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=== Project Websites & Social Media ===
 
=== Project Websites & Social Media ===
  
[https://www.capturingcaliforniasflowers.org CAP TCN Website]
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[https://twitter.com/CalPhenologyTCN Data Portal]
  
[https://twitter.com/CalPhenologyTCN Twitter Page]
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[https://www.capturingcaliforniasflowers.org Project Website (protocols, news, about)]
 +
 
 +
[http://cch2.org/portal/index.php Twitter Page]
  
 
=== Citizen Science & Outreach Projects ===
 
=== Citizen Science & Outreach Projects ===
 +
 +
[https://www.zooniverse.org/projects/md68135/notes-from-nature-capturing-californias-flowers CAP TCN on Notes from Nature]
  
 
=== Project Leadership  ===
 
=== Project Leadership  ===
 
''Project sponsor:'' California Polytechnic State University San Luis Obispo [http://www.nsf.gov/awardsearch/showAward?AWD_ID=1802301 (NSF Award #1802301)]
 
''Project sponsor:'' California Polytechnic State University San Luis Obispo [http://www.nsf.gov/awardsearch/showAward?AWD_ID=1802301 (NSF Award #1802301)]
  
''Principal Investigator (PI):'' Jennifer Yost<br>
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''Principal Investigator (PI):'' Jenn Yost<br>
''Project Manager:'' Katie Pearson<br>
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''Project Manager:'' [mailto:kdpearso@calpoly.edu Katie Pearson]<br>
 
''Data Manager:'' Jason Alexander<br>
 
''Data Manager:'' Jason Alexander<br>
  
 
=== Project Collaborators  ===
 
=== Project Collaborators  ===
  
=====California Polytechnic State University San Luis Obispo=====
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 +
====Digitizing Institutions====
 +
 
 +
=====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)]
  
=====University of California - Berkeley=====
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=====University of California - Berkeley (UC/JEPS)=====
 
Brent Mischler, (PI), University of California - Berkeley [http://www.nsf.gov/awardsearch/showAward?AWD_ID=1802163 (NSF Award #1802163)]<br>
 
Brent Mischler, (PI), University of California - Berkeley [http://www.nsf.gov/awardsearch/showAward?AWD_ID=1802163 (NSF Award #1802163)]<br>
  
=====University of California - Santa Barbara=====
+
=====University of California - Santa Barbara (UCSB)=====
 
Susan J. Mazer, (PI), University of California - Santa Barbara [http://www.nsf.gov/awardsearch/showAward?AWD_ID=1802181 (NSF Award #1802181)]<br>
 
Susan J. Mazer, (PI), University of California - Santa Barbara [http://www.nsf.gov/awardsearch/showAward?AWD_ID=1802181 (NSF Award #1802181)]<br>
 
Katja Seltmann (Co-PI), University of California - Santa Barbara <br>
 
Katja Seltmann (Co-PI), University of California - Santa Barbara <br>
  
=====Santa Barbara Botanic Garden=====
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=====California Parks and Recreation, Colorado Desert District (BSCA)=====
Matt Guilliams, (PI) Santa Barbara Botanic Garden [http://www.nsf.gov/awardsearch/showAward?AWD_ID=1802176 (NSF Award #1802176)]<br>
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Danny McCamish, senior environmental scientist <br>
Lucie Gimmel, herbarium curatorial assistant <br>
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Jim Dice, reserve manager <br>
Kristen Lehman, laboratory manager
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Larry Hendrickson, senior park aide
  
=====San Jose State University=====
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=====California State University, Chico (CHSC)=====
Benjamin Carter, (PI), San Jose State University [http://www.nsf.gov/awardsearch/showAward?AWD_ID=1802177 (NSF Award #1802177)]<br>
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Colleen Hatfield, (PI), California State University, Chico [http://www.nsf.gov/awardsearch/showAward?AWD_ID=1802182 (NSF Award #1802182)]<br>
Lars Rosengreen, herbarium curator
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Lawrence Janeway, herbarium curator
  
=====California State University, Fresno=====
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=====California State University, Los Angeles (CSLA)=====
Katherine E. Waselkov, (PI), California State University, Fresno [http://www.nsf.gov/awardsearch/showAward?AWD_ID=1802178 (NSF Award #1802178)]<br>
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Kirsten Fisher, (PI), California State University, Los Angeles [http://www.nsf.gov/awardsearch/showAward?AWD_ID=1802191 (NSF Award #1802191)]<br>
  
=====San Diego State University=====
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=====California State University, San Bernardino (CSUSB)=====
Michael G. Simpson, (PI), San Diego State University [http://www.nsf.gov/awardsearch/showAward?AWD_ID=1802180 (NSF Award #1802180)]<br>
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Kimberlyn Williams, (PI), California State University, San Bernardino
Lluvia Flores-Renteria (Co-PI), San Diego State University <br>
+
  
