Species Distribution Modelling: Contrasting presence-only models with plot abundance data

Vitor H. F. Gomes; Stéphanie D. Ijff; Niels Raes; Iêda Leão Amaral; Rafael P. Salomão; Luiz de Souza Coelho; Francisca Dionízia de Almeida Matos; Carolina V. Castilho; Diogenes de Andrade Lima Filho; Dairon Cárdenas López; Juan Ernesto Guevara; William E. Magnusson; Oliver L. Phillips; Florian Wittmann; Marcelo de Jesus Veiga Carim; Maria Pires Martins; Mariana Victória Irume; Daniel Sabatier; Jean-François Molino; Olaf S. Bánki; José Renan da Silva Guimarães; Nigel C. A. Pitman; Maria Teresa Fernandez Piedade; Abel Monteagudo Mendoza; Bruno Garcia Luize; Eduardo Martins Venticinque; Evlyn Márcia Moraes de Leão Novo; Percy Núñez Vargas; Thiago Sanna Freire Silva; Angelo Gilberto Manzatto; John Terborgh; Neidiane Farias Costa Reis; Juan Carlos Montero; Katia Regina Casula; Beatriz S. Marimon; Ben-Hur Marimon; Euridice N. Honorio Coronado; Ted R. Feldpausch; Alvaro Duque; Charles Eugene Zartman; Nicolás Castaño Arboleda; Timothy J. Killeen; Bonifacio Mostacedo; Rodolfo Vasquez; Jochen Schöngart; Rafael L. Assis; Marcelo Brilhante Medeiros; Marcelo Fragomeni Simon; Ana Andrade; William F. Laurance; José Luís Camargo; Layon O. Demarchi; Susan G. W. Laurance; Emanuelle de Sousa Farias; Henrique Eduardo Mendonça Nascimento; Juan David Cardenas Revilla; Adriano Quaresma; Flavia R. C. Costa; Ima Célia Guimarães Vieira; Bruno Barçante Ladvocat Cintra; Hernán Castellanos; Roel Brienen; Pablo R. Stevenson; Yuri Feitosa; Joost F. Duivenvoorden; Gerardo A. Aymard C.; Hugo F. Mogollón; Natalia Targhetta; James A. Comiskey; Alberto Vicentini; Aline Lopes; Gabriel Damasco; Nállarett Dávila; Roosevelt García-Villacorta; Carolina Levis; Juliana Schietti; Priscila Souza; Thaise Emilio; Alfonso Alonso; David Neill; Francisco Dallmeier; Leandro Valle Ferreira; Alejandro Araujo-Murakami; Daniel Praia; Dário Dantas Do Amaral; Fernanda Antunes Carvalho; Fernanda Coelho de Souza; Kenneth Feeley; Luzmila Arroyo; Marcelo Petratti Pansonato; Rogerio Gribel; Boris Villa; Juan Carlos Licona; Paul V. A. Fine; Carlos Cerón; Chris Baraloto; Eliana M. Jimenez; Juliana Stropp; Julien Engel; Marcos Silveira; Maria Cristina Peñuela Mora; Pascal Petronelli; Paul Maas; Raquel Thomas-Caesar; Terry W. Henkel; Doug Daly; Marcos Ríos Paredes; Tim R. Baker; Alfredo Fuentes; Carlos A. Peres; Jerome Chave; Jose Luis Marcelo Pena; Kyle G. Dexter; Miles R. Silman; Peter Møller Jørgensen; Toby Pennington; Anthony Di Fiore; Fernando Cornejo Valverde; Juan Fernando Phillips; Gonzalo Rivas-Torres; Patricio von Hildebrand; Tinde R. van Andel; Ademir R. Ruschel; Adriana Prieto; Agustín Rudas; Bruce Hoffman; César I. A. Vela; Edelcilio Marques Barbosa; Egleé L. Zent; George Pepe Gallardo Gonzales; Hilda Paulette Dávila Doza; Ires Paula de Andrade Miranda; Jean-Louis Guillaumet; Linder Felipe Mozombite Pinto; Luiz Carlos de Matos Bonates; Natalino Silva; Ricardo Zárate Gómez; Stanford Zent; Therany Gonzales; Vincent A. Vos; Yadvinder Malhi; Alexandre A. Oliveira; Angela Cano; Bianca Weiss Albuquerque; Corine Vriesendorp; Diego Felipe Correa; Emilio Vilanova Torre; Geertje van Der Heijden; Hirma Ramirez-Angulo; José Ferreira Ramos; Kenneth R. Young; Maira Rocha; Marcelo Trindade Nascimento; Maria Natalia Umaña Medina; Milton Tirado; Ophelia Wang; Rodrigo Sierra; Armando Torres-Lezama; Casimiro Mendoza; Cid Ferreira; Cláudia Baider; Daniel Villarroel; Henrik Balslev; Italo Mesones; Ligia Estela Urrego Giraldo; Luisa Fernanda Casas; Manuel Augusto Ahuite Reategui; Reynaldo Linares-Palomino; Roderick Zagt; Sasha Cárdenas; William Farfan-Rios; Adeilza Felipe Sampaio; Daniela Pauletto; Elvis H. Valderrama Sandoval; Freddy Ramirez Arevalo; Isau Huamantupa-Chuquimaco; Karina Garcia-Cabrera; Lionel Hernandez; Luis Valenzuela Gamarra; Miguel N. Alexiades; Susamar Pansini; Walter Palacios Cuenca; William Milliken; Joana Ricardo; Gabriela Lopez-Gonzalez; Edwin Pos; Hans ter Steege

