The activities of the California Phenology Network have dramatically increased the number and diversity of publicly-available, digitized herbarium specimens; however, the work is not done. Many herbaria across the state--generally small, regional collections--remain undigitized. These herbaria contain unique specimens that are critical to a complete understanding of the local flora, and the need to digitize these collections is underscored by their vulnerability to natural disasters such as wildfires.
Two such herbaria are the Inyo National Forest Herbarium (INF) and the newly-minted BLM Bishop Field Office Herbarium (BLMBI). These relatively small collections, numbering fewer than 5000 specimens apiece, reside at the Inyo National Forest and BLM Inyo and Mono County headquarters building in the small town of Bishop, CA. Here, at over 4000 ft. elevation, these collections stoically preserve the flora of the rugged surrounding landscape: the towering Sierra Nevada to the west, the arid expanse of Owens Valley, and the rocky White Mountains to the north and east.
Knowing full well of the importance of the INF and BLMBI collections, and having heard of the digitization work of the California Phenology Network, National Forest botanist Blake Engelhardt contacted the Cal Poly Hoover Herbarium about getting these small collections digitized, and we were eager to help! The Cal Poly Herbarium lent the INF and BLMBI herbaria imaging equipment and, in a brief trip to Bishop, trained their staff and volunteers in the digitization process. Over the course of only a few short weeks, INF imaged their entire collection with these few, critical tools...and a lot of help from passionate botanists.
Even the Inyo National Forest Botanist of 17 years, Kathleen Nelson, took time out of her retirement to pitch in. Botanists took shifts imaging for several hours during a 3-day digitization blitz, photographing hundreds of specimens per day.
With the complete imaging of the INF herbarium, the team is now working on the BLMBI specimens and will soon turn to processing and uploading the images to CCH2. Using a similar workflow to the CAP Network, the INF and BLMBI herbaria will then be able to transcribe and georeference their specimens directly in the portal with the help of volunteers, staff, and interns. Interested in helping out? Contact the CAP project manager for more information.
Congratulations INF and BLMBI!
Nestled in the northeast foothills the Napa Valley sits a small, charming liberal arts college, surrounded by aged oaks, manzanitas, and madrones. One of the time-honored buildings on the verdant campus houses the Gilbert J. Muth Herbarium of Pacific Union College, an active herbarium that consists of over 80,000 accessioned specimens. In 2020, the herbarium at Pacific Union College (official herbarium acronym: PUA), joined the California Phenology Network through a Partner-To-Existing Network grant from the NSF, which is funding the imaging of this unique collection's specimens.
The PUA herbarium has a rich history of curation by Gilbert "Gibby" Muth and the current director, Aimee Wyrick. Thanks to hard work over the years, the majority of specimens in this collection are already databased and georeferenced, and many specimens include robust data on soil type, habitat, and plant phenology at the time and place of collection. As with most collections, there is a backlog of work to do, but with dedicated students and strong leadership, this collection is moving forward with a purpose.
This week we highlight an article hot off the press in the new year, a review penned by Dr. Mason Heberling at the Carnegie Natural History Museum. In this paper, Heberling describes how herbarium specimens have, can, and should be used to study plant functional traits.
Functional traits, as defined in the article, are "any morpho-physio-chemical-phenological characteristics that serve as proxies for understanding individual fitness" (Heberling 2022). In other words: anything that is measured from or on a plant that is used to approximate how successful that plant is. Ecologists have turned their attentions toward functional traits relatively recently; Heberling cites landmark works from as early as 1997. Still, an offhand search of Web of Science with the keyword "functional trait" or "functional traits" results in over 11,000 papers (our research, not Heberling's), clearly revealing high interest in trait-related research. However, Heberling noted that few studies in this particular arena use herbarium specimens, despite the stupendous spatiotemporal and taxonomic coverage that specimens can provide. He calculated that, if you measured only a single trait on all 396 million specimens that are estimated to exist, you could grow the most commonly used trait database, TRY, by 3400%. This could be a functional trait windfall.