=====California State University, Chico=====
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=====University of California - Davis (DAV)=====
Colleen Hatfield, (PI), California State University, Chico [http://www.nsf.gov/awardsearch/showAward?AWD_ID=1802182 (NSF Award #1802182)]<br>
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Daniel Potter, (PI), University of California - Davis [http://www.nsf.gov/awardsearch/showAward?AWD_ID=1802203 (NSF Award #1802203)]<br>
Lawrence Janeway, herbarium curator
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Ellen Dean, herbarium curator <br>
 +
Teri Barry, collections manager
  
=====Rancho Santa Ana Botanic Garden=====
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=====California State University, Fresno (FSC)=====
Mare Nazaire, (PI), Rancho Santa Ana Botanic Garden [http://www.nsf.gov/awardsearch/showAward?AWD_ID=1802183 (NSF Award #1802183)]<br>
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Katherine E. Waselkov, (PI), California State University, Fresno [http://www.nsf.gov/awardsearch/showAward?AWD_ID=1802178 (NSF Award #1802178)]<br>
Lucinda McDade (co-PI), Claremont Graduate University <br>
+
  
=====Humboldt State University=====
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=====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>
 
Robin Bencie, collections manager
 
Robin Bencie, collections manager
  
=====San Diego Natural History Museum=====
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=====University of California - Irvine (IRVC)=====
Layla Aerne Haines, (PI), San Diego Natural History Museum [http://www.nsf.gov/awardsearch/showAward?AWD_ID=1802186 (NSF Award #1802186)]<br>
+
Peter A. Bowler, (PI), University of California - Irvine [http://www.nsf.gov/awardsearch/showAward?AWD_ID=1802312 (NSF Award #1802312)]<br>
Jon Rebman, (co-PI), San Diego Natural History Museum <br>
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Rebecca Crowe, nursery manager
 
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=====California State University, Los Angeles=====
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Kirsten Fisher, (PI), California State University, Los Angeles [http://www.nsf.gov/awardsearch/showAward?AWD_ID=1802191 (NSF Award #1802191)]<br>
+
 
+
=====California State University, Long Beach=====
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Amanda E. Fisher, (PI),California State University, Long Beach [http://www.nsf.gov/awardsearch/showAward?AWD_ID=1802192 (NSF Award #1802192)]<br>
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+
=====California State University, Northridge=====
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Paul S. Wilson, (PI), California State University, Northridge [http://www.nsf.gov/awardsearch/showAward?AWD_ID=1802194 (NSF Award #1802194)]<br>
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Jim Hogue, database manager
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=====University of California - Los Angeles=====
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=====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>
 
Thomas Huggins, herbarium coordinator
 
Thomas Huggins, herbarium coordinator
  
=====California State University, Fullerton=====
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=====California State University, Long Beach (LOB)=====
 +
Amanda E. Fisher, (PI),California State University, Long Beach [http://www.nsf.gov/awardsearch/showAward?AWD_ID=1802192 (NSF Award #1802192)]<br>
 +
 
 +
=====California State University, Fullerton (MACF)=====
 
Joshua P. Der, (PI), California State University, Fullerton [http://www.nsf.gov/awardsearch/showAward?AWD_ID=1802200 (NSF Award #1802200)]<br>
 
Joshua P. Der, (PI), California State University, Fullerton [http://www.nsf.gov/awardsearch/showAward?AWD_ID=1802200 (NSF Award #1802200)]<br>
 
Jochen Schenk, (Co-PI), California State University, Fullerton <br>
 
Jochen Schenk, (Co-PI), California State University, Fullerton <br>
  
=====University of California - Davis=====
+
=====Rancho Santa Ana Botanic Garden (RSA)=====
Daniel Potter, (PI), University of California - Davis [http://www.nsf.gov/awardsearch/showAward?AWD_ID=1802203 (NSF Award #1802203)]<br>
+
Mare Nazaire, (PI), Rancho Santa Ana Botanic Garden [http://www.nsf.gov/awardsearch/showAward?AWD_ID=1802183 (NSF Award #1802183)]<br>
Ellen Dean, herbarium curator <br>
+
Lucinda McDade (co-PI), Claremont Graduate University <br>
Teri Barry, collections manager
+
  
=====University of California - Irvine=====
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=====Santa Barbara Botanic Garden (SBBG)=====
Peter A. Bowler, (PI), University of California - Irvine [http://www.nsf.gov/awardsearch/showAward?AWD_ID=1802312 (NSF Award #1802312)]<br>
+
Matt Guilliams, (PI) Santa Barbara Botanic Garden [http://www.nsf.gov/awardsearch/showAward?AWD_ID=1802176 (NSF Award #1802176)]<br>
Rebecca Crowe, nursery manager
+
Lucie Gimmel, herbarium curatorial assistant <br>
 +
Kristen Lehman, laboratory manager
  
