Published July 22, 2026 | Version v2
Software Open

Modelling data and codebase for Sakhalkar, S.P. et al., (2026). Global patterns in plant–pollinator specialisation. Nature Ecology & Evolution (accepted)

Authors/Creators

  • 1. Department of Ecology, Faculty of Science, Charles University, Prague, Czechia; Institute of Microbiology of the Czech Academy of Sciences, Prague, Czechia
  • 2. Ecological Networks Lab, Department of Biology, Technische Universität Darmstadt, Darmstadt, Germany
  • 3. Department of Ecology, Montana State University, Bozeman, MT, USA
  • 4. Chicago Botanic Garden, Negaunee Institute for Plant Science and Action, Glencoe, IL, USA; Rocky Mountain Biological Laboratory, Crested Butte, CO, USA; Plant Biology & Conservation, Northwestern University, Evanston, IL, USA
  • 5. Section for Molecular Ecology & Evolution, Globe Institute, University of Copenhagen, Denmark
  • 6. Biometry & Environmental System Analysis, University of Freiburg, Freiburg, Germany
  • 7. Centre for Ecology and Conservation, Faculty of Environment, Science and Economy, University of Exeter, Cornwall Campus, Penryn, UK
  • 8. Department of Species Interaction Ecology, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany; German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany; Department of Science and Conservation, National Tropical Botanical Garden, Kalāheo, HI, USA
  • 9. Faculty of Arts, Science and Technology, University of Northampton, Waterside Campus, Northampton, UK; Key Laboratory for Plant Diversity and Biogeography of East Asia, Chinese Academy of Sciences, Kunming Institute of Botany, Kunming, China
  • 10. Rocky Mountain Biological Laboratory, Crested Butte, CO, USA
  • 11. Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Frankfurt (Main), Germany; Department of Biology, Philipps-Universität Marburg, Marburg, Germany; Cluster of Excellence (EXC 3121): TERRA—Terrestrial Geo-Biosphere Interactions in a Changing World, University of Tübingen, Tübingen, Germany
  • 12. Argentine Institute for Dryland Research, CONICET & National University of Cuyo, Mendoza, Argentina; Faculty of Exact and Natural Sciences, National University of Cuyo, Mendoza, Argentina
  • 13. Department of Biology, Missouri State University, Springfield, MO, USA
  • 14. Department of Biology, California State University Channel Islands, Camarillo, CA, USA
  • 15. Laboratório de Ecologia da Polinização e Interações (LEPI), Department of Biodiversity and Biostatistics, Institute of Biosciences, São Paulo State University, Botucatu, SP, Brazil
  • 16. Centro de Síntese Ecológica e Conservação, Departamento de Genética, Ecologia e Evolução - ICB, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil; Programa de Pós-Graduação em Ecologia, Conservação e Manejo da Vida Silvestre, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
  • 17. Department of Ecology, Faculty of Science, Charles University, Prague, Czechia
  • 18. Department of Ecology and Evolution, Estación Biológica de Doñana, EBD-CSIC, Seville, Spain
  • 19. University of the Basque Country (UPV-EHU), Leioa, Spain; Basque Centre for Climate Change (BC3), Leioa, Spain
  • 20. Dokuz Eylül Üniversitesi, Rektörlük, İzmir, Türkiye
  • 21. Plant Biology & Conservation, Northwestern University, Evanston, IL, USA; Chicago Botanic Garden, Negaunee Institute for Plant Science and Action, Glencoe, IL, USA; Oklahoma Biological Survey, University of Oklahoma, Norman, OK, USA
  • 22. School of Geography and Natural Sciences, Northumbria University, Newcastle upon Tyne, UK
  • 23. Centre for Conservation and Restoration Science, Edinburgh Napier University, Edinburgh, UK
  • 24. Division of Environmental Science, Texas Woman's University, Denton, TX, USA
  • 25. Institute of Botany of the Czech Academy of Sciences, Třeboň, Czechia
  • 26. Department of Entomology, University of Agricultural Sciences, Bangalore, India
  • 27. Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milano, Italy
