Dear IBSS,
Fall 2023 was an exciting time, and we ended the year with some notable events as you can see in this newsletter! On Oct. 30th, we welcomed the new Chief of Strategic Partnerships and Managing Director of Science and Education, Dr. Amber Mace. Amber kicked off this new position for the Academy as executive sponsor of the Strategic Initiatives. Our SSI students made an amazing showing at the SACNAS 2023 Annual Conference in Portland, Oct. 26th-28th; two of our students won best presentation awards - Amy Wu (mentor Laurel Allen) and Alizee Gamber (mentor Durrell Kapan) - and another student Joy Falotico (mentor Elora López-Nandam) was awarded special recognition for their poster. Another of the many excitements was our convening on “Past, Present, and Future Biodiversity,” Nov. 30-Dec. 1, with almost 50 participants including many of our staff as well as academics, conservationists, and land managers regionally and beyond. Together we discussed how species occurrence data from the past (e.g., museum collections) to present day (e.g., community science data) could be used, along with future projections (e.g., species distribution models) to prioritize conservation and regenerative practices, and ultimately influence policy.
Warm regards,
Shannon
IZ Collections grew by over 2000 specimens during this quadrimester. Specimens of note include National Park Service voucher specimens of the endangered California freshwater shrimp, Syncaris pacifica, specimens collected in the Maldives by Dr. Terry Gosliner and the Mesophotic Team as part of the Academy’s Hope For Reefs Initiative, and NOAA/National Marine Fisheries Service benthic marine invertebrate vouchers collected during Alaskan Survey Cruises.
IZ Curatorial Collection Staff and Volunteers have been making great progress with prioritized curatorial projects: DigIn Marine Invertebrate Data Digitization (NSF funded TCN), EPA Project (funded in part by the California Initiative), NOAA/NMFS Alaskan Survey Cruise Voucher Project (Contract funded), J.A. Scott Seashell Colln., photo slide scanning, image metadata capture, specimen label scanning and label transcription.
As part of our DigIn Project, IZ committed to scanning our non-molluscan photoslides. Since beginning the project in June 2022, Volunteer Polly Thacher has numbered and scanned 2753 photoslides, capturing copyright data and labeling the image files, completing this project. Congratulations and thank you, Polly! Polly enjoyed this scanning project, viewing beautiful invertebrate images and is looking forward to scanning our molluscan holdings.
Bob Byers donated 77 mineral specimens to the Geology collection in December 2023. This donation includes more excellent pieces from his stibnite collection, as well as a conichalcite specimen from Greece. In September and November 2023, paleontologist Wayne Thompson donated 48 invertebrate specimens from the Purisima formation in Santa Cruz county. Dr. Masaki Matsukawa, Professor of Environmental Sciences, Tokyo Gakugei University visited the Geology collection for 6 weeks last fall. He is working on re-describing Frank Marion Anderson ammonite type specimens.
Entomology hosted 10 visiting researchers and received a partial donation of about 2,000 specimens from Joseph L. Furnish of aquatic insects from the Western USA and Okinawa, Japan.
The Picturae conveyor belt project managed to image over 500k specimens since the start of the project in March 2023; all California herbarium holdings are now imaged and pending upload to our database; work on the remaining North American holdings progresses. A garden club member made a substantial donation to the Botany department, for research and curatorial activities, following a tour for 50 garden club members with stops in the herbarium, prep room & conveyor belt. Several new conveyor belt contractors were hired. Melanie Zhao and Jen Pagel are currently operating the equipment.
Insect barcoding project - The CCG insect barcoding team is operating in full swing. Despite the challenge of dealing with old samples from the collection, we have successfully extracted 3882 samples and obtained 1096 barcodes, covering 88 different insect families from the years 1980 to 2019.
