TCN: Collaborative Research: Digitization and Enrichment of U.S. Herbarium Data from Tropical Africa to Enable Urgent Quantitative Conservation Assessments

Collaborative Research: Digitization and Enrichment of U.S. Herbarium Data from Tropical Africa to Enable Urgent Quantitative Conservation Assessments

Digitization and Enrichment of U.S. Herbarium Data from Tropical Africa to Enable Urgent Quantitative Conservation Assessments
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Project Summary

Biological diversity has been the subject of hundreds of years of work by botanists and zoologists, accumulating rich stores of specimens and associated data in museums and herbaria around the world. These rich information resources, however, too often remain in analog format only, and have not been digitized and “enabled” in the service of science. This project aims to digitize, enrich, and share openly the rich data resources held in United States herbaria that correspond to plants of tropical Africa. By the close of the project, it will have captured data from 1.1 million herbarium specimens, and will augment digital accessible data records for the African continent by more than 15-fold. It will also have created a broad, international, intercontinental network of scientists and students interested in and experienced with management and analysis of such data. This combination of information resources and human capacity will enrich and improve biodiversity conservation planning across Africa.

Herbarium specimens represent a rich source of data on plant diversity. This project will focus on the tropical African seed plant specimen holdings of 21 U.S. herbaria, which will be imaged, associated data captured, and data records georeferenced and quality-controlled. Imaging and data capture will be carried out at each of the herbaria, and data will be aggregated for efficient georeferencing. For most records, georeferencing will be performed automatically; however, a small portion will be georeferenced manually by plant scientists in Ghana, Rwanda, Malawi, and Gabon. Finally, project data will be subjected to detailed quality-control assessment, and served openly to the scientific community via a dedicated “African Plants” portal on Symbiota, as well as integration into iDigBio.org and the Global Biodiversity Information Facility (GBIF.org). These rich data resources will be used to understand the conservation status of African plant species in much greater detail than has been possible to date.

Project Websites & Social Media

African Plants Collaborative Biodiversity Portal

The African Plants Portal provides a unique access point to millions of primary biodiversity records of plants from African countries.

https://african-plants.org/portal/index.php

Tropical African Plants Thematic Collections Network (TAP-TCN) website

The TAP TCN website provides information about this project, including outcomes, collaborators, partners, and contact information for researchers and students interested in using data from the project or for herbaria that would like to contribute data to the African Plants Portal.

https://sites.google.com/view/tap-tcn/home

African Plants Transcribers Network Google Group

In August 2024, the project team at the University of Kansas (DBI-2223875) formed a Google Group for the African Plants Transcribers Network, a group for researchers and staff who are transcribing records for African plant specimens for this project. The purpose of this group is to facilitate communication across project teams. This project involves teams at 11 core institutions (MO, GH, NY, F, RSA, UC, MIN, PH, CM, YU, and PUL/PUR), plus 9 additional herbaria who are contributing relevant specimens as part of this TCN (US, BRIT, KSP, BRU, LSU, DAV, BRY, ARIZ and UT).

https://groups.google.com/g/african-plants-transcribers-network

Citizen Science & Outreach Projects

The Field Museum (FM) hosted community scientists to participate in digitization projects at the Field Museum Collections Club. Fourteen community scientists attended an event in December 2022, learned about this project and its main objectives, and barcoded ~1800 specimens of flowering plants from Africa; in January 2023, 32 community scientists barcoded a further 5271 specimens.

In April 2023, FM hosted a WeDigBio Event, wherein community scientists were invited to participate in digitization projects at the Field Museum. FM also hosted a Bank of America Community Volunteering Program, where 18 people attended and barcoded 2976 African plant specimens. Finally, FM Members' Night events provided FM members with the opportunity to visit behind-the-scenes areas to meet scientists and learn about their research projects, including a display about this project in the Imaging Lab.

In August 2023, a Newsletter Celebrating plant power! 20,000+ plant specimens from Tropical Africa digitized, was featured in News From the Field Museum of Natural History (FMNH), an e-newsletter with current and recent news of collections, research, and conservation efforts at FMNH distributed to members of the museum.

In April and July 2024, interested members of the public were invited to attend open tours at the University and Jepson Herbaria (UCJEPS) at the University of California, Berkeley. The tours of the herbarium including a demo of the digitizing lab, showing people the process of digitizing and using African specimens as an example.

