NAMPHORA: An Open-access Database of Fossil and Modern Pollen Records from the Mediterranean, Arabian and Northern Africa regions

Authors

Affiliations

Irene Solano

Department of Evolution, Ecology and Behaviour, University of Liverpool, Liverpool, UK

Jakob Bro-Jorgensen

Department of Evolution, Ecology and Behaviour, University of Liverpool, Liverpool, UK

Ignacio A. Lazagabaster

Department of Evolution, Ecology and Behaviour, University of Liverpool, Liverpool, UK

Centro Nacional de Investigación Sobre Evolución Humana CENIEH, Burgos, Spain

Chris D. Thomas

Leverhulme Centre for Anthropocene Biodiversity, Department of Biology, University of York, York, UK

Saúl Manzano

Área de Botánica, Departamento de Biodiversidad y Gestión Ambiental, Facultad de Ciencias Biológicas y Ambientales, Universidad de León, León, Spain

Abstract

Northern Africa’s climate and vegetation underwent significant changes throughout the Holocene, particularly in connection to the termination of the African Humid Period ca. 5500 years ago. Fossil pollen records are crucial for reconstructing past vegetation and climate, offering insights into the origin and distribution of past flora. However, existing pollen databases, especially concerning Northern Africa, have several limitations, including the unavailability of some unpublished data and the absence of standardised information on plant traits. To address these issues, we introduce the Northern African, Arabian, and Mediterranean Pollen Holocene Records Archive (NAMPHORA)—a comprehensive, machine-readable database compiling fossil and modern pollen records alongside plant functional traits, and a pollen taxonomic harmonisation proposal. This database will significantly improve the accuracy of palaeoecological reconstructions, enhance biogeographical analyses, and refine climate models for Northern Africa during the Holocene. It enables direct data retrieval via programming languages such as R, and all datasets and code are openly available via GitHub, with contributions and feedback welcomed.

Keywords

Pollen records, Plant functional traits, Palaeoecology, Holocene, African Humid Period (AHP), Open-access database, NAMPHORA database

1 Table of Contents

1. Introduction

2. Project structure

3. Data pipeline

   3.1. Project set up

   3.2. Data Preparation

   3.3. Data Visualisation

   3.4. Metadata

   3.5. Functions

4. References

2 Introduction

The NAMPHORA (Northern Africa, Arabian, and Mediterranean Pollen HOlocene Records Archive) is an open-access database that compiles fossil and modern pollen records from North Africa, Arabia, and the Mediterranean. The database includes fossil and modern pollen records, as well as uncalibrated and calibrated radiocarbon dates (in calendar years). The database also provides information on growth form (habit), phytogeographic affinity, and plant functional traits (PFTs) for each taxon in the database.

Pollen records and radiocarbon dates were sourced from Neotoma (https://www.neotomadb.org/) and African Pollen Database (APD: https://africanpollendatabase.ipsl.fr/#/home), and unpublished data were obtained directly from the authors. Growth form and phytogeographic affinity data for each harmonised pollen type were compiled using the Global Biodiversity Information Facility (GBIF: https://www.gbif.org/), the Plants of the World Online (POWO: https://powo.science.kew.org/) website, and relevant literature, while plant functional traits were retrieved from the Botanical Information and Ecology Network (BIEN: https://bien.nceas.ucsb.edu/bien/) (Enquist et al. 2016) and TRY Plant Trait Database (TRY: https://www.try-db.org/TryWeb/Home.php) (Kattge et al. 2020) databases.

3 Project structure

Different sections (folders) of the project are structured as follows:

• data/: All raw and processed data are stored in this folder.

  • /raw_data: Contains raw data on the following sub-folders:

    • /age_data: Contains information on radiocarbon dates and their calibration for each dated pollen record.

      • /calibration: Contains calibration data for each dated fossil pollen record. If more than two radiocarbon dates are available, calibration is performed using a Bayesian age-depth model with the rbacon R package (Bacon_runs folder). If only a single date is reported, calibration is performed using the rice R package (Single_depth_calibration folder).

      • /radiocarbon: Contains the raw radiocarbon dates for each dated fossil pollen record. Obtained from the APD (https://africanpollendatabase.ipsl.fr/#/home), from Neotoma (https://www.neotomadb.org/), from Giesecke et al. (2014), and directly from the authors.

    • /mapping_data: Contains the following:

      • /EcoregionsWWF_2017: Includes the WWF terrestrial ecoregions of the world shapefile (retrieved from https://www.worldwildlife.org/publications/terrestrial-ecoregions-of-the-world).

      • /Regions_WWF_2017: Includes a shapefile with the regions for Europe and the Arabian Peninsula modified from the WWF terrestrial ecoregions of the world shapefile in QGIS v. 3.28.1 - Firenze.