=====University of California - Riverside=====
+
=====San Diego Natural History Museum (SD)=====
 +
Layla Aerne Haines, (PI), San Diego Natural History Museum [http://www.nsf.gov/awardsearch/showAward?AWD_ID=1802186 (NSF Award #1802186] and [https://www.nsf.gov/awardsearch/showAward?AWD_ID=2001535 #2001535)]<br>
 +
Jon Rebman, (co-PI), San Diego Natural History Museum <br>
 +
 
 +
=====San Diego State University (SDSU)=====
 +
Michael G. Simpson, (PI), San Diego State University [http://www.nsf.gov/awardsearch/showAward?AWD_ID=1802180 (NSF Award #1802180)]<br>
 +
Lluvia Flores-Renteria (Co-PI), San Diego State University <br>
 +
 
 +
=====California State University, Northridge (SFV)=====
 +
Paul S. Wilson, (PI), California State University, Northridge [http://www.nsf.gov/awardsearch/showAward?AWD_ID=1802194 (NSF Award #1802194)]<br>
 +
Jim Hogue, database manager
 +
 
 +
=====San Jose State University (SJSU)=====
 +
Benjamin Carter, (PI), San Jose State University [http://www.nsf.gov/awardsearch/showAward?AWD_ID=1802177 (NSF Award #1802177)]<br>
 +
Lars Rosengreen, herbarium curator
 +
 
 +
=====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
  
=====University of California - Santa Cruz=====
+
=====University of California - Santa Cruz (UCSC)=====
 
Karen Holl, (PI), University of California - Santa Cruz <br>
 
Karen Holl, (PI), University of California - Santa Cruz <br>
 
Al Keuter, herbarium manager <br>
 
Al Keuter, herbarium manager <br>
Ken Kellman
+
Chris Lay, curator, Kenneth Norris Center for Natural History <br>
  
=====California Parks and Recreation, Colorado Desert District=====
+
==== 2020 PEN Participants ====
Danny McCamish, senior environmental scientist <br>
+
 
Jim Dice, reserve manager <br>
+
=====California Department of Food and Agriculture (CDA)=====
Larry Hendrickson, senior park aide
+
Genevieve Walden, senior plant systematist
 +
 
 +
=====Oregon State University (OSC)=====
 +
Aaron Liston, professor and herbarium director [https://www.nsf.gov/awardsearch/showAward?AWD_ID=2001644 (NSF Award #2001644)]
 +
 
 +
=====Pacific Union College (PUA)=====
 +
Aimee Wyrick-Brownsworth, chair and associate professor of biology [https://www.nsf.gov/awardsearch/showAward?AWD_ID=2001644 (NSF Award #2001644)]
 +
 
 +
=====San Francisco State University (SFSU)=====
 +
Jason Cantley, assistant professor [https://www.nsf.gov/awardsearch/showAward?AWD_ID=2001641 (NSF Award #2001641)]
 +
 
 +
=====California State University, Stanislaus (SHTC)=====
 +
Andrew Gardner, assistant professor of botany [https://www.nsf.gov/awardsearch/showAward?AWD_ID=2001644 (NSF Award #2001644)]
 +
 
 +
=====University of Nevada, Las Vegas (UNLV)=====
 +
Lloyd Stark, associate professor [https://www.nsf.gov/awardsearch/showAward?AWD_ID=2001644 (NSF Award #2001644)]
  
 
=== Protocols & Workflows ===
 
=== Protocols & Workflows ===
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=== Publications ===
 
=== Publications ===
Alexander, Jason A. (2019). Upcoming changes in the Consortium of California Herbaria, ''Madroño'', ''66''(1), 37-38. https://doi.org/10.3120/0024-9637-66.1.37
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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:[https://academic.oup.com/bioscience/article/70/7/610/5825721 10.1093/biosci/biaa044]
 +
 
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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:[https://bsapubs.onlinelibrary.wiley.com/doi/full/10.1002/aps3.11276 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:[https://bioone.org/journals/madro%C3%B1o/volume-66/issue-4/0024-9637-66.4.130/THE-CALIFORNIA-PHENOLOGY-COLLECTIONS-NETWORK--USING-DIGITAL-IMAGES-TO/10.3120/0024-9637-66.4.130.full 10.3120/0024-9637-66.4.130]
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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. [https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6426157/ doi:10.1002/aps3.1233]
 +
 
