The Key to the Cabinets: Building and Sustaining a Research Database for a Global Biodiversity Hotspot
- 1 Digitization TCN: The Key to the Cabinets: Building and Sustaining a Research Database for a Global Biodiversity Hotspot
- 2 PENs
- 2.1 Digitization PEN: Filling in Knowledge Gaps with Key Herbaria for Understanding Vascular Plant Diversity in the Atlantic Coastal Plain
- 2.2 Digitization PEN: Integrating the Herbaria of Peninsular Florida, a Biodiversity Hotspot of Endemism, Rarity, and Richness
- 2.3 Integrating the unique collections of southern Illinois at SIU to improve coverage of the Southeastern US Flora in SERNEC
Digitization TCN: The Key to the Cabinets: Building and Sustaining a Research Database for a Global Biodiversity Hotspot
|The Key to the Cabinets (SERNEC - TCN)|
The southeastern USA is botanically rich, with areas of high global biodiversity in both the Appalachians and the coastal plain. Millions of plant specimens have been collected from this region over the past four centuries, and these specimens and the information they contain currently reside in museums, or herbaria, at universities across the area. Scientists study these specimens intently; however, it is difficult to retrieve information at broad geographic and taxonomic scales without pipelines to move the information electronically from the specimen to an accessible pool of data. SERNEC, or the SouthEast Regional Network of Expertise and Collections, is a large regional network of botanical experts and collections that has, through an NSF-sponsored research coordination network (RCN) project, developed critical skills in biodiversity informatics. The current project will allow the SERNEC group to make data available for over 3 million specimens using the latest photography and information capture tools and to engage citizen scientists and students to assist in transcribing and georeferencing this large dataset. The research generated through this project can help regional planners, land managers and communities to manage their natural resources in our ever-changing environment.
The interaction of scientists, citizen scientists, and students will provide a synergy to build a research tool of an unparalleled scale and scope. The ultimate goal of this project is to develop an imaged and databased set of over 3 million specimens from over 100 herbaria in one of the most floristically diverse regions in North America and a global hotspot of plant diversity. This will represent a valuable data source for research on the response of vegetation to climate change, human development, and rapid migrations of introduced species. This region has been a biodiversity hotspot for 100 million years and this project should encourage research on changes over time to develop better predictive models as areas of biodiversity change. By partnering with Symbiota, Notes from Nature, GEOLocate, Adler Planetarium, iPlant/TACC, and Specify, the project will develop ways to best integrate various efforts for data accessibility. This award is made as part of the National Resource for Digitization of Biological Collections through the Advancing Digitization of Biological Collections program, and all data resulting from this award will be available through the national resource (iDigBio.org).
This project proposes to utilize plant collection data to determine the threats to the native biota of the southeastern region of North America, including:
- climate change
- invasive species
- human population growth
- species extinction.
Compare geographic distributions and habitat requirements of endemic species with non-endemics.
Determine the origins of biogeographic richness of the region and maintenance of diversity over geologic time.
Ecological niche or species distribution modeling of current and future distributions of rare and endemic species.
Project Websites & Social Media
Citizen Science & Outreach Projects
This project will utilize Notes From Nature (http://www.notesfromnature.org) which will serve to engage citizen scientists in museum related science activities.
The project has developed Notes From Nature-based lesson plans to target state-based standards of learning (SOLs) for grades 6-12. These along with other educational resources can be found at http://sernec.appstate.edu/education-outreach
FSU's Robert K. Godfrey Herbarium hosted a successful crowdfunding campaign in 2014, raising more than $2000 to provision six 1-day citizen science events in 2015. 100+ citizen scientists from the Tallahassee region were brought onto campus to learn about local biodiversity and the role of biodiversity specimens in research and education. The longer-term, bigger-picture goal is to develop a new model for sustaining biodiversity data creation by providing resources to the nation's 1500 museums, universities, field stations, and other institutions with similar collections so that they find it easier to do something similar. Those collections together house about a billion specimens—plants, fossils, birds, mammals, sponges, insects, etc. The plan is to establish a virtuous circle in which, as the collections engage more people in their local communities in the events, the crowdfunding support for those events grows. Visit http://spark.fsu.edu/Projects/121/Blazing-a-New-Trail-for-Sustainability-with-Citizen-Science for more information.