      • /Africa_Vegetation_White_1983: Contains the phytoregions shapefile, which were defined by White (1983) (retrieved from https://www.miramon.cat/mmr/examples/miombo/docs/database/white/index.htm)

      • The elevation raster file (elevation.tiff) used in this study was obtained from Lazagabaster et al. (2024). This raster was generated by calculating elevation based on the CHELSA-Trace21K paleo-orographic simulations (Karger et al. 2023).

    • /plant_functional_types: Contains the /TRY folder, which includes plant functional trait data (i.e. leaf_type_TRY.txt) downloaded from the TRY database.

    • /pollen_data: Contains raw fossil (/fossil folder) and modern (/modern folder) pollen records, obtained from the APD (https://africanpollendatabase.ipsl.fr/#/home), from Neotoma (https://www.neotomadb.org/) using the neotoma2 package and the Neotoma API, and from the authors directly.

    • /taxonomy: Contains the following sub-folders:

      • harmonisation_lists: Includes taxonomic harmonisation resources, including harmonisation tables from Lézine et al. (2009), Mottl et al. (2021), and the APD taxonomy list (https://africanpollendatabase.ipsl.fr/#/taxon-dict).

      • raw_taxa_list: Contains the raw_pollen_types.csv file, which lists the raw pollen types from all pollen records compiled in the NAMPHORA database.

      • GBIF_species_list: Contains the GBIF_species_list.csv file, which lists all plant species filtered by the study area, directly obtained from the GBIF website (GBIF.org, 2025).

  • /processed_data: Contains processed data on the following sub-folders:

    • /age_calibrated: Contains recalibrated radiocarbon dates for each dated pollen record.

    • /mapping_data: Contains the merged phytogeographic_regions shapefile (a combination of both Olson et al. 2001 and White 1983 phytogeographic regions maps)

    • /plant_functional_types: Contains the final plant functional traits data in the file total_pfts.csv.

    • /pollen_data: Contains harmonised fossil (/fossil folder) and modern (/modern folder) pollen records. Each folder includes:

      • /harmonised_counts: Harmonised pollen records with original counts.

      • /harmonised_percentages: Harmonised pollen records with calculated percentages.

    •  /taxonomy: Contains the following:

      • The harmonised_taxonomy_list.csv file, which contains a list of the original taxa and their corresponding harmonised names.

      • The taxa_pollen_types_list.csv file lists individual taxa for each pollen type. When a pollen type includes multiple genera (e.g., Diospyros/Euclea t.), it is divided into multiple rows, with each row representing a single genus linked to the same pollen type (only for angiosperms and gymnosperms).

      • The taxa_species_names.csv file, which contains a list of the taxa from taxa_pollen_types_list and all the species names associated to them (only for angiosperms and gymnosperms).

      • The species_pollen_types_list.csv file, which contains the final list of the species belonging to the pollen type within our study area (only for angiosperms and gymnosperms).

      • The phytogeographic_affinity.csv file, which contains a list of the phytogeographic affinities for each harmonised pollen type.

      • The phytogeographic_affinity_list_columns.csv file, which contains the phytogeographic affinities categories in columns for each harmonised pollen type (in rows)

      • The habit_list.csv file, which contains a list of the habits for each harmonised pollen type.

• docs/

  • /supplementary_info: Includes the following:

    • /original_excel_files_received_from_authors, which stores the original files provided by the authors.

    • Table S1.docx file, which includes a list with all contributing authors who provided data to the database.

• images/: Contains the PNG files of the database workflow, pollen harmonisation and plant traits processing workflow and the database logo.

• index_files/: The files created when rendered this html document.

• metadata/

  • /age_calibrated: Contains the following:

    • calibration_information.csv: A file that provides details on the calibration process for each record.

    • calibration_metadata.csv: A file that contains metadata for the calibration_information.csv file.

    • calibration_metadata.html: An html file that contains metadata for the calibration_information.csv file.

    • /calibration_metadata_files: The files created when rendered the script calibration_metadata.qmd.

  • /plant_functional_types: Contains the following:

    • pfts_categories.csv: A file that provides a definition for each plant functional trait and the corresponding reference.

    • pfts_metadata.csv: A file that contains metadata for the total_pfts.csv file.

    • pfts_metadata.html: An html file that contains metadata for the total_pfts.csv file.

    • /pfts_metadata_html_files: The files created when rendered the script pfts_metadata.qmd.

  • /pollen_data: Contains the following:

    • database.csv: A file that contains the metadata information for all the pollen records compiled in the NAMPHORA database.

    • pollen_metadata.csv: This file provides details descriptions of each column in the database.csv file.

    • database.html: An html file that contains metadata for the database.csv file.

    • /pollen_metadata_files: The files created when rendered the script pollen_metadata.qmd.

  • /references: Contains the database_references.csv file, which lists references for each dataset (i.e. pollen records/age data, taxonomy, habit, phytogeographic affinity and plants functional traits).

  • /taxonomy: Contains the following:

    • phytogeographic_affinity_categories.csv: A file that provides a definition for each phytogeographic affinity category and the corresponding reference.

    • taxonomy_metadata.csv: A file that provides an explanation for each column of the harmonised_taxonomy_list.csv file.

