023.107999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 11/10/2023] [Accepted: 12/25/2023] [Indexed: 01/03/2024]
Abstract
Traditional classification of many animals, including birds, has been highly dependent on external morphological characters like plumage coloration. However, both bioacoustics and genetic or genomic data have revolutionized our understanding of the relationships of certain lineages and led to sweeping taxonomic re-organizations. In this study, we present a case of erroneous delimitation of genus boundaries in the species-rich flycatcher subfamily Niltavinae. Genera within this subfamily have historically been delineated based on blue versus brown male body plumage until recent studies based on a few mitochondrial and nuclear loci unearthed several cases of generic misclassification. Here we use extensive bioacoustic data from 43 species and genomic data from 28 species for a fundamental reclassification of species in the Niltavinae. Our study reveals that song is an important trait to classify these birds even at the genus level, whereas plumage traits exhibit ample convergence and have led to numerous historic misattributions. Our taxonomic re-organization leads to new biogeographic limits of major genera, such that the genus Cyornis now only extends as far east as the islands of Sulawesi, Sula, and Banggai, whereas Eumyias is redefined to extend far beyond Wallace's Line to the islands of Seram and Timor. Our conclusions advise against an over-reliance on morphological traits and underscore the importance of integrative datasets.
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Affiliation(s)
- Kritika M Garg
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore; Centre for Interdisciplinary Archaeological Research, Ashoka University, Sonipat, India; Department of Biology, Ashoka University, Sonipat, India
| | - Chyi Yin Gwee
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore; Division of Evolutionary Biology, Faculty of Biology, LMU Munich, Munich, Germany
| | - Balaji Chattopadhyay
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore; Department of Biology, Ashoka University, Sonipat, India; Trivedi School of Biosciences, Ashoka University, Sonipat, India
| | - Nathaniel S Ng
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Dewi M Prawiradilaga
- Research Center for Biosystematics and Evolution, National Research and Innovation Agency (BRIN), Bogor-Cibinong, West Java, Indonesia
| | - Gabriel David
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore; Animal Ecology, Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-752 36 Uppsala, Sweden; Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing, China
| | - Jérôme Fuchs
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, 22 S U, EPHE, UA CP51, Paris, France
| | - Hung Le Manh
- Institute of Ecology and Biological Resources, Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | | | - Urban Olsson
- Systematics and Biodiversity, Department of Biology and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden; Gothenburg Global Biodiversity Center, Göteborg, Sweden
| | - Vuong Tan Tu
- Institute of Ecology and Biological Resources, Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Sophea Chhin
- Department of Biodiversity, General Directorate of Policy and Strategy, Ministry of Environment, Phnom Penh, Cambodia
| | - Per Alström
- Animal Ecology, Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-752 36 Uppsala, Sweden; Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Fumin Lei
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing, China; Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
| | - Frank E Rheindt
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore.
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2
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Rössler T, Mioduszewska B, O'Hara M, Huber L, Prawiradilaga DM, Auersperg AMI. The Innovation Arena: A Method for Comparing Innovative Problem-Solving Across Groups. J Vis Exp 2022. [PMID: 35635458 DOI: 10.3791/63026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2024] Open
Abstract
Problem-solving tasks are commonly used to investigate technical, innovative behavior but a comparison of this ability across a broad range of species is a challenging undertaking. Specific predispositions, such as the morphological toolkit of a species or exploration techniques, can substantially influence performance in such tasks, which makes direct comparisons difficult. The method presented here was developed to be more robust with regard to such species-specific differences: the Innovation Arena presents 20 different problem-solving tasks. All tasks are presented simultaneously. Subjects are confronted with the apparatus repeatedly, which allows a measurement of the emergence of innovations over time - an important next step for investigating how animals can adapt to changing environmental conditions through innovative behavior. Each individual was tested with the apparatus until it ceased to discover solutions. After testing was concluded, we analyzed the video recordings and coded successful retrieval of rewards and multiple apparatus-directed behaviors. The latter were analyzed using a Principal Component Analysis and the resulting components were then included in a Generalized Linear Mixed Model together with session number and the group comparison of interest to predict the probability of success. We used this approach in a first study to target the question of whether long-term captivity influences the problem-solving ability of a parrot species known for its innovative behavior: the Goffin´s cockatoo. We found an effect in degree of motivation but no difference in the problem-solving ability between short- and long-term captive groups.
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Affiliation(s)
- Theresa Rössler
- Comparative Cognition, Messerli Research Institute, University of Veterinary Medicine Vienna, University of Vienna, Medical University of Vienna; Department of Cognitive Biology, University of Vienna;
| | - Berenika Mioduszewska
- Comparative Cognition, Messerli Research Institute, University of Veterinary Medicine Vienna, University of Vienna, Medical University of Vienna; Max Planck Institute for Ornithology
| | - Mark O'Hara
- Comparative Cognition, Messerli Research Institute, University of Veterinary Medicine Vienna, University of Vienna, Medical University of Vienna; Research Center for Biology, National Research and Innovation Agency (BRIN)
| | - Ludwig Huber
- Comparative Cognition, Messerli Research Institute, University of Veterinary Medicine Vienna, University of Vienna, Medical University of Vienna
| | | | - Alice M I Auersperg
- Comparative Cognition, Messerli Research Institute, University of Veterinary Medicine Vienna, University of Vienna, Medical University of Vienna
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3
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Tobias JA, Sheard C, Pigot AL, Devenish AJM, Yang J, Sayol F, Neate-Clegg MHC, Alioravainen N, Weeks TL, Barber RA, Walkden PA, MacGregor HEA, Jones SEI, Vincent C, Phillips AG, Marples NM, Montaño-Centellas FA, Leandro-Silva V, Claramunt S, Darski B, Freeman BG, Bregman TP, Cooney CR, Hughes EC, Capp EJR, Varley ZK, Friedman NR, Korntheuer H, Corrales-Vargas A, Trisos CH, Weeks BC, Hanz DM, Töpfer T, Bravo GA, Remeš V, Nowak L, Carneiro LS, Moncada R AJ, Matysioková B, Baldassarre DT, Martínez-Salinas A, Wolfe JD, Chapman PM, Daly BG, Sorensen MC, Neu A, Ford MA, Mayhew RJ, Fabio Silveira L, Kelly DJ, Annorbah NND, Pollock HS, Grabowska-Zhang AM, McEntee JP, Carlos T Gonzalez J, Meneses CG, Muñoz MC, Powell LL, Jamie GA, Matthews TJ, Johnson O, Brito GRR, Zyskowski K, Crates R, Harvey MG, Jurado Zevallos M, Hosner PA, Bradfer-Lawrence T, Maley JM, Stiles FG, Lima HS, Provost KL, Chibesa M, Mashao M, Howard JT, Mlamba E, Chua MAH, Li B, Gómez MI, García NC, Päckert M, Fuchs J, Ali JR, Derryberry EP, Carlson ML, Urriza RC, Brzeski KE, Prawiradilaga DM, Rayner MJ, Miller ET, Bowie RCK, Lafontaine RM, Scofield RP, Lou Y, Somarathna L, Lepage D, Illif M, Neuschulz EL, Templin M, Dehling DM, Cooper JC, Pauwels OSG, Analuddin K, Fjeldså J, Seddon N, Sweet PR, DeClerck FAJ, Naka LN, Brawn JD, Aleixo A, Böhning-Gaese K, Rahbek C, Fritz SA, Thomas GH, Schleuning M. AVONET: morphological, ecological and geographical data for all birds. Ecol Lett 2022; 25:581-597. [PMID: 35199922 DOI: 10.1111/ele.13898] [Citation(s) in RCA: 130] [Impact Index Per Article: 65.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 04/10/2021] [Accepted: 09/10/2021] [Indexed: 01/02/2023]
Abstract
Functional traits offer a rich quantitative framework for developing and testing theories in evolutionary biology, ecology and ecosystem science. However, the potential of functional traits to drive theoretical advances and refine models of global change can only be fully realised when species-level information is complete. Here we present the AVONET dataset containing comprehensive functional trait data for all birds, including six ecological variables, 11 continuous morphological traits, and information on range size and location. Raw morphological measurements are presented from 90,020 individuals of 11,009 extant bird species sampled from 181 countries. These data are also summarised as species averages in three taxonomic formats, allowing integration with a global phylogeny, geographical range maps, IUCN Red List data and the eBird citizen science database. The AVONET dataset provides the most detailed picture of continuous trait variation for any major radiation of organisms, offering a global template for testing hypotheses and exploring the evolutionary origins, structure and functioning of biodiversity.