Project Sponsor: Appalachian State University (NSF Award 1410069)
Principal Investigator (PI): Zack Murrell
Project Manager: Michael Denslow
Data Manager: Herrick Brown
Collaboratoring Award PIs:
Alan Harvey, Georgia Southern University; Alan Weakley, University of North Carolina - Chapel Hill; Alexander Krings, North Carolina State University; Allen Risk, Morehead State University; Andrea Weeks, George Mason University; Ashley Morris, Middle Tennessee State University; Austin Mast, Florida State University; Ben Montgomery, University of South Carolina Upstate; Brad Ruhfel, Eastern Kentucky University; Charles Horn, Newberry College; Daniel Stanzione, iPlant, University of Texas; Dayle Saar, Murray State University; Dixie Damrel, Clemson University; Donna Ford-Werntz, West Virginia University; Douglas Jensen, Converse College; Ed Gilbert, Arizona State University; Emily Gillespie, Marshall University; Eran Kilpatrick, University of South Carolina - Salkehatchie; Erika Gonzalez, Longwood College; George Johnson, Arkansas Tech University; Gerald Long, Francis Marion University; Hank Bart, Tulane University; James Carter, Valdosta State University; Joe Pollard, Furman University; Joey Shaw, University of Tennessee - Chattanooga; John Clark, University of Alabama - Tuscaloosa; John Nelson, University of South Carolina - Columbia; Jon Evans, University of the South; Katherine Mathews, Western Carolina University; Kelly Major, University of South Alabama; Kunsiri Grubbs, Winthrop University; L. D. Estes, Botanical Research Institute of Texas; Laura Trouille, Adler Plantarium; Leslie Goertzen, Auburn University; Lisa Krueger, University of Tennessee - Martin; Lisa Wallace, Mississippi State University; Mary (Maggie) Whitson, Northern Kentucky University; Mary Priestley, University of the South; Michael Windham, Duke University; Nelson Rios, Tulane University; Nico Franz, Arizona State University; Norris Williams, University of Florida, Florida Museum of Natural History; Rachel Jabaily, Rhodes College; Robert Guralnick, University of Florida; Shawn Krosnick, Tennessee Technological University; Thomas Sasek, University of Louisiana – Monroe; Timothy McDowell, East Tennessee State University; Travis Marsico, Arkansas State University - Jonesboro; Wendy Zomlefer, University of Georgia
Appalachian State University, I. W. Carpenter, Jr. Herbarium (BOON) (NSF Award 1410069)
Arkansas Natural Heritage Commission (ANHC)
Arkansas State University (STAR) (NSF Award 1410098)
Arkansas Tech University (APCR)
Armstrong State University (AASU)
Auburn University, John D. Freeman Herbarium (AUA) (NSF Award 1410200)
Austin Peay State University (APSC)
Berea College (BEREA)
Bridgewater College (BDWR)
Campbell University (CAU)
City of Alexandria Herbarium (AVCH)
Clemson University, Bob and Betsy Campbell Museum of Natural History (CLEMS) (NSF Award 1410094)
Columbus State University (COLG)
Converse College (CONV)
Delta State University (DSC)
Duke University (DUKE)
East Carolina University (ECUH)
East Tennessee State University (ETSU)
Eastern Kentucky University, Ronald L. Jones Herbarium (EKY) (NSF Award 1410077)
Florida Department of Agriculture and Consumer Services (PIHG)
Florida Museum of Natural History (FLAS)
Florida State University (FSU) (NSF Award 1410288)
Francis Marion University (FMUH)
Furman University (FUGR)
George Mason University, Ted R. Bradley Herbarium (GMUF) (NSF Award 1410086)
Georgia Southern University (GAS)
Georgia Southwestern State University (GSW)
Gulf Coast Research Laboratory (HGCRL)
Henderson State University (HEND)
Hendrix College (HXC)
Institute for Botanical Exploration (IBE)
James Madison University (JMUH)
Longwood University, Harvill-Stevens Herbarium (FARM)
Lord Fairfax Community College (LFCC)
Louisiana State University, Baton Rouge, Shirley C. Tucker Herbarium (LSU)
Louisiana State University, Shreveport, D. T. MacRoberts Herbarium (LSUS)
Louisiana Tech University (LTU)
Lynchburg College, Ramsey-Freer Herbarium (LYN)
Marie Selby Botanical Gardens (SEL)
Marshall University (MUHW) (NSF Award 1410143)
McNeese State University (MCN)
Mecklenburg County Park and Recreation Herbarium (UNCC)
Middle Tennessee State University (MTSU)
Mississippi Museum of Natural Science (MMNS)
Mississippi State University (MISSA) (NSF Award 1410092)
Morehead State University (MDKY)
Murray State University (MUR)
Newberry College (NBYC)
Nicholls State University (THIB)
North Carolina Zoological Park (NCZP)
Northern Kentucky University, John W. Thieret Herbarium (KNK)
Northwestern State University (NATC)
Rhodes College (SWMT)
Salem College (SC)
Southeastern Louisiana University (SELU)
Southern Research Station (SFRP)
Tennessee Technological University (HTTU)
Tulane University (NO)
University of Alabama (UNA)
University of Arkansas (UARK )
University of Arkansas at Monticello (UAM)
University of Central Arkansas (UCAC)
University of Central Florida (FTU)
University of Georgia, Georgia Museum of Natural History (GA) (NSF Award 1410081)
University of Louisiana at Monroe (NLU) (NSF Award 1410445)
