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Kahanamoku-Meyer SS, Samuels-Fair M, Kamel SM, Stewart D, Wu B, Kahn LX, Titcomb M, Mei YA, Bridge RC, Li YS, Sinco C, Moreno J, Epino JT, Gonzalez-Marin G, Latt C, Fergus H, Duijnstee IAP, Finnegan S. An 800-year record of benthic foraminifer images and 2D morphometrics from the Santa Barbara Basin. Sci Data 2024; 11:144. [PMID: 38291058 PMCID: PMC10828449 DOI: 10.1038/s41597-024-02934-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 01/09/2024] [Indexed: 02/01/2024] Open
Abstract
The Santa Barbara Basin is an extraordinary archive of environmental and ecological change, where varved sediments preserve microfossils that provide an annual to decadal record of the dynamics of surrounding ecosystems. Of the microfossils preserved in these sediments, benthic foraminifera are the most abundant seafloor-dwelling organisms. While they have been extensively utilized for geochemical and paleoceanographic work, studies of their morphology are lacking. Here we use a high-throughput imaging method (AutoMorph) designed to extract 2D data from photographic images of fossils to produce a large image and 2D shape dataset of recent benthic foraminifera from two core records sampled from the center of the Santa Barbara Basin that span an ~800-year-long interval during the Common Era (1249-2008 CE). Information on more than 36,000 objects is included, of which more than 22,000 are complete or partially-damaged benthic foraminifera. The dataset also includes other biogenic microfossils including ostracods, pteropods, diatoms, radiolarians, fish teeth, and shark dermal denticles. We describe our sample preparation, imaging, and identification techniques, and outline potential data uses.
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Affiliation(s)
- Sara S Kahanamoku-Meyer
- Department of Integrative Biology and Museum of Paleontology, University of California at Berkeley, Berkeley, CA, 94720, USA.
- School of Ocean and Earth Sciences and Technology, University of Hawai'i at Mānoa, Honolulu, HI, 96822, USA.
| | - Maya Samuels-Fair
- Department of Integrative Biology and Museum of Paleontology, University of California at Berkeley, Berkeley, CA, 94720, USA
- School of Ocean and Earth Sciences and Technology, University of Hawai'i at Mānoa, Honolulu, HI, 96822, USA
| | - Sarah M Kamel
- Department of Psychology, University of California at Berkeley, Berkeley, CA, 94720, USA
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA, 94720, USA
| | - Da'shaun Stewart
- Department of Environmental Science, Policy, and Management, University of California at Berkeley, Berkeley, CA, 94720, USA
| | - Bryan Wu
- Department of Electrical Engineering and Computer Sciences, University of California at Berkeley, Berkeley, CA, 94720, USA
| | - Leah X Kahn
- Department of Integrative Biology and Museum of Paleontology, University of California at Berkeley, Berkeley, CA, 94720, USA
- Department of Earth and Planetary Science, University of California at Berkeley, Berkeley, CA, 94720, USA
- School of Ocean and Earth Sciences and Technology, University of Hawai'i at Mānoa, Honolulu, HI, 96822, USA
| | - Max Titcomb
- Scripps Institution of Oceanography, University of California at San Diego, La Jolla, CA, 92093, USA
| | - Yingyan Alyssa Mei
- Department of Integrative Biology and Museum of Paleontology, University of California at Berkeley, Berkeley, CA, 94720, USA
- School of Ocean and Earth Sciences and Technology, University of Hawai'i at Mānoa, Honolulu, HI, 96822, USA
| | - R Cheyenne Bridge
- Department of Earth and Planetary Science, University of California at Berkeley, Berkeley, CA, 94720, USA
- College of Chemistry, University of California at Berkeley, Berkeley, CA, 94720, USA
| | - Yuerong Sophie Li
- Department of Environmental Science, Policy, and Management, University of California at Berkeley, Berkeley, CA, 94720, USA
| | - Carolina Sinco
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA, 94720, USA
| | - Julissa Moreno
- Department of Environmental Science, Policy, and Management, University of California at Berkeley, Berkeley, CA, 94720, USA
| | - Josef T Epino
- Department of Sociology, University of California at Berkeley, Berkeley, CA, 94720, USA
| | - Gerson Gonzalez-Marin
- Department of Environmental Science, Policy, and Management, University of California at Berkeley, Berkeley, CA, 94720, USA
- Department of Earth and Planetary Science, University of California at Berkeley, Berkeley, CA, 94720, USA
| | - Chloe Latt
- Department of Environmental Science, Policy, and Management, University of California at Berkeley, Berkeley, CA, 94720, USA
| | - Heather Fergus
- Department of Environmental Science, Policy, and Management, University of California at Berkeley, Berkeley, CA, 94720, USA
| | - Ivo A P Duijnstee
- Department of Integrative Biology and Museum of Paleontology, University of California at Berkeley, Berkeley, CA, 94720, USA
- School of Ocean and Earth Sciences and Technology, University of Hawai'i at Mānoa, Honolulu, HI, 96822, USA
| | - Seth Finnegan
- Department of Integrative Biology and Museum of Paleontology, University of California at Berkeley, Berkeley, CA, 94720, USA
- School of Ocean and Earth Sciences and Technology, University of Hawai'i at Mānoa, Honolulu, HI, 96822, USA
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Klinkenbuß D, Metz O, Reichert J, Hauffe T, Neubauer TA, Wesselingh FP, Wilke T. Performance of 3D Morphological Methods in the Machine Learning Assisted Classification of Closely Related Fossil Bivalve Species of the Genus Dreissena. MALACOLOGIA 2020. [DOI: 10.4002/040.063.0109] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Affiliation(s)
- Denise Klinkenbuß
- Department of Animal Ecology & Systematics, Justus Liebig University Giessen, Heinrich-Buff-Ring 26, 35392 Giessen, Germany
| | - Olivia Metz
- Department of Animal Ecology & Systematics, Justus Liebig University Giessen, Heinrich-Buff-Ring 26, 35392 Giessen, Germany
| | - Jessica Reichert
- Department of Animal Ecology & Systematics, Justus Liebig University Giessen, Heinrich-Buff-Ring 26, 35392 Giessen, Germany
| | - Torsten Hauffe
- Department of Animal Ecology & Systematics, Justus Liebig University Giessen, Heinrich-Buff-Ring 26, 35392 Giessen, Germany
| | - Thomas A. Neubauer
- Department of Animal Ecology & Systematics, Justus Liebig University Giessen, Heinrich-Buff-Ring 26, 35392 Giessen, Germany
| | - Frank P. Wesselingh
- Naturalis Biodiversity Center, P.O. Box 9517, 2300 RA Leiden, The Netherlands
| | - Thomas Wilke
- Department of Animal Ecology & Systematics, Justus Liebig University Giessen, Heinrich-Buff-Ring 26, 35392 Giessen, Germany
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