Dear community scientists, transcribers, volunteers, stay-at-homers, and data entry extraordinaires,
We couldn't do it without you! Watching our numbers of transcribed specimens climb is so exciting for the community of herbarium directors, curators, collections managers, and in-person volunteers. Your work matters, and it demonstrates that people outside the herbarium walls also believe that natural history specimens matter.
With your help, over 25,000 specimen records have been transcribed for the herbaria at seven California institutions: CSU Los Angeles, CSU Fresno, CSU Long Beach, CSU Cal Poly SLO, CSU Humboldt, UC Irvine, and UCLA. Although housed at California herbaria, these specimens have been collected across the nation—and often across the globe—for hundreds of years.
Take, for example, the specimens from the most recently completed expedition, which featured the herbarium at Humboldt State University. Notes from Nature volunteers transcribed over 2,000 specimens for this NW California herbarium. The oldest specimen was collected in 1885 by Wilhelm N. Suksdorf, an autodidactic German-American botanist who specialized on the flora of the Pacific Northwest U.S. The newest specimen was collected only five years ago by one J. Mueller in Nevada, for whom the Humboldt State Herbarium only has three specimens catalogued to date. The majority of specimens were collected in the 1960s and 1970s, as shown in the graph below.
Humboldt State had a strong prior history of digitizing their California specimens, so the majority of specimens in this expedition were found outside California, indeed, all across the United States!
The plants these specimens encapsulate are not only geographically and temporally diverse, but also phylogenetically diverse (i.e., diverse in terms of species). This single expedition included over 800 different taxa, from the stately Emory oak (Quercus emoryi) to the delicate one-flowered wintergreen (Moneses uniflora). The top ten genera in this expedition included fleabanes (Erigeron), oaks (Quercus), buttercups (Ranunculus), popcorn flowers (Cryptantha), phacelias (Phacelia), larkspurs (Delphinium), bluebells (Mertensia), rabbitbrushes (Chrysothamnus), clovers (Trifolium), and huckleberries/blueberries (Vaccinium): a rainbow of flowering plants spanning the country and including several species endemic to California.
The data from the Humboldt State expedition, as well as all the expeditions before it, have been carefully cleaned and uploaded into the public portal of the Consortium of California Herbaria, CCH2, where they are accessed daily by botanists, ecologists, educators, land managers, and so many more. It truly takes a dedicated community to create, curate, and capitalize on these fantastic pieces of data and botanical history. Thanks a million!
The California Phenology Network
Herbarium specimens tell not only stories of scholarly botanists on formal collecting expeditions; they also hint of epic travels of adventurers and nature-lovers, serving as small glimpses into past scenes of beauty and wonderment.
While transcribing online through Notes from Nature, an online volunteer by the username "lofl" discovered one such delightful example in the elegant script and delicate flowers and leaves mounted on 100-year old paper. Looking more closely, this volunteer recognized that the specimen represented, in fact, two separate expeditions in 1910 and 1912 to similar, but not identical locations.
The specimens were collected by Winona Bailey, an avid outdoorswoman and member of an outdoors club of Seattle, Washington called The Mountaineers. Still running today, this club leads hiking and mountaineering trips throughout the rugged Pacific Northwest. Winona Bailey was a Latin teacher by profession but adventurer by nature. She traveled the world, explored, and climbed mountains (even falling 75 ft. off of a mountainside at one point, receiving only minor injuries!).
In the 1910 mountaineering expedition, Winona Bailey joined forces with Dr. Cora Eaton to describe the botanical observations of the trip in the Mountaineers' regular publication The Mountaineer. Dr. Eaton was a strong, independent woman and herself a champion of the outdoors. She became the first woman to practice medicine in North Dakota in 1892 and was an active advocate for women's suffrage, even carrying a pennant proclaiming "Votes for Women" to the top of Mount Rainier on one expedition of the Mountaineers.
Eaton and Bailey reported over 60 species of tree, wildflower, and shrub in this Mountaineer article, frequently commenting on the stunning beauty of each. "[N]othing more frequently claims the attention of the Mountaineer and calls forth his expressions of delight than the flowers that carpet the hillside, or hide modestly under cliff or brush" (18-19). Apparently, they and other botanists also collected voucher specimens during their journeys, allowing us to scientifically verify their observations. Perhaps more poetically, they enable us to peek into the past, perhaps catching a glimpse in our mind's eye of the glorious sights these adventurers and scientists beheld. Herbarium specimens tell us real stories of the people, places, and plants of historical times and hopefully help us preserve them for the future.
