Species Distribution Modelling: Contrasting presence-only models with plot abundance data
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.
Main Authors: | , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , |
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Format: | article biblioteca |
Language: | eng |
Subjects: | F70 - Taxonomie végétale et phytogéographie, K01 - Foresterie - Considérations générales, modélisation, distribution des populations, biodiversité, écologie des populations, écologie forestière, peuplement forestier, http://aims.fao.org/aos/agrovoc/c_230ab86c, http://aims.fao.org/aos/agrovoc/c_6113, http://aims.fao.org/aos/agrovoc/c_33949, http://aims.fao.org/aos/agrovoc/c_37336, http://aims.fao.org/aos/agrovoc/c_3044, http://aims.fao.org/aos/agrovoc/c_28080, http://aims.fao.org/aos/agrovoc/c_32372, |
Online Access: | http://agritrop.cirad.fr/597715/ http://agritrop.cirad.fr/597715/1/597715.pdf |
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F70 - Taxonomie végétale et phytogéographie K01 - Foresterie - Considérations générales modélisation distribution des populations biodiversité écologie des populations écologie forestière peuplement forestier http://aims.fao.org/aos/agrovoc/c_230ab86c http://aims.fao.org/aos/agrovoc/c_6113 http://aims.fao.org/aos/agrovoc/c_33949 http://aims.fao.org/aos/agrovoc/c_37336 http://aims.fao.org/aos/agrovoc/c_3044 http://aims.fao.org/aos/agrovoc/c_28080 http://aims.fao.org/aos/agrovoc/c_32372 F70 - Taxonomie végétale et phytogéographie K01 - Foresterie - Considérations générales modélisation distribution des populations biodiversité écologie des populations écologie forestière peuplement forestier http://aims.fao.org/aos/agrovoc/c_230ab86c http://aims.fao.org/aos/agrovoc/c_6113 http://aims.fao.org/aos/agrovoc/c_33949 http://aims.fao.org/aos/agrovoc/c_37336 http://aims.fao.org/aos/agrovoc/c_3044 http://aims.fao.org/aos/agrovoc/c_28080 http://aims.fao.org/aos/agrovoc/c_32372 |
spellingShingle |
F70 - Taxonomie végétale et phytogéographie K01 - Foresterie - Considérations générales modélisation distribution des populations biodiversité écologie des populations écologie forestière peuplement forestier http://aims.fao.org/aos/agrovoc/c_230ab86c http://aims.fao.org/aos/agrovoc/c_6113 http://aims.fao.org/aos/agrovoc/c_33949 http://aims.fao.org/aos/agrovoc/c_37336 http://aims.fao.org/aos/agrovoc/c_3044 http://aims.fao.org/aos/agrovoc/c_28080 http://aims.fao.org/aos/agrovoc/c_32372 F70 - Taxonomie végétale et phytogéographie K01 - Foresterie - Considérations générales modélisation distribution des populations biodiversité écologie des populations écologie forestière peuplement forestier http://aims.fao.org/aos/agrovoc/c_230ab86c http://aims.fao.org/aos/agrovoc/c_6113 http://aims.fao.org/aos/agrovoc/c_33949 http://aims.fao.org/aos/agrovoc/c_37336 http://aims.fao.org/aos/agrovoc/c_3044 http://aims.fao.org/aos/agrovoc/c_28080 http://aims.fao.org/aos/agrovoc/c_32372 Gomes, Vitor H.F. IJff, Stéphanie D. Raes, Niels Amaral, Iêda Leão Salomão, Rafael P. de Souza Coelho, Luiz de Almeida Matos, Francisca Dionízia Castilho, Carolina V. de Andrade Lima Filho, Diogenes López, Dairon Cárdenas Guevara, Juan Ernesto Magnusson, William