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Affiliation(s)
- Joseph A Tobias
- Department of Life Sciences, Imperial College London, Ascot, UK.,Department of Zoology, University of Oxford, Oxford, UK
| | - Catherine Sheard
- Department of Zoology, University of Oxford, Oxford, UK.,School of Earth Sciences, University of Bristol, Bristol, UK
| | - Alex L Pigot
- Department of Zoology, University of Oxford, Oxford, UK.,Centre for Biodiversity and Environment Research, Department of Genetics, Evolution and Environment, University College London, London, UK
| | | | - Jingyi Yang
- Department of Life Sciences, Imperial College London, Ascot, UK
| | - Ferran Sayol
- Centre for Biodiversity and Environment Research, Department of Genetics, Evolution and Environment, University College London, London, UK
| | - Montague H C Neate-Clegg
- Department of Zoology, University of Oxford, Oxford, UK.,School of Biological Sciences, University of Utah, Salt Lake City, Utah, USA
| | - Nico Alioravainen
- Department of Zoology, University of Oxford, Oxford, UK.,Natural Resources Institute Finland, Natural resources - Migratory fish and regulated rivers, Oulu, Finland
| | - Thomas L Weeks
- Department of Life Sciences, Imperial College London, Ascot, UK.,Department of Life Sciences, Natural History Museum, London, UK
| | - Robert A Barber
- Department of Life Sciences, Imperial College London, Ascot, UK
| | - Patrick A Walkden
- Department of Life Sciences, Imperial College London, Ascot, UK.,Department of Life Sciences, Natural History Museum, London, UK
| | - Hannah E A MacGregor
- Department of Zoology, University of Oxford, Oxford, UK.,School of Biological Sciences, University of Bristol, Bristol, UK
| | - Samuel E I Jones
- Department of Zoology, University of Oxford, Oxford, UK.,School of Biological Sciences, Royal Holloway, University of London, Egham, UK
| | - Claire Vincent
- UN Environment Programme World Conservation Monitoring Centre (UNEP-WCMC), Cambridge, UK
| | - Anna G Phillips
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Frankfurt am Main, Germany
| | - Nicola M Marples
- Department of Zoology, School of Natural Sciences, Trinity College Dublin, Dublin, Ireland
| | - Flavia A Montaño-Centellas
- Instituto de Ecología, Universidad Mayor de San Andres, La Paz, Bolivia.,Department of Wildlife Ecology and Conservation, University of Florida, Gainesville, Florida, USA
| | - Victor Leandro-Silva
- Laboratório de Ecologia e Evolução de Aves, Departamento de Zoologia, Universidade Federal de Pernambuco, Recife, Brazil
| | - Santiago Claramunt
- Department of Natural History, Royal Ontario Museum, Toronto, Ontario, Canada.,Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
| | - Bianca Darski
- Departamento de Ecologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Benjamin G Freeman
- Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Tom P Bregman
- Department of Zoology, University of Oxford, Oxford, UK.,Future-Fit Foundation, Spitalfields, London, UK
| | | | - Emma C Hughes
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK
| | - Elliot J R Capp
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK
| | - Zoë K Varley
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK.,Bird Group, Department of Life Sciences, The Natural History Museum, Tring, UK
| | - Nicholas R Friedman
- Biodiversity and Biocomplexity Unit, Okinawa Institute of Science and Technology Graduate University, Kunigami-gun, Okinawa, Japan
| | - Heiko Korntheuer
- Department of Ecology, Institute of Zoology, Johannes Gutenberg University Mainz, Mainz, Germany
| | - Andrea Corrales-Vargas
- Central American Institute for Studies on Toxic Substances (IRET), Universidad Nacional de Costa Rica, Heredia, Costa Rica
| | - Christopher H Trisos
- Department of Zoology, University of Oxford, Oxford, UK.,African Climate and Development Initiative, University of Cape Town, Cape Town, South Africa.,Centre for Statistics in Ecology, the Environment and Conservation, University of Cape Town, Cape Town, South Africa
| | - Brian C Weeks
- School for Environment and Sustainability, University of Michigan, Ann Arbor, Michigan, USA.,Department of Ornithology, American Museum of Natural History, New York, New York, USA
| | - Dagmar M Hanz
- Biogeography and Biodiversity Lab, Institute of Physical Geography, Goethe University Frankfurt, , Frankfurt am Main, Germany
| | - Till Töpfer
- Ornithology Section, Zoological Research Museum Alexander Koenig, Bonn, Germany
| | - Gustavo A Bravo
- Museum of Comparative Zoology, Harvard University, Cambridge, Massachusetts, USA.,Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Vladimír Remeš
- Department of Zoology, Palacký University, Olomouc, Czech Republic.,Department of Ecology, Faculty of Science, Charles University, Praha, Czech Republic
| | - Larissa Nowak
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Frankfurt am Main, Germany.,Institute for Ecology, Evolution and Diversity, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Lincoln S Carneiro
- Coordenação de Zoologia, Museu Paraense Emílio Goeldi, Belém, Pará, Brazil
| | - Amilkar J Moncada R
- CATIE (Centro Agronómico Tropical de Investigación y Enseñanza), Cartago, Turrialba, Costa Rica
| | | | | | | | - Jared D Wolfe
- College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, Michigan, USA
| | | | | | - Marjorie C Sorensen
- Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada
| | - Alexander Neu
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Frankfurt am Main, Germany.,Department of Biological Sciences, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Michael A Ford
- South African Ringing Unit, University of Cape Town, Rondebosch, Cape Town, South Africa
| | - Rebekah J Mayhew
- Biological and Environmental Sciences, University of Stirling, Stirling, UK
| | - Luis Fabio Silveira
- Museu de Zoologia da Universidade de Sao Paulo (MZUSP), São Paulo, SP, Brazil
| | - David J Kelly
- Department of Zoology, School of Natural Sciences, Trinity College Dublin, Dublin, Ireland
| | - Nathaniel N D Annorbah
- Department of Biological, Physical and Mathematical Sciences, University of Environment and Sustainable Development, Somanya, Ghana
| | - Henry S Pollock
- Department of Natural Resources and Environmental Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | | | - Jay P McEntee
- Department of Biology, Missouri State University, Springfield, Missouri, USA
| | - Juan Carlos T Gonzalez
- Department of Zoology, University of Oxford, Oxford, UK.,Museum of Natural History, University of the Philippines Los, Baños, Los Baños, Laguna, Philippines.,Animal Biology Division, Institute of Biological Sciences, College of Arts and Sciences, University of the Philippines Los, Baños, Los Baños, Laguna, Philippines
| | - Camila G Meneses
- Museum of Natural History, University of the Philippines Los, Baños, Los Baños, Laguna, Philippines
| | - Marcia C Muñoz
- Programa de Biología, Universidad de la Salle, Bogotá, Colombia
| | - Luke L Powell
- Institute of Animal Health and Comparative Medicine, Graham Kerr Building, University of Glasgow, Glasgow, UK.,Biodiversity Initiative, Houghton, Michigan, USA.,CIBIO-InBIO, Research Centre in Biodiversity and Genetic Resources, University of Porto, Vairão, Portugal
| | - Gabriel A Jamie
- Department of Zoology, University of Cambridge, Cambridge, UK.,FitzPatrick Institute of African Ornithology, University of Cape Town, Rondebosch, Cape Town, South Africa
| | - Thomas J Matthews
- GEES (School of Geography, Earth and Environmental Sciences) and Birmingham Institute of Forest Research, University of Birmingham, Birmingham, UK.,CE3C (Centre for Ecology, Evolution and Environmental Changes/Azorean Biodiversity Group and Universidade, dos Açores), Depto de Ciências Agráriase Engenharia do Ambiente, Angra do Heroísmo, Açores, Portugal
| | - Oscar Johnson
- Department of Biological Sciences and Museum of Natural Science, Louisiana State University, Baton Rouge, Louisina, USA
| | - Guilherme R R Brito
- Depto. de Ecologia e Zoologia, Centro de Ciências Biológicas, Universidade Federal de Santa Catarina, Florianópolis, Brazil
| | - Kristof Zyskowski
- Peabody Museum of Natural History, Yale University, New Haven, Connecticut, USA
| | - Ross Crates
- Fenner School of Environment and Society, Australian National University, Canberra, Australia
| | - Michael G Harvey
- Department of Biological Sciences and Biodiversity Collections, The University of Texas at El Paso, El Paso, Texas, USA
| | | | - Peter A Hosner
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.,Center for Macroecology, Evolution and Climate, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | | | - James M Maley
- Moore Laboratory of Zoology, Occidental College, Los Angeles, California, USA