doi:10.1038/s41598-017-18927-1

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Species Distribution Modelling: Contrasting presence-only models with plot abundance data

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Species Distribution Modelling: Contrasting presence-only models with plot abundance data

Vitor H. F. Gomes, Stéphanie D. Ijff, Niels Raes, Iêda Leão Amaral, Rafael P. Salomão, Luiz de Souza Coelho, Francisca Dionízia de Almeida Matos, Carolina V. Castilho, Diogenes de Andrade Lima Filho, Dairon Cárdenas López, …

Scientific Reports, Vol.8(1)

2018

DOI: https://doi.org/10.1038/s41598-017-18927-1

Abstract

biodiversité

Species distribution models (SDMs) are widely used in ecology and conservation. Presence-only SDMs such as MaxEnt frequently use natural history collections (NHCs) as occurrence data, given their huge numbers and accessibility. NHCs are often spatially biased which may generate inaccuracies in SDMs. Here, we test how the distribution of NHCs and MaxEnt predictions relates to a spatial abundance model, based on a large plot dataset for Amazonian tree species, using inverse distance weighting (IDW). We also propose a new pipeline to deal with inconsistencies in NHCs and to limit the area of occupancy of the species. We found a significant but weak positive relationship between the distribution of NHCs and IDW for 66% of the species. The relationship between SDMs and IDW was also significant but weakly positive for 95% of the species, and sensitivity for both analyses was high. Furthermore, the pipeline removed half of the NHCs records. Presence-only SDM applications should consider this limitation, especially for large biodiversity assessments projects, when they are automatically generated without subsequent checking. Our pipeline provides a conservative estimate of a species’ area of occupancy, within an area slightly larger than its extent of occurrence, compatible to e.g. IUCN red list assessments.