  • 28. Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden; Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
  • 29. Programa de Pós-Graduação em Ciência Florestal, Universidade Federal dos Vales do Jequitinhonha e Mucuri, Diamantina, MG, Brazil
  • 30. CREAF, Bellaterra, Spain
  • 31. Centro de Síntese Ecológica e Conservação, Departamento de Genética, Ecologia e Evolução - ICB, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil; Ecologia, Conservação e Biodiversidade, Universidade Federal de Uberlândia, Belo Horizonte, MG, Brazil
  • 32. UMR CNRS 7261, Institut de Recherche sur la Biologie de l'Insecte, Université de Tours, Tours, France
  • 33. Department of Entomology, University of Maryland, College Park, MD, USA; Yale School of the Environment, New Haven, CT, USA
  • 34. Unidad de Investigación para el Conocimiento, Uso y Valoración de la Biodiversidad, Centro de Estudios Conservacionistas, Facultad de Ciencias Químicas y Farmacia, Universidad de San Carlos de Guatemala, Guatemala City, Guatemala
  • 35. Department of Biology, Faculty of Engineering and Natural Sciences, Kırıkkale University, Kırıkkale, Türkiye
  • 36. Naturpark Fränkische Schweiz - Frankenjura, Pottenstein/Kirchenbirkig, Germany
  • 37. Centre for Environmental and Climate Science, Lund University, Lund, Sweden
  • 38. Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, Australia
  • 39. School of Biological Sciences, University of East Anglia, Norwich, UK
  • 40. Programas de Pós-Graduação em Biologia Animal, Universidade Federal dos Vales do Jequitinhonha e Mucuri, Diamantina, MG, Brazil
  • 41. CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vila do Conde, Portugal; BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vila do Conde, Portugal
  • 42. Red de Ecoetología, Instituto de Ecología AC, Xalapa, Veracruz, Mexico; Laboratorio Nacional de Biología del Cambio Climático, Mexico City, Mexico
  • 43. Instituto de Ecología, Universidad Mayor de San Andrés, La Paz, Bolivia
  • 44. Department of Biology, University of the Balearic Islands, Palma, Spain; MUCBO – Museu Balear de Ciències Naturals (FJBS-MBCN), Sóller, Illes Balears, Spain
  • 45. Department of Zoology, University of Cambridge, Cambridge, UK
  • 46. Bioeconomy Science Institute, Lincoln, New Zealand; School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
  • 47. Biology Department, University of Nevada Reno, NV, USA
  • 48. International Centre of Insect Physiology and Ecology (icipe), Nairobi, Kenya; Social Insects Research Group (SIRG), Department of Zoology & Entomology, University of Pretoria, Pretoria, Republic of South Africa; Department of Biological Sciences, University of Lethbridge, Lethbridge, AB, Canada
  • 49. Unidad de Investigación para el Conocimiento, Uso y Valoración de la Biodiversidad, Centro de Estudios Conservacionistas, Facultad de Ciencias Químicas y Farmacia, Universidad de San Carlos de Guatemala, Guatemala City, Guatemala; Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico
  • 50. Biology Centre of the Czech Academy of Sciences, Institute of Entomology, České Budějovice, Czechia; School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
  • 51. Department of Environmental Conservation, University of Massachusetts Amherst, Amherst, MA, USA
  • 52. Global Change Research Institute (IICG-URJC), Rey Juan Carlos University (URJC), Madrid, Spain; Departamento de Biología y Geología, Física y Química Inorgánica, Universidad Rey Juan Carlos, Móstoles, Spain
  • 53. School of Science, Western Sydney University, Penrith, NSW, Australia; Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, Australia
  • 54. Centro de Síntese Ecológica e Conservação, Departamento de Genética, Ecologia e Evolução - ICB, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil; Laboratório de Genética da Conservação de Abelhas (LaBee), Instituto de Ciências Biológicas e da Saúde, Universidade Federal de Viçosa, Campus Florestal, Florestal, MG, Brazil
