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

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

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''Project Manager:'' [mailto:kdpearso@calpoly.edu Katie Pearson]<br>
''Project Manager:'' [mailto:kdpearso@calpoly.edu Katie Pearson]<br>
''Data Manager:'' Jason Alexander<br>
''Data Manager:'' Jason Alexander<br>
=== 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 [https://www.capturingcaliforniasflowers.org/phenology.html project website]. Key resources are also linked below.
*Scoring Phenological Traits Using Symbiota Tools: [[File:PhenologicalScoringCAPTCN.pdf]]
*Downloading trait data from the CCH2 portal: [https://www.capturingcaliforniasflowers.org/phenology.html#Output here]


=== Protocols & Workflows ===
=== Protocols & Workflows ===
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=== Publications ===
=== Publications ===
Pearson KD, Love NR, Ramirez Parada T, Mazer SJ, Yost JM. 2021. Phenological trends in the California poppy (Eschscholzia californica): Digitized herbarium specimens reveal intraspecific variation in the sensitivity of flowering date to climate change. ''Madroño''.
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
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,  
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,  
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====Conference Talks====
====Conference Talks====
* Yost J, Pearson KD. Digitizing California’s National Forest Herbaria. [Lightning Talk]. Northern California Botanists Symposium January 11, 2022.
* Pearson KD. A public resource for tracking invasive plants: the Consortium of California Herbaria’s CCH2 Portal. (Lightning Talk). California Invasive Plant Council 30-Year Anniversary Symposium. October 27, 2021.
*Pearson KD, Yost J, et. al. Data standards for the phenology of plant specimens. [Virtual] TDWG 2021. October 19, 2021. [https://doi.org/10.3897/biss.5.74372 Abstract]
*Pearson KD, Love N, Ramirez Parada T, Mazer S, Yost J. Phenological trends in the California poppy (Eschscholzia californica): Digitized herbarium specimens reveal intraspecific variation in the sensitivity of flowering date to climate change. [Virtual] Botany 2021. July 20, 2021.
*Pearson KD, Gilbert E, Tyrrell C, Franz N, Yost J. New tools to score, view, and download (phenological) trait data in a Symbiota portal. 5th Annual Digital Data in Biodiversity Research Conference. [Virtual]. June 9, 2021. [https://drive.google.com/file/d/12iFjriVYG13S2VMwxyfiywoNpjcDwjNW/view Recording]
*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. [https://youtu.be/YO65BPO2MIY Recording]
*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. [https://youtu.be/YO65BPO2MIY Recording]


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====Posters====
====Posters====
*Pearson KD, Love N, Ramirez Parada T, Mazer S, Yost J. Digitized herbarium specimens reveal intraspecific variation in the sensitivity of flowering date to climate change: A Case Study of the California Poppy (Eschscholzia californica). Southern California Botanists Symposium. [Virtual]. October 16, 2021.
*Pearson KD, Yost J. Capturing California’s flowers: Mobilizing phenological data from herbarium specimens. Biodiversity Digitization: Celebrating a Decade of Progress. September 22, 2021. [https://drive.google.com/file/d/13NDPRDxb53DIQ2rt1ym_IOsitocEPrbL/view?usp=sharing View Here]
*Pearson KD, Love NR, Ramirez Parada T, Mazer SJ, Yost JM. New, publicly-available source of phenological data reveals intraspecific variation in the sensitivity of flowering date to climate change: A case study of the California poppy (Eschscholzia californica). Ecological Society of America Annual Meeting. [Virtual]. August 5, 2021. [https://eventscribe.net/2021/ESA/fsPopup.asp?Mode=posterinfo&PosterID=406888 View Here]
*Waselkov K. Capturing the Flowers of the Sierra Nevada Mountains: The Contribution of the Fresno State Herbarium (FSC) to the California Phenology Network. Society for the Preservation of Natural History Collections. June 2020.  [https://spnhc.biowikifarm.net/wiki/Posters View Here]
*Pearson KD, Yost JM. Creating and mobilizing specimen-based plant phenological data: The California Phenology Network. Ecological Society of America Annual Meeting. [Virtual]. August 2020. https://www.capturingcaliforniasflowers.org/uploads/1/6/3/7/16372936/cap_tcn_esa2020_v2.pdf
*Pearson KD, Yost JM. Creating and mobilizing specimen-based plant phenological data: The California Phenology Network. Ecological Society of America Annual Meeting. [Virtual]. August 2020. https://www.capturingcaliforniasflowers.org/uploads/1/6/3/7/16372936/cap_tcn_esa2020_v2.pdf


