Carnegie Museum of Natural History

One of the Four Carnegie Museums of Pittsburgh

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Carnegie Museum of Natural History Researchers Detail Innovative Uses of Museum Collections for Understanding Global Change

herbarium specimen with large green leaves

Researchers from Carnegie Museum of Natural History and Michigan State University report plant specimens are being used in novel new ways that could influence future environmental policy, species conservation, and collections-based science. Specimen digitization and new data analysis technologies increase the relevance of herbaria for scientific research, education, and societal issues like climate change and invasive species. The study, titled “The Changing Uses of Herbarium Data in an Era of Global Change,” was published September 4, 2019 and is featured on the cover of the October issue of BioScience.

Nearly 390 million plant specimens are kept in over 3000 herbaria around the world, with more specimens collected each day. Plant collection is a centuries-old practice, and herbaria have long been critical resources for discovering and formally describing new species, a core function that continues today. However, collections use is expanding to provide clues about how global changes impact certain species.

The new uses of herbarium specimens documented by Mason Heberling, Assistant Curator of Botany at Carnegie Museum of Natural History, Stephen Tonsor, Director of Science at Carnegie Museum of Natural History, and Alan Prather, Associate Professor of Plant Biology at Michigan State University, illustrate the increased value of specimens and herbaria in the Anthropocene, our current era. Changing use of specimens is part of a larger trend of change in the roles of natural history museums from repositories of knowledge to active leaders in scientific research that has a direct impact on life today.

“Museum specimens are being leveraged in innovative and powerful ways that most collectors and curators couldn’t even dream of a century, or even decades, ago,” says Heberling, “Natural history collections are perhaps more relevant than ever. These specimens have important stories to tell to understand the past, present, and future of life.”

The entire study is available online.

The Changing Uses of Herbarium Data in an Era of Global Change

Abstract: Widespread specimen digitization has greatly enhanced the use of herbarium data in scientific research. Publications using herbarium data have increased exponentially over the last century. Here, we review changing uses of herbaria through time with a computational text analysis of 13,702 articles from 1923 to 2017 that quantitatively complements traditional review approaches. Although maintaining its core contribution to taxonomic knowledge, herbarium use has diversified from a few dominant research topics a century ago (e.g., taxonomic notes, botanical history, local observations), with many topics only recently emerging (e.g., biodiversity informatics, global change biology, DNA analyses). Specimens are now appreciated as temporally and spatially extensive sources of genotypic, phenotypic, and biogeographic data. Specimens are increasingly used in ways that influence our ability to steward future biodiversity. As we enter the Anthropocene, herbaria have likewise entered a new era with enhanced scientific, educational, and societal relevance.

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30 years ago today: A milestone for Botany at the Carnegie Museum of Natural History

Bonnie Isaac in the museum herbarium
Bonnie in the lower herbarium at the Carnegie Museum in the early 1990s.

On August 7, 1989, Bonnie Isaac started at the Carnegie Museum. She was initially hired at the museum to work on a project to database the plant collection, making it searchable and therefore more useable to understand the occurrence and distribution of plants across Pennsylvania (and beyond). Since then, a lot has happened. Thirty years later, Bonnie is now Collection Manager in the Section of Botany and Co-chair of Collections.

It is no exaggeration to say Bonnie’s influence on the Section of Botany has been monumental. And continues to be.

As one of the top plant collectors over the Carnegie Museum’s 120+ year history, she has actively contributed to the growth of the herbarium, collecting several tens of thousands of specimens from across Pennsylvania and North America. These specimens now reside in herbaria across the world and are actively used by researchers around the world to make exciting discoveries.

yellow jewelweed specimen collected by Bonnie Isaac and Joe Isaac
Collected on this day, eight years after she started working at the Carnegie Museum, this specimen of pale touch-me-not (aka yellow jewelweed; Impatiens pallida) was collected by Bonnie Isaac (and her spouse, Joe Isaac) on August 7, 1997 along the roadside at Neff Barrens, Huntington County, PA. Largely thanks to Bonnie, this specimen (and many more!) can be found online.

Bonnie played a pivotal role in the digitization of the Carnegie Museum herbarium, one of the first of its size to have all specimens in the entire collection with label data entered into a database and publicly available online. A huge accomplishment that took over a decade of her career to complete, the collection database has increased the research value and led to a massive increase in specimen use. The digitization of the herbarium continues today through a project facilitated by Bonnie and funded by the National Science Foundation to make high resolution digital images and georeferences (assign latitude/longitude to plot on a map) to all specimens collected in the region.

Bonnie Isaac collecting plants
Bonnie pressing plants in the field in 2017.

Although she’s humble about it, Bonnie is an incredible field botanist and leading expert on the plants of Pennsylvania, especially those rare and threatened species of conservation concern. An expert in natural history collections management and methods, Bonnie has a specialized diploma on herbarium techniques from Royal Botanic Garden, Kew, England. She has a master’s degree from Youngstown State University, where she studied the ecology and distribution of a rare species.