PromethION 2 solo - We have completed the first sequencing run on the new PromethION 2 solo. We also received hands-on training from a local Nanopore sequencing specialist. Although running the P2 machine is not without challenges, we're excited about the enhanced in-house sequencing capacity and the potential it brings, including ultra-long read sequencing, adaptive sequencing, and increased data for metabarcoding projects
Milwaukie Public Museum visit - In December, the CCG hosted Dr. Nick Dowdy, Head of Zoology & Director of Collections Informatics at the Milwaukie Public Museum (MPM), along with Kat Sullivan, a PhD student working with Nick. They brought along a collection of twenty-four 100-year-old tiger moths from MPM's archives. Together, we successfully created libraries and gathered valuable data from all of the specimens. MPM is interested in starting a core genomic lab to conduct genomic research using their natural history collections. Currently, they outsource most of their genomic projects, which is both expensive and often unsuccessful, particularly with older samples. Their main goal in visiting us was to learn museum genomic techniques and understand the equipment and expertise needed to run such a lab successfully. We look forward to our continued collaboration with them.
The Reefscape Genomics Lab returned to Curaçao in November/December for three weeks to survey the impacts of the anomalously high temperatures that affected the Caribbean last year. The expedition not only marked a critical time point in our time series, but also the 10th milestone of resurveying our plots for the "CoralScape 20K" project, where we are tracking >20,000 individually catalogued corals.
Underwater 3D imaging - Working together with our close collaborators at the CARMABI Research Station, and the support of several diving volunteers from the community, we successfully reimaged 30 of our plots (100m2 each). Due to the combined effects of both Stony Coral Tissue Loss Disease (SCTLD) and coral bleaching, more than half of the corals across all sites were observed to be affected – although impacts were much less pronounced at mesophotic depths. We also complemented the high-resolution surveys with much larger area imaging (~2,500m2) at each location, to allow for mapping of rare/endangered and highly abundant species, aligning with our newly granted Inkfish project. In collaboration with the Norwegian University of Science and Technology, this project aims to develop new Autonomous Underwater Vehicles (AUVs) to scale up our underwater imaging capabilities in the future.
Coral tissue collections - An integral part of the "CoralScape 20K" project is to understand the variability in stress responses in natural populations, by coupling the time series of individual coral colonies with genomic information. Representing the third bleaching event in our 4.5 years of monitoring (!), this "natural" experiment has provided us with an unique mass-screening for stress tolerance across multiple temperature anomalies and across the entire reef community (with temporal context for every single coral colony). Over the years we have cumulatively sequenced the genomes of ~3,000 organisms in our plots, but given the high predicted mortality during this current event we prioritized expanding these efforts during this latest fieldwork. With a team of 6 divers jointly spending well over 100 hours underwater, we managed to obtain tissue vouchers for >1,500 additional coral colonies in our digital collection. This included >400 samples from "rare species" for Ale's research that were obtained by systematically combing out more than 4 acres of reef habitat. All these samples are cross-referenced to the database either through pregenerated maps (accessed by divers on underwater tablets) or position-matching through bird's eye view cameras (carried by each individual diver), and are now being prepared for genome sequencing.
Bleaching impacts - Despite the heartbreak of witnessing the reefs' deterioration and the loss of century-old colonies, there were hopeful signs of recovery and resilience. For instance, many Orbicella corals (considered key reef-builders in the shallows) were starting to regain color as temperatures are now decreasing, indicating potential recovery. The Madracis corals (the focus of Jennifer’s NSF-funded project) proved to be some of the most thermally tolerant species. Notably, even among severely affected species, we found a small proportion of unbleached individuals, possibly shielded by unique reef locations or inherent thermal resilience – a key focus of our upcoming research. Out of the water, we also had encouraging planning meetings with CARMABI's education team, and were able to see the Marine Youth Ranger team in action, keeping our spirits up!
We had most of the Reefscape Genomics Lab out in the field, including PI Pim Bongaerts, postdocs Alejandra Hernandez and Jennifer Hoey, two new PhD students that have recently started in the lab through Inkfish scholarships: Dennis van Hulten (Netherlands) and Phaedra Hernandez (Curacao), and a MSc intern: Giorgio Terzi (Italy). We also had support from the Steinhart Aquarium with Curator Kylie Lev joining us in the field to help specifically with tissue collections. A big shout out also to the DiveOps team - this trip would not have been possible without their continued logistical and safety support!
