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Sci Rep. 2018 Jan 17;8(1):1003. doi: 10.1038/s41598-017-18927-1.

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

Gomes VHF1,2, IJff SD3,4, Raes N3, Amaral IL5, Salomão RP2, de Souza Coelho L5, de Almeida Matos FD5, Castilho CV6, de Andrade Lima Filho D5, López DC7, Guevara JE8,9, Magnusson WE10, Phillips OL11, Wittmann F12,13, de Jesus Veiga Carim M14, Martins MP5, Irume MV5, Sabatier D15, Molino JF5, Bánki OS3, da Silva Guimarães JR14, Pitman NCA16, Piedade MTF17, Mendoza AM18, Luize BG19, Venticinque EM20, de Leão Novo EMM21, Vargas PN22, Silva TSF23, Manzatto AG24, Terborgh J25, Reis NFC26, Montero JC5,27, Casula KR26, Marimon BS28, Marimon BH28, Coronado ENH11,29, Feldpausch TR30, Duque A31, Zartman CE5, Arboleda NC7, Killeen TJ32, Mostacedo B33, Vasquez R18, Schöngart J17, Assis RL17, Medeiros MB34, Simon MF34, Andrade A35, Laurance WF36, Camargo JL35, Demarchi LO17, Laurance SGW36, de Sousa Farias E37,38, Nascimento HEM5, Revilla JDC5, Quaresma A17, Costa FRC5, Vieira ICG1, Cintra BBL11,17, Castellanos H39, Brienen R11, Stevenson PR40, Feitosa Y41, Duivenvoorden JF42, Aymard C GA43, Mogollón HF44, Targhetta N45, Comiskey JA46,47, Vicentini A10, Lopes A17, Damasco G8, Dávila N48, García-Villacorta R49,50, Levis C51,52, Schietti J5, Souza P5, Emilio T10,53, Alonso A47, Neill D54, Dallmeier F47, Ferreira LV1, Araujo-Murakami A55, Praia D17, do Amaral DD1, Carvalho FA10,56, de Souza FC10,11, Feeley K57,58, Arroyo L55, Pansonato MP5,59, Gribel R60, Villa B17, Licona JC27, Fine PVA8, Cerón C61, Baraloto C62, Jimenez EM63, Stropp J64, Engel J15,62, Silveira M65, Mora MCP66, Petronelli P67, Maas P3, Thomas-Caesar R68, Henkel TW69, Daly D70, Paredes MR71, Baker TR11, Fuentes A72,73, Peres CA74, Chave J75, Pena JLM76, Dexter KG50,77, Silman MR78, Jørgensen PM73, Pennington T50, Di Fiore A79, Valverde FC80, Phillips JF81, Rivas-Torres G82,83, von Hildebrand P84, van Andel TR3, Ruschel AR85, Prieto A86, Rudas A86, Hoffman B87, Vela CIA88, Barbosa EM5, Zent EL89, Gonzales GPG71, Doza HPD71, de Andrade Miranda IP5, Guillaumet JL90, Pinto LFM71, de Matos Bonates LC5, Silva N91, Gómez RZ92, Zent S89, Gonzales T93, Vos VA94,95, Malhi Y96, Oliveira AA59, Cano A40, Albuquerque BW17, Vriesendorp C16, Correa DF40,97, Torre EV98,99, van der Heijden G100, Ramirez-Angulo H98, Ramos JF5, Young KR101, Rocha M17, Nascimento MT102, Medina MNU40,103, Tirado M104, Wang O105, Sierra R104, Torres-Lezama A98, Mendoza C106,107, Ferreira C5, Baider C108, Villarroel D55, Balslev H109, Mesones I8, Giraldo LEU31, Casas LF110, Reategui MAA111, Linares-Palomino R112, Zagt R113, Cárdenas S110, Farfan-Rios W78, Sampaio AF26, Pauletto D114, Sandoval EHV115,116, Arevalo FR116, Huamantupa-Chuquimaco I22, Garcia-Cabrera K78, Hernandez L39, Gamarra LV18, Alexiades MN117, Pansini S26, Cuenca WP118, Milliken W53, Ricardo J11, Lopez-Gonzalez G11, Pos E3,119, Ter Steege H120,121.