| | - F Gary Stiles
- Instituto de Ciencias Naturales, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Hevana S Lima
- Instituto Nacional de Pesquisas da Amazônia, Manaus, Brazil
| | - Kaiya L Provost
- Department of Ornithology, American Museum of Natural History, New York, New York, USA.,Department of Evolution, Ecology and Organismal Biology, Ohio State University, Columbus, Ohio, USA
| | - Moses Chibesa
- Department of Zoology and Aquatic Sciences, Copperbelt University, Kitwe, Zambia
| | | | - Jeffrey T Howard
- Department of Biological Sciences and Museum of Natural Science, Louisiana State University, Baton Rouge, Louisina, USA.,Louisiana State University, Health Sciences Center Shreveport, Shreveport, Louisina, USA
| | - Edson Mlamba
- Department of Zoology, National Museums of Kenya, Nairobi, Kenya
| | - Marcus A H Chua
- Lee Kong Chian Natural History Museum, National University of Singapore, Singapore, Singapore.,Department of Environmental Science and Policy, George Mason University, Fairfax, Virginia, USA
| | - Bicheng Li
- Natural History Research Center, Shanghai Natural History Museum, Shanghai, China
| | - M Isabel Gómez
- Colección Boliviana de Fauna - Museo Nacional de Historia Natural, Ministerio de Medio Ambiente y Agua, La Paz, Bolivia
| | - Natalia C García
- División Ornitología, Museo Argentino de Ciencias Naturales "Bernardino Rivadavia", CONICET, Buenos Aires, Argentina
| | - Martin Päckert
- Senckenberg Natural History Collections, Museum of Zoology, Dresden, Germany
| | - Jérôme Fuchs
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, SU, EPHE, UA, Paris, France
| | - Jarome R Ali
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey, USA
| | - Elizabeth P Derryberry
- Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, Tennessee, USA
| | - Monica L Carlson
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey, USA
| | - Rolly C Urriza
- Ornithology Section, Zoology Division, Philippine National Museum, Rizal Park, Manila, Philippines
| | - Kristin E Brzeski
- College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, Michigan, USA
| | - Dewi M Prawiradilaga
- Museum Zoologicum Bogoriense, Research Centre for Biology, Indonesian Institute of Sciences (LIPI), Bogor, Indonesia
| | - Matt J Rayner
- Auckland Museum, Auckland, New Zealand.,School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | | | - Rauri C K Bowie
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California Berkeley, Berkeley, California, USA
| | - René-Marie Lafontaine
- Operational Directorate Natural Environment, Royal Belgian Institute of Natural Sciences (RBINS), Brussels, Belgium
| | | | - Yingqiang Lou
- Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Lankani Somarathna
- Natural History Section, Department of National Museum, Colombo, Sri Lanka
| | | | | | - Eike Lena Neuschulz
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Frankfurt am Main, Germany
| | - Mathias Templin
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Frankfurt am Main, Germany
| | - D Matthias Dehling
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf, Switzerland
| | | | - Olivier S G Pauwels
- Department of Recent Vertebrates, Royal Belgian Institute of Natural Sciences (RBINS), Brussels, Belgium
| | - Kangkuso Analuddin
- Department of Biotechnology, Halu Oleo University, Kendari, Sulawesi Tenggara, Indonesia
| | - Jon Fjeldså
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.,Center for Macroecology, Evolution and Climate, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Nathalie Seddon
- Nature-based Solutions Initiative, Department of Zoology, University of Oxford, Oxford, UK
| | - Paul R Sweet
- Department of Ornithology, American Museum of Natural History, New York, New York, USA
| | - Fabrice A J DeClerck
- Bioversity International, CGIAR, Parc Scientifique Agropolis II, Montpellier, France
| | - Luciano N Naka
- Laboratório de Ecologia e Evolução de Aves, Departamento de Zoologia, Universidade Federal de Pernambuco, Recife, Brazil
| | - Jeffrey D Brawn
- Department of Natural Resources and Environmental Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Alexandre Aleixo
- Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland
| | - Katrin Böhning-Gaese
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Frankfurt am Main, Germany.,Institute for Ecology, Evolution and Diversity, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Carsten Rahbek
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.,Center for Macroecology, Evolution and Climate, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.,Danish Institute for Advanced Study, University of Southern Denmark, Odense, Denmark.,Institute of Ecology, Peking University, Beijing, China
| | - Susanne A Fritz
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Frankfurt am Main, Germany.,Institut für Geowissenschaften, Goethe University, Frankfurt, Frankfurt am Main, Germany
| | - Gavin H Thomas
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK.,Bird Group, Department of Life Sciences, The Natural History Museum, Tring, UK
| | - Matthias Schleuning
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Frankfurt am Main, Germany
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4
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Tobias JA, Sheard C, Pigot AL, Devenish AJM, Yang J, Sayol F, Neate‐Clegg MHC, Alioravainen N, Weeks TL, Barber RA, Walkden PA, MacGregor HEA, Jones SEI, Vincent C, Phillips AG, Marples NM, Montaño‐Centellas FA, Leandro‐Silva V, Claramunt S, Darski B, Freeman BG, Bregman TP, Cooney CR, Hughes EC, Capp EJR, Varley ZK, Friedman NR, Korntheuer H, Corrales‐Vargas A, Trisos CH, Weeks BC, Hanz DM, Töpfer T, Bravo GA, Remeš V, Nowak L, Carneiro LS, Moncada R. AJ, Matysioková B, Baldassarre DT, Martínez‐Salinas A, Wolfe JD, Chapman PM, Daly BG, Sorensen MC, Neu A, Ford MA, Mayhew RJ, Fabio Silveira L, Kelly DJ, Annorbah NND, Pollock HS, Grabowska‐Zhang AM, McEntee JP, Carlos T. Gonzalez J, Meneses CG, Muñoz MC, Powell LL, Jamie GA, Matthews TJ, Johnson O, Brito GRR, Zyskowski K, Crates R, Harvey MG, Jurado Zevallos M, Hosner PA, Bradfer‐Lawrence T, Maley JM, Stiles FG, Lima HS, Provost KL, Chibesa M, Mashao M, Howard JT, Mlamba E, Chua MAH, Li B, Gómez MI, García NC, Päckert M, Fuchs J, Ali JR, Derryberry EP, Carlson ML, Urriza RC, Brzeski KE, Prawiradilaga DM, Rayner MJ, Miller ET, Bowie RCK, Lafontaine R, Scofield RP, Lou Y, Somarathna L, Lepage D, Illif M, Neuschulz EL, Templin M, Dehling DM, Cooper JC, Pauwels OSG, Analuddin K, Fjeldså J, Seddon N, Sweet PR, DeClerck FAJ, Naka LN, Brawn JD, Aleixo A, Böhning‐Gaese K, Rahbek C, Fritz SA, Thomas GH, Schleuning M. Cover Image: Volume 25 Number 3, March 2022. Ecol Lett 2022. [DOI: 10.1111/ele.13795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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5
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O'Hara M, Mioduszewska B, Mundry R, Yohanna, Haryoko T, Rachmatika R, Prawiradilaga DM, Huber L, Auersperg AMI. Wild Goffin's cockatoos flexibly manufacture and use tool sets. Curr Biol 2021; 31:4512-4520.e6. [PMID: 34469771 DOI: 10.1016/j.cub.2021.08.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 07/05/2021] [Accepted: 08/02/2021] [Indexed: 10/20/2022]
Abstract
The use of different tools to achieve a single goal is considered unique to human and primate technology. To unravel the origins of such complex behaviors, it is crucial to investigate tool use that is not necessary for a species' survival. These cases can be assumed to have emerged innovatively and be applied flexibly, thus emphasizing creativity and intelligence. However, it is intrinsically challenging to record tool innovations in natural settings that do not occur species-wide. Here, we report the discovery of two distinct tool manufacture methods and the use of tool sets in wild Goffin's cockatoos (Cacatua goffiniana). Up to three types of wooden tools, differing in their physical properties and each serving a different function, were manufactured and employed to extract embedded seed matter of Cerbera manghas. While Goffin's cockatoos do not depend on tool-obtained resources, repeated observations of two temporarily captive wild birds and indications from free-ranging individuals suggest this behavior occurs in the wild, albeit not species-wide. The use of a tool set in a non-primate implies convergent evolution of advanced tool use. Furthermore, these observations demonstrate how a species without hands can achieve dexterity in a high-precision task. The presence of flexible use and manufacture of tool sets in animals distantly related to humans significantly diversifies the phylogenetic landscape of technology and opens multiple avenues for future research. VIDEO ABSTRACT.
