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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
Current Research
Project Websites
Publications

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.

Current Research

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

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.

[#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 (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

Cornell University(BH)

Contact: Kevin C. Nixon

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

Publications

Professional Presentations

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.

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.

Simmons, D. Rabern; Bunch, Sidney M.; Reyes, Bryan; and Aime, M. Catherine (2024). Conference poster: African Plants in the Purdue University Herbaria Arthur (PUR) and Kriebel (PUL) Collections. Indiana Academy of Science annual meeting. Indianapolis, Indiana.

Simmons, D. Rabern; Bunch, Sidney M.; Reyes, Bryan; and Aime, M. Catherine (2024). Conference poster: Digitization of the African plants of the Arthur Fungarium (PUR) and Kriebel Herbarium (PUL) at Purdue University. 2024 American Society of Plant Biologists, Midwest Section Meeting. West Lafayette, Indiana.