Author information

1
Coordenação de Botânica, Museu Paraense Emílio Goeldi, Av. Magalhães Barata 376, C.P. 399, Belém, PA, 66040-170, Brazil.
2
Programa de Pós-Graduação em Ciência Ambientais, Universidade Federal do Pará, Rua Augusto Corrêa 01, Belém, PA, 66075-110, Brazil.
3
Biodiversity Dynamics, Naturalis Biodiversity Center, PO Box 9517, Leiden, 2300 RA, The Netherlands.
4
Marine and Coastal Management, Deltares, Boussinesqweg 1, Delft, 2629 HV, The Netherlands.
5
Coordenação de Biodiversidade, Instituto Nacional de Pesquisas da Amazônia - INPA, Av. André Araújo 2936, Petrópolis, Manaus, AM, 69067-375, Brazil.
6
EMBRAPA - Centro de Pesquisa Agroflorestal de Roraima, BR 174 km 8, Distrito Industrial, Boa Vista, RR, 69301-970, Brazil.
7
Herbario Amazónico Colombiano, Instituto SINCHI, Calle 20 No 5-44, Bogotá, DC, Colombia.
8
Department of Integrative Biology University of California, Berkeley, CA, 94720-3140, USA.
9
Universidad San Francisco de Quito, Colegio de Ciencias Biológicas, Diego de Robles y Vía Interoceánica, Quito, Pichincha, Ecuador.
10
Coordenação de Pesquisas em Ecologia, Instituto Nacional de Pesquisas da Amazônia - INPA, Av. André Araújo 2936, Petrópolis, Manaus, AM, 69067-375, Brazil.
11
School of Geography, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK.
12
Department of Wetland Ecology, Institute of Geography and Geoecology, Karlsruhe Institute of Technology - KIT, Josefstr 1, Rastatt, D-76437, Germany.
13
Biogeochemistry, Max Planck Institute for Chemistry, Hahn-Meitner Weg 1, Mainz, 55128, Germany.
14
Departamento de Botânica, Instituto de Pesquisas Científicas e Tecnológicas do Amapá - IEPA, Rodovia JK Km 10, Campus do IEPA da Fazendinha, Amapá, 68901-025, Brazil.
15
AMAP, IRD, Cirad, CNRS, INRA, Université de Montpellier, TA A-51/PS2, Bd. de la Lironde, Montpellier, 34398, France.
16
Science and Education, The Field Museum, 1400 S. Lake Shore Drive, Chicago, IL, 60605-2496, USA.
17
Coordenação de Dinâmica Ambiental, Instituto Nacional de Pesquisas da Amazônia - INPA, Av. André Araújo 2936, Petrópolis, Manaus, AM, 69067-375, Brazil.
18
Jardín Botánico de Missouri, Oxapampa, Pasco, Peru.
19
Departamento de Ecologia, Universidade Estadual Paulista - UNESP, Instituto de Biociências - IB, Av. 24 A 1515, Bela Vista, Rio Claro, SP, 13506-900, Brazil.
20
Centro de Biociências, Departamento de Ecologia, Universidade Federal do Rio Grande do Norte, Av. Senador Salgado Filho 3000, Natal, RN, 59072-970, Brazil.
21
Divisao de Sensoriamento Remoto - DSR, Instituto Nacional de Pesquisas Espaciais - INPE, Av. dos Astronautas 1758, Jardim da Granja, São José dos Campos, SP, 12227-010, Brazil.
22
Herbario Vargas, Universidad Nacional de San Antonio Abad del Cusco, Avenida de la Cultura, Nro 733, Cusco, Cuzco, Peru.
