Species distribution modelling: contrasting presence-only models with plot abundance data

Gomes, Vitor H.F., Ijff, Stéphanie D., Raes, Niels, Amaral, Iêda Leão, Salamão, Rafael P., Coelho, Luiz de Souza, De Almeida Matos, Francisca, Castilho, Carolina V., Limo Filho, Diogenes de Andrade, López, Dairon Cárdenas, Guevara, Juan Ernesto, Magnusson, William E., Phillips, Oliver L., Wittmann, Florian, Veiga Carim, Marcelo de Jesus, Martins, Maria Pires, Irume, Mariana Victória, Sabatier, Daniel, Molino, Jean-François, Bánki, Olaf S., da Silva Guimarães, José Renan, Pitman, Nigel C.A., Fernandez Piedade, Maria Teresa, Mendoza, Abel Monteagudo, Luize, Bruno Garcia, Venticinque, Eduardo Martins, de Leão Novo, Evlyn Márcia Moraes, Vargas, Percy Núñez, Silva, Thiago Sanna Freire, Manzatoo, Angelo Gilberto, Terborgh, John, Reis, Neidiane Farias Costa, Montero, Juan Carlos, Casula, Katia Regina, Marimon, Beatriz S., Marimon-junior, Ben-Hur, Honorio Coronado, N., Feldpausch, Ted R., Duque, Alvaro, Zartman, Charles Eugene, Arboleda, Nicolás Castaño, Killeen, Timothy J., Mostacedo, Bonifacio, Vásquez, Rodolfo, Schöngart, Jochen, Assis, Rafael L., Medeiros, Marcelo Brilhante, Simon, Marcelo Fragomeni, Andrade, Ana, Laurance, William F., Camargo, José Luís, Demarchi, Layon O., Laurance, Susan G.W., de Sousa Farias, Emanuelle, Nascimento, Henrique Eduardo Mendonça, Revilla, Juan David Cardenas, Quaresma, Adriano, Costa, Flavia R.C., Vieira, Ima Célia Guimarães, Cintra, Bruno Barçante Ladvocat, Castellanos, Hernán, Brienan, Roel, Stevenson, Pablo R., Feitosa, Yuri, Duivenvoorden, Joost F., Aymard C., Gerardo A., Mogollón, Hugo F., Targhetta, Natalia, Comiskey, James A., Vicentini, Alberto, Lopes, Aline, Damasco, Gabriel, Dávila, Nállarett, Garcia-Villacorta, Roosevelt, Levis, Carolina, Schietti, Juliana, Souza, Priscilla, Emilio, Thaise, Alonso, Alfonso, Neill, David, Dallmeier, Francisco, Ferreira, Leandro Valle, Araujo-Murakami, Alejandro, Praia, Daniel, do Amaral, Dário Dantas, Carvalho, Fernanda Antunes, de Souza, Fernanda Coelho, Feeley, Kenneth, Arroyo, Luzmila, Pansonato, Marcelo Petratti, Gribel, Rogerio, Villa, Boris, Licona, Juan Carlos, Fine, Paul V.A., Cerón, Carlos, Baraloto, Chris, Jiménez, Eliana M., Stropp, Juliana, Engel, Julien, Silveira, Marcos, Mora, Maria Cristina Peñuela, Petronelli, Pascal, Maas, Paul, Thomas-Caesar, Raquel, Henkel, Terry W., Daly, Doug, Paredes, Marcos Rios, Baker, Tim R., Fuentes, Alfredo, Peres, Carlos A., Chave, Jerome, Pena, Jose Luis Marcelo, Dexter, Kyle G., Silman, Miles R., Jørgensen, Peter Møller, Pennington, Toby, De Fiore, Anthony, Valverde, Fernando Cornejo, Phillips, Juan Fernando, Rivas-Torres, Gonzalo, von Hildebrand, Patricio, van Andel, Tinde R., Ruschel, Ademir R., Prieto, Adriana, Rudas, Agustín, Hoffman, Bruce, Vela, César I.A., Barbosa, Edelcilio Marques, Zent, Egleé L., Gonzales, George Pepe Gallardo, Doza, Hilda Paulette Dávila, Miranda, Irs Paula de Andrade, Guillaumet, Jean-Louis, Pinto, Linder Felipe Mozombite, Bonates, Luiz Carlos de Matos, Silva, Natalino, Gómez, Ricardo Zárate, Zent, Stanford, Gonzales, Therany, Vos, Vincent A., Malhi, Yadvinder, Oliveira, Alexandre A., Cano, Angela, Albuquerque, Bianca Weiss, Vriesendorp, Corine, Correa, Diego Felipe, Torre, Emilio Vilanova, Van Der Heijden, Geertje, Ramírez-Angulo, Hirma, Ramos, José Ferreira, Young, Kenneth R., Rocha, Maira, Nascimento, Marcelo Trindade, Medina, Maria Natalia Umaña, Tirado, Milton, Wang, Ophelia, Sierra, Rodrigo, Torres-Lezama, Armando, Mendoza, Casimiro, Ferreira, Cid, Baider, Cláudia, Villarroel, Daniel, Balslev, Henrik, Mesones, Italo, Giraldo, Ligia Estela Urrego, Casas, Luisa Fernanda, Reategui, Manuel Augusto Ahuite, Linares-Palomino, Reynaldo, Zagt, Roderick, Cárdenas, Sasha, Farfan-Rios, William, Sampaio, Adeilza Felipe, Pauletto, Daniela, Sandoval, Elvis H. Valderrama, Arevalo, Freddy Ramirez, Huamantupa-Chuquimaco, Isau, Garcia-Cabrera, Karina, Hernandez, Lionel, Gamarra, Luis Valenzuela, Alexiades, Miguel N., Pansini, Susamar, Cuenca, Walter Palacios, Milliken, William, Ricardo, Joana, López-González, Gabriela, Pos, Edwin, and ter Steege, Hans (2018) Species distribution modelling: contrasting presence-only models with plot abundance data. Scientific Reports, 8. 1003.

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Abstract

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.

Item ID: 52128
Item Type: Article (Research - C1)
ISSN: 2045-2322
Keywords: species distribution models; SDM's; conservation; occurrence data; spatial abundance model; natural history collections; biodiversity
Additional Information:

This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

Funders: CAPES
Projects and Grants: grant 407232/2013-3
Date Deposited: 25 Jan 2018 02:17
FoR Codes: 05 ENVIRONMENTAL SCIENCES > 0502 Environmental Science and Management > 050202 Conservation and Biodiversity @ 100%
SEO Codes: 96 ENVIRONMENT > 9608 Flora, Fauna and Biodiversity > 960899 Flora, Fauna and Biodiversity of Environments not elsewhere classified @ 100%
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