Capturing California's Flowers: Using Digital Images to Investigate Phenological Change in a Biodiversity Hotspot

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Digitization TCN: Capturing California's Flowers: Using Digital Images to Investigate Phenological Change in a Biodiversity Hotspot (CAP)

CAP TCN
CAPLogo.jpg
Quick Links
Project Summary
Current Research
Project Websites
Publications

Project Summary

Flowering time is an important biological phenomenon, affecting human societies through its effects on agricultural crops, pollinators, pests, and biodiversity. Given the sensitivity of flowering times to climatic conditions, a thorough understanding of how plants respond to changing environments is necessary for predicting the consequences for pollinators, herbivores, parasites, and plant populations. A record of historical flowering times is found within the nation's herbaria. This award establishes a thematic collection network (TCN) dedicated to understanding flowering time shifts in the California flora. California has the most diverse native flora of any state in the U.S., containing more than one-third of all U.S. plant species. The state is a biodiversity hotspot due to the high number of endemic species that are also threatened. The Capturing California's Flowers (CAP) TCN will record flowering times from and create images of over 900,000 herbarium specimens from the oldest records, the most diverse families, and most threatened families in California. Twenty-two institutions spanning the state, including public universities, state agencies, museums, and botanic gardens, will participate in these efforts. This project will generate data that will increase our understanding of flowering time shifts - a critical need for agriculturalists, conservation biologists, plant taxonomists, land managers, and wildlife biologists.

Digitization of each specimen in the CAP TCN will result in a high-resolution image, a databased record of collection metadata, a georeferenced point, and the reproductive status of the specimen. New tools will be developed for the public to search and display phenological data through a Symbiota portal interface. The CAP TCN will develop novel data standards for capturing and sharing trait data from specimens. Building on already successful national and regional programs, the CAP TCN will partner with schools, universities, botanical clubs, and the general public to crowd source phenological measurements through online expeditions, workshops, new college courses, and K-12 educational programs. The CAP TCN will provide a historical record of plants currently being monitored through the National Phenology Network and other regional programs. Finally, this award will expand efforts to train the "next generation" of museum curators, collectors, and researchers.

Project Websites & Social Media

Data Portal

Project Website (protocols, news, about)

Twitter Page

Project Leadership

Project sponsor: California Polytechnic State University San Luis Obispo (NSF Award #1802301)

Principal Investigator (PI): Jenn Yost
Project Manager: Katie Pearson
Data Manager: Jason Alexander

Phenological Data

The CAP TCN has developed tools, workflows, and guides for creating and storing specimen-based phenological data. The most comprehensive repository of these resources can be found on our project website. Key resources are also linked below.

Protocols & Workflows

The CAP Network has created a semi-comprehensive digitization manual that aggregates documentation from the digitization process, from imaging to image processing to transcription and georeferencing. This document is available here: File:CAP Digitization Manual.pdf

The Network also developed a manual for using their Symbiota data portal, CCH2, than can be generalized for users of other Symbiota portals: File:CAP Symbiota Guide.pdf

Additional protocols, workflows, and other documentation can be found on the project website: http://www.capturingcaliforniasflowers.org

Publications

Goëau H, Mora-Fallas A, Champ J, Love NLR, Mazer SJ, Mata-Montero E, Joly A, Bonnet P. 2020. A new fine-grained method for automated visual analysis of herbarium specimens: A case study for phenological data extraction. Applications in Plant Sciences 8(6):e11368. doi:10.1002/aps3.11368 Pearson KD, Nelson G, Aronson MFJ, Bonnet P, Brenskelle L, Davis CC, Denny EG, Ellwood ER, Goëau H, Heberling JM, Joly A, Lorieul T, Mazer SJ, Meineke EK, Stucky BJ, Sweeney P, White AE, Soltis PS. 2020. Machine learning using digitized herbarium specimens to advance phenological research. BioScience. 70(7):610-620. doi:10.1093/biosci/biaa044