In July 2024, Patricia Barberá (MOBOT), Brent Mishler (UCJEPS), Katelin Pearson (ASU), Chelsea Smith (PH), Israel Borokini, and Tiana Rehman (BRIT) led an open meeting on the Tropical African Plants Digitization TCN at the International Botanical Congress, Madrid, Spain. The meeting was an information session on this project and the utility of the data being generated by it.

[#AfricanPlants series]

https://twitter.com/WeDigBio/status/1619899508351201282 Tweet about outreach activities with volunteers who barcoded over 12,000 specimens as part of the African Plants Data Project.

Project Leadership

Project sponsor: National Science Foundation

Principal Investigators (PIs):[A. Townsend Peterson (PI/PD)] [Brent D. Mishler (PI)] [Mare Nazaire (PI)] [Nico M. Franz (PI)] [Alexander Linan (PI)] [Elena Kramer (PI)] [Nicole Tarnowsky (PI)]

Project Collaborators

University of Kansas

Principal Investigator (PI)/Project Director (PD): A. Townsend Peterson (NSF Award #2223875)

University of California, Berkeley, University Herbarium (UC) and Jepson Herbaria (JEPS)

Principal Investigator (PI): Brent D. Mishler (NSF Award #2223876)

California Botanic Garden, formerly Rancho Santa Ana (RSA) Botanic Garden

Principal Investigator (PI): Mare Nazaire (NSF Award #2223877)

Arizona State University

Principal Investigator (PI): Nico M. Franz (NSF Award #2223878)

Missouri Botanical Garden (MO)

Principal Investigator (PI): Alexander Linan Co-Principal Investigator (Co-PI): Porter Lowry Former Principal Investigator: Patricia Barberá (NSF Award #2223879)

Harvard University (GH)

Principal Investigator (PI): Elena Kramer (NSF Award #2223880)

New York Botanical Garden (NY)

Principal Investigator (PI): Nicole Tarnowsky (NSF Award #2223881)

Academy of Natural Sciences of Drexel University (PH)

Subaward Principal Investigator (Sub PI): Tatyana Livshultz (NSF Award #2223875)

Carnegie Museum of Natural History (CM)

Subaward Principal Investigator (Sub PI): Bonnie L. Isaac (NSF Award #2223875)

Field Museum of Natural History (F)

Subaward Principal Investigator (Sub PI): Maria Lucia Kawasaki (NSF Award #2223875)

Purdue University (PUL)

Subaward Principal Investigator (Sub PI): D. Rabern Simmons (NSF Award #2223875)

University of Minnesota (MIN)

Subaward Principal Investigator (Sub PI): Timothy Whitfeld (NSF Award #2223875)

Yale University (YU)

Subaward Principal Investigator (Sub PI): Patrick Sweeney (NSF Award #2223875)

Bringham and Young University (BRY)

Contact: Robert Johnson

Brown University (BRU)

Contact: Rebecca Y. Kartzinel

Louisiana State University (LSU)

Contacts: Laura Lagomarsino and Jennifer Kluse

National Museum of Natural History (US)

Contacts: Sylvia Orli and Eric Schuettpelz

Philecology Herbarium at the Botanical Research Institute of Texas (BRIT)

Contacts: Peter Fritsch and Tiana F. Rehman

Pittsburg State University (KSP)

Contact: Neil Snow

University of Arizona (ARIZ)

Contact: Michelle McMahon

University of California, Davis (DAV)

Contacts: Alison Colwell and Daniel Potter

University of Utah (UT)

Contact: Mitchell J. Power

Centre for Plant Medicine Research (CPMR), Mampong-Akuapem, Ghana

Contact: Alex Asase (Georeferencing Team Lead)

Center of Excellence in Biodiversity and Natural Resource Management at University of Rwanda, Kigali, Rwanda

Contact: Beth A. Kaplin (Georeferencing Team Lead)

L’Herbier National du Gabon, Libreville, Gabon

Contact: Nestor Engone Obiang (Georeferencing Team Lead)

Malawi University of Science and Technology, Limbe, Malawi

Contact: Tiwonge Mzumara-Gawa (Georeferencing Team Lead)

Georeferencing Coordinators

Contact: John Wieczorek, Rauthiflor LLC, Bariloche, Argentina

Contact: Paula Zermoglio, Instituto de Investigaciones en Recursos Naturales, Agroecología y Desarrollo Rural (IRNAD)

Protocols & Workflows

The Missouri Botanical Garden team initiated contact with Cyrille Chatelain from Geneva, responsible for the African Plant Database (APD), and Chatelain provided a copy of the APD for the project. The University of Minnesota team (Tim Whitfeld and George Weiblen) then quality-controlled the APD dataset, and created a clean and effective version thereof, for use by the project, which has the dual advantage of creating a controlled vocabulary for each institutional dataset, and of moving all project datasets to a common taxonomic authority.