Lupinus latifolius var. subalpinus, one of the "blue" flower species dominating what the mountaineers dubbed "National hill", "because the effect was that of the colors of the flag" (p. 21).
PC: Jason Hollinger CC-BY 2.0
The California Phenology Network kicked off the new year with another herbarium digitization internship course for students at many of our collaborating institutions. This winter quarter, 30 students joined from 9 universities and colleges: Cal Poly, CSU San Bernardino, Pacific Union College, San Francisco State University, UC Irvine, UC Los Angeles, UC Riverside, UC Santa Barbara, and UC Santa Cruz. The students learned a variety of digitization skills, including transcribing herbarium labels and identifying and converting different coordinate systems into decimal degrees. All students learned to use CCH2 to edit and curate data, as well as how herbarium specimens are used for vital scientific research. Each student read and presented a poster about a primary research article during class, and they participated in a virtual herbarium tour and virtual collecting demonstration.
Not only did the students learn valuable, transferable skills, but they also accomplished a lot in the process. Together the students transcribed and converted coordinates for 675 specimens, and they completed over 2700 Notes from Nature transcriptions and 491 transcriptions in CCH2. Because specimens require three transcriptions in Notes from Nature to be complete, this amounts to nearly 1,400 specimens transcribed overall—but that's only counting transcriptions completed during class time! Many students went above and beyond to transcribe specimens outside of class time, sharing fun discoveries and asking questions via a student-led GroupMe.
In a final reflection assignment, students were enthusiastic about the course and shared that they gained much deeper understandings about herbaria and the uses of herbarium specimens.
"I learned they [herbarium specimens] are useful in taxonomy, systematics and so much more!" wrote one student.
Another student related their experience to their plans beyond the internship: "Now, I realize just how helpful herbarium collections can be in my future career."
Many students enjoyed the course so much that they will be returning to the internship for the spring 2021 quarter. In the upcoming course, students will learn how to georeference specimens using locality information from specimen labels—potentially even the labels they transcribed during the winter quarter! The CAP Network is committed to involving the next generation of scientists in this important work, and we look forward to leading more classes across and within institutions throughout the network.
To kick off the new year, the CAP Network is leading another multi-institution herbarium digitization course. This online course of 30 students meets synchronously via Zoom, once per week, to transcribe specimen labels on Notes from Nature. Along the way, we've encountered many of the unique forms that herbarium specimens can take.
Because the most obvious features of a plant--namely the leaves--are not always the best diagnostic characters (i.e., characters that can help you identify the plant), collectors will sample other parts of the plant. Reproductive structures are often critical, but other features such as bark or a cross-section of the stem can aid in identification and further analysis.
However, in some cases, what you see on the sheet is all that the collector had to work with at the time. If you're collecting in the winter, all you might be able to find is twigs, dead leaves, and dry remnants of fruits...but that doesn't stop some collectors from documenting the occurrence anyway!
A specimen need not be beautiful to be useful. Each collection documents the conditions at a unique place and time, and it captures the status of plants at that historical point. Keep an eye on our class website for new and interesting specimen discoveries and for a tally of our progress as our students digitize these precious data snapshots.
Socially distancing can't keep us from socially digitizing California plants! For the second year running, the California Phenology Network coordinated events as part of WeDigBio, the Worldwide Engagement for Digitizing Biocollections. This annual event unites biodiversity specimen collections across the globe—from herbaria in Paris to mammal collections in Australia—in digitization events involving the community.
This year, the CAP Network went 100% digital. We held two events: WeDigBio "Happy Hour" on Thursday, October 15th at 7:00 PM, and "Waking up with WeDigBio" on Saturday, October 17th at 10:00 AM. Across both events, we had over 95 participants logging on to Zoom and learning about the importance of herbaria. Participants received a short introduction to herbaria and how they are used for research, and the CAP project manager gave a virtual tour of the Robert F. Hoover Herbarium at Cal Poly, San Luis Obispo. After a tutorial and introduction to Notes from Nature, we got to work transcribing specimen label data.