23
Departamento de Geografia, Universidade Estadual Paulista - UNESP, Instituto de Geociências e Ciências Extas - IGCE, Bela Vista, Rio Claro, SP, 13506-900, Brazil.
24
Departamento de Biologia, Universidade Federal de Rondônia, Rodovia BR 364 s/n Km 9.5, Rural, Porto Velho, RO, 76.824-027, Brazil.
25
Center for Tropical Conservation, Duke University, Nicholas School of the Environment, Durham, NC, 27708, USA.
26
Programa de Pós-Graduação em Biodiversidade e Biotecnologia - PPG-Bionorte, Universidade Federal de Rondônia, Campus Porto Velho, Km 9.5, Rural, Porto Velho, RO, 76.824-027, Brazil.
27
Instituto Boliviano de Investigacion Forestal, Av. 6 de agosto 28 Km 14, Doble via La Guardia Casilla, 6204, Santa Cruz, Santa Cruz, Bolivia.
28
Programa de Pós-Graduação em Ecologia e Conservação, Universidade do Estado de Mato Grosso, Nova Xavantina, MT, Brazil.
29
Instituto de Investigaciones de la Amazonía Peruana - IIAP, Av. A. Quiñones km 2.5, Iquitos, Loreto, 784, Peru.
30
Geography College of Life and Environmental Sciences, University of Exeter, Exeter, EX4 4RJ, UK.
31
Departamento de Ciencias Forestales, Universidad Nacional de Colombia, Calle 64 x Cra 65, Medellín, Antioquia, 1027, Colombia.
32
Agteca-Amazonica, Santa Cruz, Bolivia.
33
Facultad de Ciencias Agrícolas Universidad Autónoma Gabriel René Moreno Santa Cruz, Santa Cruz, Bolivia.
34
Prédio da Botânica e Ecologia Embrapa Recursos Genéticos e Biotecnologia Parque Estação Biológica, Av. W5 Norte, Brasilia, DF, 70770-917, Brazil.
35
Projeto Dinâmica Biológica de Fragmentos Florestais, Instituto Nacional de Pesquisas da Amazônia - INPA, Av. André Araújo 2936, Petrópolis, Manaus, AM, 69067-375, Brazil.
36
Centre for Tropical Environmental and Sustainability Science and College of Science and Engineering James Cook University, Cairns, Queensland, 4870, Australia.
37
Laboratório de Ecologia de Doenças Transmissíveis da Amazônia (EDTA), Instituto Leônidas e Maria Deane, Fiocruz, Rua Terezina 476, Adrianópolis, Manaus, AM, 69060-001, Brazil.
38
Programa de Pós-graduação em Biodiversidade e Saúde Instituto Oswaldo Cruz - IOC/FIOCRUZ Pav. Arthur Neiva - Térreo Av. Brasil 4365 - Manguinhos, Rio de Janeiro, RJ, 21040-360, Brazil.
39
Centro de Investigaciones Ecológicas de Guayana Universidad Nacional Experimental de Guayana, Calle Chile, urbaniz Chilemex, Puerto Ordaz, Bolivar, Venezuela.
40
Laboratorio de Ecología de Bosques Tropicales y Primatología Universidad de los Andes Carrera 1 # 18a- 10, Bogotá, DC, 111711, Colombia.
41
Programa de Pós-Graduação em Biologia (Botânica) Instituto Nacional de Pesquisas da Amazônia - INPA, Av. André Araújo 2936, Petrópolis, Manaus, AM, 69067-375, Brazil.
42
Institute of Biodiversity and Ecosystem Dynamics University of Amsterdam, Sciencepark 904, Amsterdam, 1098 XH, The Netherlands.
43
Programa de Ciencias del Agro y el Mar Herbario Universitario (PORT) UNELLEZ-Guanare, Guanare, Portuguesa, 3350, Venezuela.