Love NLR, Park IW, Mazer SJ. 2019. A new phenological metric for use in pheno‐climatic models: A case study using herbarium specimens of Streptanthus tortuosus. Applications in Plant Sciences 7(7): e11276. doi:10.1002/aps3.11276

Yost JM, Pearson KD, Alexander J, Gilbert E, et al. 2019. The California Phenology Collections Network: Using digital images to investigate phenological change in a biodiversity hotspot. Madroño. 66(4):130-141. doi:10.3120/0024-9637-66.4.130

Lorieul T, Pearson KD, Ellwood ER, Goëau H, Molino J-F, Sweeney PW, Yost JM, Sachs J, Mata-Montero E, Nelson G, Soltis PS, Bonnet P, Joly A. 2019. Toward a large-scale and deep phenological stage annotation of herbarium specimens: case studies from temperate, tropical, and equatorial floras. Applications in Plant Sciences. 7(3):e1233. doi:10.1002/aps3.1233

Alexander, Jason A. 2019. Upcoming changes in the Consortium of California Herbaria. Madroño, 66(1):37-38. doi:10.3120/0024-9637-66.1.37

Professional Presentations

Conference Talks

  • Pearson KD, Yost J. The California Phenology Network: Building capacity for sharing specimen-based phenological data. Ecological Society of America Annual Meeting. [Virtual]. August 2020. Recording
  • Pearson KD, Yost J, Ramirez Parada T, Love N. Creating new data, questions, and scientists: A new phenology-focused CURE using herbarium specimen data. Botany 2020. [Virtual]. July 2020. Recording
  • Yost J, Pearson KD, Alexander J, Love N, Mazer S, Mishler B. Capturing flowering time data from herbarium specimens: The California Phenology TCN. Botany 2020. [Virtual]. July 2020. Recording
  • Pearson KD, Yost J, Ramirez Parada T, Love N. Creating new data, questions, and scientists. 4th Annual Digital Data in Biodiversity Research Conference. [Virtual]. June 2, 2020. Recording
  • Pearson KD. Using Notes from Nature to digitize California herbaria. Northern California Botanists Symposium, Chico, CA. January 13, 2020. Recording
  • Yost J, Pearson KD. California Phenology TCN: Starting Year 2. ADBC Summit 2019. October 2019. Gainesville, FL. Slides
  • Pearson KD. Old plants, new tricks: Phenological revelations from herbarium specimens. Southern California Botanists Symposium, Claremont, CA. October 5, 2019.
  • Alexander J. Upcoming changes in the Consortium of California Herbaria. Northern California Botanists Symposium. January 2019. Chico, CA.
  • Yost J. Introducing the California Phenology TCN. ADBC Summit 2018. October 2019. Gainesville, FL. Recording

Posters

  • Crowe RE, Bowler PA. Reopening the UCI Herbarium (IRVC). Southern California Botanists Symposium, Claremont, CA. October 2, 2019.
  • McGowan H, Fisher AE. A Flora of the Chiquito Basin, Santa Ana Mountains, Peninsular Ranges of Southern California. Botany 2019. Tucson, AZ. July 2019.
  • Olmeda BL, Cuadra S, Barnett A, Rice M, Fisher AE. Capturing California’s Flowers at the Beach: Herbarium Specimen Imaging at Long Beach State (LOB). Botany 2019. Tucson, Arizona. July 2019.
  • Tang K, Fisher AE. A Visual Guide and Morphometric Analysis of Leaf Shapes of Common Shrubs of the Santa Ana Mountains of Southern California. Botany 2019. Tucson, AZ. July 2019.
  • Pearson KD, Yost JM. Capturing flowering time data from herbarium specimens: The California Phenology TCN. Botany 2019, Tucson, AZ. July 28, 2019.
  • Pearson KD, Yost JM. Capturing flowering time data from herbarium specimens: The California Phenology TCN. Digital Data in Biodiversity Research Conference, New Haven, CT. June 11, 2019.
  • Pearson KD, Yost JM. (Presented by A Ayers). Capturing flowering time data from herbarium specimens: The California Phenology TCN. California Botanical Society Graduate Student Symposium. San Luis Obispo, CA. April 6, 2019.
  • Pearson KD, Yost JM. Capturing flowering time data from herbarium specimens: The California Phenology TCN. Southern California Botanists Symposium, Claremont, CA. November 3, 2018.