At the close of the WeDigBio weekend, held from Thursday to Sunday, October 15-18, the online citizen science community transcribed a whopping 2,072 records, putting us that much closer to fully transcribing the thousands of specimens we are imaging as part of the CAP project. With each transcription, more valuable botanical data are made available for researchers, educators, and the public, helping us understand the spatiotemporal distribution of plants and how they change. Equally importantly, WeDigBio participants voiced having a lot of fun during the process, fostering positive associations and awareness of herbaria as interesting and irreplaceable data sources.
But there is hope in the midst of chaos. While we can't repeal the devastation of the fires, we can peer into the past to see the flora and fauna that once inhabited these now-charred regions: what may have been lost and what may yet spring back to life. Herbarium specimens retain a historical record of the plant life in recently burned regions that can help direct monitoring and restoration efforts. Even if some species had not been saved, we still possess a vital link to the past, a window into history.
Finally, herbarium specimens remind us of the plants that use fire to prosper. Many plant species are fire followers, some even requiring the heat of fires to disperse or germinate their seeds (LPFW 2013). Others simply take advantage of the new real estate and lack of competitors on the charred landscape.
Herbarium specimens of some fire-following species in California. Left: Whispering bells (Emmenanthe penduliflora), Center: Poodle-dog bush (Eriodictyon parryi), Right: Fire poppy (Papaver californicum)
Not all fire followers are native and renewing, and at times, careful management might be required to ensure burned areas are not overrun with invasive species. Still, the flourishing of life against the blackened earth and plant skeletons symbolize the cycle of rebirth and renewal that follows even the worst devastation.
flora - a (hopefully) comprehensive list of the plant species that exist within a specified region
These specimens include several unique and exciting collections. SFSU holds a comprehensive collection of manzanitas (Arctostaphylos), one of California's iconic genera of shrubs and trees with flat, often frosted leaves and peeling reddish bark. CDA contains California's collection of noxious weeds and agricultural plants, preserving a detailed record of plant introductions to California over the past 100 years.
Left: Peeling trunk of an Arctostaphylos shrub. Right: Yellow starthistle (Centaurea solstitialis) a noxious weed in the western U.S.
Each new collection contributes an important piece to the puzzle of plant diversity in the California Floristic Province. With the data produced from this new PEN, we hope to better understand changes in flowering time across the whole CFP and among the diverse taxonomic groups in this region and beyond.
To learn more about these new grants, visit their NSF award pages, linked below:
CFP: Adapted from Noah Elhardt, https://creativecommons.org/licenses/by-sa/3.0/deed.en
Manzanita: Paul Asman and Jill Lenoble, https://creativecommons.org/licenses/by/2.0/
Yellow starthistle: creative commons
With the COVID-19 pandemic raging on, scientific conferences across the world were canceled, delayed, and overall faced with chaos, leading to much disappointment throughout the community. Dissemination of research and discussing new ideas are essential elements of the scientific process, and conferences are important environments for these activities. The CAP Network was looking forward to sharing about the new undergraduate research course they developed in spring 2020, as well as continue to bring our data to the attention of potential collaborators, at Botany 2020, the annual, international conference of plant scientists. The pandemic seemed to stymie these plans.
Fortunately, the Botany conference pressed on. With a heroic effort, the organizers pivoted to an all-digital conference that, perhaps unsurprisingly, resulted in a massive uptick in registrations. Over a thousand plant scientists across the globe participated in the conference, despite juggling the innumerable challenges of COVID-19 life, from child care to online teaching to navigating different time zones.
Another benefit of the digital Botany 2020 conference is that nearly all the presentations were pre-recorded or recorded during the session, resulting in hundreds of high-quality scientific presentations digitally preserved and available for further dissemination. The CAP Network has uploaded our presentations to our YouTube channel. We hope you enjoy learning about recent developments in the CAP Network. Look out for more Botany 2020 presentations coming online in the next few weeks as scientists eagerly share their work.
Presentation by Katie Pearson on July 28, 2020.
Presentation by Dr. Jenn Yost on July 30, 2020.
Halfway into year 2 of the California Phenology Network project, we were faced with a dilemma. With thousands of herbarium specimen images being added to the CCH2 portal each week, the potential for uncovering new information about plant phenological events, such as climate-induced changes in flowering times, was also growing. How can we effectively harness these new data, given the wild diversity of our beautiful state? More still, how can we empower more scientists to do the same?