E Phillips, Oliver L. Wittmann, Florian de Jesus Veiga Carim, Marcelo Pires Martins, Maria Irume, Victória Irume Sabatier, Daniel Molino, Jean-François Banki, Olaf da Silva Guimarães, José Renan Pitman, Nigel C. A. Fernandez Piedade, Maria Teresa Mendoza, Abel Monteagudo Garcia Luize, Bruno Venticinque, Eduardo Martins Moraes de Leão Novo, Evlyn Márcia Vargas, Percy Núñez Silva, Thiago Sanna Freire Manzatto, Angelo Gilberto Terborgh, John Costa Reis, Neidiane Farias Montero, Juan Carlos Casula, Katia Regina Marimon, Beatriz Schwantes Marimon Junior, Ben Hur Coronado, Euridice N. Honorio Feldpausch, Ted R. Duque, Alvaro Zartman, Charles Eugene Castaño Arboleda, Nicolás Killeen, Timothy J. Mostacedo, Bonifacio Vasquez, Rodolfo Schöngart, Jochen Assis, Rafael L. Medeiros, Marcelo Brilhante Fragomeni Simon, Marcelo Andrade, Ana Laurance, William F. Camargo, Jose Luis C. Demarchi, Layon O. Laurance, Susan G.W. de Sousa Farias, Emmanuelle Mendonça Nascimento, Henrique Eduardo Cardenas Revilla, Juan David Quaresma, Adriano Costa, Flávia R.C Guimarães Vieira, Ima Célia Barçante Ladvocat Cintra, Bruno Castellanos, Hernán Brienen, 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 Davila, Nallarett García-Villacorta, Roosevelt Levis, Carolina Schietti, Juliana Souza, Priscila Emilio, Thaise Alonso, Alfonso Neill, David Dallmeier, Francisco Ferreira, Leandro V. Araujo-Murakami, Alejandro Praia, Daniel do Amaral, Dário Dantas Carvalho, Fernanda Antunes de Souza, Fernanda Coelho Feeley, Kenneth J. Arroyo, Luzmila Pansonato, Marcelo Petratti Gribel, Rogerio Villa, Boris Licona, Juan Carlos Fine, Paul V.A. Cerón, Carlos Baraloto, Christopher Jimenez, Eliana Stropp, Juliana Engel, Julien Silveira, Marcos Peñuela Mora, Maria Cristina Petronelli, Pascal et al., Species Distribution Modelling: Contrasting presence-only models with plot abundance data |
description |
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. |
format |
article |
topic_facet |
F70 - Taxonomie végétale et phytogéographie K01 - Foresterie - Considérations générales modélisation distribution des populations biodiversité écologie des populations écologie forestière peuplement forestier http://aims.fao.org/aos/agrovoc/c_230ab86c http://aims.fao.org/aos/agrovoc/c_6113 http://aims.fao.org/aos/agrovoc/c_33949 http://aims.fao.org/aos/agrovoc/c_37336 http://aims.fao.org/aos/agrovoc/c_3044 http://aims.fao.org/aos/agrovoc/c_28080 http://aims.fao.org/aos/agrovoc/c_32372 |
author |
Gomes, Vitor H.F. IJff, Stéphanie D. Raes, Niels Amaral, Iêda Leão Salomão, Rafael P. de Souza Coelho, Luiz de Almeida Matos, Francisca Dionízia Castilho, Carolina V. de Andrade Lima Filho, Diogenes López, Dairon Cárdenas Guevara, Juan Ernesto Magnusson, William E Phillips, Oliver L. Wittmann, Florian de Jesus Veiga Carim, Marcelo Pires Martins, Maria Irume, Victória Irume Sabatier, Daniel Molino, Jean-François Banki, Olaf da Silva Guimarães, José Renan Pitman, Nigel C. A. Fernandez Piedade, Maria Teresa Mendoza, Abel Monteagudo Garcia Luize, Bruno Venticinque, Eduardo Martins Moraes de Leão Novo, Evlyn Márcia Vargas, Percy Núñez Silva, Thiago Sanna Freire Manzatto, Angelo Gilberto Terborgh, John Costa Reis, Neidiane Farias Montero, Juan Carlos