Mobilizing New England Vascular Plant Specimen Data

Digitization TCN: Mobilizing New England Vascular Plant Specimen Data to Track Environmental Change (NEVP)

New England Vascular Plants TCN
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Project Summary
Current Research
Project Websites
Network Map
Publications
PENs

Project Summary

Herbarium specimens provide a source of historical information useful to the study of global environmental change. The goal of this project is to provide data to support studies of the nature and consequences of environmental change in the New England region over the last three centuries. This project will digitally capture specimen data and images from about 1.3 million vascular plant specimens from herbaria across New England, enhancing the data with georeferencing, habitat, and phonological information. The digitization process will integrate with existing community efforts and will develop novel high-throughput digitization technologies to increase efficiency and decrease costs. All resulting data and images will be freely available on-line.

The data from this project will be of immediate use to scientists who study climate and land-use change, and will provide a better understanding of how global changes will impact the distribution of native and introduced plant species. This project will benefit research in taxonomy, ecology, morphology, biogeography, and evolutionary history by making available data on an entire regional flora in an electronic format. The methodologies developed will provide a model for other regions around the nation. In addition the project will utilize citizen scientists, school groups, and students providing training, research, and educational opportunities. . This award is made as part of the National Resource for Digitization of Biological Collections through the Advancing Digitization of Biodiversity Collections program and all data resulting from this award will be available through the national resource (iDigBio.org).

Current Research

Understanding the effects of rising temperature on the phenology (flowering and leafing-out stage) for New England taxa.

Impact on landscape of human activity through deforestation, agriculture, and the development of human infrastructure on New England habitat.

Intersection of climate change and land use and effects on biotic systems in New England, such as sensitivity of habitats, changes in species abundance and phenology.

Documentation and conservation of biological diversity, including assessing the distribution of rare and endangered species, changes in species abundance over time, arrival and expansion of non-native and invasive species.

Project Websites & Social Media

NEVP Website http://nevp.org
Consortium of Northeastern Herbaria http://portal.neherbaria.org/portal

Project Leadership

Project Sponsor: Yale University (NSF Award 1209149)

Principal Investigators (PIs): Patrick Sweeney (PI), Michael Donoghue (Co-PI)

Project Collaborators

Map of Collaborating Institutions

Bartlett Arboretum
Berkshire Museum
Boston University (NSF Award 1208989)
Brown University (NSF Award 1208972)
Central Connecticut State University
Chicago Botanic Garden, Project Budburst (no data)
Connecticut Botanical Society
Connecticut College
Harvard University (NSF Award 1208835)
Harvard University Herbarium, New England Botanical Club
Harvard University, Arnold Arboretum
Harvard University, Economic Herbarium of Oakes Ames
Harvard University, Farlow Herbarium
Harvard University, Gray Herbarium
Harvard University, Harvard Forest
Harvard University, Orchid Herbarium of Oakes Ames
Keene State College
North Carolina State University (no data)
Plymouth State University
University of Arizona National Phenology Network (no data)
University of Massachusetts - Amherst (NSF Award 1208975)
University of New Hampshire (NSF Award 1208829)
University of Oklahoma (no data)
University of Vermont (NSF Award 1208973)
Western Connecticut State University
Westfield State University
Yale University, Peabody Museum

PENs:
New York Botanical Garden (NSF Award 1502452) Project wiki page
University of Maine (NSF Award 1503583) Project wiki page

Protocols & Workflows

Digitization resources

Publications

Daru, B.H., Park, D.S., Primack, R., Willis, C.G., Barrington, D.S., Whitfeld, T.J., Seidler, T.G., Sweeney, P.W., Foster, D.R., Ellison, A.M. and Davis, C.C., (2017). Widespread sampling biases in herbaria revealed from large-scale digitization. bioRxiv, p.165480.

