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.C. Aymard; 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

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. BánkiJosé 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.C. Aymard, 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

extern

Research output: Contribution to journal › Article › Academic › peer-review

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.

Original language	English
Article number	1003
Journal	Scientific Reports
Volume	8
DOIs	https://doi.org/10.1038/s41598-017-18927-1
Publication status	Published - 1 Dec 2018

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10.1038/s41598-017-18927-1

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http://www.mendeley.com/research/species-distribution-modelling-contrasting-presenceonly-models-plot-abundance-data

Cite this

Gomes, V. H. F., Ijff, S. D., Raes, N., Amaral, I. L., Salomão, R. P., Coelho, L. D. S., Matos, F. D. D. A., Castilho, C. V., Filho, D. D. A. L., López, D. C., Guevara, J. E., Magnusson, W. E., Phillips, O. L., Wittmann, F., Carim, M. D. J. V., Martins, M. P., Irume, M. V., Sabatier, D., Molino, J. F., ... Ter Steege, H. (2018). Species Distribution Modelling: Contrasting presence-only models with plot abundance data. Scientific Reports, 8, Article 1003 . https://doi.org/10.1038/s41598-017-18927-1

@article{2345fd3f180a4065ac1fa0cc07e89d62,

title = "Species Distribution Modelling: Contrasting presence-only models with plot abundance data",

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{\textquoteright} area of occupancy, within an area slightly larger than its extent of occurrence, compatible to e.g. IUCN red list assessments.",

