Leveraging Herbaria Specimens: A New 3D Imaging Protocol and Analyses of Diversity of West Virginia Rosids
Date of Award
College of Science
Type of Degree
Dr. Pamela Puppo, Committee Chairperson
Dr. Anne Axel
Dr. Kyle Palmquist
Dr. Herman Mays
Herbaria are repositories of plant natural history, whose data can provide insights into the life histories of plant taxa over space and time. Recent initiatives to digitize herbarium data have made studies over broad geographic and taxonomic extents possible, with the ability of scientists to access data from large databases of herbaria. Most of the digitization initiatives have focused on flat 2D herbaria sheets, but herbaria also include 3D collections, such as fungi, mosses, lichens, and dry fruits. In Chapter 1 we propose an easy and cost-effective workflow that uses free photogrammetry software to produce 3D images of 3D herbaria specimens. We tested four free to use photogrammetry software and created 3D images of five types of 3D specimens: a fungus, a moss, a lichen, a pinecone, and a compound fruit. With our workflow using equipment already present in most herbarium digitization stations, we produced 3D specimens in less than an hour. The software 3DF Zephyr Free gave the best results across each specimen type. Our workflow has provided an easy and low-cost method of producing 3D images that can be used to digitize 3D specimens in a similar manner to 2D herbaria sheets. In Chapter 2 we used herbaria data to analyze the spatial patterns of diversity of a major clade of plants, the Rosids, that contain most hardwood trees in West Virginia, and are the dominant plant species in the state. We used phylogenetic diversity to assess the diversity of this clade across the Level IV Ecoregions of West Virginia. Phylogenetic diversity (PD) is a metric that incorporates the evolutionary history of an area of interest. Ecoregions are defined by the Environmental Protection Agency (EPA) as areas of similar habitat, climate, and species composition. Our results indicated high PD in the eastern portion of the state in the Monongahela National Forest and low PD in the southern portion of the state in the Dissected Appalachian Plateau ecoregion. Analyses such as ours are important for informing conservation priorities, as they identify specific areas that are more biodiverse.
United States. – Environmental Protection Agency.
Herbaria – West Virginia.
Herbaria – Digitization.
Museum objects – Digitization.
Photogrammetry – Digital techniques.
Photogrammetry – Instruments.
Phylogeny – Data processing.
Shamblin, Zachary Scott, "Leveraging Herbaria Specimens: A New 3D Imaging Protocol and Analyses of Diversity of West Virginia Rosids" (2022). Theses, Dissertations and Capstones. 1681.