Heberling explains that there is a cornucopia of questions that could be investigated using specimen-derived functional traits. Researchers can measure plant and leaf size and shape; density and patterns of leaf veins and stomata (small pore-like openings in the surface of the leaf that allow the exchange of gases); tissue chemistry; pollen shape, size, and composition; presence of symbiotic organisms; plant phenological traits (e.g., flowering or fruiting status); and many other traits yet unexplored. These all can be related to the time, place, and conditions in which the plant was collected to inform our understanding of these plants' ecological roles and evolutionary strategies. The few studies that have dived into this data source have already discovered critical patterns, such as significant morphological shifts in introduced species over only 150 years (Buswell et al. 2011), and a decrease in leaf nitrogen (an important component in the structures that conduct photosynthesis) in the last 100 years (McLauchlan et al. 2010). Such research can pave the way for further studies of the ecological, evolutionary, and economic impact of these changes.
All this being said, Heberling posits that realizing the potential of herbariums specimens for functional trait research relies not only upon ecologists recognizing these specimens as a viable source of data, but also on (1) the continued development of ways to account for well-documented biases in specimen-based datasets, and (2) improved collection practices that capture trait variation and other key data. With attention paid to these two aspects, Heberling writes, and "Bolstered by more than a decade of digitization and emerging initiatives, the role of herbaria in modern research should only strengthen" (110).
Heberling JM. 2022. Herbaria as big data sources of plant traits. International Journal of Plant Sciences. 183(2):87-118.
Buswell JM, Moles AT, & S Hartley 2011 Is rapid evolution common in introduced plant species? Journal of Ecology. 99:214–224.
McLauchlan KK, Ferguson CJ, Wilson IE, Ocheltree TW, & JM Craine. 2010 Thirteen decades of foliar isotopes indicate declining nitrogen availability in central North American grasslands. New Phytologist. 187:1135–1145.
Each completed Notes from Nature expedition or transcription project uncovers historical treasures in the annals of botanical exploration. Each specimen has a story to tell, and every collector could be the subject of their own tome, much less a blog post. Here we highlight a few of our favorite people and plants from the most recent expedition of specimens from the UCLA herbarium.
After three years of gathering phenological data from herbarium specimens, the Consortium of California Herbaria's CCH2 portal now includes phenological scorings for over 1.6 million herbarium specimens (more info about our methods here). Now, we're excited to introduce a new tool for visualizing these data.
You can now view phenological data for a given taxon aggregated across specimens in the portal. In other words, you can see when, on average, a taxon is budding, flowering, or fruiting. The phenological data are displayed as carefully labeled graphs. You can see how many specimens were included in the count and when the data were analyzed. The graphs are generated on the fly, meaning that as more specimens are scored for their phenological status, they will be automatically added to the graphs.
Shown below is an example of the taxon page for baby blue eyes, Nemophila menziesii, in CCH2. The flowering traits are displayed in the Traits Plots tab. You can switch between the different types of plot by clicking one of the icons at the top of the window, and you can view plots for other traits by scrolling down.
The taxon pages in CCH2 are still under construction—we would like to see more thorough descriptions from published treatments, as well as more field images—but the addition of these phenological data represent a significant and celebrated advance in the availability of these data for end users.
To find the phenological data for your favorite taxon, conduct a search in the portal through the Search Collections tab, clicking List Display to view your options. Then, in the search results, click the name of the taxon on of the records. If the taxon is an angiosperm, you'll likely find a load of data aggregated and displayed on the Traits Plots page.
This tool was developed due to the hard work of Dr. Chris Tyrrell, and we are very grateful for his efforts! Chris designed the code in such a way that it can be used to visualize any time-related traits that have been coded in a Symbiota portal. The code has been integrated into the main Symbiota code and can be integrated into other portals as desired.
As the California Polytechnic State University herbarium team embarked on digitizing their collection, the Robert F. Hoover Herbarium, they came upon a recurring theme: hundreds of the yet un-digitized specimens told of a far-away place called "Ovamboland." This led to some obvious questions: where is (or was) Ovamboland, and why do we have so many specimens from this mysterious place? Notes from Nature volunteers may have asked these same questions as they have transcribed over 4000 specimens from the Cal Poly Hoover Herbarium.
Where is Ovamboland?
Why does the Cal Poly herbarium have so many specimens from Ovamboland?
The flora of Ovamboland is featured in the Cal Poly Hoover herbarium due to the work of Robert J. Rodin, an accomplished botanist with an impressive resume of exploration. Born a Californian, Rodin was stationed in Guam and China while serving in WWII, explored southern Africa as a postdoc, worked as a professor in West Pakistan for several years (during which time he made forays into the Himalayas), spent a year as a Fulbright Professor in Delhi (India), and participated in a National Geographic Expedition to Ovamboland. Rodin was a botany professor at Cal Poly for 23 years, from 1953-1976, and as such, he loaded the herbarium with specimens from his travels and studies.