author = "Gomes, {Vitor H.F.} and Ijff, {St{\'e}phanie D.} and Niels Raes and Amaral, {I{\^e}da Le{\~a}o} and Salom{\~a}o, {Rafael P.} and Coelho, {Luiz De Souza} and Matos, {Francisca Dion{\'i}zia De Almeida} and Castilho, {Carolina V.} and Filho, {Diogenes De Andrade Lima} and L{\'o}pez, {Dairon C{\'a}rdenas} and Guevara, {Juan Ernesto} and Magnusson, {William E.} and Phillips, {Oliver L.} and Florian Wittmann and Carim, {Marcelo De Jesus Veiga} and Martins, {Maria Pires} and Irume, {Mariana Vict{\'o}ria} and Daniel Sabatier and Molino, {Jean Fran{\c c}ois} and B{\'a}nki, {Olaf S.} and Guimar{\~a}es, {Jos{\'e} Renan Da Silva} and Pitman, {Nigel C.A.} and Piedade, {Maria Teresa Fernandez} and Mendoza, {Abel Monteagudo} and Luize, {Bruno Garcia} and Venticinque, {Eduardo Martins} and Novo, {Evlyn M{\'a}rcia Moraes De Le{\~a}o} and Vargas, {Percy N{\'u}{\~n}ez} and Silva, {Thiago Sanna Freire} and Manzatto, {Angelo Gilberto} and John Terborgh and Reis, {Neidiane Farias Costa} and Montero, {Juan Carlos} and Casula, {Katia Regina} and Marimon, {Beatriz S.} and Marimon, {Ben Hur} and Coronado, {Euridice N.Honorio} and Feldpausch, {Ted R.} and Alvaro Duque and Zartman, {Charles Eugene} and Arboleda, {Nicol{\'a}s Casta{\~n}o} and Killeen, {Timothy J.} and Bonifacio Mostacedo and Rodolfo Vasquez and Jochen Sch{\"o}ngart and Assis, {Rafael L.} and Medeiros, {Marcelo Brilhante} and Simon, {Marcelo Fragomeni} and Ana Andrade and Laurance, {William F.} and Camargo, {Jos{\'e} Lu{\'i}s} and Demarchi, {Layon O.} and Laurance, {Susan G.W.} and Farias, {Emanuelle De Sousa} and Nascimento, {Henrique Eduardo Mendon{\c c}a} and Revilla, {Juan David Cardenas} and Adriano Quaresma and Costa, {Flavia R.C.} and Vieira, {Ima C{\'e}lia Guimar{\~a}es} and Cintra, {Bruno Bar{\c c}ante Ladvocat} and Hern{\'a}n Castellanos and Roel Brienen and Stevenson, {Pablo R.} and Yuri Feitosa and Duivenvoorden, {Joost F.} and Aymard, {Gerardo A.C.} and Mogoll{\'o}n, {Hugo F.} and Natalia Targhetta and Comiskey, {James A.} and Alberto Vicentini and Aline Lopes and Gabriel Damasco and N{\'a}llarett D{\'a}vila and Roosevelt Garc{\'i}a-Villacorta and Carolina Levis and Juliana Schietti and Priscila Souza and Thaise Emilio and Alfonso Alonso and David Neill and Francisco Dallmeier and Ferreira, {Leandro Valle} and Alejandro Araujo-Murakami and Daniel Praia and {Do Amaral}, {D{\'a}rio Dantas} and Carvalho, {Fernanda Antunes} and {De Souza}, {Fernanda Coelho} and Kenneth Feeley and Luzmila Arroyo and Pansonato, {Marcelo Petratti} and Rogerio Gribel and Boris Villa and Licona, {Juan Carlos} and Fine, {Paul V.A.} and Carlos Cer{\'o}n and Chris Baraloto and Jimenez, {Eliana M.} and Juliana Stropp and Julien Engel and Marcos Silveira and Mora, {Maria Cristina Pe{\~n}uela} and Pascal Petronelli and Paul Maas and Raquel Thomas-Caesar and Henkel, {Terry W.} and Doug Daly and Paredes, {Marcos R{\'i}os} and Baker, {Tim R.} and Alfredo Fuentes and Peres, {Carlos A.} and Jerome Chave and Pena, {Jose Luis Marcelo} and Dexter, {Kyle G.} and Silman, {Miles R.} and J{\o}rgensen, {Peter M{\o}ller} and Toby Pennington and {Di Fiore}, Anthony and Valverde, {Fernando Cornejo} and Phillips, {Juan Fernando} and Gonzalo Rivas-Torres and {Von Hildebrand}, Patricio and {Van Andel}, {Tinde R.} and Ruschel, {Ademir R.} and Adriana Prieto and Agust{\'i}n Rudas and Bruce Hoffman and Vela, {C{\'e}sar I.A.} and Barbosa, {Edelcilio Marques} and Zent, {Egle{\'e} L.} and Gonzales, {George Pepe Gallardo} and Doza, {Hilda Paulette D{\'a}vila} and Miranda, {Ires Paula De Andrade} and Guillaumet, {Jean Louis} and Pinto, {Linder Felipe Mozombite} and Bonates, {Luiz Carlos De Matos} and Natalino Silva and G{\'o}mez, {Ricardo Z{\'a}rate} and Stanford Zent and Therany Gonzales and Vos, {Vincent A.} and Yadvinder Malhi and Oliveira, {Alexandre A.} and Angela Cano and Albuquerque, {Bianca Weiss} and Corine Vriesendorp and Correa, {Diego Felipe} and Torre, {Emilio Vilanova} and {Van Der Heijden}, Geertje and Hirma Ramirez-Angulo and Ramos, {Jos{\'e} Ferreira} and Young, {Kenneth R.} and Maira Rocha and Nascimento, {Marcelo Trindade} and Medina, {Maria Natalia Uma{\~n}a} and Milton Tirado and Ophelia Wang and Rodrigo Sierra and Armando Torres-Lezama and Casimiro Mendoza and Cid Ferreira and Cl{\'a}udia Baider and Daniel Villarroel and Henrik Balslev and Italo Mesones and Giraldo, {Ligia Estela Urrego} and Casas, {Luisa Fernanda} and Reategui, {Manuel Augusto Ahuite} and Reynaldo Linares-Palomino and Roderick Zagt and Sasha C{\'a}rdenas and William Farfan-Rios and Sampaio, {Adeilza Felipe} and Daniela Pauletto and Sandoval, {Elvis H.Valderrama} and Arevalo, {Freddy Ramirez} and Isau Huamantupa-Chuquimaco and Karina Garcia-Cabrera and Lionel Hernandez and Gamarra, {Luis Valenzuela} and Alexiades, {Miguel N.} and Susamar Pansini and Cuenca, {Walter Palacios} and William Milliken and Joana Ricardo and Gabriela Lopez-Gonzalez and Edwin Pos and {Ter Steege}, Hans",