  • 55. Department of Entomology, Pennsylvania State University, University Park, PA, USA
  • 56. Ecology of Tropical Agricultural Systems, University of Hohenheim, Stuttgart, Germany; Center for Biodiversity and Integrative Taxonomy (KomBioTa), University of Hohenheim, Stuttgart, Germany
  • 57. Department of Biology, University of Florida, Gainesville, Florida, USA
  • 58. Wildlife Ecology & Health Group (WE&H), Departament de Medicina i Cirurgia Animals, Facultat de Veterinària, Universitat Autònoma de Barcelona (UAB), Cerdanyola del Vallès, Spain; Insect Ecology Group, Department of Ecology, Faculty of Environmental Sciences, Czech University of Life Sciences Prague (CZU), Prague, Czechia
  • 59. Centre for Functional Ecology (CFE), Associate Laboratory TERRA, Department of Life Sciences, University of Coimbra, Coimbra, Portugal
  • 60. Department of Animal Ecology and Tropical Biology, Biocenter, University of Würzburg, Würzburg, Germany
  • 61. Cultural Landscape Günztal Foundation, Ottobeuren, Germany; Department of Animal Ecology and Tropical Biology, Biocenter, University of Würzburg, Würzburg, Germany
  • 62. Department of Biology of Ecosystems, Faculty of Science, University of South Bohemia, České Budějovice, Czechia
  • 63. Department of Integrative Biology and Lady Bird Johnson Wildflower Center, University of Texas at Austin, Austin, TX, USA
  • 64. Department of Environmental Systems Science, ETH Zurich, Zurich, Switzerland
  • 65. Department of Biology and the Environment, University of Haifa – Oranim, Tivon, Israel
  • 66. General Zoology, Institute for Biology, Martin Luther University Halle-Wittenberg, Halle, Germany; Unidad de Investigación para el Conocimiento, Uso y Valoración de la Biodiversidad, Centro de Estudios Conservacionistas, Facultad de Ciencias Químicas y Farmacia, Universidad de San Carlos de Guatemala, Guatemala City, Guatemala
  • 67. School of Life Sciences, University of KwaZulu-Natal, Westville Campus, Durban, South Africa
  • 68. Justus Liebig University of Gießen, Institute of Animal Ecology and Systematics, Gießen, Germany
  • 69. CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, China
  • 70. Department of Biology, Lund University, Lund, Sweden; Instituto de Ecología, Universidad Mayor de San Andrés, La Paz, Bolivia
  • 71. Bokwaongo Village Forest Management Committee (BVFMC), Bokwaongo, Cameroon; Mount Cameroon National Park, Buea, Cameroon
  • 72. Grupo de Investigación en Ecología y Evolución en los Trópicos-EETROP, Universidad de las Américas, Quito, Ecuador
  • 73. Departamento de Zoologia, Universidade de Brasília, Brasília, Brazil
  • 74. Programa de Pos-Graduação em Biologia Vegetal, Universidade Federal de Pernambuco, Recife, PE, Brazil
  • 75. Basque Centre for Climate Change (BC3), Leioa, Spain; Ikerbasque, Basque Foundation for Science, Bilbao, Spain
  • 76. Swiss Ornithological Institute, Sempach, Switzerland; Conservation Biology Lab, University of Neuchâtel, Neuchâtel, Switzerland
  • 77. Centro de Síntese Ecológica e Conservação, Departamento de Genética, Ecologia e Evolução - ICB, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
  • 78. Graduate School of Environment and Information Sciences, Yokohama National University, Yokohama, Japan
  • 79. Department of Ecology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
  • 80. Plant-Insect Interactions, School of Life Sciences, Technical University of Munich, Freising, Germany
  • 81. Departamento de Biología y Geología, Física y Química Inorgánica, Universidad Rey Juan Carlos, Móstoles, Spain; Global Change Research Institute (IICG-URJC), Rey Juan Carlos University (URJC), Madrid, Spain
  • 82. Global Change Research Institute (IICG-URJC), Rey Juan Carlos University (URJC), Madrid, Spain; Departamento de Biología y Geología, Física y Química Inorgánica, Universidad Rey Juan Carlos, Móstoles, Spain; Plant Evolutionary Ecology, Institute of Ecology, Evolution and Diversity, Faculty of Biological Sciences, Goethe University Frankfurt, Frankfurt am Main, Germany