Details of taxonomy list:

458 families, 6666 genera, 38193 species (accepted names), 43960 species synonyms, 5466 subspecies (accepted names), 1256 subspecies synonyms, 3714 varieties (accepted names), 6768 variety synonyms, 166 forms (accepted names), and 464 form synonyms for consistency among project partners on this project. Csv file in UTF-8.

Publications

von Konrat M, Rodriguez Y, Bailey C, Gwilliam III GF, Christian C, Aguero B, Ahn J, Albion Z, Allen JR, Bailey C, Blake E, Blake W, Blake G, Briscoe L, Budke JM, Campbell T, Chansler M, Clark D, Delapena R, Denslow M, Dodinval D, Dux E, Ellis S, Ellwood E, Enkhbayer M, Ens B, Evans NM, Fabian A, Ferguson A, Gaswick W, Golembiewski K, Grant S, Hancock L, Hansen K, Janney B, Jones J, Kachian Z, Kawasaki ML, Kellum K, Leek O, Lichamer A, Maier C, Mast A, Martinec JL, Mayer P, Mladek M, Nadhifah A, Neefus C, Nodulman M, Oliver M, Overberg K, Townsend Peterson A, Qazi-Lampert A, Rothfels C, Ryan ZA, Salm R, Schreiner D, Schreiner M, Tepe EJ, Turcatel M, Vega A, Wade H, Webbink K, Weinand D, Widhelm T, Zwingelberg M (2024) From spectators to stewards: Transforming public involvement in natural history collections. Natural History Collections and Museomics 1: 1-33. https://doi.org/10.3897/nhcm.1.138247

Herbst, R., D. Stille, G. F. Gwilliam III, M. von Konrat, T. Campbell, W. Gaswick, F. Grewe, K. Hansen, F. Iacobelli, K. Jellema, M. L. Kawasaki, D. Kreider, R. Ree, Y. Rodriguez, A. Wolpert. (In press). Unlocking the Past: The Potential of Large Language Models to Revolutionize Transcription of Natural History Collections. Data Intelligence.

Professional Presentations

Asase, A., Bissiengou, P., & Peterson, A. T. (2025, August). The Tropical African Plants Initiative: Mobilizing large-scale herbarium data for science and conservation [Symposium]. XXIII AETFAT Congress, Accra, Ghana. https://aetfat.ug.edu.gh/sites/aetfat.ug.edu.gh/files/2025-04/symposia_abstracts.pdf

Appau, Y., & Derkyi, A. A. M. (2025, August). Assessing people's knowledge, attitudes, and practices in a community-driven ecological restoration initiative: Insight from Ghana [Conference abstract]. XXIII AETFAT Congress, Accra, Ghana.

Barberá, P., Asase, A., Borokini, I. T., Colwell, A., Davis, C. C., Franz, N. M., Fritsch, P., Gilbert, E., Isaac, B. L., Johnson, R., Kaplin, B. A., Kartzinel, R. Y., Kawasaki, M. L., Kennedy, J., Kluse, J., Kramer, E. M., Lagomarsino, L., Livshultz, T., Lowry, P. P., McMahon, M., Mishler, B. D., Mzumara, T. I., Nazaire, M., Nixon, K. C., Engone Obiang, N., Orli, S., Pearson, K., Peterson, A. T., Potter, D., Power, M. J., Rehman, T. F., Schmidt, H., Simmons, D. R., Schmull, M., Schuettpelz, E., Smith, C. R., Snow, N., Sweeney, P. W., Tarnowsky, N., Teisher, J. K., Weiblen, G. D., Whitfeld, T. J. S., Wieczorek, J., & Zermoglio, P. (2024, July). Digitization and enrichment of U.S. herbarium data from Tropical Africa to enable urgent quantitative conservation assessments. Paper presented at the XX International Botanical Congress (IBC 2024), in the symposium "African Taxonomy: A Collaborative Effort Towards Biodiversity Conservation," Madrid, Spain.