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Title: Species Distribution Modelling: Contrasting presence-only models with plot abundance data
Creators - without role: Vitor H. F. Gomes - Museu Paraense Emílio Goeldi
Stéphanie D. Ijff - Naturalis Biodiversity Center
Niels Raes - Naturalis Biodiversity Center
Iêda Leão Amaral - National Institute of Amazonian Research
Rafael P. Salomão - Universidade Federal do Pará
Luiz de Souza Coelho - National Institute of Amazonian Research
Francisca Dionízia de Almeida Matos - National Institute of Amazonian Research
Carolina V. Castilho - Brazilian Agricultural Research Corporation
Diogenes de Andrade Lima Filho - National Institute of Amazonian Research
Dairon Cárdenas López - Instituto Sinchi
Juan Ernesto Guevara - University of California, Berkeley
William E. Magnusson - National Institute of Amazonian Research
Oliver L. Phillips - University of Leeds
Florian Wittmann - Karlsruhe Institute of Technology
Marcelo de Jesus Veiga Carim - Instituto de Pesquisas Tecnológicas
Maria Pires Martins - National Institute of Amazonian Research
Mariana Victória Irume - National Institute of Amazonian Research
Daniel Sabatier - Université de Montpellier, BotAnique et Modélisation de l'Architecture des Plantes et des végétations - AMAP
Jean-François Molino - Université de Montpellier, BotAnique et Modélisation de l'Architecture des Plantes et des végétations - AMAP
Olaf S. Bánki - Naturalis Biodiversity Center
José Renan da Silva Guimarães - Instituto de Pesquisas Tecnológicas
Nigel C. A. Pitman - Field Museum of Natural History
Maria Teresa Fernandez Piedade - National Institute of Amazonian Research
Abel Monteagudo Mendoza
Bruno Garcia Luize - Universidade Estadual Paulista (Unesp)
Eduardo Martins Venticinque - Universidade Federal do Rio Grande do Norte
Evlyn Márcia Moraes de Leão Novo - National Institute for Space Research
Percy Núñez Vargas - National University of Saint Anthony the Abbot in Cuzco
Thiago Sanna Freire Silva - Universidade Estadual Paulista (Unesp)
Angelo Gilberto Manzatto - Universidade Federal de Rondônia
John Terborgh - Duke University
Neidiane Farias Costa Reis - Universidade Federal de Rondônia
Juan Carlos Montero - National Institute of Amazonian Research
Katia Regina Casula - Universidade Federal de Rondônia
Beatriz S. Marimon - Universidade do Estado de Mato Grosso
Ben-Hur Marimon - Universidade do Estado de Mato Grosso
Euridice N. Honorio Coronado - University of Leeds
Ted R. Feldpausch - University of Exeter
Alvaro Duque - Universidad Nacional de Colombia
Charles Eugene Zartman - National Institute of Amazonian Research
Nicolás Castaño Arboleda - Instituto Sinchi
Timothy J. Killeen - Universidad Nacional del Oriente
Bonifacio Mostacedo - Gabriel René Moreno Autonomous University
Rodolfo Vasquez
Jochen Schöngart - National Institute of Amazonian Research
Rafael L. Assis - National Institute of Amazonian Research
Marcelo Brilhante Medeiros
Marcelo Fragomeni Simon - Brazilian Agricultural Research Corporation
Ana Andrade - National Institute of Amazonian Research
William F. Laurance - James Cook University
José Luís Camargo - National Institute of Amazonian Research
Layon O. Demarchi - National Institute of Amazonian Research
Susan G. W. Laurance - James Cook University
Emanuelle de Sousa Farias
Henrique Eduardo Mendonça Nascimento - National Institute of Amazonian Research
Juan David Cardenas Revilla - National Institute of Amazonian Research
Adriano Quaresma - National Institute of Amazonian Research
Flavia R. C. Costa - National Institute of Amazonian Research
Ima Célia Guimarães Vieira - Museu Paraense Emílio Goeldi
Bruno Barçante Ladvocat Cintra - University of Leeds
Hernán Castellanos - Universidad Nacional Experimental de Guayana
Roel Brienen - University of Leeds
Pablo R. Stevenson - Universidad de Los Andes
Yuri Feitosa - National Institute of Amazonian Research
Joost F. Duivenvoorden - University of Amsterdam
Gerardo A. Aymard C.
Hugo F. Mogollón
Natalia Targhetta - National Institute of Amazonian Research
James A. Comiskey - National Park Service
Alberto Vicentini - National Institute of Amazonian Research
Aline Lopes - National Institute of Amazonian Research
Gabriel Damasco - University of California, Berkeley
Nállarett Dávila - Universidade Estadual de Campinas (UNICAMP)
Roosevelt García-Villacorta - University of Edinburgh
Carolina Levis - National Institute of Amazonian Research
Juliana Schietti - National Institute of Amazonian Research
Priscila Souza - National Institute of Amazonian Research
Thaise Emilio - National Institute of Amazonian Research
Alfonso Alonso - Smithsonian Conservation Biology Institute
David Neill - Universidad Estatal Amazónica
Francisco Dallmeier - Smithsonian Conservation Biology Institute
Leandro Valle Ferreira - Museu Paraense Emílio Goeldi
Alejandro Araujo-Murakami - Gabriel René Moreno Autonomous University
Daniel Praia
Dário Dantas Do Amaral
Fernanda Antunes Carvalho - National Institute of Amazonian Research
Fernanda Coelho de Souza - University of Leeds
Kenneth Feeley - University of Miami