University of Louisiana, Lafayette (USLH / LAF)
University of Mississippi, Thomas M. Pullen Herbarium (MISS)
University of New Orleans (NOLS)
University of North Carolina, Chapel Hill (NCU) (NSF Award 1410439)
University of North Carolina, Pembroke (PEMB)
University of Richmond (URV)
University of South Alabama (USAM)
University of South Carolina Upstate (USCS)
University of South Carolina, Columbia, A. C. Moore Herbarium (USCH)
University of South Carolina, Salkehatchie (SALK)
University of Southern Mississippi (USMS)
University of Tennessee (TENN)
University of Tennessee, Chattanooga (UCHT) (NSF Award 1410087)
University of Tennessee, Martin (UTM)
University of the South (UOS)
University of West Florida, Michael I. Cousens Herbarium (UWFP)
University of West Georgia (WGC)
Valdosta State University (VSC)
Vanderbilt University (VDB)
Virginia Commonwealth University, Lewis Ginter Botanical Garden (VCU)
Virginia Military Institute (VMIL)
Virginia Polytechnic Institute and State University, Massey Herbarium (VPI)
West Virginia University (WVA)
Western Carolina University (WCUH)
Weymouth Woods (WEWO)
Winthrop University (WINU)
Adler Planetarium (Notes from Nature)
Arizona State University (Symbiota)
iPlant (now CyVerse), University of Texas
Tulane University (GEOLocate)
University of Florida (Notes From Nature)
University of Kansas (Specify)
Emory University Herbarium (GEO)
St. Andrews University (SAPCL)
University of Mary Washington Herbarium (MWCF)
University of Memphis Herbarium (MEM)
Wake Forest University (WFU)
Protocols & Workflows
The SERNEC website has a section with various resources including documentation, tutorials and webinars.
Digitization Methods: Rapid imaging coupled with citizen science based label transcription and collaborative georeferencing.
Franz, N., Gilbert, E., Ludäscher, B. and Weakley, A., 2016. Controlling the taxonomic variable: Taxonomic concept resolution for a southeastern United States herbarium portal. Research Ideas and Outcomes, 2, p.e10610.
Nelson, G., Sweeney, P., Wallace, L.E., Rabeler, R.K., Allard, D., Brown, H., Carter, J.R., Denslow, M.W., Ellwood, E.R., Germain-Aubrey, C.C., Gilbert, E., Gillespie, E., Goertzen, L.R., Legler, B., Marchant, D.B., Marsico, T.D., Morris, A.B., Murrell, Z., Nazaire, M., Neefus, C., Oberreiter, S., Paul, D., Ruhfel, B.R., Sasek, T., Shaw, J., Soltis, P.S., Watson, K., Weeks, A., Mast, A.R., 2015. Digitization Workflows for Flat Sheets and Packets of Plants, Algae, and Fungi. Applications in Plant Sciences 3(9): 1500065 doi:10.3732/apps.1500065.
Powell, C., Motley, J., Qin, H., & Shaw, J. (2019). A born‐digital field‐to‐database solution for collections‐based research using collNotes and collBook. Applications in Plant Sciences, e11284.
Zomlefer, W. B., Carter, J. R., Allison, J. R., Baker, W. W., Giannasi, D. E., Hughes, S. C., Lance, R. W., Lowe, P.D., Lynch, P.S., Miller, J. T.,Patrick, T. S., Protsko,E., Sewell, S. Y. S., & Weakley, A. 2018. Additions to the Flora of Georgia Vouchered at the University of Georgia (GA) and Valdosta State University (VSC) Herbaria. Castanea, 83(1), 124-139.
Other project documentation
Digitization PEN: Filling in Knowledge Gaps with Key Herbaria for Understanding Vascular Plant Diversity in the Atlantic Coastal Plain
The Southeast Regional Network of Expertise and Collections (SERNEC) is developing one of the most comprehensive data sets of plant diversity in North America. Through SERNEC, more than 4.5 million herbarium specimens from the southeastern U.S. will be digitized for online access through a project portal and the iDigBio Specimen Portal. In this Partner to Existing Network (PEN) project, three additional herbaria at the College of William and Mary, Old Dominion University, and University of Mary Washington will contribute digitized and georeferenced herbarium records from southeastern Virginia to these efforts. Plant diversity in this region is of interest because of the high degree of turnover due to southern species reaching their northern limit and northern species reaching their southern limit in southeastern Virginia. These records join the SERNEC data set that contribute information about plant diversity in the North American Coastal Plain, an area rich in rare, unique species. The SERNEC data set is a one-stop resource for taxonomic and ecological research and botanical education and aids in the revision of state checklists of plants and specimen curation. Student interns will have opportunities to develop professional skills in team work, communication, and goal-setting, as well as exploring potential career options in museum management. Citizen-scientists aiding in digitization will have opportunities to interact with project personnel and learn about the importance of natural history collections in education and research and local plant diversity. Educational materials developed for K-12 classes will enhance botanical literacy and illustrate plant diversity, structure and geographical range in the Southeast.
