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; Bruce Hoffman

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, Bruce Hoffman

School of Geography & Sustainable Development

Research output: Contribution to journal › Article › 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 - 17 Jan 2018

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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., ... Hoffman, B. (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{fe99ca846dea4a47a72bfb484e470751,

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' 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 Ben-Hur Marimon 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 Bruce Hoffman",

note = "V. H. F. Gomes, H. ter Steege and R. P. Salomao are supported by grant 407232/2013-3 -PVE - MEC/MCTI/ CAPES/CNPq/FAPs. ",

year = "2018",

month = jan,

day = "17",

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

language = "English",

volume = "8",

journal = "Scientific Reports",

issn = "2045-2322",

publisher = "Nature publishing group",

}

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, B-H, 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 & Hoffman, B 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

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 - Hoffman, Bruce

N1 - V. H. F. Gomes, H. ter Steege and R. P. Salomao are supported by grant 407232/2013-3 -PVE - MEC/MCTI/ CAPES/CNPq/FAPs.

PY - 2018/1/17

Y1 - 2018/1/17

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

AN - SCOPUS:85041379841

SN - 2045-2322

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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