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
When you first learn about stacks of plant specimens housed in herbaria, it is tempting to envision these collections as quiet, inanimate storage spaces. You can imagine the smells of paper and dust, the quiet hum of florescent lights, and imposing rows of tightly shut cabinets. Indeed, many California herbaria are currently fated to this state with the shelter-at-home order still in place, but this was not always the case. Herbaria can be bustling hubs of creating, tending, discovering, and learning, and without constant care and curation, years of hard-earned data can be imperiled. Even when students learn from home and researchers keep to their desks, herbaria still require resources and attention.
Herbarium specimens are like delicate archival books: subject to rot, insect infestation, and general decay when not properly cared for. This is particularly important in warm environments, where heat and humidity can accelerate deterioration, the growth of mold, and the proliferation of pests. In California, one such infamous pest is the cigarette beetle, a tiny but destructive creature that can consume all plant matter on an herbarium specimen (and leave holes in the mounting paper, to boot!). Book lice are even smaller pests—about the size of a grain of sand—that nevertheless have huge appetites and can munch through herbarium specimens at startling speed. Flowers and fruits, perhaps the most important features for conclusively identifying most plant species, are often the first parts to be targeted.
Controlling pests is a continuous battle. Historically, curators and collections managers used pesticides, but since these substances are often toxic to humans as well as pests, modern managers typically rely on integrated pest management: maintaining an environment that prevent pests and controlling outbreaks by freezing infected specimens. While safer, this approach takes a lot of work. The environmental conditions of the herbarium must be monitored for appropriate temperature and humidity, and cabinets must be constantly checked for new infestations. Once an outbreak is discovered, the cabinet must be sanitized and its entire contents frozen for several weeks. Without regular and careful observation, major and irreversible damage can occur in a relatively short amount of time.
Herbarium curation also includes repairing damaged specimens, organizing specimens that were pulled for research or other use, and—in most collections—keeping up with the backlog of specimens that have been deposited in the herbarium over time. (The latter task can be surprisingly formidable; large herbaria may have full-time staff whose sole responsibility is to mount specimens!) In addition, when not sheltering-at-home, herbarium staff lead tours of students and naturalist groups, and they help researchers, land managers, and the public find the botanical resources they need. All in the day's work for a curator of one of the world's most important sources of botanical data.
Don't let the tall, steel doors and stacks of papers fool you; herbaria are active spaces that need constant, careful support to preserve the irreplaceable data held within. These institutions safeguard centuries of botanical knowledge and hold the keys to countless future discoveries.
While many herbarium collections across the state are sitting in silence, their curators, data managers, technicians, and volunteers are doing quite the opposite. Herbarium databases are a flurry of activity as faculty, staff, and citizen scientists take advantage of the past years of digitization efforts to create and expand herbarium specimen data. Thousands of the >560,000 specimens imaged by the California Phenology Network since January 2019 still need to have their label data entered in the database. These and many thousands more still need to be georeferenced—assigned latitude and longitude coordinates from the location data on the label. Each of these tasks can be done remotely, thanks to the California Phenology Network's online database (CCH2.org) and citizen science platforms like Notes from Nature.
Volunteers have especially showed up during these difficult times—a true testament to the passion and determination of hundreds of citizen scientists across the globe. (A few extra hours to spare can't hurt, too!) The graph below shows the daily number of transcriptions (specimens that have had their label data entered) on Notes from Nature since mid-February. Since the beginning of the shelter-at-home order in California (red line), transcription numbers have shot up and now remain consistently higher than before.
Students and staff who previously spent hours imaging specimens now find themselves at the computer, learning to transcribe label data and georeference specimen records. Weekly "Zoom office hours" bring these dedicated workers together from across the state to check in, ask and answer questions, and build synergy. In the words of the project manager: "We may be isolated, but we're not alone."
As California begins the long road to re-opening, on-site digitization activities at herbaria will slowly resume at a currently unknown rate. One thing is for sure: the herbarium community and plant enthusiasts are certainly not putting their time to waste.
To learn more about getting involved in at-home digitization activities, contact the CAP project manager, Katie Pearson.
Notes from Nature volunteers may not have known it at the time, but while they transcribed the label of this small and unassuming plant specimen, they were documenting the occurrence of a rare, threatened species.
Phacelia mustelina, comically called "weasel phacelia" or more elegantly "Death Valley round-leaved phacelia" is an uncommon annual herb of eastern California and western Nevada. The California Native Plant Society ranks this species as rare, threatened, and endangered in California and elsewhere, and indeed, in our database (CCH2.org), only 39 herbarium specimens exist from the past 100+ years.
This newly rediscovered specimen tells us an interesting story about this unique species. Originating from 1972 in Nye county, Nevada, this specimen was collected as part of a botanical inventory of the Nevada Test Site, an outdoor laboratory for nuclear testing that was established by the U.S. Atomic Energy Commission soon after World War II. Many specimens from this inventory ended up at the CSU Long Beach Herbarium, where they remained undigitized and thus largely unknown for several decades. With recent digitization efforts from the California Phenology Network, however, these specimens were imaged and included in one of our latest expeditions on Notes from Nature.
By transcribing information from specimen labels, citizen scientists helped us rediscover this historical occurrence of the rare Phacelia mustelina. These data are critical for assessing the conservation status of this species; if we know where this plant grew historically, we can better know where it might likely still exist. Once we know where and how abundantly this species exists, we can determine whether it needs protection and how to effectively do so.
If you ever wonder whether your help matters, remember the weasel phacelia. Bringing "dark data" to light can us help protect biodiversity on Earth.
Note: Although the image above doesn't show it, documentation of this species in Nevada does exist in other data portals, so this collection at the CSU Long Beach herbarium does not necessarily represent a range extension of the species.
This blog is curated by the project manager of the California Phenology Network, Katie Pearson.