Bonnie’s science and botanical knowledge impacts conservation decisions. Since 2001, she has served as a member of the Vascular Plant Technical Committee of the Pennsylvania Biological Survey, serving at various times over the past decades as president and recording secretary, which advised the state in determining the status of endangered and threatened plant species. She is currently working on a project funded by the Pennsylvania Department of Conservation and Natural Resources through the Wild Resources Conservation Program, revisiting many historic sites of 10 threatened species across the state to assess their current rarity status.

Beyond the walls of the museum, Bonnie has a huge impact on botanical research in Pennsylvania and fosters a public appreciation for the role of plants in our lives and ecosystem health. She is a founding member of the “Pennsylvania Botany Symposium,” a group of committed volunteers who provide education and networking opportunities for professionals, amateurs, and students of botany, including a biennial symposium that gathers Pennsylvania botanists of all levels. Bonnie is also very active in the Botanical Society of Western Pennsylvania, one of the oldest botanical organizations in the country.  She has served as President of the organization since 2005.

And if that is not enough – she is friendly, too!

Happy work-iversary, Bonnie!

Check back for more! Botanists at the Carnegie Museum of Natural History share digital specimens from the herbarium on dates they were collected. 

Mason Heberling is Assistant Curator of Botany at the Carnegie Museum of Natural History. Museum employees are encouraged to blog about their unique experiences and knowledge gained from working at the museum.

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Poison Ivy – Collected on This Day

poison ivy growing as a shrub

Watch out for poison ivy!  It is a fascinatingly cool plant but can also be dangerous.  This flowering specimen of poison ivy was collected on May 31, 1903 by John Shafer (the first curator of botany at Carnegie Museum) and O.P. Medsger in the Laurel Highlands of southwestern PA.

poison ivy herbarium sheet

What is Poison Ivy?

Poison ivy (Toxicodendron radicans) is a woody vine found in forest understories, but does especially well on forest edges. It is very common in urban and suburban areas. It takes many forms, climbing high up a tree, along the ground, or even a short shrubby thing. The leaves take a range of shapes, but as the adage goes (“leaves of 3, let it be”), it has three leaflets.

poison ivy in a tree

Poison Ivy Chemistry – What Causes the Rash?

Poison ivy is known for its chemistry, producing a class of organic compounds call urushiol. These are found in the plant’s sap and on leaves/stems/roots. Urushiol causes a nasty rash to those who touch it. Not all people have a reaction (but most are sensitive). Don’t be too confident if you haven’t had a rash before – it can develop with repeated exposure.  Incredibly itchy, the rash can become a serious health issue if infected, especially if its oils get in contact with your eyes, face, or throat.  The rash can appear days after exposure and can last for weeks.

poison ivy rash

Research indicates poison ivy will get more poisonous with climate change, both in terms of growth and producing higher quantities of forms of urushiol particularly toxic to humans.

Is Poison Ivy a Weed?

Some people call Poison ivy because of its fear-causing rash, but it is native to eastern North America.  The species has a wide distribution across our region, and across the world (native subspecies in China). Although native, the species seems to be getting more common as we create more forest edge habitat.   The colorful foliage can be quite beautiful in the fall, and the berries are a food source for birds and other animals. Humans seem to be the only ones allergic to it.

poison ivy colored foliage in autumn
poison ivy berries

Plants Similar to Poison Ivy

Poison ivy is often confused with other non-poisonous and poisonous plants.

Some common confusions:

  1. Virginia creeper (Parthenocissus quinquefolia), a vine in the grape but different leaves, and not with leaves of three
  2. Box elder maple (Acer negundo), a tree that has compound leaves unlike most stereotypical maples,  but with samaras (aka “helicopter” seeds)

Poison ivy and some other rash-causing plants are in the cashew family (Anacardiaceae) – which also includes poison oak (not found in Pennsylvania, but in western USA), staghorn sumac (not rash causing), poison sumac (rash causing, but you likely won’t come across it unless in very wet habitats)….and even a few familiar species like  pistachio,  cashew, and mango (some people are allergic).

What an amazing plant.

This specimen image is now publicly available online: http://midatlanticherbaria.org/portal/collections/individual/index.php?occid=12232529&clid=0

Check back for more! Botanists at the Carnegie Museum of Natural History share digital specimens from the herbarium on their collection dates. They have embarked on a three-year project to digitize nearly 190,000 plant specimens collected in the region (like Poison ivy!) making images and other data publicly available online. This effort is part of the Mid-Atlantic Megalopolis Project (mamdigitization.org), a network of thirteen herbaria spanning the densely populated urban corridor from Washington, D.C. to New York City to achieve a greater understanding of our urban areas, including the unique industrial and environmental history of the greater Pittsburgh region. This project is made possible by the National Science Foundation under grant no. 1801022.  