One of Rodin's specialties was the ethnobotany of Ovamboland. Accordingly, many of his specimens from the region include the Kwanyama (a local language) name for the plant and descriptions of how the locals use the plant. These notes are fascinating windows into the culture of the Ovambo people and speak to a rich relationship of the people with their natural resources. Some species were used as remedies for nosebleeds, swelling, and infertility. Others found uses as arrow shafts, fences, or in the construction of huts.
Thanks to Robert Rodin and many others, we have the privilege of learning how other people around the globe view and treasure their natural resources. These notes remind us that no matter where you are, we as humans are unified in our dependence on plants.
Digitization reveals unexpected discoveries, not only in botany, but in history. Each specimen represents a plant and at least one person: their journey, their interests, and their circumstances.
Prior to the California Phenology Network, the Cal State Herbarium (CSLA) was in "the dark." No specimen data had been transcribed and no specimens were imaged. Now, thanks to digitization efforts from students, technicians, and hundreds of dedicated volunteers (especially on Notes from Nature!), new stories are coming to light.
This month, Notes from Nature volunteers polished off the 5th expedition of CSLA herbarium specimens, containing over 2,800 records from across the globe. The spatial and temporal range of specimens in this collection continues to amaze. Specimens from Australia, Canada, Ireland, and Malaysia were included in the mix, ranging in collection date from 1874 to 2001.
These any many more specimens are being uncovered by digitization efforts of the California Phenology Network and countless others. In aggregate, the data enable powerful research that reveal trends in ecology and evolution. Singularly, the specimens provide snapshots into times past, representing the stories of people, places, and the plants the undergird them all.
One of the primary goals of the California Phenology Network has been to develop data standards for phenological data: community-developed guidelines for formatting and storing phenological data (e.g., data on whether plants are flowering or fruiting). If data standards are developed and widely adopted, phenological data can be shared across the many organizations that gather these data, and researchers can more easily use data from multiple data sources to conduct research.
Let's say, for example, that a graduate student would like to investigate whether the flowering times of red maple (Acer rubrum) have changed over time, and whether this change is different between the West and East Coasts of the U.S. (these types of questions are a hot topic right now...just check out our phenological research page!). This grad student could use phenological data from herbarium specimens in CCH2 to look at West Coast maples, then herbarium-based phenological data from the Consortium of Northeastern Herbaria (CNH) portal for East Coast maples. But what if the data aren't in the same format? How can the grad student be sure that a specimen recorded as "flower present" in the CCH2 follows the same rules as the specimen recorded as "in flower" by the CNH? What if she wants to go a step further and incorporate data from iNaturalist?
Combining datasets from different sources can be a huge headache, especially when data collection protocols data differ widely between sources. For example, some phenological datasets come from herbarium specimens, some from human observers in the field (e.g., the US National Phenology Network), and some from phenocam images (e.g., the National Ecological Observatory Network). To empower greater integration of these data--and therefore phenological research at greater scales than previously possible--the CAP Network has launched a Plant Phenology Standards Task Group within the global biodiversity data standards organization, TDWG.
This task group brings together global experts in data standards and users and providers of phenological data to determine a common format in which phenological data can be stored and shared among data providers. The task group established a charter (which can be found here) and had their first working group meeting on November 3rd, 2021. The group is now working to gather information about what phenological datasets exist, as well as what use cases researchers and data users may have that would need to be addressed by these data standards.
This Task Group is in very early stages, and we welcome input and membership from any interested parties. You can find more information on our GitHub page or by emailing the Task Group conveners, lead PI Jenn Yost and project manager Katie Pearson. Stay tuned for updates, and we're excited to move forward with the process of developing community standards.
WeDigBio is a biannual event that brings volunteers, collections, and curators together to rapidly digitize biodiversity specimens over the course of four days. The California Phenology Network has participated in this event for the past 3 years using Notes from Nature, an online platform where anyone with an internet connection can view specimen images and transcribe their labels into provided data fields.
This year, we saw fantastic engagement across the CAP Network at four events across the West Coast. CSU Long Beach, CSU Fresno, Oregon State University, and the California Polytechnic State University all led events (two of them in-person!), engaging over 250 volunteers across the United States. One virtual volunteer even tuned in from Turkey!