44
Endangered Species Coalition, 8530 Geren Rd, Silver Spring, MD, 20901, USA.
45
MAUA Working Group Instituto Nacional de Pesquisas da Amazônia - INPA Av. André Araújo 2936, Petrópolis, Manaus, AM, 69067-375, Brazil.
46
Inventory and Monitoring Program National Park Service 120 Chatham Lane, Fredericksburg, VA, 22405, USA.
47
Center for Conservation Education and Sustainability Smithsonian Conservation Biology Institute, 1100 Jefferson Dr. SW, Suite 3123, Washington, DC, 20560-0705, USA.
48
Biologia Vegetal, Universidade Estadual de Campinas, Caixa Postal 6109, Campinas, SP, 13.083-970, Brazil.
49
Institute of Molecular Plant Sciences University of Edinburgh, Mayfield Rd, Edinburgh, EH3 5LR, UK.
50
Royal Botanic Garden Edinburgh 20a Inverleith Row, Edinburgh, Scotland, EH3 5LR, UK.
51
Programa de Pós-Graduação em Ecologia, Instituto Nacional de Pesquisas da Amazônia - INPA, Av. André Araújo 2936, Petrópolis, Manaus, AM, 69067-375, Brazil.
52
Forest Ecology and Forest Management Group Wageningen University Wageningen University & Research, Droevendaalsesteeg 3, Wageningen, P.O. Box 47, 6700 AA, The Netherlands.
53
Natural Capital and Plant Health Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AB, UK.
54
Ecosistemas Biodiversidad y Conservación de Especies Universidad Estatal Amazónica, Km. 2 1/2 vía a Tena (Paso Lateral), Puyo, Pastaza, Ecuador.
55
Museo de Historia Natural Noel Kempff Mercado Universidad Autónoma Gabriel Rene Moreno, Avenida Irala 565 Casilla Postal 2489, Santa Cruz, Santa Cruz, Bolivia.
56
Centro de Biociências, Departamento de Botânica e Zoologia, Universidade Federal do Rio Grande do Norte, Campus Universitário, Lagoa Nova, Natal, RN, 59078-970, Brazil.
57
Department of Biology University of Miami Coral, Gables, FL, 33146, USA.
58
Fairchild Tropical Botanic Garden Coral, Gables, FL, 33156, USA.
59
Instituto de Biociências - Dept. Ecologia, Universidade de Sao Paulo - USP, Rua do Matão, Trav. 14, no. 321, Cidade Universitária, São Paulo, SP, 05508-090, Brazil.
60
Diretoria de Pesquisas Científicas, Instituto de Pesquisas Jardim Botânico do Rio de Janeiro, Rio de Janeiro, RJ, Brazil.
61
Escuela de Biología Herbario Alfredo Paredes Universidad Central, Ap. Postal 17.01.2177, Quito, Pichincha, Ecuador.
62
International Center for Tropical Botany (ICTB) Department of Biological Sciences Florida International University, 11200 SW 8th Street, OE 243, Miami, FL, 33199, USA.
63
Grupo de Ecología de Ecosistemas Terrestres Tropicales, Universidad Nacional de Colombia Sede Amazonía, Leticia, Amazonas, Colombia.
64
Institute of Biological and Health Sciences, Federal University of Alagoas, Av. Lourival Melo Mota, s/n, Tabuleiro do Martins, Maceio, AL, 57072-970, Brazil.
65
Museu Universitário/Centro de Ciências Biológicas e da Natureza/Laboratório de Botânica e Ecologia Vegetal, Universidade Federal do Acre, Rio Branco, AC, 69915-559, Brazil.
66
Universidad Regional Amazónica IKIAM, Km 7 via Muyuna, Tena, Napo, Ecuador.
67
Cirad UMR Ecofog AgrosParisTech CNRS INRA Univ Guyane, Campus agronomique, Kourou Cedex, 97379, France.