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====Public Presentations====
====Public Presentations====
*Waselkov K. CSUF Herbarium and its use in phenology research. Soil and Water Conservation Society, California-Nevada Chapter. October 20, 2021.
*Waselkov K, Riley R. Leafing through the past: A virtual walkthrough of the largest herbarium in the San Joaquin Valley. California Native Plant Society Sequoia Chapter. October 12, 2021.
*Yost J, Pearson KD, Love N, Ramirez Parada T, Mazer S. SPNHC Natural History Education Demo Camp. 28-29 June 2021.
*Pearson KD. 2021. Herbarium Specimens and Digitization. San Luis Obispo Master Gardeners. [Virtual]. May 13, 2021.
*Yost J. 2021. Natural History in the Digital Age. San Luis Obispo Botanical Garden. [Virtual]. February 20, 2021.
*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. 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.
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====Outreach Events====
====Outreach Events====
*Herbarium Specimens and Digitization. November 3. 2021. Taught 33 UC Irvine students how to transcribe specimens in Notes from Nature as part of biological sustainability course.
*WeDigBio CSULB. October 15, 2021. 40 participants
*WeDigBio Fresno CNPS. October 14, 2021. 11 participants
*WeDigBio Virtual, Herbarium Happy Hour. October 15, 2021. 157 participants.
*WeDigBio @ OSU. October 15, 2021. 35 participants
*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.
*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: Botany Brunch. April 10, 2021. 42 participants
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====Educational Materials====
====Educational Materials====
* Pearson K, Ramirez Parada T, Mazer S, Love N, Yost J. 2021. Exploring Plant Phenology using Herbarium Specimens: Lab or Workshop. QUBES Educational Resources. doi:[https://qubeshub.org/publications/2476/?v=1 10.25334/NBY6-5A67]
*Pearson K, Love N, Mazer S. 2020. Peek into Plant Diversity using Herbarium Specimens (Online!). QUBES Educational Resources. doi:[https://qubeshub.org/publications/2068/1 10.25334/YW7C-P170]
*Pearson K, Love N, Mazer S. 2020. Peek into Plant Diversity using Herbarium Specimens (Online!). QUBES Educational Resources. doi:[https://qubeshub.org/publications/2068/1 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:[https://qubeshub.org/publications/1956/1 10.25334/DBYN-ZX80]
*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:[https://qubeshub.org/publications/1956/1 10.25334/DBYN-ZX80]
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====Undergraduate Courses Conducted====
====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)
*Spring 2022 - Herbarium digitization internship. Directed by Cal Poly. 13 students enrolled from 7 institutions
*Winter 2021 - Herbarium specimen georeferencing Directed by Oregon State University and aided by Cal Poly. 12 students from Oregon State University.
*Winter 2022 - Herbarium digitization internship. Directed by Cal Poly. 13 students enrolled from 6 institutions
*Winter 2021 - Phenological research using herbarium specimens. Directed by Cal Poly and aided by UCSB. 11 students from Cal Poly.
*Fall 2021 – Herbarium digitization internship. Directed by Cal Poly. 31 students enrolled from 5 institutions (CSU Fullerton, OSU, SFSU, UC Irvine, UCLA)
*Spring 2021 – Phenological research using herbarium specimens. Directed by UCSB. 15 students from UCSB.
*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).
*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)
*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.
*Spring 2020 – Phenological research using herbarium specimens. Directed by Cal Poly and aided by UCSB. 19 students from Cal Poly.
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=====California Polytechnic State University San Luis Obispo (OBI)=====
=====California Polytechnic State University San Luis Obispo (OBI)=====
Jennifer Yost (Lead PI), California Polytechnic State University San Luis Obispo [http://www.nsf.gov/awardsearch/showAward?AWD_ID=1802301 (NSF Award #1802301)]
Jennifer Yost (Lead PI), California Polytechnic State University San Luis Obispo [http://www.nsf.gov/awardsearch/showAward?AWD_ID=1802301 (NSF Award #1802301)]<br>
Katie Pearson, project manager