ENTO Jacob Gorneau graduated from SF State in late December with a Master's in Biology and a Concentration in Ecology, Evolution and Conservation Biology and will join UC Berkeley as a PhD student in the Department of Environmental Science, Policy & Management with Drs. Damian Elias and Rosemary Gillespie.
HERP Bell Lab PhD student Oscar Fokou, who is based at the University of Yaoundé in Cameroon, visited the Herpetology Dept and CCG in September with support of the Lakeside Program. Oscar worked with our extensive collection of Cameroon amphibians and collected DNA-barcoding data in the CCG to confirm field IDs of specimens collected at his field site in the Dja Biosphere Reserve.
HERP Over the last several years, the frog vision research team (a global collaboration led by Rayna Bell) has been putting together a brief eBook that introduces the basic concepts of optics and vision biology, and summarizes some of the results from our NSF-NERC grant. It's only fully viewable on Mac platforms (iphone, ipad, Mac computers) because of the software we used to create it, so hopefully you're able to view it :) The IBSS scientific illustration intern from last summer, Joseph Wu, contributed several illustrations as part of his internship that was supported by Maxwell Hanrahan.
IZ IBSS staff and volunteers are celebrating Johanna Loacker who has earned her Master of Arts degree in Museum Studies from Johns Hopkins University. Please join us in congratulating her on this awesome accomplishment. This degree, along with her degree in Biology and Collections experience, shapes Johanna’s unique perspective. She welcomes engaging conversation about re-imagining the Natural History Museum!
IZ said thank you and so long to Jennifer Wong who volunteered with us since Dec 2022 and has now headed to UC San Diego to continue their studies. IZ welcomed two new volunteers: Dylan Limjoco and Yumary Rubio. Dylan and Yumary are both USF Biology majors joining the label scanning crew headed up by Johanna Loacker.
IZ Nelly Batista Delgado (SSI 2023) attended the SACNAS National Diversity in STEM Conference in Portland, OR, to present her continued work on Madracis morphological trait analyses. She received a full scholarship to attend the meeting - congrats, Nelly!
ENTO California Barcode team took to the field just once in this period, spending several nights up at University of California Sagehen Creek field station. Brisk autumnal temps made for limited collecting, but fresh apples and fall colors were everywhere.
ENTO Lakeside Scholar Diego de Pedro joined the department from his home institution of Centro de Investigación Científica y de Educación in Baja, Mexico. He visited CAS for one month working in collaboration with the BigBee NSF grant.
ENTO Project Lifeplan, a global biodiversity monitoring network, has completed a full year of surveying on the roof of the Academy! 2024 begins year 4 of a 6 year project. Traps were removed in December and will be relocated in the Presidio (near Inspiration Point), in the spring.
ICHT hosted Sri Lankan scientist Asha De Vos and a delegation from the Maldives to look at our collections in December.
IZ The Coral Regeneration Lab (CoRL) supported the most successful coral spawn to date in December. Two species of Acropora spawned over the course of two months. For the first time, we successfully closed the life cycle when a three-year old A. hyacinthus baby that was fertilized in 2020 in CoRL reached sexual maturity and spawned with the adults. Thirteen volunteers, interns, and collaborating researchers worked tirelessly to support a wide variety of research projects, including: CORDAP-funded experiments to test techniques to enhance growth and survivorship of coral recruits; selection for heat-resistant coral larvae; cryopreservation of coral sperm; and lipidomics sampling of wild- versus captive- gametes. Three collaborators from the Roatán Marine Park, supported by a Lakeside Fellowship, spent several weeks on-site learning husbandry techniques and collaborating on spawning experiments. We supported three interns (two undergraduates, one graduate), and we hosted a lab from Stanford (Dr. Manu Prakash and students) on-site for two weeks to investigate larval plasticity and swimming behavior. We also provided material to two labs at Berkeley to pursue a variety of projects involving coral symbiosis. KQED's Deep Look team was on-site and filmed a coral spawning episode (link in Outreach section).