  • 83. Centre for Sustainable Agricultural Systems, University of Southern Queensland, Toowoomba, QLD, Australia
  • 84. Department of Geography, University of the Aegean, Mytilene, Greece
  • 85. Department of Landscape and Biodiversity, Norwegian Institute for Bioeconomy Research (NIBIO), Ås, Norway
  • 86. Department of Evolutionary and Environmental Biology, University of Haifa, Haifa, Israel; Department of Natural Science and Environmental Education, Oranim College of Education, Tivon, Israel
  • 87. Instituto de Investigaciones en Ecología y Sustentabilidad (IIES), Laboratorio de Interacciones Bióticas en Habitats Alterados, Universidad Nacional Autónoma de México, Campus Morelia, Morelia, México
  • 88. Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
  • 89. Laboratory of Biogeography & Ecology, Department of Geography, University of the Aegean, Mytilene, Greece
  • 90. Social Insects Research Group (SIRG), Department of Zoology & Entomology, University of Pretoria, Pretoria, Republic of South Africa
  • 91. Centre for Sustainable Agricultural Systems, University of Southern Queensland, Toowoomba, QLD, Australia; School of Molecular and Life Science, Curtin University, Bentley, WA, Australia
  • 92. Biology Department, Boston University, Boston, MA, USA
  • 93. Facultad de Ciencias Agrarias, Universidad Nacional de Jujuy (FCA-UNJu), San Salvador de Jujuy, Argentina
  • 94. UMR CNRS 7267, Ecologie et Biologie des Interactions, Université de Poitiers, Poitiers, France; UMR CNRS 7261, Institut de Recherche sur la Biologie de l'Insecte, Université de Tours, Tours, France
  • 95. Departamento Engenharia e Meio Ambiente, Universidade Federal da Paraíba, PB, Brazil
  • 96. Programas de Pós-Graduação em Biologia Animal, Ciência Florestal e Estudos Rurais, Universidade Federal dos Vales do Jequitinhonha e Mucuri, Diamantina, MG, Brazil
  • 97. Laboratory of Zoology, Research Institute for Biosciences, University of Mons, Mons, Belgium
  • 98. Instituto Interuniversitario de Investigación del Sistema Tierra de Andalucía, Universidad de Jaén, Jaén, Spain; Departmento de Biología Animal, Biología Vegetal y Ecología, Universidad de Jaén, Jaén, Spain
  • 99. Instituto de Biologia – INBIO, Universidade Federal de Uberlândia, Uberlândia, MG, Brazil
  • 100. Autonomous University of Barcelona (UAB), Bellaterra, Spain; CREAF, Bellaterra, Spain
  • 101. Data Science Division, University of Texas at Arlington, Arlington, TX, USA
  • 102. Departamento de Biología y Geología, Física y Química Inorgánica, Universidad Rey Juan Carlos, Móstoles, Spain
  • 103. Department of Biological Sciences, Universidade Estadual de Feira de Santana, Feira de Santana, BA, Brasil
  • 104. Graduate School of Environment and Information Sciences, Yokohama National University, Yokohama, Japan; Institute for Multidisciplinary Sciences, Yokohama National University, Yokohama, Japan
  • 105. School of Environmental and Rural Science, University of New England, Armidale, NSW, Australia
  • 106. The Woodland Trust, Grantham, UK
  • 107. Global Change Research Group, Mediterranean Institute for Advanced Studies, Mallorca, Spain
  • 108. Functional Agrobiodiversity & Agroecology, University of Göttingen, Göttingen, Germany
  • 109. Department of Ecology, Faculty of Science, Charles University, Prague, Czechia; Department of Zoology, Faculty of Science, University of South Bohemia, České Budějovice, Czechia
  • 110. The Xerces Society for Invertebrate Conservation, Columbus, NJ, USA; Yale College, Yale University, New Haven, CT, USA
  • 111. Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands
  • 112. Department of Ecology, Faculty of Science, Charles University, Prague, Czechia; Biology Centre of the Czech Academy of Sciences, Institute of Entomology, České Budějovice, Czechia