year = "2018",

month = dec,

day = "1",

doi = "10.1038/s41598-017-18927-1",

language = "English",

volume = "8",

journal = "Scientific Reports",

publisher = "NLM (Medline)",

}

Gomes, VHF, Ijff, SD, Raes, N, Amaral, IL, Salomão, RP, Coelho, LDS, Matos, FDDA, Castilho, CV, Filho, DDAL, López, DC, Guevara, JE, Magnusson, WE, Phillips, OL, Wittmann, F, Carim, MDJV, Martins, MP, Irume, MV, Sabatier, D, Molino, JF, Bánki, OS, Guimarães, JRDS, Pitman, NCA, Piedade, MTF, Mendoza, AM, Luize, BG, Venticinque, EM, Novo, EMMDL, Vargas, PN, Silva, TSF, Manzatto, AG, Terborgh, J, Reis, NFC, Montero, JC, Casula, KR, Marimon, BS, Marimon, BH, Coronado, ENH, Feldpausch, TR, Duque, A, Zartman, CE, Arboleda, NC, Killeen, TJ, Mostacedo, B, Vasquez, R, Schöngart, J, Assis, RL, Medeiros, MB, Simon, MF, Andrade, A, Laurance, WF, Camargo, JL, Demarchi, LO, Laurance, SGW, Farias, EDS, Nascimento, HEM, Revilla, JDC, Quaresma, A, Costa, FRC, Vieira, ICG, Cintra, BBL, Castellanos, H, Brienen, R, Stevenson, PR, Feitosa, Y, Duivenvoorden, JF, Aymard, GAC, Mogollón, HF, Targhetta, N, Comiskey, JA, Vicentini, A, Lopes, A, Damasco, G, Dávila, N, García-Villacorta, R, Levis, C, Schietti, J, Souza, P, Emilio, T, Alonso, A, Neill, D, Dallmeier, F, Ferreira, LV, Araujo-Murakami, A, Praia, D, Do Amaral, DD, Carvalho, FA, De Souza, FC, Feeley, K, Arroyo, L, Pansonato, MP, Gribel, R, Villa, B, Licona, JC, Fine, PVA, Cerón, C, Baraloto, C, Jimenez, EM, Stropp, J, Engel, J, Silveira, M, Mora, MCP, Petronelli, P, Maas, P, Thomas-Caesar, R, Henkel, TW, Daly, D, Paredes, MR, Baker, TR, Fuentes, A, Peres, CA, Chave, J, Pena, JLM, Dexter, KG, Silman, MR, Jørgensen, PM, Pennington, T, Di Fiore, A, Valverde, FC, Phillips, JF, Rivas-Torres, G, Von Hildebrand, P, Van Andel, TR, Ruschel, AR, Prieto, A, Rudas, A, Hoffman, B, Vela, CIA, Barbosa, EM, Zent, EL, Gonzales, GPG, Doza, HPD, Miranda, IPDA, Guillaumet, JL, Pinto, LFM, Bonates, LCDM, Silva, N, Gómez, RZ, Zent, S, Gonzales, T, Vos, VA, Malhi, Y, Oliveira, AA, Cano, A, Albuquerque, BW, Vriesendorp, C, Correa, DF, Torre, EV, Van Der Heijden, G, Ramirez-Angulo, H, Ramos, JF, Young, KR, Rocha, M, Nascimento, MT, Medina, MNU, Tirado, M, Wang, O, Sierra, R, Torres-Lezama, A, Mendoza, C, Ferreira, C, Baider, C, Villarroel, D, Balslev, H, Mesones, I, Giraldo, LEU, Casas, LF, Reategui, MAA, Linares-Palomino, R, Zagt, R, Cárdenas, S, Farfan-Rios, W, Sampaio, AF, Pauletto, D, Sandoval, EHV, Arevalo, FR, Huamantupa-Chuquimaco, I, Garcia-Cabrera, K, Hernandez, L, Gamarra, LV, Alexiades, MN, Pansini, S, Cuenca, WP, Milliken, W, Ricardo, J, Lopez-Gonzalez, G, Pos, E & Ter Steege, H 2018, 'Species Distribution Modelling: Contrasting presence-only models with plot abundance data', Scientific Reports, vol. 8, 1003 . https://doi.org/10.1038/s41598-017-18927-1

TY - JOUR

T1 - Species Distribution Modelling: Contrasting presence-only models with plot abundance data

AU - Gomes, Vitor H.F.