We were saddened by the death of our long-time Research Associate and former Collection Manager, Bruce Bartholomew, in September of 2023. We recently held a memorial to honor his important contributions to botanical research and the CAS herbarium. Notably, Bruce was an important editor and contributor to the Flora of China project where he authored 22 taxonomic treatments. He continued pursuing his botanical interests and dedication to herbaria well into his retirement as a CAS Research Associate and herbarium volunteer. During this time Bruce published numerous papers and worked steadily to contribute to the curation of his many Chinese collections. A memorial plaque has been installed in the garden along with an oak tree to commemorate him.
GEO welcomed Ariel Berenyi-Tonesi, the new curatorial assistant in the geologic collections. Arie is a recent graduate from UC Davis in Biology with a minor in Geology. She speaks two languages, Italian and English, and holds dual citizenships. Like many others in the field of paleontology, Arie grew up loving dinosaurs and museums. "Having lived in the East Bay my whole life, I quickly learned to love Bay Area paleontology and wanted to work towards aiding in the preservation of natural resources as a whole. Outside of work I enjoy hiking, traveling, and chatting with friends."
HERP Islands 2030 welcomed Dr. Michael Yuan as the postdoctoral researcher for the Lesser Antilles STEM Leadership Cohort.
IZ welcomed Matt Schmidt whose previous experience with marine invertebrates is a perfect match for our current project to curate, identify and digitize marine invertebrate voucher specimens collected on NOAA/NMFS Alaskan Survey Cruises. Funding comes from a federal contract awarded to IZ earlier this year. Matt, the Renaissance Person that he is, can also be found working in Ichthyology and O&M.
IZ Elora López-Nandam was promoted from postdoctoral researcher to research scientist as part of the CORDAP award between the Roatán Marine Park and the Academy to advance coral restoration science. This award runs from 2023-2026.
CCG This month, we are excited to welcome Kate Richards as our CCG intern in the CCG insect barcoding team. Kate brings a fresh perspective and enthusiasm to the team.
The second annual Solstice Sea Star Search held from December 10 - 27, was a success with over 2,800 observations of 11 different sea stars along the California coast made by 333 people. While there was not a Sunflower Sea Star spotted during our campaign, there was one spotted on January 11th in Mendocino! Locally, the Center for Biodiversity and Community Science held a public event at Pillar Point on December 12th with over 50 people in attendance. There were events held along the entire coast from Del Norte to San Diego counties. Our team also attended and supported a local event in a budding partnership with QueerSurf and the Greater Farallones Association. We are excited for more partnerships and tidepooling events for Snapshot Cal Coast happening this summer for the entire month of June this year, keep an eye out for public events announced soon!
On California Biodiversity Day, September 7th, the Academy hosted a press conference to announce Reimagining San Francisco—an alliance of more than two dozen local nonprofits and government agencies. The group’s vision is relatively simple: A San Francisco where people and nature thrive together. But their goals are bold: By 2030, 30% of San Francisco is biodiverse greenspace and everyone in San Francisco has easy access to nearby nature. This announcement is the culmination of more than a year of collaborative work led by Thriving California Co-directors Rebecca Johnson and Alison Young and Project Coordinator Sydney Davenport.
The Academy celebrated California Biodiversity Day with a 12-Hour Nature Extravaganza led by the Digital Engagement team with over 50 special guests including many CAS staff, IBSS researchers, students and more! The goal was for the group to read out the scientific names of as many groups of California plants, animals, and fungi as humanly possible…in 12 HOURS. That evening, Nightlife hosted California Love to celebrate all things California Biodiversity. This event included a talk by Dr. Sarah Jacobs, Academy Curator of Botany, about what biodiversity means and how it is measured followed by California Biodiversity Trivia hosted by Sydney Davenport. California Academy of Sciences’ Entomology Department and Christine Wilkinson each held their own tables as part of the event alongside some incredible local San Francisco groups sharing about biodiversity in the Bay Area!