Education and Outreach

Citizen Science Engagement

The CAP Network engages citizen scientists and volunteers through Notes from Nature expeditions.

Public Presentations

  • Yost J. 2021. Natural History in the Digital Age. San Luis Obispo Botanical Garden. [Virtual]. February 20, 2021.
  • Pearson KD. Capturing California's Flowers: Building community, capacity, and discovery by digitizing herbarium specimens. Friends of the Chico State Herbarium Annual Meeting. [Virtual]. October 22, 2020.
  • Pearson KD. Green Guardians: How plants protect biodiversity (and you can help from home!). San Luis Obispo Coast District Biodiversity Week. [Virtual]. September 12, 2020. https://www.youtube.com/watch?v=V8NCB413TII
  • Yost J, Pearson KD. Capturing California’s flowers. California Native Plant Society North Coast Chapter. [Virtual]. May 20, 2020. https://www.youtube.com/watch?v=2sIQ4YKpg4Y

Outreach Events

  • Herbarium Specimens and Digitization. April 21, 2021. Taught UC Irvine students how to transcribe specimens in Notes from Nature as part of biological sustainability course.
  • WeDigBio Spring 2021: Botany Brunch. April 10, 2021. 42 participants
  • WeDigBio Spring 2021: Herbarium Happy Hour. April 8, 2021. 55 participants
  • Herbarium Specimens and Digitization. January 20, 2021. Taught 22 UC Irvine students how to transcribe specimens in Notes from Nature as part of biological sustainability course.
  • Waking Up with WeDigBio. October 17, 2020. Cumulative with Happy Hour: 95 participants
  • WeDigBio Happy Hour. October 15, 2020.
  • Citizen science workshop: Help science study wildflowers! Led by Katie Pearson and aided by Annie Ayers, Josiah Gilbert, and Hunter Johnson. Audience: CNPS-SLO chapter. November 7, 2019.
  • WeDigBio. October 2019. Volunteer mounters (approx. 95 students) participated in transcription via Notes from Nature.
  • Citizen Science Day. April 13, 2019. Over 20 students learned to transcribe records in Notes from Nature.
  • Cal Poly Open House. April 12-13, 2019. Tour to over 60 prospective students and their parents.

Educational Materials

  • Pearson K, Love N, Mazer S. 2020. Peek into Plant Diversity using Herbarium Specimens (Online!). QUBES Educational Resources. doi:10.25334/YW7C-P170
  • Pearson K, Love N, Parada T, Yost J. 2020. A New Phenology-focused CURE using Herbarium Specimen Data. Cultivating Scientific Curiosity, QUBES Educational Resources. doi:10.25334/DBYN-ZX80
  • Fisher A. 2019. An Introduction to Biodiversity Databases and Specimen Images. Fall 2019 BLUE FMN, QUBES Educational Resources. doi:10.25334/1NCG-T718

Undergraduate Courses Conducted

  • Spring 2021 - Advanced herbarium digitization internship. Directed by Cal Poly. 18 students enrolled from 7 institutions (CSU San Bernardino, Pacific Union University, CSU San Francisco, UC Irvine, UC Los Angeles, UC Santa Barbara, UC Santa Cruz)
  • Winter 2021 - Herbarium specimen georeferencing Directed by Oregon State University and aided by Cal Poly. 12 students from Oregon State University.
  • Winter 2021 - Phenological research using herbarium specimens. Directed by Cal Poly and aided by UCSB. 11 students from Cal Poly.
  • Winter 2021 – Herbarium digitization internship. Directed by Cal Poly. 31 students enrolled from 10 institutions (Cal Poly, CSU Fresno, CSUSB, Pacific Union College, SFSU, UC Irvine, UCLA, UC Riverside, UCSB, UCSC).
  • Fall 2020 - Herbarium digitization internship. Directed by Cal Poly. Completed by 58 students from 6 institutions (Cal Poly, CSU Long Beach, Oregon State, UC Irvine, UC Santa Barbara, UC Santa Cruz)
  • Spring 2020 - Phenological research using herbarium specimens. Directed by Cal Poly and aided by UCSB. 19 students from Cal Poly.