Casula, Katia Regina Marimon, Beatriz Schwantes Marimon Junior, Ben Hur Coronado, Euridice N. Honorio Feldpausch, Ted R. Duque, Alvaro Zartman, Charles Eugene Castaño Arboleda, Nicolás Killeen, Timothy J. Mostacedo, Bonifacio Vasquez, Rodolfo Schöngart, Jochen Assis, Rafael L. Medeiros, Marcelo Brilhante Fragomeni Simon, Marcelo Andrade, Ana Laurance, William F. Camargo, Jose Luis C. Demarchi, Layon O. Laurance, Susan G.W. de Sousa Farias, Emmanuelle Mendonça Nascimento, Henrique Eduardo Cardenas Revilla, Juan David Quaresma, Adriano Costa, Flávia R.C Guimarães Vieira, Ima Célia Barçante Ladvocat Cintra, Bruno Castellanos, Hernán Brienen, 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 Davila, Nallarett García-Villacorta, Roosevelt Levis, Carolina Schietti, Juliana Souza, Priscila Emilio, Thaise Alonso, Alfonso Neill, David Dallmeier, Francisco Ferreira, Leandro V. Araujo-Murakami, Alejandro Praia, Daniel do Amaral, Dário Dantas Carvalho, Fernanda Antunes de Souza, Fernanda Coelho Feeley, Kenneth J. Arroyo, Luzmila Pansonato, Marcelo Petratti Gribel, Rogerio Villa, Boris Licona, Juan Carlos Fine, Paul V.A. Cerón, Carlos Baraloto, Christopher Jimenez, Eliana Stropp, Juliana Engel, Julien Silveira, Marcos Peñuela Mora, Maria Cristina Petronelli, Pascal et al., |
author_facet |
Gomes, Vitor H.F. IJff, Stéphanie D. Raes, Niels Amaral, Iêda Leão Salomão, Rafael P. de Souza Coelho, Luiz de Almeida Matos, Francisca Dionízia Castilho, Carolina V. de Andrade Lima Filho, Diogenes López, Dairon Cárdenas Guevara, Juan Ernesto Magnusson, William E Phillips, Oliver L. Wittmann, Florian de Jesus Veiga Carim, Marcelo Pires Martins, Maria Irume, Victória Irume Sabatier, Daniel Molino, Jean-François Banki, Olaf da Silva Guimarães, José Renan Pitman, Nigel C. A. Fernandez Piedade, Maria Teresa Mendoza, Abel Monteagudo Garcia Luize, Bruno Venticinque, Eduardo Martins Moraes de Leão Novo, Evlyn Márcia Vargas, Percy Núñez Silva, Thiago Sanna Freire Manzatto, Angelo Gilberto Terborgh, John Costa Reis, Neidiane Farias Montero, Juan Carlos Casula, Katia Regina Marimon, Beatriz Schwantes Marimon Junior, Ben Hur Coronado, Euridice N. Honorio Feldpausch, Ted R. Duque, Alvaro Zartman, Charles Eugene Castaño Arboleda, Nicolás Killeen, Timothy J. Mostacedo, Bonifacio Vasquez, Rodolfo Schöngart, Jochen Assis, Rafael L. Medeiros, Marcelo Brilhante Fragomeni Simon, Marcelo Andrade, Ana Laurance, William F. Camargo, Jose Luis C. Demarchi, Layon O. Laurance, Susan G.W. de Sousa Farias, Emmanuelle Mendonça Nascimento, Henrique Eduardo Cardenas Revilla, Juan David Quaresma, Adriano Costa, Flávia R.C Guimarães Vieira, Ima Célia Barçante Ladvocat Cintra, Bruno Castellanos, Hernán Brienen, 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 Davila, Nallarett García-Villacorta, Roosevelt Levis, Carolina Schietti, Juliana Souza, Priscila Emilio, Thaise Alonso, Alfonso Neill, David Dallmeier, Francisco Ferreira, Leandro V. Araujo-Murakami, Alejandro Praia, Daniel do Amaral, Dário Dantas Carvalho, Fernanda Antunes de Souza, Fernanda Coelho Feeley, Kenneth J. Arroyo, Luzmila Pansonato, Marcelo Petratti Gribel, Rogerio Villa, Boris Licona, Juan Carlos Fine, Paul V.A. Cerón, Carlos Baraloto, Christopher Jimenez, Eliana Stropp, Juliana Engel, Julien Silveira, Marcos Peñuela Mora, Maria Cristina Petronelli, Pascal et al., |