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Affiliation(s)
- Mark O'Hara
- Comparative Cognition, Messerli Research Institute, University of Veterinary Medicine Vienna, Medical University Vienna, University of Vienna, Veterinaerplatz 1, 1210 Vienna, Austria.
| | - Berenika Mioduszewska
- Comparative Cognition, Messerli Research Institute, University of Veterinary Medicine Vienna, Medical University Vienna, University of Vienna, Veterinaerplatz 1, 1210 Vienna, Austria.
| | - Roger Mundry
- Comparative Cognition, Messerli Research Institute, University of Veterinary Medicine Vienna, Medical University Vienna, University of Vienna, Veterinaerplatz 1, 1210 Vienna, Austria; Platform for Bioinformatics and Biostatistics, University of Veterinary Medicine Vienna, Veterinaerplatz 1, 1210 Vienna, Austria
| | - Yohanna
- Museum Zoologicum Bogoriense, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Jl. Raya Jakarta, Bogor Km.46 Cibinong, 16911 Bogor, Indonesia
| | - Tri Haryoko
- Museum Zoologicum Bogoriense, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Jl. Raya Jakarta, Bogor Km.46 Cibinong, 16911 Bogor, Indonesia
| | - Rini Rachmatika
- Museum Zoologicum Bogoriense, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Jl. Raya Jakarta, Bogor Km.46 Cibinong, 16911 Bogor, Indonesia
| | - Dewi M Prawiradilaga
- Museum Zoologicum Bogoriense, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Jl. Raya Jakarta, Bogor Km.46 Cibinong, 16911 Bogor, Indonesia
| | - Ludwig Huber
- Comparative Cognition, Messerli Research Institute, University of Veterinary Medicine Vienna, Medical University Vienna, University of Vienna, Veterinaerplatz 1, 1210 Vienna, Austria
| | - Alice M I Auersperg
- Comparative Cognition, Messerli Research Institute, University of Veterinary Medicine Vienna, Medical University Vienna, University of Vienna, Veterinaerplatz 1, 1210 Vienna, Austria
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6
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Shakya SB, Haryoko T, Irham M, Suparno, Prawiradilaga DM, Sheldon FH. Genomic investigation of colour polymorphism and phylogeographic variation among populations of black-headed bulbul (Brachypodius atriceps) in insular southeast Asia. Mol Ecol 2021; 30:4757-4770. [PMID: 34297854 DOI: 10.1111/mec.16089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 07/15/2021] [Accepted: 07/19/2021] [Indexed: 11/27/2022]
Abstract
Intraspecific polymorphism in birds, especially plumage colour polymorphism, and the mechanisms that control it are an area of active research in evolutionary biology. The black-headed bulbul (Brachypodius atriceps) is a polymorphic species with two distinct morphs, yellow and grey. This species inhabits the mainland and virtually all continental islands of Southeast Asia where yellow morphs predominate, but on two islands in the Sunda region, Bawean and Maratua, grey morphs are common or exclusive. Here, we generated a high-quality reference genome of a yellow individual and resequenced genomes of multiple individuals of both yellow and grey morphs to study the genetic basis of coloration and population history of the species. Using PCA and STRUCTURE analysis, we found the Maratua Island population (which is exclusively grey) to be distinct from all other B. atriceps populations, having been isolated c. 1.9 million years ago (Ma). In contrast, Bawean grey individuals (a subset of yellow and grey individuals on that island) are embedded within an almost panmictic Sundaic clade of yellow birds. Using FST and dxy to compare variable genomic segments between Maratua and yellow individuals, we located peaks of divergence and identified candidate loci involved in the colour polymorphism. Tests of selection among coding-proteins in high FST regions, however, did not indicate selection on the candidate genes. Overall, we report on some loci that are potentially responsible for the grey/yellow polymorphism in a species that otherwise shows little genetic diversification across most of its range.
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Affiliation(s)
- Subir B Shakya
- Museum of Natural Science and Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, USA
| | - Tri Haryoko
- Museum Zoologicum Bogoriense, Research Centre for Biology, Indonesian Institute of Sciences (LIPI), Cibinong, Indonesia
| | - Mohammad Irham
- Museum Zoologicum Bogoriense, Research Centre for Biology, Indonesian Institute of Sciences (LIPI), Cibinong, Indonesia
| | - Suparno
- Museum Zoologicum Bogoriense, Research Centre for Biology, Indonesian Institute of Sciences (LIPI), Cibinong, Indonesia
| | - Dewi M Prawiradilaga
- Museum Zoologicum Bogoriense, Research Centre for Biology, Indonesian Institute of Sciences (LIPI), Cibinong, Indonesia
| | - Frederick H Sheldon
- Museum of Natural Science and Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, USA
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7
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Baveja P, Garg KM, Chattopadhyay B, Sadanandan KR, Prawiradilaga DM, Yuda P, Lee JGH, Rheindt FE. Using historical genome-wide DNA to unravel the confused taxonomy in a songbird lineage that is extinct in the wild. Evol Appl 2021; 14:698-709. [PMID: 33767745 PMCID: PMC7980273 DOI: 10.1111/eva.13149] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 10/13/2020] [Indexed: 11/29/2022] Open
Abstract
Urgent conservation action for terminally endangered species is sometimes hampered by taxonomic uncertainty, especially in illegally traded animals that are often cross-bred in captivity. To overcome these problems, we used a genomic approach to analyze historical DNA from museum samples across the Asian Pied Starling (Gracupica contra) complex in tropical Asia, a popular victim of the ongoing songbird crisis whose distinct Javan population ("Javan Pied Starling") is extinct in the wild and subject to admixture in captivity. Comparing genomic profiles across the entire distribution, we detected three deeply diverged lineages at the species level characterized by a lack of genomic intermediacy near areas of contact. Our study demonstrates that the use of historical DNA can be instrumental in delimiting species in situations of taxonomic uncertainty, especially when modern admixture may obfuscate species boundaries. Results of our research will enable conservationists to commence a dedicated ex situ breeding program for the Javan Pied Starling, and serve as a blueprint for similar conservation problems involving terminally endangered species subject to allelic infiltration from close congeners.
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Affiliation(s)
- Pratibha Baveja
- Department of Biological SciencesNational University of SingaporeSingaporeSingapore
| | - Kritika M. Garg
- Department of Biological SciencesNational University of SingaporeSingaporeSingapore
- Institute of Bioinformatics and Applied BiotechnologyBangaloreIndia
| | - Balaji Chattopadhyay
- Department of Biological SciencesNational University of SingaporeSingaporeSingapore
| | - Keren R. Sadanandan
- Department of Biological SciencesNational University of SingaporeSingaporeSingapore
- Max Planck Institute for OrnithologySeewiesenGermany
| | | | - Pramana Yuda
- Fakultas TeknobiologiUniversitas Atma Jaya YogyakartaYogyakartaIndonesia
| | - Jessica G. H. Lee
- Department of Conservation and ResearchWildlife Reserves SingaporeSingaporeSingapore
| | - Frank E. Rheindt
- Department of Biological SciencesNational University of SingaporeSingaporeSingapore
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8
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Gwee CY, Garg KM, Chattopadhyay B, Sadanandan KR, Prawiradilaga DM, Irestedt M, Lei F, Bloch LM, Lee JGH, Irham M, Haryoko T, Soh MCK, Peh KSH, Rowe KMC, Ferasyi TR, Wu S, Wogan GOU, Bowie RCK, Rheindt FE. Phylogenomics of white-eyes, a 'great speciator', reveals Indonesian archipelago as the center of lineage diversity. eLife 2020; 9:e62765. [PMID: 33350381 PMCID: PMC7775107 DOI: 10.7554/elife.62765] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 12/21/2020] [Indexed: 01/09/2023] Open
Abstract
Archipelagoes serve as important 'natural laboratories' which facilitate the study of island radiations and contribute to the understanding of evolutionary processes. The white-eye genus Zosterops is a classical example of a 'great speciator', comprising c. 100 species from across the Old World, most of them insular. We achieved an extensive geographic DNA sampling of Zosterops by using historical specimens and recently collected samples. Using over 700 genome-wide loci in conjunction with coalescent species tree methods and gene flow detection approaches, we untangled the reticulated evolutionary history of Zosterops, which comprises three main clades centered in Indo-Africa, Asia, and Australasia, respectively. Genetic introgression between species permeates the Zosterops phylogeny, regardless of how distantly related species are. Crucially, we identified the Indonesian archipelago, and specifically Borneo, as the major center of diversity and the only area where all three main clades overlap, attesting to the evolutionary importance of this region.