68
Iwokrama International Programme for Rainforest Conservation, Georgetown, Guyana.
69
Department of Biological Sciences, Humboldt State University, 1 Harpst Street, Arcata, CA, 95521, USA.
70
New York Botanical Garden 2900 Southern Blvd, Bronx, New York, NY, 10458-5126, USA.
71
Servicios de Biodiversidad EIRL, Jr. Independencia 405, Iquitos, Loreto, 784, Peru.
72
Herbario Nacional de Bolivia, Universitario UMSA, Casilla 10077 Correo Central, La Paz, La Paz, Bolivia.
73
Missouri Botanical Garden, P.O. Box 299, St. Louis, MO, 63166-0299, USA.
74
School of Environmental Sciences, University of East Anglia, Norwich, NR4 7TJ, UK.
75
Laboratoire Evolution et Diversité Biologique CNRS and Université Paul Sabatier UMR 5174 EDB, Toulouse, 31000, France.
76
Department of Forestry Management, Universidad Nacional Agraria La Molina, Avenido La Molina, Apdo. 456, La Molina, Lima, Peru.
77
School of Geosciences University of Edinburgh, 201 Crew Building, King's Buildings, Edinburgh, EH9 3JN, UK.
78
Biology Department and Center for Energy, Environment and Sustainability, Wake Forest University, 1834 Wake Forest Rd, Winston Salem, NC, 27106, USA.
79
Department of Anthropology University of Texas at Austin, SAC 5.150, 2201 Speedway Stop C3200, Austin, TX, 78712, USA.
80
Andes to Amazon Biodiversity Program, Madre de Dios, Madre de Dios, Peru.
81
Fundación Puerto Rastrojo, Cra 10 No. 24-76 Oficina 1201, Bogotá, DC, Colombia.
82
Colegio de Ciencias Biológicas y Ambientales-COCIBA & Galapagos Institute for the Arts and Sciences-GAIAS, Universidad San Francisco de Quito-USFQ, Quito, Pichincha, Ecuador.
83
Department of Wildlife Ecology and Conservation University of Florida, 110 Newins-Ziegler Hall, Gainesville, FL, 32611, USA.
84
Fundación Estación de Biología, Cra 10 No. 24-76 Oficina 1201, Bogotá, DC, Colombia.
85
Embrapa Amazônia Oriental, Trav. Dr. Enéas Pinheiro s/nº, Belém, PA, 66095-100, Brazil.
86
Instituto de Ciencias Naturales, Universidad Nacional de Colombia, Apartado, 7945, Bogotá, DC, Colombia.
87
Amazon Conservation Team, Doekhieweg Oost #24, Paramaribo, Suriname.
88
Facultad de Ciencias Forestales y Medio Ambiente, Universidad Nacional de San Antonio Abad del Cusco, Jirón San Martín 451, Puerto Maldonado, Madre de Dios, Peru.
89
Laboratory of Human Ecology, Instituto Venezolano de Investigaciones Científicas - IVIC, Ado 20632, Caracas, Caracas, 1020A, Venezuela.
90
Departement EV, Muséum national d'histoire naturelle de Paris, 16 rue Buffon, Paris, 75005, France.
91
Instituto de Ciência Agrárias, Universidade Federal Rural da Amazônia, Av. Presidente Tancredo Neves 2501, Belém, PA, 66.077-901, Brazil.
92
PROTERRA, Instituto de Investigaciones de la Amazonía Peruana (IIAP), Av. A. Quiñones km 2 5, Iquitos, Loreto, 784, Peru.
93
ACEER Foundation, Jirón Cusco N° 370, Puerto Maldonado, Madre de Dios, Peru.
94
Universidad Autónoma del Beni José Ballivián, Campus Universitario Final Av. Ejercito, Riberalta, Beni, Bolivia.
95
Regional Norte Amazónico, Centro de Investigación y Promoción del Campesinado, C/Nicanor Gonzalo Salvatierra N° 362, Riberalta, Beni, Bolivia.