Project Collaborators

Digitizing Institutions

California Polytechnic State University San Luis Obispo (OBI)

Jennifer Yost (Lead PI), California Polytechnic State University San Luis Obispo (NSF Award #1802301)
Katie Pearson, project manager

University of California - Berkeley (UC/JEPS)

Brent Mishler, (PI), University of California - Berkeley (NSF Award #1802163)
Jason Alexander, data manager

University of California - Santa Barbara (UCSB)

Susan J. Mazer, (PI), University of California - Santa Barbara (NSF Award #1802181)
Katja Seltmann (Co-PI), University of California - Santa Barbara
Greg Wahlert, collections manager

California Parks and Recreation, Colorado Desert District (BSCA)

Danny McCamish, senior environmental scientist
Jim Dice, reserve manager
Larry Hendrickson, senior park aide

California State University, Chico (CHSC)

Colleen Hatfield, (PI), California State University, Chico (NSF Award #1802182)
Lawrence Janeway, herbarium curator

California State University, Los Angeles (CSLA)

Kirsten Fisher, (PI), California State University, Los Angeles (NSF Award #1802191)

California State University, San Bernardino (CSUSB)

Kimberlyn Williams, (PI), California State University, San Bernardino
Lua Lopez, assistant professor

University of California - Davis (DAV)

Daniel Potter, (PI), University of California - Davis (NSF Award #1802203)
Ellen Dean, herbarium curator
Teri Barry, collections manager

California State University, Fresno (FSC)

Katherine E. Waselkov, (PI), California State University, Fresno (NSF Award #1802178)

Humboldt State University (HSC)

Michael R. Mesler, (PI), Humboldt State University (NSF Award #1802185)
Oscar Vargas, assistant professor
Robin Bencie, collections manager

University of California - Irvine (IRVC)

Peter A. Bowler, (PI), University of California - Irvine (NSF Award #1802312)
Rebecca Crowe, nursery manager

University of California - Los Angeles (LA)

Philip Rundel, (PI), University of California - Los Angeles (NSF Award #1802199)
Victoria Sork, herbarium director
Thomas Huggins, herbarium coordinator

California State University, Long Beach (LOB)

Amanda E. Fisher, (PI),California State University, Long Beach (NSF Award #1802192)

California State University, Fullerton (MACF)

Joshua P. Der, (PI), California State University, Fullerton (NSF Award #1802200)
Jochen Schenk, (Co-PI), California State University, Fullerton

Rancho Santa Ana Botanic Garden (RSA)

Mare Nazaire, (PI), Rancho Santa Ana Botanic Garden (NSF Award #1802183)
Lucinda McDade (co-PI), Claremont Graduate University

Santa Barbara Botanic Garden (SBBG)

Matt Guilliams, (PI) Santa Barbara Botanic Garden (NSF Award #1802176)
Susana Delgadillo, collections assistant

San Diego Natural History Museum (SD)

Layla Aerne Haines, (PI), San Diego Natural History Museum (NSF Award #1802186 and #2001535)
Jon Rebman, (co-PI), San Diego Natural History Museum

San Diego State University (SDSU)

Michael G. Simpson, (PI), San Diego State University (NSF Award #1802180)
Lluvia Flores-Renteria (Co-PI), San Diego State University

California State University, Northridge (SFV)

Paul S. Wilson, (PI), California State University, Northridge (NSF Award #1802194)
Jim Hogue, database manager

San Jose State University (SJSU)

Benjamin Carter, (PI), San Jose State University (NSF Award #1802177)
Lars Rosengreen, herbarium curator