Borokini, I. T., Mishler, B. D., & Laffan, S. (2024, July). Revisiting the patterns of African flora biodiversity using spatial phylogenetics [Conference presentation]. XX International Botanical Congress (IBC 2024), Symposium: Tropical Plant Evolution Across Spatial and Temporal Scales, Madrid, Spain. https://ibcmadrid2024.com/?seccion=scientificArea&subSeccion=detailAbstract&id=872

Borokini, I. T., Mishler, B. D., & Laffan, S. (2025, August). Spatial phylogenetics of native African seed plants [Conference abstract]. XXIII AETFAT Congress, Accra, Ghana.

Kaunda, N. D., & Haindi, A. J. (2025, August). Medicinal plants use and knowledge in Malawi: The case of genus Aloe [Conference abstract]. XXIII AETFAT Congress, Accra, Ghana.

Kayuni, B., & Mzumara, T. I. (2025, August). Improving spatial accuracy for historical African plant records in the herbaria [Conference abstract]. XXIII AETFAT Congress, Accra, Ghana.

Klein, M., Mount, K., Bunch, S., Reyes, B., Simmons, D. R., & Aime, M. C. (2025, March). African rust fungi (Basidiomycota, Pucciniales) in the Purdue University Arthur Fungarium (PUR): An unrecognized resource for the study of Ugandan plant pathology [Poster presentation]. Indiana Academy of Science Annual Meeting, Indianapolis, Indiana, United States.

Klein, M., Mount, K., Bunch, S., Reyes, B., Simmons, D. R., & Aime, M. C. (2025, April). African rust fungi (Basidiomycota, Pucciniales) in the Purdue University Arthur Fungarium (PUR): An unrecognized resource for the study of Ugandan plant pathology [Poster presentation]. Purdue University Spring Undergraduate Research Exposition, Purdue University, West Lafayette, Indiana, United States.

Linan, A. G., Schmidt, H. H., Pearson, K., Asase, A., Borokini, I. T., Colwell, A., Davis, C., Franz, N. M., Fritsch, P. W., Gilbert, E., Isaac, B. L., Johnson, R., Kaplin, B. A., Kartzinel, R. Y., Kawasaki, M. L., Kennedy, J., Kluse, J., Kramer, E. M., Lagomarsino, L., Livshultz, T., McMahon, M., Mishler, B. D., Mzumara, T. I., Nazaire, M., Obiang, N. E., Orli, S., Peterson, A. T., Potter, D., Power, M. J., Rehman, T., Schmull, M., Schuettpelz, E., Simmons, D. R., Smith, C. R., Snow, N., Sweeney, P. W., Tarnowsky, N., Teisher, J. K., Weiblen, G. D., Whitfeld, T. J. S., Wieczorek, J., & Zermoglio, P. (2025, July). Digitization and enrichment of U.S. herbarium data from tropical Africa to enable urgent quantitative conservation assessments [Poster presentation]. Botany 2025 Annual Meeting, Palm Springs, California, United States.

Mboma, R., & Engone Obiang, N. (2025, August). Effort d'investigation sur Guibourtia tessmannii (Harms) J. Léonard (Fabaceae) [Conference abstract]. XXIII AETFAT Congress, Accra, Ghana.

M’manga, G. M., Mwafongo, E., M’bwana, B., Namoto, M., & Mzumara-Gawa, T. I. (2025, August). Assessing the conservation status of Malawi’s endemic flora: Urgent needs and challenges [Conference abstract]. XXIII AETFAT Congress, Accra, Ghana.

Nazaire, Mare (2023). Enriching the Internship Experience Through Digitization of the RSA Herbarium. Society for the Preservation of Natural History Collections (SPNHC) 2023. San Francisco, California.

Nkhata, A., Chingaipe, A., & Mzumara, T. I. (2025, August). Leveraging iNaturalist for plant species mobilization and identification in Malawi [Conference abstract]. XXIII AETFAT Congress, Accra, Ghana.

Peterson, A. Townsend (2022). Digitization and Enrichment of U.S. Herbarium Data from Tropical Africa to Enable Urgent Quantitative Conservation Assessments. 2022 Biodiversity Digitization Conference (BioDigiCon). Virtual.

Peterson, A. Townsend (2024). Managing Biodiversity Data in the Blockchain: Full Tracking of All Data Transactions Through Time in Managing Systematic Collections. iDigBio Digital Data 2024: Synthesizing & Harmonizing Data for Integrated Biodiversity Research. Lawrence, Kansas.