Mason Heberling is Assistant Curator of Botany at the Carnegie Museum of Natural History. Museum employees are encouraged to blog about their unique experiences and knowledge gained from working at the museum.

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A Lot to be Fascinated By in the Herbarium

wildflowers in the woods

Are you fascinated by plants? Fascination of Plants Day is upon us (don’t worry, we didn’t know it was a thing either, but agree celebration is in order!). As you might guess, we in the Section of Botany at the Carnegie Museum of Natural History are definitely into any and all things plants. Plants are inextricable from our daily lives and play critical roles in our environment.  Plus, they are just pretty cool, too. Amid chirping birds or a lion chasing a gazelle, they might be easy to overlook, but they are well worth your attention. From the sidewalk cracks in front of the museum to a remote tropical rainforest, there is a lot to celebrate.

With over half a million plant specimens in the Carnegie Museum herbarium, we have a lot to be fascinated by. Botanists here at the museum and across the world are making new discoveries about plants through these collections. On this 5th annual Fascination of Plants Day, I’d like to share some exciting new work in our collection – extracting fungal DNA from herbarium specimen roots collected over a hundred years ago.

plant specimen with long roots on herbarium sheet

Unexpected inspiration often comes from looking at old specimens in new ways. Museum specimens were collected for many different reasons. The uses of specimens are many, and recently, being used in new ways.  Museum specimens have a lot to tell us. If we look.

Recently, I became fascinated by something often ignored – roots on herbarium specimens. Why do herbarium specimens have roots?

dried plant specimen on herbarium sheet

It is standard practice for botanists to collect the entire plant when possible.  Of course, that isn’t possible for a huge tree, but many plants can fit nicely on an herbarium sheet, roots and all. And  not only do many specimens have roots, but they have soil too.

For some plants, roots can be very helpful for identification. But for the most part, roots on herbarium specimens have not been generally used. But what can 100-year-old roots tell us?

With this new fascination with herbarium specimen roots, I contacted  Dr. David Burke, a microbial ecologist and expert in belowground forest ecology at the Holden Arboretum in Kirkland, Ohio. David studies belowground microbial soil communities and their interactions with plant roots. Nearly 75% of all flowering plant species form close relationships with mycorrhizal fungi. Many plant species in our forests across the eastern United States rely upon these mycorrhizal fungi to obtain water and nutrients necessary for growth. In return, the fungi get food (sugars) from the plant.

herbarium sheet of dried flower with roots

Can herbarium specimen roots tell us about relationships between mycorrhizal fungi and plants?  And perhaps more importantly: Have human activities affected these plant-fungal relationships over the past century?

David Burke had not extracted fungal DNA from herbarium specimen roots, but he was eager to try. (In fact, to our knowledge, no one had done this with herbarium specimen roots before.)  We sampled roots from herbarium specimens of four common forest wildflowers collected in western Pennsylvania between 1881 to 2008. These species included some favorites familiar in our area: red trillium, large-flowered trillium, false Solomon’s seal, and jack-in-the-pulpit.

red-purple flower in the woods

David was able to extract and sequence fungal DNA from plant roots as old as 137 years old! We published our results in a special issue on belowground botany in Applications in Plant Sciences. You can read the full study here.  While there is still much to be done, we showed that museum collections across the world hold enormous potential to provide new insights in the basic belowground biology of plants. They can also help us understand how human activities may affect the web of life in overlooked ways.

Herbarium specimen roots have a lot to tell us about the past, present, and future of our forests in the Anthropocene. And that is fascinating!

woods with many spring wildflowers in bloom

Mason Heberling is Assistant Curator of Botany at the Carnegie Museum of Natural History. Museum employees are encouraged to blog about their unique experiences and knowledge gained from working at the museum.

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Expanding the value of herbarium specimens with citizen science app, iNaturalist

By Mason Heberling

Biological collections are at the heart of the natural history museum. Biological collections are large and diverse, with specimens of shells, bugs, birds, fossils, bones, plants, and more. They were collected anywhere from the sidewalk in front of the museum this past spring to a remote jungle on the other side of the world a century ago.

Each of the roughly 22 million objects at the Carnegie Museum of Natural History have valuable scientific stories to tell. Knowledge derived from museum specimens motivate or inform nearly every aspect of museum practice. Specimens are used directly in museum exhibitions and programming. Specimens are sources of scientific data, used by researchers both at the museum and across the world to understand the past, present, and future of life. And these specimens continue to be used in new and innovative ways to inform us about the world and the impact of humans in the Anthropocene.

Collecting from nature for admiration and study is an ancient practice, with plant collecting among the oldest. The oldest known collection of plants, known as an herbarium (plural: herbaria), dates to 16thcentury Italy!