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Affiliation(s)
- Chyi Yin Gwee
- National University of Singapore, Department of Biological SciencesSingaporeSingapore
| | - Kritika M Garg
- National University of Singapore, Department of Biological SciencesSingaporeSingapore
| | - Balaji Chattopadhyay
- National University of Singapore, Department of Biological SciencesSingaporeSingapore
| | - Keren R Sadanandan
- National University of Singapore, Department of Biological SciencesSingaporeSingapore
- Max Planck Institute for OrnithologySeewiesenGermany
| | - Dewi M Prawiradilaga
- Division of Zoology, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Cibinong Science CenterCibinongIndonesia
| | - Martin Irestedt
- Department of Bioinformatics and Genetics, Swedish Museum of Natural HistoryStockholmSweden
| | - Fumin Lei
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of SciencesBeijingChina
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of SciencesKunmingChina
| | - Luke M Bloch
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, BerkeleyBerkeleyUnited States
| | | | - Mohammad Irham
- Division of Zoology, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Cibinong Science CenterCibinongIndonesia
| | - Tri Haryoko
- Division of Zoology, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Cibinong Science CenterCibinongIndonesia
| | - Malcolm CK Soh
- University of Western Australia, School of Biological SciencesPerthAustralia
| | - Kelvin S-H Peh
- University of Southampton, School of Biological Sciences, UniversitySouthamptonUnited Kingdom
| | - Karen MC Rowe
- Sciences Department, Museums VictoriaMelbourneAustralia
| | - Teuku Reza Ferasyi
- Faculty of Veterinary Medicine, Universitas Syiah KualaDarussalamIndonesia
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, School of Life Sciences, Jiangsu Normal UniversityXuzhouChina
| | - Shaoyuan Wu
- Department of Biochemistry and Molecular Biology, 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, School of Basic Medical Sciences, Tianjin Medical UniversityTianjinChina
- Center for Tropical Veterinary Studies – One Health Collaboration Center, Universitas Syiah KualaDarussalamIndonesia
| | - Guinevere OU Wogan
- Museum of Vertebrate Zoology and Department of Environmental Science, Policy, and Management, University of California, BerkeleyBerkeleyUnited States
| | - Rauri CK Bowie
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, BerkeleyBerkeleyUnited States
| | - Frank E Rheindt
- National University of Singapore, Department of Biological SciencesSingaporeSingapore
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9
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Darras KF, Deppe F, Fabian Y, Kartono AP, Angulo A, Kolbrek B, Mulyani YA, Prawiradilaga DM. High microphone signal-to-noise ratio enhances acoustic sampling of wildlife. PeerJ 2020; 8:e9955. [PMID: 33150056 PMCID: PMC7585376 DOI: 10.7717/peerj.9955] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 08/25/2020] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND Automated sound recorders are a popular sampling tool in ecology. However, the microphones themselves received little attention so far, and specifications that determine the recordings' sound quality are seldom mentioned. Here, we demonstrate the importance of microphone signal-to-noise ratio for sampling sonant animals. METHODS We tested 12 different microphone models in the field and measured their signal-to-noise ratios and detection ranges. We also measured the vocalisation activity of birds and bats that they recorded, the bird species richness, the bat call types richness, as well as the performance of automated detection of bird and bat calls. We tested the relationship of each one of these measures with signal-to-noise ratio in statistical models. RESULTS Microphone signal-to-noise ratio positively affects the sound detection space areas, which increased by a factor of 1.7 for audible sound, and 10 for ultrasound, from the lowest to the highest signal-to-noise ratio microphone. Consequently, the sampled vocalisation activity increased by a factor of 1.6 for birds, and 9.7 for bats. Correspondingly, the species pool of birds and bats could not be completely detected by the microphones with lower signal-to-noise ratio. The performance of automated detection of bird and bat calls, as measured by its precision and recall, increased significantly with microphone signal-to-noise ratio. DISCUSSION Microphone signal-to-noise ratio is a crucial characteristic of a sound recording system, positively affecting the acoustic sampling performance of birds and bats. It should be maximised by choosing appropriate microphones, and be quantified independently, especially in the ultrasound range.
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Affiliation(s)
- Kevin F.A. Darras
- Agroecology, University of Göttingen, Göttingen, Niedersachsen, Germany
| | - Franziska Deppe
- Agroecology, University of Göttingen, Göttingen, Niedersachsen, Germany
| | - Yvonne Fabian
- Agroecology, University of Göttingen, Göttingen, Niedersachsen, Germany
- Agroscope FAL Reckenholz, Swiss Federal Research Station for Agroecology and Agriculture, Zurich, Switzerland
| | - Agus P. Kartono
- Department of Forest Resources, Conservation and Ecotourism, Bogor Institute of Agriculture, Bogor, Indonesia
| | - Andres Angulo
- Agroecology, University of Göttingen, Göttingen, Niedersachsen, Germany
| | - Bjørn Kolbrek
- Celestion International, Ipswich, Suffolk, United Kingdom
| | - Yeni A. Mulyani
- Department of Forest Resources, Conservation and Ecotourism, Bogor Institute of Agriculture, Bogor, Indonesia
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10
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Sadanandan KR, Low GW, Sridharan S, Gwee CY, Ng EYX, Yuda P, Prawiradilaga DM, Lee JGH, Tritto A, Rheindt FE. The conservation value of admixed phenotypes in a critically endangered species complex. Sci Rep 2020; 10:15549. [PMID: 32968132 PMCID: PMC7511927 DOI: 10.1038/s41598-020-72428-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 08/17/2020] [Indexed: 11/19/2022] Open
Abstract
In today's environmental crisis, conservationists are increasingly confronted with terminally endangered species whose last few surviving populations may be affected by allelic introgression from closely related species. Yet there is a worrying lack of evidence-based recommendations and solutions for this emerging problem. We analyzed genome-wide DNA markers and plumage variability in a critically endangered insular songbird, the Black-winged Myna (BWM, Acridotheres melanopterus). This species is highly threatened by the illegal wildlife trade, with its wild population numbering in the low hundreds, and its continued survival urgently depending on ex-situ breeding. Its three subspecies occur along a geographic gradient of melanism and are variably interpreted as three species. However, our integrative approach revealed that melanism poorly reflects the pattern of limited genomic differentiation across BWM subspecies. We also uncovered allelic introgression into the most melanistic subspecies, tertius, from the all-black congeneric Javan Myna (A. javanicus), which is native to the same islands. Based on our results, we recommend the establishment of three separate breeding programs to maintain subspecific traits that may confer local adaptation, but with the option of occasional cross-breeding between insurance populations in order to boost genetic diversity and increase overall viability prospects of each breeding program. Our results underscore the importance of evidence-based integrative approaches when determining appropriate conservation units. Given the rapid increase of terminally endangered organisms in need of ex-situ conservation, this study provides an important blueprint for similar programs dealing with phenotypically variable species.
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Affiliation(s)
- Keren R Sadanandan
- Department of Biological Sciences, National University of Singapore, Singapore, 117558, Singapore
- Max Planck Institute for Ornithology, 82319, Seewiesen, Germany
| | - Gabriel W Low
- Department of Biological Sciences, National University of Singapore, Singapore, 117558, Singapore
- School of Biological Sciences, Monash University, Clayton, VIC, 3800, Australia
| | - Sheeraja Sridharan
- Department of Biological Sciences, National University of Singapore, Singapore, 117558, Singapore
- Department of Biological Sciences, University of Alberta, 116 St & 85 Ave, Edmonton, AB, T6G 2R3, Canada
| | - Chyi Yin Gwee
- Department of Biological Sciences, National University of Singapore, Singapore, 117558, Singapore
| | - Elize Y X Ng
- Department of Biological Sciences, National University of Singapore, Singapore, 117558, Singapore
| | - Pramana Yuda
- Universitas Atma Jaya, Jl. Babarsari 44, Janti, Caturtunggal, Kec. Depok, Kabupaten Sleman, Daerah Istimewa Yogyakarta, 55281, Indonesia
| | - Dewi M Prawiradilaga
- Division of Zoology, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Jalan Raya Jakarta Bogor KM 46, Cibinong Science Center, Cibinong, 16911, Indonesia
| | - Jessica G H Lee
- Wildlife Reserves Singapore, 80 Mandai Lake Road, Singapore, 729826, Singapore
| | - Anaïs Tritto
- Wildlife Reserves Singapore, 80 Mandai Lake Road, Singapore, 729826, Singapore
| | - Frank E Rheindt
- Department of Biological Sciences, National University of Singapore, Singapore, 117558, Singapore.
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11
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Rheindt FE, Prawiradilaga DM, Ashari H, Suparno, Gwee CY, Lee GWX, Wu MY, Ng NSR. A lost world in Wallacea: Description of a montane archipelagic
avifauna. Science 2020; 367:167-170. [DOI: 10.1126/science.aax2146] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Accepted: 11/21/2019] [Indexed: 12/16/2022]
Abstract
Birds are the best-known animal class, with only about five or six new
species descriptions per year since 1999. Integrating genomic and phenotypic
research with arduous fieldwork in remote regions, we describe five new songbird
species and five new subspecies from a small area near Sulawesi, Indonesia, all
collected in a single 6-week expedition. Two factors contributed to the
description of this large number of species from such a small geographic area: (i)
Knowledge of Quaternary Period land connections helped pinpoint isolated islands
likely to harbor substantial endemism and (ii) studying accounts of historic
collectors such as Alfred Wallace facilitated the identification of undercollected
islands. Our findings suggest that humans’ understanding of biogeographically
complex regions such as Wallacea remains incomplete.