96
Environmental Change Institute, Oxford University Centre for the Environment, Dyson Perrins Building, South Parks Road, Oxford, England, OX1 3QY, UK.
97
School of Agriculture and Food Sciences - ARC Centre of Excellence for Environmental Decisions CEED, The University of Queensland, St. Lucia, QLD 4072, Australia.
98
Instituto de Investigaciones para el Desarrollo Forestal (INDEFOR), Universidad de los Andes, Conjunto Forestal, C.P. 5101, Mérida, Mérida, Venezuela.
99
School of Environmental and Forest Sciences, University of Washington, Seattle, WA, 98195-2100, USA.
100
University of Nottingham, University Park, Nottingham, NG7 2RD, UK.
101
Geography and the Environment, University of Texas at Austin, 305 E. 23rd Street, CLA building, Austin, TX, 78712, USA.
102
Laboratório de Ciências Ambientais, Universidade Estadual do Norte Fluminense, Av. Alberto Lamego 2000, Campos dos Goyatacazes, RJ, 28013-620, Brazil.
103
Department of Biology, University of Maryland, College Park, MD, 20742, USA.
104
GeoIS, El Día 369 y El Telégrafo, 3° Piso, Quito, Pichincha, Ecuador.
105
Environmental Science and Policy, Northern Arizona University, Flagstaff, AZ, 86011, USA.
106
FOMABO, Manejo Forestal en las Tierras Tropicales de Bolivia, Sacta, Cochabamba, Bolivia.
107
Escuela de Ciencias Forestales (ESFOR), Universidad Mayor de San Simon (UMSS), Sacta, Cochabamba, Bolivia.
108
Agricultural Services, Ministry of Agro-Industry and Food Security, Agricultural Services, Ministry of Agro-Industry and Food Security, The Mauritius Herbarium, Reduit, Mauritius.
109
Department of Bioscience, Aarhus University, Building 1540 Ny Munkegade, Aarhus C, Aarhus, DK-8000, Denmark.
110
Ciencias Biológicas, Universidad de Los Andes, Carrera 1 # 18a- 10, Bogotá, DC, 111711, Colombia.
111
Medio Ambiente, PLUSPRETOL, Iquitos, Loreto, Peru.
112
Center for Conservation Education and Sustainability, Smithsonian's National Zoo & Conservation Biology Institute, National Zoological Park, 3001 Connecticut Ave, Washington, DC, 20008, USA.
113
Tropenbos International, Lawickse Allee 11 PO Box 232, Wageningen, 6700 AE, The Netherlands.
114
Instituto de Biodiversidade e Floresta, Universidade Federal do Oeste do Pará, Rua Vera Paz, Campus Tapajós, Santarém, PA, 68015-110, Brazil.
115
Department of Biology, University of Missouri, St. Louis, MO, 63121, USA.
116
Facultad de Biologia, Universidad Nacional de la Amazonia Peruana, Pevas 5ta cdra, Iquitos, Loreto, Peru.
117
School of Anthropology and Conservation, University of Kent, Marlowe Building, Canterbury, Kent, CT2 7NR, UK.
118
Herbario Nacional del Ecuador, Universidad Técnica del Norte, Quito, Pichincha, Ecuador.
119
Ecology & Biodiversity Group, Utrecht University, Padualaan 8, Utrecht, 3584 CH, The Netherlands.
120
Biodiversity Dynamics, Naturalis Biodiversity Center, PO Box 9517, Leiden, 2300 RA, The Netherlands. hans.tersteege@naturalis.nl.
121
Systems Ecology, Free University, De Boelelaan 1087, Amsterdam, 1081 HV, Netherlands. hans.tersteege@naturalis.nl.

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.

PMID:
29343741
PMCID:
PMC5772443
DOI:
10.1038/s41598-017-18927-1
[Indexed for MEDLINE]
Free PMC Article

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