University of California - Riverside (UCR)

Amy Litt, (PI), University of California - Riverside (NSF Award #1802188)
Andy Sanders, curator
Mike Cohen, volunteer collections manager

University of California - Santa Cruz (UCSC)

Karen Holl, (PI), University of California - Santa Cruz
Al Keuter, herbarium manager
Chris Lay, curator, Kenneth Norris Center for Natural History

2020 PEN Participants

Oregon State University (OSC)

Aaron Liston (lead PI), professor and herbarium director (NSF Award #2001644)
James Mickley, herbarium curator

California Department of Food and Agriculture (CDA)

Genevieve Walden (PI), senior plant systematist

Pacific Union College (PUA)

Aimee Wyrick-Brownsworth (PI), chair and associate professor of biology (NSF Award #2001644)

San Francisco State University (SFSU)

Jason Cantley (PI), assistant professor (NSF Award #2001641)

California State University, Stanislaus (SHTC)

Andrew Gardner (PI), assistant professor of botany (NSF Award #2001644)

University of Nevada, Las Vegas (UNLV)

Lloyd Stark (PI), associate professor (NSF Award #2001644)
Mat Sharples, digitization manager

PENs

Digitization PEN: Expanding and enhancing the California Phenology TCN

Flowering time is an important biological phenomenon, affecting human societies through its effects on agricultural crops, pollinators, pests, and biodiversity. Given the sensitivity of flowering times to climatic conditions, a thorough understanding of how plants respond to changing environments is necessary for predicting the consequences for pollinators, herbivores, parasites, and plant populations. A record of historical flowering times is found within the nation's herbaria ? collections of dried and pressed plants. In 2018, the California Phenology Thematic Collections Network (CAP-TCN) was established to advance our understanding of flowering time changes over time. The network brought together 22 California universities, research stations, natural history collections, and botanical gardens, with the goal of imaging and recording the flowering status of approximately one million herbarium specimens collected over the past 150 years. These data are freely available through the newly established Consortium of California Herbaria (CCH2) portal. This project will add a partnership of seven new collections and six new institutions to the CAP-TCN, contributing an additional 150,000 herbarium specimens. The project participants will be fully integrated into CAP-TCN training and outreach activities including Notes from Nature online expeditions, which educate and involve members of the public in learning about herbarium specimens and flowering phenology.

By expanding the geographic scope to encompass Oregon and the northern Baja California peninsula, the CAP-TCN will now cover the entire California Floristic Province, a biodiversity hotspot of global significance. This will increase the number of species with imaged specimens across their entire range from 1,217 to 1,850, a 55% increase. The addition of 80,000 Oregon and Baja California specimens to CCH2 will facilitate efficient specimen-based analyses of the entire California Floristic Province and for the first time allow a more objective and reproducible specimen-based delineation of its geographic boundaries. Three institutions in California and Nevada will fill key geographic gaps for northwestern California, the northern San Joaquin Valley, and the Mojave Desert. Two additional institutions will significantly increase CAP-TCN representation of 1) the ecologically important and taxonomically complex genus Arctostaphylos (manzanita); and 2) introduced and invasive species of importance to California agriculture, rangelands, and native ecosystems. An estimated 25 additional undergraduates will participate in digitizing activities. Ongoing public outreach efforts about the floras of Oregon and Baja California at Oregon State University and the San Diego Natural History Museum will also benefit from the newly imaged specimens. Data will be shared through online resources, including iDigBio.org.

Project Sponsors: Oregon State University (NSF Award 2001644), San Francisco State University (NSF Award 2001641), and San Diego Natural History Museum (NSF Award 2001535)

Principal Investigators (PIs): Aaron Liston (OSC), Genevieve Walden (CDA), Jenn Yost (OBI), Aimee Wyrick-Brownworth (PUA), Layla Aerne Hains (SD), Jon Rebman (SD), Jason Cantley (SFSU), Andrew Gardner (SHTC), and Lloyd Stark (UNLV)