author_sort |
Gomes, Vitor H.F. |
title |
Species Distribution Modelling: Contrasting presence-only models with plot abundance data |
title_short |
Species Distribution Modelling: Contrasting presence-only models with plot abundance data |
title_full |
Species Distribution Modelling: Contrasting presence-only models with plot abundance data |
title_fullStr |
Species Distribution Modelling: Contrasting presence-only models with plot abundance data |
title_full_unstemmed |
Species Distribution Modelling: Contrasting presence-only models with plot abundance data |
title_sort |
species distribution modelling: contrasting presence-only models with plot abundance data |
url |
http://agritrop.cirad.fr/597715/ http://agritrop.cirad.fr/597715/1/597715.pdf |
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dig-cirad-fr-5977152024-01-29T03:22:13Z http://agritrop.cirad.fr/597715/ http://agritrop.cirad.fr/597715/ Species Distribution Modelling: Contrasting presence-only models with plot abundance data. Gomes Vitor H.F., IJff Stéphanie D., Raes Niels, Amaral Iêda Leão, Salomão Rafael P., de Souza Coelho Luiz, de Almeida Matos Francisca Dionízia, Castilho Carolina V., de Andrade Lima Filho Diogenes, López Dairon Cárdenas, Guevara Juan Ernesto, Magnusson William E, Phillips Oliver L., Wittmann Florian, de Jesus Veiga Carim Marcelo, Pires Martins Maria, Irume Victória Irume, Sabatier Daniel, Molino Jean-François, Banki Olaf, da Silva Guimarães José Renan, Pitman Nigel C. A., Fernandez Piedade Maria Teresa, Mendoza Abel Monteagudo, Garcia Luize Bruno, Venticinque Eduardo Martins, Moraes de Leão Novo Evlyn Márcia, Vargas Percy Núñez, Silva Thiago Sanna Freire, Manzatto Angelo Gilberto, Terborgh John, Costa Reis Neidiane Farias, Montero Juan Carlos, Casula Katia Regina, Marimon Beatriz Schwantes, Marimon Junior Ben Hur, Coronado Euridice N. Honorio, Feldpausch Ted R., Duque Alvaro, Zartman Charles Eugene, Castaño Arboleda Nicolás, Killeen Timothy J., Mostacedo Bonifacio, Vasquez Rodolfo, Schöngart Jochen, Assis Rafael L., Medeiros Marcelo Brilhante, Fragomeni Simon Marcelo, Andrade Ana, Laurance William F., Camargo Jose Luis C., Demarchi Layon O., Laurance Susan G.W., de Sousa Farias Emmanuelle, Mendonça Nascimento Henrique Eduardo, Cardenas Revilla Juan David, Quaresma Adriano, Costa Flávia R.C, Guimarães Vieira Ima Célia, Barçante Ladvocat Cintra Bruno, Castellanos Hernán, Brienen 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, Davila Nallarett, García-Villacorta Roosevelt, Levis Carolina, Schietti Juliana, Souza Priscila, Emilio Thaise, Alonso Alfonso, Neill David, Dallmeier Francisco, Ferreira Leandro V., Araujo-Murakami Alejandro, Praia Daniel, do Amaral Dário Dantas, Carvalho Fernanda Antunes, de Souza Fernanda Coelho, Feeley Kenneth J., Arroyo Luzmila, Pansonato Marcelo Petratti, Gribel Rogerio, Villa Boris, Licona Juan Carlos, Fine Paul V.A., Cerón Carlos, Baraloto Christopher, Jimenez Eliana, Stropp Juliana, Engel Julien, Silveira Marcos, Peñuela Mora Maria Cristina, Petronelli Pascal, et al.. 2018. Scientific Reports, 8:1003, 12 p.https://doi.org/10.1038/s41598-017-18927-1 <https://doi.org/10.1038/s41598-017-18927-1> Species Distribution Modelling: Contrasting presence-only models with plot abundance data Gomes, Vitor H.F. IJff, Stéphanie D. Raes, Niels Amaral, Iêda Leão Salomão, Rafael P. de Souza Coelho, Luiz de Almeida Matos, Francisca Dionízia Castilho, Carolina V. de Andrade Lima Filho, Diogenes López, Dairon Cárdenas Guevara, Juan Ernesto Magnusson, William E Phillips, Oliver L. Wittmann, Florian de Jesus Veiga Carim, Marcelo Pires Martins, Maria Irume, Victória Irume Sabatier, Daniel Molino, Jean-François Banki, Olaf da Silva Guimarães, José Renan Pitman, Nigel C. A. Fernandez Piedade, Maria Teresa Mendoza, Abel Monteagudo Garcia Luize, Bruno Venticinque, Eduardo Martins Moraes de Leão Novo, Evlyn Márcia Vargas, Percy Núñez Silva, Thiago Sanna Freire Manzatto, Angelo Gilberto Terborgh, John Costa Reis, Neidiane Farias Montero, Juan Carlos Casula, Katia Regina Marimon, Beatriz Schwantes Marimon Junior, Ben Hur Coronado, Euridice N. Honorio Feldpausch, Ted R. Duque, Alvaro Zartman, Charles Eugene Castaño Arboleda, Nicolás Killeen, Timothy J. Mostacedo, Bonifacio Vasquez, Rodolfo Schöngart, Jochen Assis, Rafael L. Medeiros, Marcelo Brilhante Fragomeni Simon, Marcelo Andrade, Ana Laurance, William F. Camargo, Jose Luis C. Demarchi, Layon O. Laurance, Susan G.W. de Sousa Farias, Emmanuelle Mendonça Nascimento, Henrique Eduardo Cardenas Revilla, Juan David Quaresma, Adriano Costa, Flávia R.C Guimarães Vieira, Ima Célia Barçante Ladvocat Cintra, Bruno Castellanos, Hernán Brienen, 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 Davila, Nallarett García-Villacorta, Roosevelt Levis, Carolina Schietti, Juliana Souza, Priscila Emilio, Thaise Alonso, Alfonso Neill, David Dallmeier, Francisco Ferreira, Leandro V. Araujo-Murakami, Alejandro Praia, Daniel do Amaral, Dário Dantas Carvalho, Fernanda Antunes de Souza, Fernanda Coelho Feeley, Kenneth J. Arroyo, Luzmila Pansonato, Marcelo Petratti Gribel, Rogerio Villa, Boris Licona, Juan Carlos Fine, Paul V.A. Cerón, Carlos Baraloto, Christopher Jimenez, Eliana Stropp, Juliana Engel, Julien Silveira, Marcos Peñuela Mora, Maria Cristina Petronelli, Pascal et al., eng 2018 Scientific Reports F70 - Taxonomie végétale et phytogéographie K01 - Foresterie - Considérations générales modélisation distribution des populations biodiversité écologie des populations écologie forestière peuplement forestier http://aims.fao.org/aos/agrovoc/c_230ab86c http://aims.fao.org/aos/agrovoc/c_6113 http://aims.fao.org/aos/agrovoc/c_33949 http://aims.fao.org/aos/agrovoc/c_37336 http://aims.fao.org/aos/agrovoc/c_3044 http://aims.fao.org/aos/agrovoc/c_28080 Amazonie http://aims.fao.org/aos/agrovoc/c_32372 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. article info:eu-repo/semantics/article Journal Article info:eu-repo/semantics/publishedVersion http://agritrop.cirad.fr/597715/1/597715.pdf text cc_by info:eu-repo/semantics/openAccess https://creativecommons.org/licenses/by/4.0/ https://doi.org/10.1038/s41598-017-18927-1 10.1038/s41598-017-18927-1 info:eu-repo/semantics/altIdentifier/doi/10.1038/s41598-017-18927-1 info:eu-repo/semantics/altIdentifier/purl/https://doi.org/10.1038/s41598-017-18927-1 |