AU - Ijff, Stéphanie D.

AU - Raes, Niels

AU - Amaral, Iêda Leão

AU - Salomão, Rafael P.

AU - Coelho, Luiz De Souza

AU - Matos, Francisca Dionízia De Almeida

AU - Castilho, Carolina V.

AU - Filho, Diogenes De Andrade Lima

AU - López, Dairon Cárdenas

AU - Guevara, Juan Ernesto

AU - Magnusson, William E.

AU - Phillips, Oliver L.

AU - Wittmann, Florian

AU - Carim, Marcelo De Jesus Veiga

AU - Martins, Maria Pires

AU - Irume, Mariana Victória

AU - Sabatier, Daniel

AU - Molino, Jean François

AU - Bánki, Olaf S.

AU - Guimarães, José Renan Da Silva

AU - Pitman, Nigel C.A.

AU - Piedade, Maria Teresa Fernandez

AU - Mendoza, Abel Monteagudo

AU - Luize, Bruno Garcia

AU - Venticinque, Eduardo Martins

AU - Novo, Evlyn Márcia Moraes De Leão

AU - Vargas, Percy Núñez

AU - Silva, Thiago Sanna Freire

AU - Manzatto, Angelo Gilberto

AU - Terborgh, John

AU - Reis, Neidiane Farias Costa

AU - Montero, Juan Carlos

AU - Casula, Katia Regina

AU - Marimon, Beatriz S.

AU - Marimon, Ben Hur

AU - Coronado, Euridice N.Honorio

AU - Feldpausch, Ted R.

AU - Duque, Alvaro

AU - Zartman, Charles Eugene

AU - Arboleda, Nicolás Castaño

AU - Killeen, Timothy J.

AU - Mostacedo, Bonifacio

AU - Vasquez, Rodolfo

AU - Schöngart, Jochen

AU - Assis, Rafael L.

AU - Medeiros, Marcelo Brilhante

AU - Simon, Marcelo Fragomeni

AU - Andrade, Ana

AU - Laurance, William F.

AU - Camargo, José Luís

AU - Demarchi, Layon O.

AU - Laurance, Susan G.W.

AU - Farias, Emanuelle De Sousa

AU - Nascimento, Henrique Eduardo Mendonça

AU - Revilla, Juan David Cardenas

AU - Quaresma, Adriano

AU - Costa, Flavia R.C.

AU - Vieira, Ima Célia Guimarães

AU - Cintra, Bruno Barçante Ladvocat

AU - Castellanos, Hernán

AU - Brienen, Roel

AU - Stevenson, Pablo R.

AU - Feitosa, Yuri

AU - Duivenvoorden, Joost F.

AU - Aymard, Gerardo A.C.

AU - Mogollón, Hugo F.

AU - Targhetta, Natalia

AU - Comiskey, James A.

AU - Vicentini, Alberto

AU - Lopes, Aline

AU - Damasco, Gabriel

AU - Dávila, Nállarett

AU - García-Villacorta, Roosevelt

AU - Levis, Carolina

AU - Schietti, Juliana

AU - Souza, Priscila

AU - Emilio, Thaise

AU - Alonso, Alfonso

AU - Neill, David

AU - Dallmeier, Francisco

AU - Ferreira, Leandro Valle

AU - Araujo-Murakami, Alejandro

AU - Praia, Daniel

AU - Do Amaral, Dário Dantas

AU - Carvalho, Fernanda Antunes

AU - De Souza, Fernanda Coelho

AU - Feeley, Kenneth

AU - Arroyo, Luzmila

AU - Pansonato, Marcelo Petratti

AU - Gribel, Rogerio

AU - Villa, Boris

AU - Licona, Juan Carlos

AU - Fine, Paul V.A.