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Affiliation(s)
- Frank E. Rheindt
- National University of Singapore, Department of Biological Sciences, 14 Science Drive 4, Singapore 117543
| | - Dewi M. Prawiradilaga
- Division of Zoology, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Jalan Raya Jakarta Bogor KM 46, Cibinong Science Center, Cibinong 16911, Indonesia
| | - Hidayat Ashari
- Division of Zoology, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Jalan Raya Jakarta Bogor KM 46, Cibinong Science Center, Cibinong 16911, Indonesia
| | - Suparno
- Division of Zoology, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Jalan Raya Jakarta Bogor KM 46, Cibinong Science Center, Cibinong 16911, Indonesia
| | - Chyi Yin Gwee
- National University of Singapore, Department of Biological Sciences, 14 Science Drive 4, Singapore 117543
| | - Geraldine W. X. Lee
- National University of Singapore, Department of Biological Sciences, 14 Science Drive 4, Singapore 117543
| | - Meng Yue Wu
- National University of Singapore, Department of Biological Sciences, 14 Science Drive 4, Singapore 117543
| | - Nathaniel S. R. Ng
- National University of Singapore, Department of Biological Sciences, 14 Science Drive 4, Singapore 117543
- Department of Conservation and Research, Wildlife Reserves Singapore, 80 Mandai Lake Road, Singapore 729826
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12
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Gwee CY, Eaton JA, Garg KM, Alström P, Van Balen S(B, Hutchinson RO, Prawiradilaga DM, Le MH, Rheindt FE. Cryptic diversity in Cyornis (Aves: Muscicapidae) jungle-flycatchers flagged by simple bioacoustic approaches. Zool J Linn Soc 2019. [DOI: 10.1093/zoolinnean/zlz003] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Affiliation(s)
- Chyi Yin Gwee
- Department of Biological Sciences, National University of Singapore, Singapore
| | - James A Eaton
- Birdtour Asia Ltd, Littleover, Derby, United Kingdom
| | - Kritika M Garg
- Department of Biological Sciences, National University of Singapore, Singapore
| | - Per Alström
- Department of Ecology and Genetics, Animal Ecology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
- Swedish Species Information Centre, Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | | | | | - Dewi M Prawiradilaga
- Research Centre for Biology, Indonesian Institute of Sciences (LIPI), Cibinong Science Centre, Jalan Raya Jakarta Bogor, Indonesia
| | - Manh Hung Le
- Graduated University of Science and Technology, Vietnam Academy of Science and Technology (VAST), Caugiay, Hanoi, Vietnam
| | - Frank E Rheindt
- Department of Biological Sciences, National University of Singapore, Singapore
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13
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Ng NSR, Prawiradilaga DM, Ng EYX, Suparno, Ashari H, Trainor C, Verbelen P, Rheindt FE. A striking new species of leaf warbler from the Lesser Sundas as uncovered through morphology and genomics. Sci Rep 2018; 8:15646. [PMID: 30353148 PMCID: PMC6199301 DOI: 10.1038/s41598-018-34101-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Accepted: 09/27/2018] [Indexed: 11/09/2022] Open
Abstract
Leaf warblers (Aves; Phylloscopidae) are a diverse clade of insectivorous, canopy-dwelling songbirds widespread across the Old World. The taxonomy of Australasian leaf warblers is particularly complex, with multiple species-level divergences between island taxa in the region requiring further scrutiny. We use a combination of morphology, bioacoustics, and analysis of thousands of genome-wide markers to investigate and describe a new species of Phylloscopus leaf warbler from the island of Rote in the Lesser Sundas, Indonesia. We show that this new Rote Leaf Warbler is morphologically and genomically highly distinct from its congenerics, but do not find vocal differentiation between different island taxa. We discuss the behaviour and ecology of this highly distinctive new species, and make recommendations about its conservation status. We believe this constitutes the first description of a novel bird species that is partly based on insights from massive amounts of genome-wide DNA markers.
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Affiliation(s)
- Nathaniel S R Ng
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore, 129801, Singapore
| | - Dewi M Prawiradilaga
- Division of Zoology, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Jalan Raya Jakarta Bogor KM 46, Cibinong Science Center, Cibinong, 16911, Indonesia
| | - Elize Y X Ng
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore, 129801, Singapore
| | - Suparno
- Division of Zoology, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Jalan Raya Jakarta Bogor KM 46, Cibinong Science Center, Cibinong, 16911, Indonesia
| | - Hidayat Ashari
- Division of Zoology, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Jalan Raya Jakarta Bogor KM 46, Cibinong Science Center, Cibinong, 16911, Indonesia
| | - Colin Trainor
- Research Institute for the Environment and Livelihoods, Charles Darwin University, Darwin, NT, 0909, Australia
| | | | - Frank E Rheindt
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore, 129801, Singapore.
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14
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Alström P, Rheindt FE, Zhang R, Zhao M, Wang J, Zhu X, Gwee CY, Hao Y, Ohlson J, Jia C, Prawiradilaga DM, Ericson PGP, Lei F, Olsson U. Complete species-level phylogeny of the leaf warbler (Aves: Phylloscopidae) radiation. Mol Phylogenet Evol 2018; 126:141-152. [PMID: 29631054 DOI: 10.1016/j.ympev.2018.03.031] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Revised: 02/24/2018] [Accepted: 03/28/2018] [Indexed: 10/17/2022]
Abstract
The leaf warbler radiation (Aves: Phylloscopidae) has undergone a c. 50% increase in the number of recognised species over the last three decades, mainly as a result of analyses of vocalisations and DNA. Using a multilocus dataset for all of the species in this family, and multispecies coalescent-based as well as concatenation methods, we provide the first complete species-level phylogeny for this important group, as well as an estimate of the timing of diversification. The most recent common ancestor for the family was dated at 11.7 million years ago (mya) (95% highest posterior density 9.8-13.7 mya), and divergence times between sister species ranged from 0.5 mya (0.3-0.8 mya) to 6.1 mya (4.8-7.5 mya). Based on our results, we support synonymising Seicercus with Phylloscopus, which results in a monogeneric Phylloscopidae. We discuss the pros and cons of this treatment,and we argue againstproliferation of taxonomic names,and conclude that a large monogeneric Phylloscopidae leads to the fewest taxonomic changes compared to traditional classifications. We briefly discuss morphological evolution in the light of the phylogeny. The time calibrated phylogeny is a major improvement compared to previous studies based on a smaller number of species and loci and can provide a basis for future studies of other aspects of phylloscopid evolution.
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Affiliation(s)
- Per Alström
- Department of Ecology and Genetics, Animal Ecology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, 752 36 Uppsala, Sweden; Swedish Species Information Centre, Swedish University of Agricultural Sciences (SLU), Box 7007, Uppsala SE-750 07, Sweden; Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.