Images and associated label data for approximately 118,000 vascular plant specimens in the three herbaria will be captured digitally and accessible online at the SERNEC Symbiota Portal and the iDigBio Specimen Portal. If lacking, georeferenced coordinates for the collection location of each specimen will be determined and added to the database. These activities expand the use of software packages that were enhanced for use in the SERNEC project, including Symbiota, GEOLocate, and Zooniverse. Original data, including images and text, will be retained long-term at institutional repositories of the herbaria involved in this project. Specimen digitization will be conducted by undergraduate student interns at each of the institutions and citizen-scientists, including the Virginia Master Naturalists and volunteers working in Notes from Nature.
Project Sponsor: Old Dominion University Research Foundation (NSF Award 1802342)
Principal Investigators (PIs): Lisa Wallace (PI), Martha Case (Co-PI)
Project Sponsor: University of Mary Washington (NSF Award 1802129)
Principal Investigators (PIs): April Wynn (PI)
Digitization PEN: Integrating the Herbaria of Peninsular Florida, a Biodiversity Hotspot of Endemism, Rarity, and Richness
This Partner to Existing Network (PEN) will join the South East Regional Network of Expertise and Collections (SERNEC) Thematic Collection Network (TCN), a collaboration that is digitizing and making data accessible for over 3 million plant specimens. These specimens document over 8,000 species of native or naturalized vascular plants in this region, a biodiversity hotspot. This project will extend the collaboration to add a quarter million herbarium specimen data records to SERNEC from the herbaria of Fairchild Tropical Botanic Garden (FTG) and the University of South Florida (USF), which together document over 4,000 plant species in the southeastern USA. As biodiversity is inextricably linked to productivity, ecosystem services, and human health, the addition of these two herbaria will fill a crucial gap in the knowledge base, maximizing the data available to address environmental change and resource management among a growing human population.
The most important botanical collections of the FTG and USF herbaria are the 125,000 specimens from central and south Florida, more than found in any other herbarium. Unique features of this region include the Lakes Wales Ridge, Everglades, Atlantic Coastal Ridge, and Florida Keys, all of which have experienced significant habitat loss and degradation. Among the 8,000 native or naturalized vascular plant species in the southeastern USA, about 1,200 are known only from central and south Florida. This number includes about 290 threatened or endangered, 130 endemic, 570 non-native, and 90 invasive plant species. The plant diversity of this region is of primary importance to the management of its resources, including air, water, and soil quality, agriculture, mining, construction, land reclamation, recreation, and biodiversity conservation. By engaging volunteers and high school and undergraduate students, FTG and USF will increase access to their vast collection of herbarium specimens, bolstering scientific and educational knowledge of plants in the region. These data are shared as a public resource through SERNEC and iDigBio (www.idigbio.org).
Project Sponsor: University of South Florida (NSF Award 1701683)
Principal Investigators (PIs): Alan Franck, Brett Jestrow
Integrating the unique collections of southern Illinois at SIU to improve coverage of the Southeastern US Flora in SERNEC
Through this award the Southern Illinois University (SIU) Herbarium will join the SERNEC Thematic Collections Network (TCN). The SIU collections house an estimated 90,000 specimens of plants, primarily representing the regional flora, including many historically important specimens. While providing diverse data useful to various basic scientific fields, this project be fundamental to the greater understanding of plant sciences in southern Illinois and the surrounding regions. It will also provide information for more applied fields, such as natural area conservation, ecosystem restoration, and ecological impacts of human activities. On a local level, the digital resources will be integrated into courses at SIU, used in outreach activities at university sponsored events and in a local nature recreation park, and promoted to the general public.
The herbarium at SIU will digitize the collection to gather and provide label transcriptions, georeferences, and specimen imaging online as part of the Southeast Regional Network of Expertise and Collections (SERNEC). The flora of southern Illinois is closely allied to the southeastern US floristically. This project will proceed with a pre-digitization check of specimens, followed by barcoding, verification of label data, label transcription, digital imaging, image editing, and georeferencing. Finally, data will be transferred to SERNEC for public access, and added to the national resource at iDigBio.org.
Project Sponsor: Southern Illinois University at Carbondate (NSF Award #2002400)
Principal Investigator: Kurt Neubig (PI), Nancy Garwood (co-PI)