AU - Cerón, Carlos

AU - Baraloto, Chris

AU - Jimenez, Eliana M.

AU - Stropp, Juliana

AU - Engel, Julien

AU - Silveira, Marcos

AU - Mora, Maria Cristina Peñuela

AU - Petronelli, Pascal

AU - Maas, Paul

AU - Thomas-Caesar, Raquel

AU - Henkel, Terry W.

AU - Daly, Doug

AU - Paredes, Marcos Ríos

AU - Baker, Tim R.

AU - Fuentes, Alfredo

AU - Peres, Carlos A.

AU - Chave, Jerome

AU - Pena, Jose Luis Marcelo

AU - Dexter, Kyle G.

AU - Silman, Miles R.

AU - Jørgensen, Peter Møller

AU - Pennington, Toby

AU - Di Fiore, Anthony

AU - Valverde, Fernando Cornejo

AU - Phillips, Juan Fernando

AU - Rivas-Torres, Gonzalo

AU - Von Hildebrand, Patricio

AU - Van Andel, Tinde R.

AU - Ruschel, Ademir R.

AU - Prieto, Adriana

AU - Rudas, Agustín

AU - Hoffman, Bruce

AU - Vela, César I.A.

AU - Barbosa, Edelcilio Marques

AU - Zent, Egleé L.

AU - Gonzales, George Pepe Gallardo

AU - Doza, Hilda Paulette Dávila

AU - Miranda, Ires Paula De Andrade

AU - Guillaumet, Jean Louis

AU - Pinto, Linder Felipe Mozombite

AU - Bonates, Luiz Carlos De Matos

AU - Silva, Natalino

AU - Gómez, Ricardo Zárate

AU - Zent, Stanford

AU - Gonzales, Therany

AU - Vos, Vincent A.

AU - Malhi, Yadvinder

AU - Oliveira, Alexandre A.

AU - Cano, Angela

AU - Albuquerque, Bianca Weiss

AU - Vriesendorp, Corine

AU - Correa, Diego Felipe

AU - Torre, Emilio Vilanova

AU - Van Der Heijden, Geertje

AU - Ramirez-Angulo, Hirma

AU - Ramos, José Ferreira

AU - Young, Kenneth R.

AU - Rocha, Maira

AU - Nascimento, Marcelo Trindade

AU - Medina, Maria Natalia Umaña

AU - Tirado, Milton

AU - Wang, Ophelia

AU - Sierra, Rodrigo

AU - Torres-Lezama, Armando

AU - Mendoza, Casimiro

AU - Ferreira, Cid

AU - Baider, Cláudia

AU - Villarroel, Daniel

AU - Balslev, Henrik

AU - Mesones, Italo

AU - Giraldo, Ligia Estela Urrego

AU - Casas, Luisa Fernanda

AU - Reategui, Manuel Augusto Ahuite

AU - Linares-Palomino, Reynaldo

AU - Zagt, Roderick

AU - Cárdenas, Sasha

AU - Farfan-Rios, William

AU - Sampaio, Adeilza Felipe

AU - Pauletto, Daniela

AU - Sandoval, Elvis H.Valderrama

AU - Arevalo, Freddy Ramirez

AU - Huamantupa-Chuquimaco, Isau

AU - Garcia-Cabrera, Karina

AU - Hernandez, Lionel

AU - Gamarra, Luis Valenzuela

AU - Alexiades, Miguel N.

AU - Pansini, Susamar

AU - Cuenca, Walter Palacios

AU - Milliken, William

AU - Ricardo, Joana

AU - Lopez-Gonzalez, Gabriela

AU - Pos, Edwin

AU - Ter Steege, Hans

PY - 2018/12/1

Y1 - 2018/12/1

N2 - 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.

AB - 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.

U2 - 10.1038/s41598-017-18927-1

DO - 10.1038/s41598-017-18927-1

M3 - Article

C2 - 29343741

VL - 8

JO - Scientific Reports

JF - Scientific Reports

M1 - 1003

ER -

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

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