Davis, C. C., Willis, C. G., Connolly, B., Kelly, C., & Ellison, A. M. (2015). Herbarium records are reliable sources of phenological change driven by climate and provide novel insights into species’ phenological cueing mechanisms. American Journal of Botany, 102(10), 1599-1609.doi:10.3732/ajb.1500237

Ellwood, E. R., Kimberly, P., Guralnick, R., Flemons, P., Love, K., Ellis, S., ... & Costello, R. (2018). Worldwide Engagement for Digitizing Biocollections (WeDigBio): The Biocollections Community's Citizen-Science Space on the Calendar. BioScience, 68. doi:10.1093/biosci/bix143

Everill, Peter H., Primack, Richard B., Ellwood, Elizabeth R. and Melaas, Eli K.(2014). Determining Past Leaf-Out Times of New England?s Deciduous Forests From Herbarium Specimens, American Journal of Botany,101,1293. doi:10.3732/ajb.1400045

Lorieul, T., Pearson, K. D., Ellwood, E. R., Goëau, H., Molino, J. F., Sweeney, P. W., ... & Soltis, P. S. (2019). Toward a large‐scale and deep phenological stage annotation of herbarium specimens: Case studies from temperate, tropical, and equatorial floras. Applications in Plant Sciences, 7(3).

Nelson, G., Sweeney, P. and Gilbert, E.(2018). Use of globally unique identifiers (GUIDs) to link herbarium specimen records to physical specimens,Applications in Plant Sciences, 6, e1027. doi:10.1002/aps3.1027

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.P., 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. Watson, K., Weeks A., & Mast, A.R. (2015). Digitization workflows for flat sheets and packets of plants, algae, and fungi Applications in Plant Sciences, doi:10.3732/apps.1500065

Pearse, W. D., Davis, C. C., Inouye, D. W., Primack, R. B., & Davies, T. J. (2017). A statistical estimator for determining the limits of contemporary and historic phenology. Nature ecology & evolution, 1(12), 1876. doi:10.1038/s41559-017-0350-0

Schorn, C., Weber, E., Bernardos, R., Hopkins, C., & Davis, C. (2016). The New England Vascular Plants Project: 295,000 specimens and counting. Rhodora, 118(975), 324.https://doi.org/10.3119/15-34

Sweeney, P. and Gilbert, E. (2017). Documenting Reproductive Phenology using Herbarium Specimens: Experiences from the New England Vascular Plants Project Biodiversity Information Science and Standards, v.1, p. e20430. doi:10.3897/tdwgproceedings.1.20430

Sweeney, P.W., Starly, B., Morris, P.J., Xu, Y., Jones, A., Radhakrishnan, S., ... & Davis, C.C. (2018). Large-scale digitization of herbarium specimens: Development and usage of an automated, high-throughput conveyor system. Taxon, 67(1), 165-178. https://doi.org/10.12705/671.9

Whitfeld, T., McCauley, K, & Edwards, E.J. (2014). Calling attention to the new Brown University Herbarium, Rhodora, 116. doi:10:3119/14-02

Willis, C.G., Ellwood, E.R., Primack, R.B., Davis, C.C., Pearson, K.D., Gallinat, A.S., ... & Sparks, T.H. (2017). Old Plants, New Tricks: Phenological Research Using Herbarium Specimens. Trends in ecology & evolution. 32(7), 531-546. https://doi.org/10.1016/j.tree.2017.03.015 208835

Willis, C. G., Law, E., Williams, A. C., Franzone, B. F., Bernardos, R., Bruno, L., Hopkins, C., Schorn, C., Weber, E., Park, D. S. and Davis, C. C. (2017), CrowdCurio: an online crowdsourcing platform to facilitate climate change studies using herbarium specimens. New Phytol, 215: 479–488. doi:10.1111/nph.14535

Yost, J.M., Sweeney, P.W., Gilbert, E., Nelson, G., Guralnick, R., Gallinat, A.S., Ellwood, E.R., Rossington, N., Willis, C.G., Blum, S.D. and Walls, R.L. (2018). Digitization protocol for scoring reproductive phenology from herbarium specimens of seed plants. Applications in Plant Sciences, 6,e1022. doi:10.1002/aps3.1022

Professional Presentations

iDigBio Summit V, 2015

PENs

Digitization PEN: Partnership to the New England Vascular Plant Network for the University of Maine Herbarium

Data from Maine fills an important gap in the study of environmental changes in New England. The state comprises about half the total area of New England, extending about 2.5 degrees north and 3 degrees east of the rest of New England. Plant specimens in the University of Maine Herbarium record both the spatial and temporal distribution of species over the past 170 years. These specimens, along with associated data, inform the study of environmental changes in Maine and New England. In this project the University of Maine Herbarium will complete the databasing of specimen records and generate high-quality digital images of 55,000 plant specimens. These digitized data will contribute to the accomplishment of the research and outreach goals of the New England Vascular Plant Network.