| | - Frank E Rheindt
- Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, 117558 Singapore, Singapore
| | - Ruiying Zhang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Min Zhao
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jing Wang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiaojia Zhu
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Chyi Yin Gwee
- Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, 117558 Singapore, Singapore
| | - Yan Hao
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jan Ohlson
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Box 50007, Stockholm SE-10405, Sweden
| | - Chenxi Jia
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Dewi M Prawiradilaga
- Research Centre for Biology, Indonesian Institute of Sciences (LIPI), Cibinong Science Centre, Jalan Raya Jakarta Bogor KM 46, Bogor 16911, Indonesia
| | - Per G P Ericson
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Box 50007, Stockholm SE-10405, Sweden
| | - Fumin Lei
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Urban Olsson
- Department of Biology and Environmental Science, University of Gothenburg, Box 463, SE-405 30 Gothenburg, Sweden
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15
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Shakya SB, Haryoko T, Burner RC, Prawiradilaga DM, Sheldon FH. Preliminary assessment of community composition and phylogeographic relationships of the birds of the Meratus Mountains, south-east borneo, Indonesia. ACTA ACUST UNITED AC 2018. [DOI: 10.25226/bboc.v138i1.2018.a6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Affiliation(s)
- Subir B. Shakya
- Subir B. Shakya, Dept. of Biological Sciences and Museum of Natural Science, Louisiana State University, Baton Rouge, Louisiana 70803, USA,
| | - Tri Haryoko
- Tri Haryoko, Division of Zoology, Research Centre for Biology-LIPI, Jalan Raya Bogor km 46, Cibinong-Bogor 16911, Indonesia,
| | - Ryan C. Burner
- Ryan C. Burner, Dept. of Biological Sciences and Museum of Natural Science, Louisiana State University, Baton Rouge, Louisiana 70803, USA,
| | - Dewi M. Prawiradilaga
- Dewi Prawiradilaga, Division of Zoology, Research Centre for Biology-LIPI, Jalan Raya Bogor km 46, Cibinong-Bogor 16911, Indonesia,
| | - Frederick H. Sheldon
- Frederick H. Sheldon, Dept. of Biological Sciences and Museum of Natural Science, Louisiana State University, Baton Rouge, Louisiana 70803, USA,
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16
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Chua VL, Smith BT, Burner RC, Rahman MA, Lakim M, Prawiradilaga DM, Moyle RG, Sheldon FH. Evolutionary and ecological forces influencing population diversification in Bornean montane passerines. Mol Phylogenet Evol 2017; 113:139-149. [PMID: 28545973 DOI: 10.1016/j.ympev.2017.05.016] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Revised: 04/28/2017] [Accepted: 05/16/2017] [Indexed: 01/05/2023]
Abstract
The mountains of Borneo are well known for their high endemicity and historical role in preserving Southeast Asian rainforest biodiversity, but the diversification of populations inhabiting these mountains is poorly studied. Here we examine the genetic structure of 12 Bornean montane passerines by comparing complete mtDNA ND2 gene sequences of populations spanning the island. Maximum likelihood and Bayesian phylogenetic trees and haplotype networks are examined for common patterns that might signal important historical events or boundaries to dispersal. Morphological and ecological characteristics of each species are also examined using phylogenetic generalized least-squares (PGLS) for correlation with population structure. Populations in only four of the 12 species are subdivided into distinct clades or haplotype groups. Although this subdivision occurred at about the same time in each species (ca. 0.6-0.7Ma), the spatial positioning of the genetic break differs among the species. In two species, northeastern populations are genetically divergent from populations elsewhere on the island. In the other two species, populations in the main Bornean mountain chain, including the northeast, are distinct from those on two isolated peaks in northwestern Borneo. We suggest different historical forces played a role in shaping these two distributions, despite commonality in timing. PGLS analysis showed that only a single characteristic-hand-wing index-is correlated with population structure. Birds with longer wings, and hence potentially more dispersal power, have less population structure. To understand historical forces influencing montane population structure on Borneo, future studies must compare populations across the entirety of Sundaland.
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Affiliation(s)
- Vivien L Chua
- Museum of Natural Science and Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA.
| | - Brian Tilston Smith
- Department of Ornithology, American Museum of Natural History, New York 10024, USA
| | - Ryan C Burner
- Museum of Natural Science and Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Mustafa Abdul Rahman
- Faculty of Resource Science and Technology, Universiti Malaysia Sarawak, 94300 Kota Samarahan, Sarawak, Malaysia
| | - Maklarin Lakim
- Sabah Parks, P.O. Box 10626, 88806 Kota Kinabalu, Sabah, Malaysia
| | - Dewi M Prawiradilaga
- Division of Zoology, Research Centre for Biology-LIPI, Jl. Raya Bogor km. 46, Cibinong-Bogor 16911, Indonesia
| | - Robert G Moyle
- Biodiversity Institute and Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS 66045, USA
| | - Frederick H Sheldon
- Museum of Natural Science and Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
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17
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Harris JBC, Tingley MW, Hua F, Yong DL, Adeney JM, Lee TM, Marthy W, Prawiradilaga DM, Sekercioglu CH, Winarni N, Wilcove DS. Measuring the impact of the pet trade on Indonesian birds. Conserv Biol 2017; 31:394-405. [PMID: 28146342 DOI: 10.1111/cobi.12729] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2015] [Revised: 02/14/2016] [Accepted: 03/25/2016] [Indexed: 06/06/2023]
Abstract
The trade in wild animals involves one-third of the world's bird species and thousands of other vertebrate species. Although a few species are imperiled as a result of the wildlife trade, the lack of field studies makes it difficult to gauge how serious a threat it is to biodiversity. We used data on changes in bird abundances across space and time and information from trapper interviews to evaluate the effects of trapping wild birds for the pet trade in Sumatra, Indonesia. To analyze changes in bird abundance over time, we used data gathered over 14 years of repeated bird surveys in a 900-ha forest in southern Sumatra. In northern Sumatra, we surveyed birds along a gradient of trapping accessibility, from the edge of roads to 5 km into the forest interior. We interviewed 49 bird trappers in northern Sumatra to learn which species they targeted and how far they went into the forest to trap. We used prices from Sumatran bird markets as a proxy for demand and, therefore, trapping pressure. Market price was a significant predictor of species declines over time in southern Sumatra (e.g., given a market price increase of approximately $50, the log change in abundance per year decreased by 0.06 on average). This result indicates a link between the market-based pet trade and community-wide species declines. In northern Sumatra, price and change in abundance were not related to remoteness (distance from the nearest road). However, based on our field surveys, high-value species were rare or absent across this region. The median maximum distance trappers went into the forest each day was 5.0 km. This suggests that trapping has depleted bird populations across our remoteness gradient. We found that less than half of Sumatra's remaining forests are >5 km from a major road. Our results suggest that trapping for the pet trade threatens birds in Sumatra. Given the popularity of pet birds across Southeast Asia, additional studies are urgently needed to determine the extent and magnitude of the threat posed by the pet trade.
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Affiliation(s)
- J Berton C Harris
- Woodrow Wilson School of Public and International Affairs, Princeton University, Princeton, NJ, 08544, U.S.A
- Rainforest Trust, 7078 Airlie Road, Warrenton, VA, 20187, U.S.A
| | - Morgan W Tingley
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, 06269, U.S.A
| | - Fangyuan Hua
- Woodrow Wilson School of Public and International Affairs, Princeton University, Princeton, NJ, 08544, U.S.A
| | - Ding Li Yong
- Fenner School of Environment and Society, The Australian National University, Barry Drive, Acton, ACT, 0200, Australia
- South-east Asian Biodiversity Society, 504 Choa Chu Kang Street 51, 680504, Singapore
| | - J Marion Adeney
- Nicholas School of the Environment, Duke University, Durham, NC, 27708, U.S.A
| | - Tien Ming Lee
- Woodrow Wilson School of Public and International Affairs, Princeton University, Princeton, NJ, 08544, U.S.A
| | - William Marthy
- Wildlife Conservation Society-Indonesia Programme, Jl. Atletik No. 8, Tanah Sareal, Bogor, 16161, Indonesia
| | - Dewi M Prawiradilaga
- Division of Zoology, Research Centre for Biology-LIPI, Jl. Raya Bogor Km 46, Cibinong Science Centre, Bogor, 16911, Indonesia
| | - Cagan H Sekercioglu
- Department of Biology, University of Utah, Salt Lake City, UT, 84112, U.S.A
- KuzeyDoğa Derneği, Ortakapı Mah, Șehit Yusuf Cad., No 93/1, 36100, Kars, Turkey
| | - Nurul Winarni
- Research Center for Climate Change, Universitas Indonesia, Gd. PAU lt. 8,5. Kampus UI Depok, Depok, 16422, Indonesia
| | - David S Wilcove
- Woodrow Wilson School of Public and International Affairs, Princeton University, Princeton, NJ, 08544, U.S.A
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, 08544, U.S.A
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18
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Harris JBC, Rasmussen PC, Yong DL, Prawiradilaga DM, Putra DD, Round PD, Rheindt FE. A new species of Muscicapa flycatcher from Sulawesi, Indonesia. PLoS One 2014; 9:e112657. [PMID: 25419968 PMCID: PMC4242539 DOI: 10.1371/journal.pone.0112657] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2014] [Accepted: 10/07/2014] [Indexed: 11/18/2022] Open
Abstract
The Indonesian island of Sulawesi, a globally important hotspot of avian endemism, has been relatively poorly studied ornithologically, to the extent that several new bird species from the region have been described to science only recently, and others have been observed and photographed, but never before collected or named to science. One of these is a new species of Muscicapa flycatcher that has been observed on several occasions since 1997. We collected two specimens in Central Sulawesi in 2012, and based on a combination of morphological, vocal and genetic characters, we describe the new species herein, more than 15 years after the first observations. The new species is superficially similar to the highly migratory, boreal-breeding Gray-streaked Flycatcher Muscicapa griseisticta, which winters in Sulawesi; however, the new species differs strongly from M. griseisticta in several morphological characters, song, and mtDNA. Based on mtDNA, the new species is only distantly related to M. griseisticta, instead being a member of the M. dauurica clade. The new species is evidently widely distributed in lowland and submontane forest throughout Sulawesi. This wide distribution coupled with the species' apparent tolerance of disturbed habitats suggests it is not currently threatened with extinction.
