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 (US) |
|---|---|
| Article number | 1003 |
| Journal | Scientific reports |
| Volume | 8 |
| Issue number | 1 |
| DOIs | |
| State | Published - Dec 1 2018 |
ASJC Scopus subject areas
- General
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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.; Coelho, Luiz De Souza; Matos, Francisca Dionízia De Almeida; Castilho, Carolina V.; Filho, Diogenes De Andrade Lima; López, Dairon Cárdenas; Guevara, Juan Ernesto; Magnusson, William E.; Phillips, Oliver L.; Wittmann, Florian; Carim, Marcelo De Jesus Veiga; Martins, Maria Pires; Irume, Mariana Victória; Sabatier, Daniel; Molino, Jean François; Bánki, Olaf S.; Guimarães, José Renan Da Silva; Pitman, Nigel C.A.; Piedade, Maria Teresa Fernandez; Mendoza, Abel Monteagudo; Luize, Bruno Garcia; Venticinque, Eduardo Martins; Novo, Evlyn Márcia Moraes De Leão; Vargas, Percy Núñez; Silva, Thiago Sanna Freire; Manzatto, Angelo Gilberto; Terborgh, John; Reis, Neidiane Farias Costa; Montero, Juan Carlos; Casula, Katia Regina; Marimon, Beatriz S.; Marimon, Ben Hur; Coronado, Euridice N.Honorio; Feldpausch, Ted R.; Duque, Alvaro; Zartman, Charles Eugene; Arboleda, Nicolás Castaño; Killeen, Timothy J.; Mostacedo, Bonifacio; Vasquez, 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.; Farias, Emanuelle De Sousa; Nascimento, Henrique Eduardo Mendonça; Revilla, Juan David Cardenas; Quaresma, Adriano; Costa, Flavia R.C.; Vieira, Ima Célia Guimarães; Cintra, Bruno Barçante Ladvocat; Castellanos, Hernán; Brienen, Roel; Stevenson, Pablo R.; Feitosa, Yuri; Duivenvoorden, Joost F.; Aymard, Gerardo A.C.; Mogollón, Hugo F.; Targhetta, Natalia; Comiskey, James A.; Vicentini, Alberto; Lopes, Aline; Damasco, Gabriel; Dávila, Nállarett; García-Villacorta, Roosevelt; Levis, Carolina; Schietti, Juliana; Souza, Priscila; 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; Jimenez, 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 Ríos; 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; Di 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, Ires 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; Ramirez-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; Lopez-Gonzalez, Gabriela; Pos, Edwin; Ter Steege, Hans.
In: Scientific reports, Vol. 8, No. 1, 1003, 01.12.2018.Research output: Contribution to journal › Article
}
TY - JOUR
T1 - Species Distribution Modelling
T2 - 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.
UR - http://www.scopus.com/inward/record.url?scp=85041379841&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=85041379841&partnerID=8YFLogxK
U2 - 10.1038/s41598-017-18927-1
DO - 10.1038/s41598-017-18927-1
M3 - Article
C2 - 29343741
AN - SCOPUS:85041379841
VL - 8
JO - Scientific Reports
JF - Scientific Reports
SN - 2045-2322
IS - 1
M1 - 1003
ER -