Digitized plant collection to answer how living in a megalopolis affects flora

With support from the National Science Foundation, botanists at Morris Arboretum are assembling a digital record of plants from the mid-Atlantic region

Skema specimens 2018
A massive effort to digitize hundreds of thousands of plant specimens, led by Penn's Morris Arboretum, will enable botanists to answer questions about how plants fare in urban areas. (Images: Morris Arboretum)

Densely populated and developed, the region encompassing Washington, D.C., Baltimore, Philadelphia, and New York City is one dominated by the presence of humans. Often referred to as a megalopolis, the mid-Atlantic’s urban influence is felt on all life forms, plants included.

How can these effects be documented and investigated? An effort underway at the University of Pennsylvania’s Morris Arboretum aims to do just that. The Mid-Atlantic Megalopolis (MAM) project, supported by a grant from the National Science Foundation (NSF), will create digital records of roughly 800,000 plant specimens collected in five states—Maryland, Pennsylvania, Delaware, New Jersey, and New York—plus Washington, D.C. 

Skema, Cindy with specimens.2018
Cynthia Skema, a botanist at Morris Arboretum, is leading the Mid-Atlantic Megalopolis project. (Image: Morris Arboretum)

The end result will be a digital herbarium, a modernized, accessible database of plants collected during the past 400 years, that includes super-high-resolution images of the specimens, as well as a host of informative metadata.

Cynthia Skema, a botanist at Morris Arboretum and principal investigator of MAM, says, “Just as important as the physical plant specimen is the information that comes with it: who collected it, where they collected it, when they collected it, and sometimes a little bit of additional information.”

Together, these data have the potential to inform large-scale, “big data” studies of how plant communities have changed over time in response to urbanization. Which species thrive in soils disturbed by development? Which tolerate pollution? Which ones adapt to the urban “heat island” effect and which die out? The MAM team hopes its digital collection will one day help address these questions and more.

A modern approach

Traditionally, the term herbarium has been used to refer to a physical collection of plants, collected and processed in a standardized fashion: pressed and then sewn or glued onto an acid-free, 11-by-18 sheet of paper. “It’s basically a library of dried, dead plants,” Skema says. 

Museums, universities, and institutions across the world possess such collections, but employing them in scientific study can be a logistical challenge. Previously, collections were only accessible to those able to visit them or to receive shipped specimens on loan, both costly undertakings. 

With the digitization project, Skema says she hopes to imbue some of these collections with new life. After joining the Arboretum staff in 2013, she set as a goal to bring Morris’s existing herbarium into the 21st century. Aware that the NSF supported efforts to digitize natural history collections, she began reaching out to other universities and institutions to collaboratively apply for one of these grants, known as Thematic Collections Networks (TCN). Existing TCN grants already covered the Northeast and Southeast, so framing one around the mid-Atlantic region “was kind of a no-brainer,” says Skema. The urban research theme followed from there. “We’re the only megalopolis on the East Coast; it’s massive, it’s historic, and there’s nothing like it anywhere else in the country.”

The initial MAM project included 11 institutions, representing all of the mid-Atlantic states, with a goal of digitizing 700,000 specimens. An added partnership with Penn State University brought the total closer to 800,000 specimens, and another partnership with Pittsburgh’s Carnegie Museum of Natural History is pending. Drexel University’s Academy of Natural Sciences and the New York Botanical Garden possess the largest collections in the project, at roughly 270,000 and 200,000, respectively, but smaller collections are important as well.

Barber, Anne in herbarium.2018
Anne Barber, pictured in the Morris Arboretum herbarium, is the project coordinator for the digitization effort. (Image: Morris Arboretum)

To some extent, digitizing herbarium collections is straightforward. Volunteers and staff photograph each specimen with a high-resolution camera, capturing fine details of each plant specimen. Then they transcribe the metadata from the images to the database. For older specimens, this may involve deciphering the eccentricities of centuries-old handwritten notes about where and when the plant was found. 

But the slowest part of processing records, particularly older ones, is georeferencing, estimating the coordinates of where the specimen was collected from the available location information. In modern botanical collecting, hand-held GPS units allow for the on-the-spot recording of precise latitude and longitude coordinates. But even for recent collections, not every specimen has associated GPS coordinates. And historical collections certainly do not. In these cases, researchers must use any location provided to narrow down a set of coordinates, factoring in place names and distances provided by the collector.

“This is the onerous part of this work,” Skema says.

Big data

Capturing high-resolution images and collating the metadata in an organized, consistent fashion generates a dataset to potentially answer the types of questions that drive Skema and others to collect plants in the first place. For instance, the New England Vascular Plant Network, the NSF-funded TCN for the Northeastern U.S., focuses on phenology, the study of the timing of natural events—an aspect of biodiversity that has been affected by climate change. Part of processing each specimen involves nailing down which stage the plant is in. If researchers consistently see plants flowering earlier in the spring than they used to, it may offer insight into how the climate is affecting that organism’s phenology.

With MAM, Skema hopes digitizing all these mid-Atlantic plant specimens will help researchers answer questions related to the effects of urbanization. 

“In cities, you’ve got these filters that are affecting what species can be there,” she says. “You’ve got the heat island effect because there are higher temperatures in cities, you’ve got habitat destruction and fragmentation. Soil disturbance and soil contamination are other possible factors.”

Additional issues that manifest uniquely in urban areas are altered water management regimes, changes in pollination, and the introduction of non-native plant species through a variety of channels. While researchers have been probing how these issues affect plant species for decades, a robust database will significantly enhance the heft and value of such studies.

“It can be hard to get the dataset together,” Skema says, “but once you have it, it’s powerful.”

Drawing connections

In addition to benefiting science, an outreach component of MAM is helping bring urban residents in closer contact with the nature that exists all around them. Not only does MAM itself incorporate the work of citizen scientists—volunteers can assist with transcription or contribute observation records to the data portal—but the scientists involved have taken their work on the road to talk about the goals of the project. 

“It’s amazing what people don’t know [about the natural world], and I think that disconnect may be a little more true in cities,” says Skema.

To bridge the gap, Skema and others have given talks and trainings, written articles, and maintain a website (mamdigitization.org) with information about the project and how to participate. For example, at Philadelphia’s Crefeld School, high school students who had never even heard of a herbarium learned about the project. “They were like, ‘What do you mean it’s a bunch of dead plants?!’” Skema says. 

An embedded element of the project that was planned with intention is the inclusion of two historically black colleges and universities, Howard University and Delaware State University. “We were excited about that because we feel like we’re actually representing what the megalopolis is,” Skema says. “At least some of the diversity that is in these states is also in our grant.” 

Roughly halfway through the three-year grant, the researchers are beginning to see glimmers of trends and patterns that may turn into research projects down the line. And though the digitization adds value to the collections, it is in no way meant to undercut the value of the physical specimen itself, Skema emphasizes. Such specimens contribute myriad other data, opening up many other avenues for research questions. For example, scientists can conduct chemical analyses of the samples to look for pollutant levels as a proxy for air or soil pollution in certain areas at certain times. Trained in part as a molecular biologist, Skema is interested in ways that molecular tools can be used to study historic specimens, such as extracting DNA from museum specimens to see how plants have evolved at a genetic level.

“These collections are invaluable,” Skema says. “Part of this work is convincing people—ecologists, developers, urban planners, the public—that natural history collections are critical to understanding our world.”

Cynthia Skema is a botanical scientist at the University of Pennsylvania’s Morris Arboretum.  

Skema megalopolis yellow flower
Images captured with a high-resolution camera allow botanists to study fine details of each plant specimen. (Image: Morris Arboretum)