But specimen collecting is not a dated practice; it is not just something botanists used to do. Plant collecting remains to this day an active and necessary part of botanical science. With over half a million plant specimens, the Carnegie Museum herbarium is not stagnant.  Our collection continues to grow. New specimens are collected and added to the herbarium each year, expanding the scope of the collection and therefore its scientific and societal relevance. In fact, in the recent era of rapid environmental change, new collections are all the more important.

Despite the continued importance of this practice, the standard process for collecting new specimens has change remarkably little through time. Major changes in collection practices include the use of GPS coordinates and to a lesser extent, specific sampling methods for genetic analyses.

In the Section of Botany, Bonnie Isaac (Collections Manager) and I are developing innovative ways to maximize the future use of our collections. One way we are doing this is by linking our collections to the popular citizen science platform, iNaturalist (inaturalist.org). iNaturalist is a free resource available online or as a mobile app that allows users to record biodiversity observations. We are using iNaturalist in the field and in the herbarium to facilitate new collections and expand the research value of specimens.

Herbarium specimen of large flowered trillium (Trillium grandiflorum) with QR code on label
Herbarium specimen of large flowered trillium (Trillium grandiflorum) with QR code on label that directs researchers to the associated iNaturalist observation, including images of the plant in the wild.

Before collecting a specimen, we take images in the field of the specimen in real life. These images are uploaded to iNaturalist, including other data such as date, time, location, and species identification. Other iNaturalist users can also contribute directly through verifying the identity of the specimen or making other comments.

Back in the herbarium, we export this information from iNaturalist to create unique herbarium labels for each specimen. We are using QR codes to link the specimens to the online iNaturalist observation. These QR codes can be read by most mobile devices. Among other information, the iNaturalist observation account online permanently links images from the field to the physical specimens in the herbarium.

What color were the flower petals? What was the size of the plant? Did it have a unique pattern on the bark?  What was the branching pattern? These questions and more can be asked to place herbarium specimens in a more complete context.

We envision a future where researchers can go through the herbarium with a mobile device such as a tablet or smart phone, scan QR codes on specimens, and be immediately directed to images of the specimen in the field.

Our article outlining this approach is available for free online:

Heberling, J. M., and B. L. Isaac. 2018. iNaturalist as a tool to expand the research value of museum specimens. Applications in Plant Sciences 6(11): e1193.  https://bsapubs.onlinelibrary.wiley.com/doi/epdf/10.1002/aps3.1193

Mason Heberling is Assistant Curator of Botany at the Carnegie Museum of Natural History.

 

Check back for more! Botanists at the Carnegie Museum of Natural History have embarked on a three-year project to digitize nearly 190,000 plant specimens collected in the region, making images and other data publicly available online. This effort is part of the Mid-Atlantic Megalopolis Project (mamdigitization.org), a network of thirteen herbaria spanning the densely populated urban corridor from Washington, D.C. to New York City to achieve a greater understanding of our urban areas, including the unique industrial and environmental history of the greater Pittsburgh region. This project is made possible by the National Science Foundation under grant no. 1801022. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.

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Hidden Treasure of Pittsburgh Found

by Bonnie Isaac

Recently I received a call from a woman who had bought an estate and discovered a hidden treasure in the basement. The basement contained 28 boxes of herbarium specimens. These boxes contained the private herbarium of Charles Boardman. Boardman was a research associate of Botany here at the museum from 1951 until his death on January 5, 1983. He had built his own herbarium space in his basement. These specimens are already mounted and in remarkably good shape for having been stored in a basement unattended for over 30 years.

Herbarium space built in the basement of Charles Boardman’s house with boxes of specimens.
Herbarium space built in the basement of Charles Boardman’s house with boxes of specimens.

Amazingly enough, there was also a letter with the collection with some details about his life. Charles Boardman was born in Buffalo, New York in 1903. Mr. Boardman attended the Massachusetts Institute of Technology and became a professional engineer. Charles was especially interested in mosses which led to his affiliation with Carnegie’s own Otto Jennings. Boardman accompanied Jennings on many field trips and collected specimens for the Manual of Mosses of Western Pennsylvania written and illustrated by Jennings. Boardman’s moss collection was donated to Duke University at his request shortly after his death. His vascular plant collection remained hidden in his basement until just a few weeks ago.

Water lily specimen
Water lily specimen found in Boardman’s personal herbarium.

Most of the specimens are from the 1930’s and 1940’s collected from Pennsylvania and beyond. In the coming weeks and months, we will process this amazing gift to see how many specimens are in this hidden treasure and put them into the main herbarium here at the museum for researchers to use in the future. You never know where a historic treasure may be lurking.

Bonnie Isaac is the Collection Manager in the Section of Botany. Museum employees are encouraged to blog about their unique experiences and knowledge gained from working at the museum.