Schmidt, H. H., Linan, A. G., Pearson, K., Asase, A., Borokini, I. T., Colwell, A., Davis, C., Franz, N. M., Fritsch, P. W., Gilbert, E., Isaac, B. L., Johnson, R., Kaplin, B. A., Kartzinel, R. Y., Kawasaki, M. L., Kennedy, J., Kluse, J., Kramer, E. M., Lagomarsino, L., Livshultz, T., McMahon, M., Mishler, B. D., Mzumara, T. I., Nazaire, M., Obiang, N. E., Orli, S., Peterson, A. T., Potter, D., Power, M. J., Rehman, T., Schmull, M., Schuettpelz, E., Simmons, D. R., Smith, C. R., Snow, N., Sweeney, P. W., Tarnowsky, N., Teisher, J. K., Weiblen, G. D., Whitfeld, T. J. S., Wieczorek, J., & Zermoglio, P. (2025, July). Digitization and enrichment of U.S. herbarium data from tropical Africa to enable urgent quantitative conservation assessments [Oral presentation]. Botany 2025 Annual Meeting, Palm Springs, California, United States.

Simmons, D. R., Bunch, S. M., Reyes, B., & Aime, M. C. (2024, March). African plants in the Purdue University Herbaria Arthur (PUR) and Kriebel (PUL) collections [Poster presentation]. Indiana Academy of Science Annual Meeting, Indianapolis, Indiana, United States.

Simmons, D. R., Bunch, S. M., Reyes, B., & Aime, M. C. (2024, April). Digitization of the African plants of the Arthur Fungarium (PUR) and Kriebel Herbarium (PUL) at Purdue University [Poster presentation]. 2024 American Society of Plant Biologists, Midwest Section Meeting, West Lafayette, Indiana, United States.

Simmons, D. R., Bunch, S. M., Reyes, B., & Aime, M. C. (2024, June). Digitization of the African rust fungi (Pucciniales) of the Arthur Fungarium (PUR) in the Purdue University Herbaria [Poster presentation]. Mycological Society of America 2024 Annual Meeting, Markham, Ontario, Canada.

Sinclair, D., & Mzumara, T. I. (2025, August). The food plants of Mylothris sagala and the endangered Oreocnemis phoenix [Conference abstract]. XXIII AETFAT Congress, Accra, Ghana.

Smith, C. (2025, May). Digitization of specimens from Africa housed in the PH Herbarium (Philadelphia, Pennsylvania) [Poster presentation]. Society for the Preservation of Natural History Collections (SPNHC) Spring 2025 Annual Meeting, University of Kansas, Lawrence, Kansas, United States. https://virtual.oxfordabstracts.com/event/74160/submission/205.

Uwase, A. S. (2025, August). The national herbarium of Rwanda - A five-year redevelopment history (2020-2025) [Conference abstract]. XXIII AETFAT Congress, Accra, Ghana.

Other project documentation

Recordings of each live class and Q&A session of the African Plants Georeferencing Train the Trainers Workshop shared on YouTube at https://tinyurl.com/AfricanPlantsGeorefCourseYT, as presented to the georeferencing teams in Ghana, Gabon, Rwanda, and Malawi for this project by the georeferencing coordinators, Paula Zermoglio and John Wieczorek

Adventures in the Herbarium: Preserving African Plants (Episodes 1 & 2), two podcasts prepared by the Summer interns from Education Department at the Field Museum, shared on https://rss.com/podcasts/teenstudio/

The St. Louis Dispatch published an article in July 2024 discussing the incorporation of AI in the digitization of African plant records at Missouri Botanical Garden (DBI-2223879). Desalvio, Serina. (2024, July 8). Missouri Botanical Garden: AI used to learn how trees move. St. Louis Post-Dispatch, Vol. 146, No. 190. https://www.stltoday.com/news/local/metro/mobot-uses-ai-to-learn-how-trees-move-and-to-save-millions-of-plantspecimens/article_fb9f9660-3885-11ef-8f5a-57b61f2acc14.html

In February 2025, New York Botanical Garden’s storytelling platform, The Hand Lens, published a story that uses digitized herbarium specimens to talk about making Antemoro paper in Madagascar (DBI-2223881): Mitra, J. (2025, February 19). Exploring Antemoro paper. The William & Lynda Steere Herbarium, New York Botanical Garden. https://sweetgum.nybg.org/science/the-hand-lens/explore/narratives-details/?irn=7771