The Center for Biodiversity and Community Science also partnered with the California Natural Resources Agency for an iNaturalist campaign across the state from Sept. 2 to Sept. 10, for California Biodiversity Week: Can you find and document 30 species in California? The "Find 30 Species for CA 30x30" Biodiversity Week Challenge was inspired by the state’s goal of protecting 30% of land and coastal waters by 2030. Our team partnered with a team of state agencies to help support this event, and we created a fun infographic highlighting some of the species seen across the state during the challenge. In addition to the challenge, our team also helped organize and lead a California Biodiversity Day bioblitz at Effie Yeaw Nature Center with CNRA, California Department of Fish & Wildlife, 30x30 California, California Biodiversity Network and had special guest Jennifer Norris, Deputy Secretary for Biodiversity and Habitat join us for the bioblitz alongside local families in Sacramento.
Eight Academy staff, including Executive Director Scott Sampson, connected with other natural history museums, environmental nonprofits, and government agencies and shared updates about recent work at the 30x30 Partnership Gathering last month. Olivia VanDamme and Sydney Davenport from the Academy’s Center for Biodiversity and Community Science hosted a “Stories of Success” table featuring the City Nature Challenge, Snapshot Cal Coast, and Reimagining San Francisco. On the conference’s second day, hosted by the California Biodiversity Network (CBN), Rebecca Johnson, co-director of Thriving California and a member of the CBN steering committee, spoke on the work of the Biodiversity Informatics and Community Science Roundtable to more than 250 people. Johnson co-chairs the roundtable with Alison Young, also co-director of Thriving California, and Shannon Bennett, the Academy’s Chief of Science, who helped organize the second day. Esther Oh and Samantha Delucchi from the Government Affairs team also attended the conference and joined the Academy attendees at a meeting with staff from the Natural History Museum of Los Angeles and the San Diego Natural History Museum to discuss collaborations and deeper contributions to 30x30 goals.
IZ Jennifer Hoey & Elora López-Nandam met with Sarah Cohen’s SFSU Marine Invertebrate Zoology class in September 2023. Jennifer and Elora introduced 20 students to corals, coral reproduction, and coral research at CAS.
IZ Jennifer completed a Coral Reef Mentorship with two Careers in Science interns. The interns are qualitatively categorizing the position of Jennifer’s Madracis corals in 3D reef models. These qualitative categorizations will help to ground-truth the quantitative habitat measurements that are being developed in the Reefscape Genomics Lab. By helping to determine how accurate our habitat measurements are, the interns are playing an important role in developing novel analyses that use 3D data for coral conservation.
IZ Ale gave talks about her postdoc project on rare and endangered coral species for Cafecito (in Spanish) and for Members (in English) in December. If you missed her talk, you can watch the Member's talk here.
IZ KQED's Deep Look team filmed and produced a Coral Spawning episode. With the exception of the reef shots, all footage was filmed in the Coral Regeneration Lab during the December spawn.
HERP The Herpetology Department received funding through the Department of Defense to survey herpetological diversity at military installations across the state of California
IZ Pim Bongaerts is a co-PI on a successful Marsden Grant awarded by the Royal Society of New Zealand: “Uncovering the functioning and importance of temperate mesophotic ecosystems”, working with Alice Rogers (PI), James Bell and Sarah Bury at the Victoria University of Wellington
ENTO Chris Grinter received a grant to support the Soil Arthropod Biodiversity Pilot Project: $254,706, as well as a Collections Rapid Grant ($26,460)
The Fall Biodiversity Seminar Series featured seminars from CAS researchers and affiliates, as well as Indigenous researchers invited by the Indigenous Solidarity Committee with support from Thriving California.
