You can do a lot of science with 3 million herbarium specimen records.

By making our digitized specimen data available not only through the CCH2 portal, but also through global aggregators GBIF and iDigBio, researchers across the world can view and use this valuable resource for studies in their fields. Research topics vary from species endemism and distributions, to invasive species, to human health and fire ecology. In this and upcoming blog posts, we will highlight recently-published papers from research communities outside of California that nevertheless use data from California herbarium specimens to explore and explain our natural world in new and exciting ways.

Alpine ecosystems are characterized by inhospitable abiotic conditions; bitter cold, high UV exposure, harsh winds, and rocky, eroding soil are just a few factors that plant species in these areas have faced over evolutionary time. Despite this, thousands of species (2,937 of which are included in this paper) have evolved to live in these environments, and Figueroa et al. wanted to understand how they came to be. Figueroa et al. used species distribution models to compare patterns of diversity due to phylogenetic (i.e., evolutionary relatedness) and abiotic factors. They found that different alpine communities across the Americas—for example, Patagonian versus Rocky Mountain communities--showed different patterns of diversity, suggesting that each region assembled due to unique factors. In other words, harsh climatic conditions alone don't necessarily determine which species can exist in an area, yet assembly does not depend solely on species being at the right place at the right time (the history-filtering hypothesis). They also found that species richness did not follow a simple latitudinal gradient (species in other environments and taxonomic groups have been shown to display a latitudinal gradient in species richness, with highest diversity around the equator).

​This work represents an important use of millions of herbarium specimen records to answer a foundational question in evolutionary biology; and many hundreds of thousands (over 600,000, to be more precise) of these specimens originated from our very own California herbaria! The dataset included specimens from the San Diego Natural History Museum Herbarium, UC Riverside Herbarium, CSU Chico Herbarium, Robert F. Hoover Herbarium at Cal Poly State University, and several others. California herbaria play an important role in shaping our understanding of global evolutionary patterns.

Drought: it's a reality for the warm, Mediterranean climatic region of California, especially as human land use changes the landscape and greenhouse grasses trap heat.

Drought can affect plants in many ways. On a physiological level, lack of water produces stress, which can inhibit plant growth and reproduction. Some plants change in appearance or stature under drought stress, often remaining small in size or limiting fruit set, like what might have happened to the Gilia on the left below. Some plants' foliage may wilt, shrivel, and/or die back, like the discoloring manzanita on the right.

In the face of annual "droughts" during the summer months, many species in California have evolved to be "drought deciduous", meaning they die back in the summer and resume growth and reproduction after winter and spring rains. The iconic species black sage (Salvia mellifera) and California sagebrush (Artemisia californica), for example, are drought deciduous and will often turn brown and lose their leaves in the hot summer months. Still, these plants can be negatively affected by long-term droughts. Too many drought years in a row can kill individuals of even these hardy, well-adapted species.

Drought can also alter plant communities, for example, by allowing drought-tolerant, often "weedy" species to take advantage of the open real estate and weakened competition. The specimens below serve as striking examples; as Laguna Lake in San Luis Obispo shrunk into a cracked, dry bed during the 2012-2016 California drought, three different species of opportunistic goosefoot (Chenopodium) sprung up abundantly in its absence.

Other species can temporarily (or permanently) disappear in the face of ongoing drought, as one astute collector noted in some of her collections. She discovered populations of the native annual "clustered tarweed" (Hemizonia/Deinandra fasciculata) the year after the severe drought of 2002, even though the species was "not seen at all in 2002 during severe drought year" (check out the specimen here!).

​Herbarium specimens document botanical changes and can help us understand the changing distributions of plants as environmental factors shift, as demonstrated by the examples above. We're so lucky to have such a dedicated community of collectors and botanists who are creating and caring for this resource.

​With the end of each academic year, we in the CAP Network often find ourselves reflecting: what have we accomplished? How have we grown? We are happy to share this reflection with you, the community that has supported us and helped us get things done. There is yet much to do, but look how far we've come!

These collections come in many shapes and sizes, from the small, localized Sagehen Creek Field Station (just over 1,800 specimens) to the massive holdings of the Jepson and University Herbaria at UC Berkeley (over 560,000 digitized vascular plant records to date). Thirty-three CCH2 collections (56%) contain fewer than 10,000 digitized specimens, and eight (14%) consist of fewer than 1,000! Although smaller in size, these herbaria are vital sources of often unique, specialized collections that document specific regions or the activities of lesser-known collectors. They fill critical gaps in our understanding of these special places (Monfils et al. 2020), yet are often in greater peril of shutting down due to lack of funding or attention. The infrastructure and community bolstered by the CAP Network and the Consortium of California Herbaria may help these smaller collections gain the recognition and help they deserve.