High quality images of herbarium specimens can be used to study shifts in the abundance, distribution, and reproduction of plants, as influenced by environmental change, document the number of populations of rare plants and the introduction and spread of invasive plants. They can also be used to gather information indicative of plant response to change, and train the public and professionals in techniques of plant identification, structure and developmental changes over time. The project will directly train undergraduates and members of an amateur botanical society. 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).

Project Sponsor: University of Maine
(NSF Award 1503583)

Principal Investigator (PIs): Christopher Campbell

Digitization PEN: Partnership to the Existing New England Vascular Plant Network for Collections at the New York Botanical Garden

The New York Botanical Garden's William and Lynda Steere Herbarium (NY) proposes to join the existing Thematic Collections Network (TCN) entitled, Mobilizing New England Vascular Plant Specimen Data to Track Environmental Changes. The goal of this project is to mine data from preserved plant specimens in order to support studies of the nature and consequences of environmental change in the New England region over the last three centuries. The New York Botanical Garden will contribute approximately 150,000 digitized specimens to the 1.3 million specimens that will be digitized at other institutions.

Data generated through this project will be of immediate use to scientists who study climate and land-use change, and will provide a better understanding of how global changes will impact the distribution of native and introduced plant species in the future. The project will provide career-relevant management training for a recent college graduate, and will provide employment and job experience for college undergraduates, exposing these young people to an aspect of environmental science not commonly taught in universities. Citizen scientists will be invited to participate in this project by helping to transcribe label data, georeferencing, and scoring specimens for phenological state. 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).

Project Sponsor: New York Botanical Garden
(NSF Award 1502452)

Principal Investigator (PIs): Barbara Thiers

Partnership to the New England Vascular Plant Network (NEVP) for the Environmental Management and Monitoring Alliance (EMMA)

Herbaria, collections of pressed and dried plant specimens, provide windows into the past. They tell us what kinds of plants were present, where those plants were, and when the plants were there. With this information we can track changes over time, such as the return of wildflowers and forest trees to previously farmed land, and the introduction and spread of invasive plant species. Herbarium specimens are also records of past seasonal events such as when wildflowers bloomed, and when trees leafed out in the spring and dropped their leaves in fall. The information stored in herbaria can help us understand past environmental changes, and also to predict and prepare for future change. This project will allow six members of the Hudson Valley Environmental Monitoring and Management Alliance (EMMA) to digitize their collections. Making the images and label information available online to anyone in the world will immeasurably increase the research and societal value of the EMMA herbaria. The images and information will help the Alliance address urgent threats to ecosystem health in the Hudson Valley, including climate change, invasive species, habitat loss and fragmentation, and deer overabundance. The EMMA herbarium information will also contribute to numerous other projects with scopes beyond the Hudson Valley.

The EMMA herbaria participating in this project are the Louis Calder Center of Fordham University, the Highstead Arboretum, the E.N. Huyck Preserve, the Mohonk Preserve, Pace University, and Vassar College. Together, they will partner with the existing New England Vascular Plant Network (NEVP). Approximately 22,250 specimens will be digitized, of which around 13,550 are from New York State. This project will provide training opportunities for undergraduate students at Pace and Vassar, who will digitize specimens from those herbaria onsite. A travelling team will carry out most of the digitization work at the other four herbaria. This will increase the NEVP?s New York specimens by 27%. Images and data will be made available through the Consortium of Northeastern Herbaria portal and through iDigBio.org. Along with the herbarium data, site-specific weather and phenology data will be available to researchers through the Forest Ecosystems Monitoring Cooperative platform and the EMMA website. Phenology data will also be available through the USA-National Phenology Network.

Project Sponsor: Vassar College (NSF Award #2001321)

Principal Investigators: Mark Schlessman (PI), Keri VanCamp, Nicole Scalessa (co-PIs)