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

Gomes, Vitor H.F.; IJff, St?phanie D.; Raes, Niels; Amaral, I?da Le?o; Salom?o, Rafael P.; de Souza Coelho, Luiz; de Almeida Matos, Francisca Dion?zia; Castilho, Carolina V.; de Andrade Lima Filho, Diogenes; L?pez, Dairon C?rdenas; Guevara, Juan Ernesto; Magnusson, William E.; Phillips, Oliver L.; Wittmann, Florian; de Jesus Veiga Carim, Marcelo; Martins, Maria Pires; Irume, Mariana Vict?ria; Sabatier, Daniel; Molino, Jean-Fran?ois; B?nki, Olaf S.; da Silva Guimar?es, Jos? Renan; Pitman, Nigel C.A.; Piedade, Maria Teresa Fernandez; Mendoza, Abel Monteagudo; Luize, Bruno Garcia; Venticinque, Eduardo Martins; de Le?o Novo, Evlyn M?rcia Moraes; Vargas, Percy N??ez; 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, Nicol?s Casta?o; Killeen, Timothy J.; Mostace...

Authors

Vitor H.F. Gomes

IJff

Niels Raes

Amaral

Rafael P.

Luiz de Souza Coelho

de Almeida Matos

Carolina V. Castilho

Diogenes de Andrade Lima Filho

Juan Ernesto Guevara

William E. Magnusson

Oliver L. Phillips

Florian Wittmann

Marcelo de Jesus Veiga Carim

Maria Pires Martins

Irume

Daniel Sabatier

Molino

Olaf S.

Nigel C.A. Pitman

Maria Teresa Fernandez Piedade

Abel Monteagudo Mendoza

Bruno Garcia Luize

Eduardo Martins Venticinque

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

Arboleda

Timothy J. Killeen

Bonifacio Mostacedo

Rodolfo Vasquez

Jochen

Rafael L. Assis

Marcelo Brilhante Medeiros

Marcelo Fragomeni Simon

Ana Andrade

William F. Laurance

Camargo

Layon O. Demarchi

Susan G.W. Laurance

Emanuelle de Sousa Farias

Nascimento

Juan David Cardenas Revilla

Adriano Quaresma

Costa

Vieira

Cintra

Castellanos

Roel Brienen

Pablo R. Stevenson

Yuri Feitosa

Joost F. Duivenvoorden

Gerardo A. Aymard C.

Hugo F.

Natalia Targhetta

James A. Comiskey

Alberto Vicentini

Aline Lopes

Gabriel Damasco

Roosevelt

Carolina Levis

Juliana Schietti

Priscila Souza

Thaise Emilio

Alfonso Alonso

David Neill

Francisco Dallmeier

Leandro Valle Ferreira

Alejandro Araujo-Murakami

Daniel Praia

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

Chris Baraloto

Eliana M. Jimenez

Juliana Stropp

Julien Engel

Marcos Silveira

Mora

Pascal Petronelli

Paul Maas

Raquel Thomas-Caesar

Terry W. Henkel

Doug Daly

Paredes

Tim R. Baker

Alfredo Fuentes

Carlos A. Peres

Jerome Chave

Jose Luis Marcelo Pena

Kyle G. Dexter

Miles R. Silman

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

Rudas

Bruce Hoffman

Vela

Edelcilio Marques Barbosa

Zent

George Pepe Gallardo Gonzales

Doza

Ires Paula de Andrade Miranda

Jean-Louis Guillaumet

Linder Felipe Mozombite Pinto

Luiz Carlos de Matos Bonates

Natalino Silva

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

Hirma Ramirez-Angulo

Ramos

Kenneth R. Young

Maira Rocha

Marcelo Trindade Nascimento

Medina

Milton Tirado

Ophelia Wang

Rodrigo Sierra

Armando Torres-Lezama

Casimiro Mendoza

Cid Ferreira

Baider

Daniel Villarroel

Henrik Balslev

Italo Mesones

Ligia Estela Urrego Giraldo

Luisa Fernanda Casas

Manuel Augusto Ahuite Reategui

Reynaldo Linares-Palomino

Roderick Zagt

Sasha

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



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.

Citation

Gomes, V. H., IJff, S. D., Raes, N., Amaral, I. L., Salomão, R. P., de Souza Coelho, L., …ter Steege, H. (in press). Species distribution modelling: contrasting presence-only models with plot abundance data. Scientific Reports, 8(1), Article 1003. https://doi.org/10.1038/s41598-017-18927-1

Journal Article Type Article
Acceptance Date Dec 20, 2017
Online Publication Date Jan 17, 2018
Deposit Date Feb 26, 2018
Journal Scientific Reports
Electronic ISSN 2045-2322
Publisher Nature Publishing Group
Peer Reviewed Peer Reviewed
Volume 8
Issue 1
Article Number 1003
DOI https://doi.org/10.1038/s41598-017-18927-1
Keywords biodiversity; ecological modelling
Public URL https://nottingham-repository.worktribe.com/output/905023
Publisher URL https://doi.org/10.1038/s41598-017-18927-1