The CAP Network decided to start with the rising generation of scientists. Lead-PI Jenn Yost, project manager Katie Pearson, and two graduate students at UC Santa Barbara, Natalie Love and Tadeo Ramirez Parada, designed a 10-week course-based undergraduate research experience (CURE) that focused on using digitized herbarium data to study plant phenological change. Almost all the materials were created from the ground up, from assignments to the R code that students would use to analyze their data. After iterative development with four advanced students in the winter quarter, the course was ready for its pilot run at Cal Poly for the spring 2020 quarter. Little did we know that the commencement of the course would correspond with the shutdown of California due to Covid-19.
The course was quickly migrated online and shortened to nine weeks, yet registration numbers continued to climb to 19 students. On the first day of class, all nineteen students logged into Zoom, cameras on, eager to discuss the pre-course readings and delve into crafting scientific questions.
This being the first implementation of the course, there were many challenges, many owing to the use of R (a commonly used programming language in biological sciences) to clean the data and conduct analyses. Nevertheless, the students persisted. Each student drafted a research question and selected a study species or set of species by week 2, and over the following weeks learned to generate phenological and georeference data from images of herbarium specimens in CCH2; download, manipulate, and clean specimen data; analyze the data using linear regression in R; interpret their results; and design further analyses when needed. In the end, each student summarized their research in a scientific poster. On the last day of class, the students presented their posters, showcasing the trends they discovered. Most plant species they studied responded in one way or another to changes in climate.
Two students proudly display their research posters over Zoom on the last week of the phenology course
Despite setbacks due to the global pandemic, the newness of the course, and coding problems, the results of the course were overwhelmingly positive. Students remained engaged every class, and many started to solve code and analysis problems on their own. Even in the midst of seemingly endless troubleshooting, one student remarked:
Results from a pre-course and post-course assessment, aimed at measuring learning outcomes, were also strongly positive. Students reported significant improvements in their understanding of key topics such as reading primary scientific literature and designing an experiment or analysis to answer a scientific question. Students also reported that they were now more comfortable practicing research skills like manipulating and cleaning data, analyzing data using linear regression, working with herbarium specimen data, and creating a scientific poster.
The course developers, with help from PIs Susan Mazer and Katja Seltmann, hope to improve the course over the summer and fall months with the goal of producing a more streamlined, universalizeable curriculum that can be adopted at other institutions. The course is scheduled to run again at Cal Poly during the winter quarter of 2021 and will hopefully spread across the state and beyond, building a network of students empowered with new data skills and scientific experience.
For more information about this course, visit our beta course page. As the course is developed, more content will be added to this page.
To read the Cal Poly Report article about this course, visit this page: https://www.calpoly.edu/news/botany-students-study-effects-climate-change-using-100-year-old-plants
One of the most essential pieces of data captured by an herbarium specimen is where the plant was found. Herbarium specimens underlie our understanding of where plants occur on this big, green planet. Aggregation of specimen data on large scales, enabled by mass digitization projects (e.g., our own California Phenology Network), can furthermore help us determine why plants occur where they do (Loiselle et al. 2008) and how distributions are changing (Wolf et al. 2016). Building a map of plant distributions across time and space, however, is no simple feat.
Although collaborators and volunteers in the California Phenology Network remain scattered and largely at home during this global pandemic, we are making huge advances in georeferencing California collections. The graphic below shows the georeferencing progress of just one collection, the Cal Poly Hoover Herbarium, from February to June, 2020. Over 1500 specimens were georeferenced during these few short months, and the numbers only continue to grow.
Locations of georeferenced specimens from the Cal Poly Hoover Herbarium over time. Black dots indicate all California specimens georeferenced as of February 2020, and additional colors indicate new georeferences as of the months indicated as follows: Red = March 2020, Blue = April 2020, Green = June 2020
This success is largely made possible by dedicated students, staff, and volunteers, but there is always a need for more help. Volunteers from all over the state—and beyond!—are joining the georeferencing community and contributing to this significant effort. Can you help us fill in the gaps?
References and Further Reading
This blog is curated by the project manager of the California Phenology Network, Katie Pearson.