Luzmila Arroyo - Museo de Historia Natural Noel Kempff Mercado
Marcelo Petratti Pansonato - Universidade de São Paulo
Rogerio Gribel - Instituto de Pesquisas Jardim Botânico do Rio de Janeiro
Boris Villa - National Institute of Amazonian Research
Juan Carlos Licona - Bolivian Forest Research Institute
Paul V. A. Fine - University of California, Berkeley
Carlos Cerón - Central University of Ecuador
Chris Baraloto
Eliana M. Jimenez - Universidad Nacional de Colombia
Juliana Stropp - Universidade Federal de Alagoas
Julien Engel - Université de Montpellier
Marcos Silveira - Universidade Federal do Acre
Maria Cristina Peñuela Mora - Universidad Regional Amazónica IKIAM
Pascal Petronelli - Centre de Coopération Internationale en Recherche Agronomique pour le Développement
Paul Maas - Naturalis Biodiversity Center
Raquel Thomas-Caesar - Iwokrama International Centre for Rainforest Conservation and Development
Terry W. Henkel - Humboldt State University
Doug Daly - New York Botanical Garden
Marcos Ríos Paredes
Tim R. Baker
Alfredo Fuentes - Academia Nacional de Ciencias de Bolivia
Carlos A. Peres - University of East Anglia
Jerome Chave - Université Toulouse III - Paul Sabatier
Jose Luis Marcelo Pena - Universidad Nacional Agraria La Molina
Kyle G. Dexter - Royal Botanic Garden Edinburgh
Miles R. Silman - Wake Forest University
Peter Møller Jørgensen - Missouri Botanical Garden
Toby Pennington
Anthony Di Fiore - The University of Texas at Austin
Fernando Cornejo Valverde - Amazon National University of Madre de Dios
Juan Fernando Phillips
Gonzalo Rivas-Torres - Universidad San Francisco de Quito
Patricio von Hildebrand
Tinde R. van Andel - Naturalis Biodiversity Center
Ademir R. Ruschel - Brazilian Agricultural Research Corporation
Adriana Prieto - Universidad Nacional de Colombia
Agustín Rudas - Universidad Nacional de Colombia
Bruce Hoffman - Multi Electrical System
César I. A. Vela - National University of Saint Anthony the Abbot in Cuzco
Edelcilio Marques Barbosa - National Institute of Amazonian Research
Egleé L. Zent - Instituto Venezolano de Investigaciones Científicas
George Pepe Gallardo Gonzales
Hilda Paulette Dávila Doza
Ires Paula de Andrade Miranda - National Institute of Amazonian Research
Jean-Louis Guillaumet
Linder Felipe Mozombite Pinto
Luiz Carlos de Matos Bonates - National Institute of Amazonian Research
Natalino Silva - Universidade Federal Rural da Amazônia
Ricardo Zárate Gómez - Instituto de Investigaciones de la Amazonía Peruana
Stanford Zent - Instituto Venezolano de Investigaciones Científicas
Therany Gonzales
Vincent A. Vos - Universidad Autónoma del Beni
Yadvinder Malhi - University of Oxford
Alexandre A. Oliveira - Universidade de São Paulo
Angela Cano - Universidad de Los Andes
Bianca Weiss Albuquerque - National Institute of Amazonian Research
Corine Vriesendorp - Field Museum of Natural History
Diego Felipe Correa - Universidad de Los Andes
Emilio Vilanova Torre
Geertje van Der Heijden - University of Nottingham
Hirma Ramirez-Angulo - University of the Andes
José Ferreira Ramos - National Institute of Amazonian Research
Kenneth R. Young - The University of Texas at Austin
Maira Rocha - National Institute of Amazonian Research
Marcelo Trindade Nascimento - State University of Norte Fluminense
Maria Natalia Umaña Medina - University of Maryland, College Park
Milton Tirado
Ophelia Wang - Northern Arizona University
Rodrigo Sierra
Armando Torres-Lezama - University of the Andes
Casimiro Mendoza - Tierra
Cid Ferreira - National Institute of Amazonian Research
Cláudia Baider - Mauritius Sugarcane Industry Research Institute
Daniel Villarroel - Gabriel René Moreno Autonomous University
Henrik Balslev - Aarhus University
Italo Mesones - University of California, Berkeley
Ligia Estela Urrego Giraldo - Universidad Nacional de Colombia
Luisa Fernanda Casas - Universidad de Los Andes
Manuel Augusto Ahuite Reategui
Reynaldo Linares-Palomino - Smithsonian Conservation Biology Institute
Roderick Zagt
Sasha Cárdenas - Universidad de Los Andes
William Farfan-Rios - Wake Forest University
Adeilza Felipe Sampaio - Universidade Federal de Rondônia
Daniela Pauletto - Universidade Federal do Oeste do Pará
Elvis H. Valderrama Sandoval - University of Missouri–St. Louis
Freddy Ramirez Arevalo - Universidad Nacional de la Amazonía Peruana
Isau Huamantupa-Chuquimaco - National University of Saint Anthony the Abbot in Cuzco
Karina Garcia-Cabrera - Wake Forest University
Lionel Hernandez - Universidad Nacional Experimental de Guayana
Luis Valenzuela Gamarra
Miguel N. Alexiades - University of Kent
Susamar Pansini - Universidade Federal de Rondônia
Walter Palacios Cuenca - Universidad Técnica del Norte
William Milliken - Royal Botanic Gardens, Kew
Joana Ricardo - University of Leeds
Gabriela Lopez-Gonzalez - University of Leeds
Edwin Pos - Utrecht University
Hans ter Steege - Vrije Universiteit Amsterdam
Publication Details: Scientific Reports, Vol.8(1)
Identifiers: 9946332509311
Academic Unit: BotAnique et Modélisation de l'Architecture des Plantes et des végétations - AMAP
Language: English
Resource Type: Journal article
Local Fields: hal-01918112