 +
Alexander, Jason A. 2019. Upcoming changes in the Consortium of California Herbaria. ''Madroño'', 66(1):37-38. [https://doi.org/10.3120/0024-9637-66.1.37 doi:10.3120/0024-9637-66.1.37]
  
 
=== Professional Presentations ===
 
=== Professional Presentations ===
  
Pearson KD, Yost JM [presented by Ayers, A]. 2019. Capturing flowering time data from herbarium specimens: The California Phenology TCN. Poster presented at: California Botanical Society Graduate Student Symposium; 2019 April 6; San Luis Obispo, CA.
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====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. https://youtu.be/YO65BPO2MIY [https://youtu.be/YO65BPO2MIY Recording]
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 +
*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. https://youtu.be/Le1zewbdOXs [https://youtu.be/Le1zewbdOXs Recording]
 +
 
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*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. https://youtu.be/rYVm5XAIQvI [Recording https://youtu.be/rYVm5XAIQvI]
 +
 
 +
*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. [https://drive.google.com/file/d/1NDFVNYzgwF3WTm13NNWgQEDulZd4_cUv/view Recording]
 +
 
 +
*Pearson KD. Using Notes from Nature to digitize California herbaria. Northern California Botanists Symposium, Chico, CA. January 13, 2020. [https://www.youtube.com/watch?v=AQv3EXy03r8&feature=youtu.be&t=1528 Recording]
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 +
*Yost J, Pearson KD. California Phenology TCN: Starting Year 2. ADBC Summit 2019. October 2019. Gainesville, FL. [https://www.idigbio.org/wiki/images/d/d7/CAP_ADBCSummit2019.pdf 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. [https://mediasite.video.ufl.edu/Mediasite/Play/1efdcec7f4414a7783798fc2b88ebe5e1d?catalog=588bdfbb38134fac83c6ef66a7c59e4e21 Recording]
 +
 
 +
====Posters====
 +
*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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 +
*Waselkov K, Riley R, Peña M, Pearson K, Yost J. 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. [Virtual]. June 2020. https://spnhc.biowikifarm.net/wiki/Posters#/media/File:Waselkov_spnhc_2020_optimized.jpg
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 +
*Cazares J, Carter BE. Capturing phenology from herbarium specimens to understand flowering period in Winecup Clarkia (Clarkia purpurea ssp. quadrivulnera, Onagraceae).  Northern California Botanists Symposium, Chico, CA. January 13-14, 2020. http://www.norcalbotanists.org/files/NCB_2020_Poster34_Cazares.pdf
 +
 
 +
*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.
 +
 
 +
== PENs ==
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 +
 
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=== Digitization PEN: Expanding and enhancing the California Phenology TCN ===
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 +
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.
  
Pearson KD, Yost JM. 2019. Capturing flowering time data from herbarium specimens: The California Phenology TCN. Poster presented at: Southern California Botanists Symposium; 2018 November 8; Claremont, CA.
+
''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)]
  
Pearson KD, Yost JM. 2019. Capturing flowering time data from herbarium specimens: The California Phenology TCN. Poster presented at: Digital Data in Biodiversity Research Conference; 2019 June 11; New Haven, CT.
+
''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)
  
=== Other project documentation ===
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''Other collaborators'': Genevieve Walden (CDA)

Latest revision as of 17:23, 13 August 2020

Contents

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.

Current Research

Project Websites & Social Media

Data Portal

Project Website (protocols, news, about)

Twitter Page

Citizen Science & Outreach Projects

CAP TCN on Notes from Nature

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

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)

University of California - Berkeley (UC/JEPS)

Brent Mischler, (PI), University of California - Berkeley (NSF Award #1802163)

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

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

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)
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)
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)
Lucie Gimmel, herbarium curatorial assistant
Kristen Lehman, laboratory manager

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

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

California Department of Food and Agriculture (CDA)

Genevieve Walden, senior plant systematist

Oregon State University (OSC)

Aaron Liston, professor and herbarium director (NSF Award #2001644)

Pacific Union College (PUA)

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

San Francisco State University (SFSU)

Jason Cantley, assistant professor (NSF Award #2001641)

California State University, Stanislaus (SHTC)

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

University of Nevada, Las Vegas (UNLV)

Lloyd Stark, associate professor (NSF Award #2001644)

Protocols & Workflows

Detailed 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. https://youtu.be/YO65BPO2MIY 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. https://youtu.be/Le1zewbdOXs 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.

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), Layla Aerne Hains (SD), Jon Rebman (SD), Jason Cantley (SFSU), Lloyd Stark (UNLV), Jenn Yost (OBI), Aimee Wyrick-Brownworth (PUA), Andrew Gardner (SHTC)

Other collaborators: Genevieve Walden (CDA)