=====University of California - Berkeley (UC/JEPS)=====
=====University of California - Berkeley (UC/JEPS)=====
Brent Mishler, (PI), University of California - Berkeley [http://www.nsf.gov/awardsearch/showAward?AWD_ID=1802163 (NSF Award #1802163)]<br>
Brent Mishler, (PI), University of California - Berkeley [http://www.nsf.gov/awardsearch/showAward?AWD_ID=1802163 (NSF Award #1802163)]<br>
Jason Alexander, data manager


=====University of California - Santa Barbara (UCSB)=====
=====University of California - Santa Barbara (UCSB)=====
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=====Humboldt State University (HSC)=====
=====Humboldt State University (HSC)=====
Michael R. Mesler, (PI), Humboldt State University [http://www.nsf.gov/awardsearch/showAward?AWD_ID=1802185 (NSF Award #1802185)]<br>
Michael R. Mesler, (PI), Humboldt State University [http://www.nsf.gov/awardsearch/showAward?AWD_ID=1802185 (NSF Award #1802185)]<br>
Oscar Vargas, assistant professor<br>
Robin Bencie, collections manager
Robin Bencie, collections manager


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=====University of California - Los Angeles (LA)=====
=====University of California - Los Angeles (LA)=====
Philip Rundel, (PI), University of California - Los Angeles [http://www.nsf.gov/awardsearch/showAward?AWD_ID=1802199 (NSF Award #1802199)]<br>
Philip Rundel, (PI), University of California - Los Angeles [http://www.nsf.gov/awardsearch/showAward?AWD_ID=1802199 (NSF Award #1802199)]<br>
Victoria Sork, herbarium director<br>
Thomas Huggins, herbarium coordinator
Thomas Huggins, herbarium coordinator


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=====Santa Barbara Botanic Garden (SBBG)=====
=====Santa Barbara Botanic Garden (SBBG)=====
Matt Guilliams, (PI) Santa Barbara Botanic Garden [http://www.nsf.gov/awardsearch/showAward?AWD_ID=1802176 (NSF Award #1802176)]<br>
Matt Guilliams, (PI) Santa Barbara Botanic Garden [http://www.nsf.gov/awardsearch/showAward?AWD_ID=1802176 (NSF Award #1802176)]<br>
Lucie Gimmel, herbarium curatorial assistant <br>
Susana Delgadillo, collections assistant
Kristen Lehman, laboratory manager


=====San Diego Natural History Museum (SD)=====
=====San Diego Natural History Museum (SD)=====
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=====University of California - Riverside (UCR)=====
=====University of California - Riverside (UCR)=====
Amy Litt, (PI), University of California - Riverside [http://www.nsf.gov/awardsearch/showAward?AWD_ID=1802188 (NSF Award #1802188)]<br>
Amy Litt, (PI), University of California - Riverside [http://www.nsf.gov/awardsearch/showAward?AWD_ID=1802188 (NSF Award #1802188)]<br>
Andy Sanders, curator
Andy Sanders, curator<br>
Mike Cohen, volunteer collections manager


=====University of California - Santa Cruz (UCSC)=====
=====University of California - Santa Cruz (UCSC)=====
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''Project Sponsors'': Oregon State University [https://www.nsf.gov/awardsearch/showAward?AWD_ID=2001644 (NSF Award 2001644)], San Francisco State University [https://www.nsf.gov/awardsearch/showAward?AWD_ID=2001641 (NSF Award 2001641)], and San Diego Natural History Museum [https://www.nsf.gov/awardsearch/showAward?AWD_ID=2001535 (NSF Award 2001535)]
''Project Sponsors'': Oregon State University [https://www.nsf.gov/awardsearch/showAward?AWD_ID=2001644 (NSF Award 2001644)], San Francisco State University [https://www.nsf.gov/awardsearch/showAward?AWD_ID=2001641 (NSF Award 2001641)], and San Diego Natural History Museum [https://www.nsf.gov/awardsearch/showAward?AWD_ID=2001535 (NSF Award 2001535)]


''Principal Investigators (PIs)'': [mailto:listona@science.oregonstate.edu Aaron Liston (OSC)], Layla Aerne Hains (SD), Jon Rebman (SD), Jason Cantley (SFSU), Lloyd Stark (UNLV), Jenn Yost (OBI), Aimee Wyrick-Brownworth (PUA), Andrew Gardner (SHTC)
''Principal Investigators (PIs)'': [mailto:listona@science.oregonstate.edu 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)
 
''Other collaborators'': Genevieve Walden (CDA)
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