Perhaps the most obvious metric of CCH success is the sheer number of herbarium specimens now digitized and available in our data portal. Many herbarium collections were never previously digitized or had never made their data public, resulting in data silos and massive unrealized potential. Now researchers and the public have access to 3.1 million herbarium specimen records of over 82,000 species across the world, and these numbers continue to grow each day.

Imaging specimens has been one of the most urgent goals of the CAP Network. With funding from this NSF grant, we purchased and assembled 17 imaging stations across the state. Not only can these critical tools be used to digitize the historic holdings of collections, but herbaria can now fold digitization into their accessioning pipelines, meaning that present and future specimen data will enter the public sphere more rapidly after collection. Indeed, we currently have over 550 records from 2021!

Images of physical specimens have the potential to unlock new discoveries as researchers can now view specimens across institutions side-by-side and measure individual specimens' traits. Broader communities across California and all over the world can now use specimen images to learn how to identify plants, where plants occur, and differences among plant populations. Specimen images are a huge and compelling resource for science and society, connecting us to the living things we find in our daily lives. We're excited for another year of advancing and enhancing this resource...and hopefully long into the future!

​Botanists and naturalists across the state are banding together to deepen our knowledge of where California plants have historically occurred. In September 2020, the California Phenology (CAP) Network launched the “100 Club,” a team of experts who are trained to “georeference” herbarium specimen records in CCH2 (cch2.org), a new data portal that serves vascular plant data from California herbaria. Members of the 100 Club have experience with one or more geographical areas, and they use this expertise to translate textual descriptions of specimen locations into latitude and longitude coordinates: dots on a map.
The CAP Network aims to georeference 300,000 herbarium specimens by 2022, and they are well on the way to achieving that goal; however, producing accurate georeferences is often challenging. This is where the expertise of local experts comes into play.
“Anyone can read a label and put a dot on the map, but in order for that dot to be accurate, you need people who know an area well. There is no re- placement for local knowledge about a place,” says Jenn Yost, professor at California Polytechnic State University and lead PI of the CAP Network. “Many of our labels refer to place names not found on any map, but if it’s your backyard, you’ll know right where it is.”
To date, the 100 Club includes 28 active members representing many vocations and locations, from self-taught botanists, to ecological consultants, to professional botanists and taxonomists, each with expertise ranging from Baja California to the Pacific Northwest. Similarly, specimens in CCH2 originate from across the state and even the globe, underscoring the importance of a diversity of experienced georeferencers. Together, the 100 Club has georeferenced over 8,000 specimen records in only a few months, yet the process has been anything but tedious.
“For me, georeferencing is a multidimensional experience,” explains Chris Hauser, manager of the Panoche Valley Preserve and avid 100 Club Member. “When I’m georeferencing an herbarium specimen, it’s as if I’m above tree line at 10,000 feet in the mountains with Dean Taylor or walking through a dark coast redwood forest with Jeff Norman. I can almost hear the wind in the trees, smell the vegetation, and feel the soil under my feet.”

​Georeferencing herbarium specimens can be an adventure into the past as members explore historical collecting locations—parks, forests, mountains, valleys, and preserves—some of which no longer exist in their natural state. Georeferencers also become familiar with historical and recent collectors, their collecting patterns, and their label styles. Each specimen is like a time capsule, embodying the tireless efforts of passionate people and their botanical escapades.
The CAP Network invites everyone with some naturalist experience to join the historical exploration by becoming part of the 100 Club. Each member completes the CAP Network’s online georeferencing training course and receives live, virtual training via Zoom. As members begin to work in the CCH2 portal, they are fully supported through additional training and communication. To sign up, fill out the interest form here: tinyurl.com/37c3m5xb.
Thanks to the dedicated efforts of this group of naturalists, more herbarium specimens are georeferenced each day, helping us build a more comprehensive understanding of where and when plants have occurred across California and beyond. These data are critical in the face of a changing climate and potential effects of those changes on California’s precious plant diversity.

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!

Sincerely,

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.

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.

For more information about how to involve herbarium specimens and digitization into your own courses, visit our Educational Materials page. Do you have students interested in participating in a future digitization course? Email the project manager, Katie Pearson, for details.

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.

​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