At the virtual event led by Cal Poly, 157 participants received an introduction to herbaria, tour of the Robert F. Hoover Herbarium, and training in how to transcribe a specimen label in Notes from Nature. For the remainder of the 2-hour event, the participants transcribed labels, keeping watch for specimens that would land them on the "Record Board." Could they find the specimen collected the furthest away from California (the winner was Malaysia)? How about a specimen collected on this day in history (we found two!)?
We saw a huge bump in productivity in Notes from Nature over the weekend, totaling over 2800 transcriptions. With 3 transcriptions per specimen, that over 900 specimens transcribed! All five current Notes from Nature expeditions saw significant advancement, and, as we write this, two huge expeditions of over 2000 specimens apiece are within 10% of being complete. That's a lot of progress!
WeDigBio not only moves our numbers forward, but it exposes students and volunteers to the vast diversity and rich history of herbarium specimens in not-too-far-away collections. Herbarium specimens are exciting, and we love passing on this excitement to people who may never have heard of biodiversity collections, much less understood their importance for preserving and protecting biodiversity. WeDigBio is a critical outreach event and a win-win situation for all. Thanks to all who participated!
As catalogs of physical plant specimens, herbaria are fantastic resources for identifying unknown plants, and this utility isn't just for scientific studies or simple curiosity. Sometimes plant identification is a matter of life or death.
Some herbaria receive samples from herders, farmers, or citizens concerned with the potential poisoning of livestock or pets. Because many plants can be poisonous, identification of unknown plants in grazing areas or farmland can be an important preventative (or investigative) measure to prevent the loss of life. Dr. Alison Colwell, curator of the UC Davis Herbarium, and her team, are frequently called upon to identify plants suspected of animal poisoning. She explains:
"Because UC Davis has a veterinary medical school with a diagnostics program, the herbarium gets referrals when animals are thought to be poisoned by plants, this can happen several times a week, mostly in the summer. There are certain plants that recurrently cause grazing animal poisoning, notably Amsinckia and Plagiobothrys in the spring, and Lupinus seeds in early summer, so I’m starting to know the Who’s Who of poisonous plants in California. Ideally, the owner of the affected animals will go around and pick the remainder of the nibbled plants and send them in. Sometimes we get a big bouquet of everything in the pen/corral/field. Often they will just send photos and if those are in focus and include diagnostic features, we can often do an ID from the photo, but we prefer fresh material to confirm ID against our herbarium specimens under the scope, as we have a very good collection of weedy and toxic species here. Sometimes we get part of a bale of hay and have to pick through it to find the weeds, we keep large plastic pans for that messy procedure. The most challenging ID is the contents of the gut of dead livestock, which is both fragrant and fragmentary. The toxicology folks kindly rinse off the plant parts before sending the sample over, but it will still smell a bit. I’ve come to recognize the odor of the contents of a rumen.
This part of my job is causing me to see landscaping in a different way – these days when I’m walking down a city street, I’m starting to see the plants in terms of their toxicity instead of their attractiveness!
Herbarium staff and other botanists use their knowledge, reference texts, and physical herbarium specimens to conduct this identification process. Not only are herbarium specimens a crucial reference for identification, but they are also used to document the establishment, distribution, and spread of potentially poisonous plants across history.
Take for example, the specimen below. On the (especially detailed) note, the collector of this plant chronicled the saga of poison hemlock. He notes, "The plant is toxic both to men and beast...." and "...In spite of its poisonous qualities it has been introduced from Europe as an ornamental plant." Poison hemlock is now widespread across the United States (just look at the distribution of this species across California in this map!). Knowing where it came from, the habitats it inhabits, and its potential pattern of spread may help us prevent it from spreading further and help us seek out where it may have quietly become established. There's no replacement for a robust herbarium record of plants, native and introduced.
By the way, did you notice that this specimen hails from the Southern Oregon University? Political boundaries weren't drawn with natural biomes in mind, and a large chunk of the the California Floristic Province is found in southwestern Oregon. To ensure the best possible coverage of the CFP, our friends at the Southern Oregon University Herbarium are now serving a copy of their data in CCH2. This has brought 22,000 new specimens to the CCH2, along with 20,000 images like the one shown above. California herbaria aren't the only ones collecting, digitizing, and curating these resources; the herbarium community is broad and more interconnected than ever in our work to catalog, protect, and promote biodiversity.
This blog is curated by the project manager of the California Phenology Network, Katie Pearson.