October 5 Dr. Lauren Esposito CAS Academy Arachnid Research Updates
October 12 Dr. Jaime Chaves SFSU Galapagos, a natural laboratory for studying evolution
October 26 Dr. Christine Wilkinson UCB/CAS Life finds a way: Exploring the social-ecology of carnivore movement and conflict
November 9 Insect Barcoding Team CAS Building a barcode library of California insect biodiversity
(Chris Grinter, Dr. Anna Holmquist, Diana Phan, Julia Betz)
December 7 Alexii Sigona UCB Tribal Stewardship of Public Lands: Amah Mutsun Biocultural Restoration and
Invasive Species Discourse Along the Central California Coast
December 14 Dr. Don Hankins CSU Chico Climate Resilience Through Ecocultural Stewardship
Bein, B., F.D. Lima, H. Lazzarotto, L.A. Rocha, T.S. Leite, S.M.Q. Lima, R.J. Pereira (2023) Population genomics of an Octopus species identify oceanographic barriers and inbreeding patterns. Marine Biology 170: 161. https://doi.org/10.1007/s00227-023-04307-z
Bernstein, J. M., de Souza, H., Murphy, J., Voris, H., Brown, R., Myers, E., ... & Ruane, S. (2023). Phylogenomics of fresh and formalin specimens resolves the systematics of Old World mud snakes (Serpentes: Homalopsidae) and expands biogeographic inference. Bulletin of the Society of Systematic Biologists, 2(1), 1-24.
Galván-Villa, C.M., F.A. Solis-Marin, K. Lopez, J. Cobb, L. Díaz-Pérez, C.R. Rezende-Ventura, N. Slivak, C.T. Ford and D.A. Janies. (2023). Occurrence of the Indo‑West Pacific starfish Luidia magnifica (Echinodermata: Asteroidea) in the Mexican Pacific and a possible introduction to the Caribbean region. Marine Biodiversity, 54(1),1-16. http://dx.doi.org/10.1007/s12526-023-01397-2
Goodman, S. M., Fisher, B. L., Glaw, F. & Phillipson, P. B. 2023. Species new to science described from Marojejy since 1988: An extraordinary area of discovery at one of Madagascar’s most biodiversity rich protected areas. In A floral and faunal inventory of the Parc National de Marojejy: Altitudinal gradient and temporal variation, eds. S. M. Goodman & M. J. Raherilalao. Malagasy Nature, 17: 41-72. Published 1 October 2023
Marshall, V. M., McLaughlin, P. J., Mengue, J. E., Bindang, L. J., Scheinberg, L. A., Irian, C., Bell, R. C., & Becker, C. G. (2023). Fungal pathogen infection intensity associated with reproductive mode and elevation in an afrotropical anuran community. Herpetological Journal, 33(4), 103-110.
Nachman, M., …L.A. Rocha…, 119 co-authors (2023) Specimen collection is essential for modern science. PLOS Biology, 21(11): e3002318. https://doi.org/10.1371/journal.pbio.3002318
Paz-Sedano, S., I. Ekimova, D. Smirnoff, T.M. Gosliner and M. Pola. (2023). Shedding light on a species complex within the genus Goniodoridella Pruvot-Fol, 1933 (Nudibranchia: Goniodorididae), with the description of three new species. Journal of Molluscan Studies, 89:eyad020, 1-13. https://doi.org/10.1093/mollus/eyad020
Paz-Sedano, S., J. Moles, D. Smirnoff, T.M. Gosliner and M. Pola. (2023). A combined phylogenetic strategy illuminates the evolution of Goniodorididae nudibranchs (Mollusca, Gastropoda, Heterobranchia). Molecular Phylogenetics and Evolution, 192(2024): 107990. https://doi.org/10.1016/j.ympev.2023.107990
Rivera, D., Zegarra, J. P., Figuerola-Hernández, C. E., Herrera-Giraldo, J. L., Hernandez-Arocho, N., Hostetter, N. J., Collazo, J., & Bell, R. C. (2023). Contemporary record and photographs of the rarely seen and poorly known Mona Blindsnake, Antillotyphlops monensis (Schmidt, 1926), with comments on its ecology and conservation. Herpetology Notes, 16, 915-918.