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Affiliation(s)
- J. Berton C. Harris
- Environment Institute and School of Earth and Environmental Sciences, University of Adelaide, Adelaide, South Australia, Australia
- Woodrow Wilson School of Public and International Affairs, Princeton University, Princeton, New Jersey, United States of America
| | - Pamela C. Rasmussen
- Michigan State University Museum and Department of Integrative Biology, East Lansing, Michigan, United States of America
- Bird Group, Department of Life Sciences, Natural History Museum at Tring, Tring, Herts, United Kingdom
| | - Ding Li Yong
- Fenner School of Environment and Society, Australian National University, Acton, Australian Capital Territory, Australia
- South-east Asian Biodiversity Society, Singapore, Republic of Singapore
| | - Dewi M. Prawiradilaga
- Division of Zoology, Research Centre for Biology, Lembaga Ilmu Pengetahuan Indonesia, Cibinong-Bogor, West Java, Indonesia
| | | | - Philip D. Round
- Department of Biology, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Frank E. Rheindt
- Department of Biological Sciences, National University of Singapore, Singapore, Republic of Singapore
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19
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Harris JBC, Dwi Putra D, Gregory SD, Brook BW, Prawiradilaga DM, Sodhi NS, Wei D, Fordham DA. Rapid deforestation threatens mid-elevational endemic birds but climate change is most important at higher elevations. DIVERS DISTRIB 2014. [DOI: 10.1111/ddi.12180] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Affiliation(s)
- J. Berton C. Harris
- Environment Institute and School of Earth and Environmental Sciences; University of Adelaide; Adelaide SA 5005 Australia
- Woodrow Wilson School of Public and International Affairs; Princeton University; Princeton NJ 08542 USA
| | - Dadang Dwi Putra
- Celebes Bird Club; Jl. Thamrin 63A Palu Central Sulawesi Indonesia
| | - Stephen D. Gregory
- Environment Institute and School of Earth and Environmental Sciences; University of Adelaide; Adelaide SA 5005 Australia
- Game and Wildlife Conservation Trust; Salmon and Trout Research Centre; Wareham BH20 6BB UK
| | - Barry W. Brook
- Environment Institute and School of Earth and Environmental Sciences; University of Adelaide; Adelaide SA 5005 Australia
| | - Dewi M. Prawiradilaga
- Division of Zoology; Research Centre for Biology-LIPI; Jl. Raya Bogor Km 46 Cibinong-Bogor 16911 Indonesia
| | - Navjot S. Sodhi
- Department of Biological Sciences; National University of Singapore; 14 Science Drive 4 Singapore 117543 Singapore
| | - Dan Wei
- Stawell Secondary College; Patrick St. Stawell Vic. 3380 Australia
| | - Damien A. Fordham
- Environment Institute and School of Earth and Environmental Sciences; University of Adelaide; Adelaide SA 5005 Australia
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20
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Sodhi NS, Wilcove DS, Lee TM, Sekercioglu CH, Subaraj R, Bernard H, Yong DL, Lim SLH, Prawiradilaga DM, Brook BW. Deforestation and avian extinction on tropical landbridge islands. Conserv Biol 2010; 24:1290-1298. [PMID: 20345403 DOI: 10.1111/j.1523-1739.2010.01495.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
There are few empirical data, particularly collected simultaneously from multiple sites, on extinctions resulting from human-driven land-use change. Southeast Asia has the highest deforestation rate in the world, but the resulting losses of biological diversity remain poorly documented. Between November 2006 and March 2008, we conducted bird surveys on six landbridge islands in Malaysia and Indonesia. These islands were surveyed previously for birds in the early 1900 s, when they were extensively forested. Our bird inventories of the islands were nearly complete, as indicated by sampling saturation curves and nonparametric true richness estimators. From zero (Pulau Malawali and Pulau Mantanani) to 15 (Pulau Bintan) diurnal resident landbird species were apparently extirpated since the early 1900 s. Adding comparable but published extinction data from Singapore to our regression analyses, we found there were proportionally fewer forest bird extinctions in areas with greater remaining forest cover. Nevertheless, the statistical evidence to support this relationship was weak, owing to our unavoidably small sample size. Bird species that are restricted to the Indomalayan region, lay few eggs, are heavier, and occupy a narrower habitat breadth, were most vulnerable to extinction on Pulau Bintan. This was the only island where sufficient data existed to analyze the correlates of extinction. Forest preservation and restoration are needed on these islands to conserve the remaining forest avifauna. Our study of landbridge islands indicates that deforestation may increasingly threaten Southeast Asian biodiversity.
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Affiliation(s)
- Navjot S Sodhi
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543, Republic of Singapore.
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21
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Abstract
The All Birds Barcoding Initiative aims to assemble a DNA barcode database for all bird species, but the 648-bp 'barcoding' region of cytochrome c oxidase subunit I (COI) can be difficult to amplify in Southeast Asian perching birds (Aves: Passeriformes). Using COI sequences from complete mitochondrial genomes, we designed a primer pair that more reliably amplifies and sequences the COI barcoding region of Southeast Asian passerine birds. The 655-bp region amplified with these primers overlaps the COI region amplified with other barcoding primer pairs, enabling direct comparison of sequences with previously published DNA barcodes.
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Affiliation(s)
- David J Lohman
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543, Division of Zoology, Research Centre for Biology-LIPI, Jl. Raya Bogor Km 46, Cibinong-Bogor, 16911, Indonesia
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22
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Lee TM, Sodhi NS, Prawiradilaga DM. The importance of protected areas for the forest and endemic avifauna of Sulawesi (Indonesia). Ecol Appl 2007; 17:1727-41. [PMID: 17913136 DOI: 10.1890/06-1256.1] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Protected areas are critical for the conservation of residual tropical forest biodiversity, yet many of these are being deforested by humans both within and outside of their administrative boundaries. Therefore, it is critical to document the significance of protected areas for conserving tropical biodiversity, particularly in mega-diverse Southeast Asia. We evaluated the importance of protected areas (national parks [NP], nature reserves [NR], and wildlife reserves [WR]) in preserving avifaunal diversity, particularly the endemic and forest species, on the island of Sulawesi. This island has one of the highest numbers of endemic avifauna genera (12) globally and is also experiencing heavy deforestation. Rarefaction analyses and species estimators showed that parks and reserves consistently recorded higher number of forest, endemic, and endemic forest bird species, in addition to larger population densities, than in their surrounding human-modified areas across eight protected areas (Gunung Manembo-nembo WR, Tangkoko-Batu Angus and Dua Saudara NR, Gunung Ambang NR, Bogani Nani Wartabone NP, Gunung Tinombala NR, Gunung Sojol NR, Lore Lindu NP, and Rawa Aopa Watumohai NP). This implies that protecting natural forests must remain as one of the fundamental conservation strategies in Sulawesi. Two small reserves (Gunung Manembo-nembo WR and Tangkoko-Batu Angus and Dua Saudara NR), however, had high number of forest and endemic bird species both within and outside their boundaries, suggesting the importance of buffer areas for augmenting small reserves so as to improve their conservation value. Ordination analyses revealed the differential response of bird species to different environmental factors (e.g., native tree cover), highlighting the significance of forested habitats with dense native vegetation cover for effective conservation of forest dependent and endemic avifauna. In addition, the distinctiveness in bird species composition among protected areas highlights the importance of establishing a reserve network across major altitudinal zones so as to achieve maximum complementarity for the conservation of Sulawesi's unique avifauna.
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Affiliation(s)
- Tien Ming Lee
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543, Republic of Singapore
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23
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Abstract
Long-term (> 50 years) extinction patterns and processes in isolated tropical forest patches are poorly understood. Considering that forest fragments are rapidly becoming the common feature of most tropical landscapes, data on the long-term conservation value of such fragments are urgently needed. We report on avifaunal turnover in a tropical woodlot (Bogor Botanical Gardens; 86 ha; 54% native and 46% introduced plants; mean 83,649 visitors/month) that has been surveyed several times before and after its isolation in 1936. By 2004 the original avifaunal richness of this woodlot declined by 59% (97 to 40 species) and its forest-dependent avifauna declined by 60% (30 to 12 species). Large-bodied birds were particularly prone to extinction before 1987, but following this time none of the species traits we studied could be considered predictive of extinction proneness. All seven forest-dependent bird species that attempted to colonize this woodlot by 1987 perished thereafter. Our results show that area reduction, isolation, intense human use, and perverse management (e.g., understory removal) of this patch have probably negatively affected the long-term sustainability of its forest avifauna.
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Affiliation(s)
- Navjot S Sodhi
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543, Republic of Singapore.
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