Description

Complete author list with affiliations is in the metadata. Corresponding authors: Sailee P. Sakhalkar,  sailee.sakha@gmail.com; Robert Tropek, robert.tropek@gmail.com

This repository contains the code and workflow for assembling, processing, and analysing data used in the research article: Sakhalkar, S.P. et al., (2026). Global patterns in plant–pollinator specialisation. Nature Ecology & Evolution (accepted). It includes scripts for project setup, database preparation, data processing, model fitting, and generation of analysis outputs.

Please note that the raw interaction data are not publicly available because they include several unpublished datasets contributed by collaborators. However, metadata, processed datasets, and all analysis scripts are provided to ensure full analytical reproducibility. The corresponding authors will facilitate contact with the respective data holders to enable access upon reasonable request.

This project is licensed under the terms of the MIT license. The MIT License applies to code in this repository. Data may be subject to separate access restrictions as described above. Please contact the author if you wish to contribute, collaborate or use part of these scripts in your own research projects.

How to run it

This analysis pipeline is written in the statistical programming language R. To run the analyses, you will need to have installed on your local computer R, and optionally RStudio Desktop.

You can download the entire project as a .zip from Zenodo. After unzipping, first run 00_setup_project.R and then scripts/00_master.R. If data/raw_data/database/lifewebs.database.db is not present, database assembly steps are skipped. Downstream analyses are then run from the processed data provided in the repository.

‼️Notes on model fitting compute

The model fitting procedure is iterative and involves three distinct fitting processes. As a result, total computation time is substantial. Benchmarks reported here were obtained on a laptop with 16 GB RAM.

On average, model runs that exclude functional-group–specific smooths require approximately 2 minutes per response variable. In contrast, models including functional-group smoothers may require up to one hour to converge, reflecting the increased complexity of the smoothing structure. Consequently, a full model-fitting workflow for a single dataset may take up to three hours to complete.

Folder structure

Data availability

⚠️The raw interaction datasets used in this study are not included in this repository because they contain unpublished data contributed by multiple collaborators.

To ensure reproducibility:

  • ⚠️ All processed datasets required to run the analyses are provided in data/processed_data/
  • All scripts used for data processing and analysis are included
  • The full workflow can be executed using the processed data

Access to the original raw datasets can be obtained from the corresponding authors upon reasonable request. Requests will be forwarded to the respective data owners where required. (Please direct requests to Sailee P. Sakhalkar,  sailee.sakha@gmail.com and Robert Tropek, robert.tropek@gmail.com.)

00_setup_project.R  # file to setup
📂 data/
│   ├─ raw_data/             # Unprocessed interaction and predictor data (not stored in repo)
│   └─ intermediate_data/       # Temporary files for joining
│   └─ processed_data/       # Cleaned and derived datasets used for analyses
│
📂 output/
│   └─ EDA/          # Exploratory analyses
│   ├─ plots/         # Figures for the manuscript
│   └─ models/          # Saved GAM outputs
│   └─ models_70/          
      # Saved GAM outputs for data thresholded at >0.7 sampling completeness
│   └─ models_estimtatesc_covariate/          
      # Saved GAM outputs for sampling completeness as covariate, not weight
│   └─ SI/          # Supplementary Information
│
📂 scripts/
│   ├─ database_scripts/    # Data cleaning and index calculations
│   │   └─ functions/       # Functions for data handling
│   ├─ predictor_scripts/   # Extract environmental and richness predictors
│   ├─ model_scripts/       # Model fitting, comparison, and figure generation
│   │   └─ comparison_covariates/  # Calculations for latitude covariates
│   │   └─ functions/  # Helper functions for modelling and plotting
│   │   └─ model_formulas/  # Lists of model formulas for datasets
│   │   └─ models_per_dataset/  # Workflows for each dataset
│   └─ SI_scripts/          # Supplementary figures and tables
│
README.md               # This file
app.R  # Used to select networks interactively, then store the query
 
 

 

Files

pollination_latitudinal_specialisation_gradient-review_version(1).zip

Files (109.3 MB)

Additional details

Software

Programming language
R
Development Status
Active