    • taxonomy_metadata.html: An html file that contains metadata for the harmonised_taxonomy_list.csv file.

    • /taxonomy_metadata_files: The files created when rendered the script taxonomy_metadata.qmd.

• outputs/: This folder contains all the outputs of the data visualisation in the form of maps (outputs/maps/) & graphs (outputs/graphs/).

• scripts/: This folder contains all scripts of the data pipeline.

• renv/: Stores all installed R packages along with a record of their versions. 

4 Data pipeline

Data extraction, processing, and visualisation are conducted in R v. 4.4.1., following this data pipeline:

Run the scripts in the following order:

4.1 Dependencies set up

setup.R (Run this script to install dependencies)

4.2 Data Preparation

01_pollen_list.R (Extracts pollen records from Neotoma using the neotoma2 v1.0.5 R package and generates a raw pollen list for taxonomic harmonisation)

02_harmonisation_lists.R (Adds the number of pollen sequences per pollen type and incorporates published harmonisation lists into the harmonised taxonomy list)

03_processing_pollen_data.R (Processes raw pollen data, including taxonomic harmonisation, radiocarbon date re-calibration, and percentage calculations)

04_species_pollen_types_list.R (Retrieves species associated with each pollen type that are exclusively found within the study region)

05_process_PFTs.R (Downloads and processes plant functional traits (PFTs) from the BIEN and TRY databases)

06_calibrate_14C_bacon.R (Calibrates radiocarbon dates using Bayesian age-depth modelling with the rbacon v3.2.0 R package)

07_calibrate_14C_single_depth.R (Calibrates radiocarbon dates for single-depth samples using the rice v1.0.0 R package)

08_altitude_sites.R (Assigns altitude values to sites lacking altitude information)

4.3 Data Visualisation

09_maps.R (Creates maps of all fossil and modern pollen records compiled in this database)

Figure 1. Map of pollen records (modern & dated and non-dated fossil records) compiled in the NAMPHORA database

Figure 2. Map of the phytogeographical regions (a) from White (1983) and Olson et al. (2001) and the biome map (b) from Olson et al. (2001).

10_description_database_figures.R (Creates graphs to summarise and describe the database)

Figure 3. Number of pollen records (sites) per biogeographic region

Figure 4. Number of pollen records (sites) per database

Figure 5. Number of dated pollen records per time period in years before present. The horizontal line indicates the African Humid Period (14,800 to 5,000 years Before Present)

Figure 7. Latitudinal distribution of pollen records (sites) according to their archive type

Figure 8. Altitudinal distribution of pollen records (sites) according to the biogeographic area

Figure 9. Proportion of harmonised pollen types per phytogeographic affinity

Figure 10. Number of taxa per plant functional trait

4.4 Metadata

pollen_metadata.qmd (Generates a csv and HTML files containing pollen metadata for the database.csv file)

taxonomy_metadata.qmd (Generates a csv and HTML files containing metadata for the harmonised_taxonomy_list.csv file)

pfts_metadata.qmd (Generates a csv and HTML files containing metadata for the total_pfts.csv file)

calibration_metadata.qmd (Generates a csv and HTML files containing metadata for the calibration_information.csv file)

4.5 Functions

functions.R (Contains custom functions used throughout the data pipeline)

5 References

1. Enquist, B. J., Condit, R., Peet, R. K., Schildhauer, M. & Thiers, B. M. Cyberinfrastructure for an integrated botanical information network to investigate the ecological impacts of global climate change on plant biodiversity. Preprint at https://doi.org/10.7287/peerj.preprints.2615v2 (2016).
2. GBIF.org (04 September 2025) GBIF Occurrence Download https://doi.org/10.15468/dl.66vbhj
3. Giesecke, T., et al. Towards mapping the late Quaternary vegetation change of Europe. Vegetation History and Archaeobotany, 23, 75–86. (2014).
4. Karger, D. N., Nobis, M. P., Normand, S., Graham, C. H., & Zimmermann, N. E. CHELSA-TraCE21k – high-resolution (1 km) downscaled transient temperature and precipitation data since the Last Glacial Maximum. Climate of the Past, 19(2), 439–456. (2023).
5. Kattge, J. et al. TRY plant trait database – enhanced coverage and open access. Global Change Biology 26, 119–188 (2020).
6. Lazagabaster, I. A., et al. Evaluating species distribution model predictions through time against paleozoological records. Ecology and Evolution, 14, e70288. (2024).
7. Lézine, A. M., Watrin, J., Vincens, A., & Hély, C. Are modern pollen data representative of West African vegetation? Review of Palaeobotany and Palynology, 156, 265–276. (2009).
8. Mott, O., et al. Global acceleration in rates of vegetation change over the past 18,000 years. Science, 372, 860–864. (2021).
9. White, F. The Vegetation of Africa: A Descriptive Memoir to Accompany the Unesco/AETFAT/UNSO Vegetation Map of Africa. (Unesco, Paris, 1983).