OVert: Open Exploration of Vertebrate Diversity in 3D
- 1 Digitization TCN: oVert: Open Exploration of Vertebrate Diversity in 3D
- 1.1 Project Summary
- 1.2 Current Research
- 1.3 Project Websites & Social Media
- 1.4 Protocols & Workflows
- 1.5 Project Leadership
- 1.6 Project Collaborators
- 1.6.1 University of Florida
- 1.6.2 Academy of Natural Sciences of Drexel University
- 1.6.3 California Academy of Sciences
- 1.6.4 Cornell University
- 1.6.5 Duke University
- 1.6.6 Field Museum of Natural History
- 1.6.7 Harvard University
- 1.6.8 Louisiana State University & Agricultural and Mechanical College
- 1.6.9 Texas A&M University
- 1.6.10 University of California, Berkeley
- 1.6.11 University of California, San Diego, Scripps Institution of Oceanography
- 1.6.12 University of Chicago
- 1.6.13 University of Kansas
- 1.6.14 University of Michigan
- 1.6.15 University of Texas, Austin
- 1.6.16 University of Washington
- 1.6.17 Virginia Institute of Marine Science
- 1.6.18 Yale University, Peabody Museum of Natural History
- 1.7 Unfunded Collaborating Institutions
- 1.8 Publications
- 1.9 Professional Presentations
- 1.10 Other project documentation
- 1.11 Educational Resources
- 2 PENs
- 2.1 Digitization PEN: oMEGA - Online Metrology of Extant Giant Animals for the oVert TCN
- 2.2 Functional Quantitative Characters for Ecology and Evolution (FuncQEE)
- 2.3 The oUTCT PEN: Outwardly Mobilizing the UTCT Vertebrate Archive for Research and Training
- 2.4 CryptoVert - Digitizing small-bodied cryptobenthic fishes for the oVertTCN
- 2.5 GalapaGateway: Unlocking Model Evolutionary Systems for Research and Education
- 2.6 oBird: 3D Photogrammetry of Museum Specimens for Phenomics across the Avian Tree of Life
- 2.7 oMeso: Opening Mesoamerican Herpetofaunal Diversity to Whole Phenome Imaging
Digitization TCN: oVert: Open Exploration of Vertebrate Diversity in 3D
The oVert (openVertebrate) Thematic Collection Network (TCN) will generate and serve high-resolution digital three-dimensional data for internal anatomy across vertebrate diversity. At a network of digitization centers across the US, we will CT-scan >20,000 fluid-preserved specimens representing >80% of the living genera of vertebrates. This will provide broad coverage for exploration and research on all major groups of vertebrates. We will also generate contrast-enhanced scans to reveal soft tissues and organs for a majority of the living vertebrate families. This collection of digital imagery and three-dimensional volumes will be open for exploration, download, and use to address questions related to the discovery of new species, documenting patterns of anatomical diversity and growth, and testing hypotheses of function and evolution. These new media will provide unprecedented global access to valuable specimens in US museum collections. Our network of leading US vertebrate collections will develop best practices and guidelines for high-throughput CT-scanning, including efficient workflows, preferred resolutions, and archival formats that optimize the variety of downstream applications. We will train museum specialists on the generation, curation, and distribution of 3D data, researchers in using 3D anatomical data, and high school and undergraduate students in the tools for creating 3D anatomical models. To drive the use of these digital specimens by K12 STEM educators, we will conduct teacher-driven workshops that generate freely available lesson plans focused on specific science standards that are based on digital and printed 3D models of specimens in US museum collections.
Data generated by oVert will serve as a catalyst for diverse research projects focused on understanding the vertebrate morphological diversity and dramatically increase the accessibility of specimens housed in US scientific collections. These anatomical phenotypes represent a common currency that facilitates integration across the fields of taxonomy, evolution, developmental biology, comparative physiology, functional anatomy, paleontology, and ecology. We will use x-ray computed tomography (CT) scanning to generate high-resolution digital anatomical data, represented as both 2D image stacks and 3D volumes and surfaces, which can be distributed globally through the on-line data portal MorphoSource. With these 3D digital specimens, US and international research communities will be able to (1) diagnose, describe, and infer patterns of relationships among both living and extinct vertebrates, (2) test hypotheses of morphological evolution such as patterns of disparity, modularity, and phenotype-environment correlations, (3) develop structure-function models for testing hypotheses about morphological adaptations related to, e.g., feeding and locomotion, and (4) explore relationships between brain and nervous system anatomy and both sensory and musculoskeletal function. We will upgrade the interface and functionality of MorphoSource, an on-line data depository for 3D data of biological specimens, improving its capacity to explore media, capture standardized metadata, ingest legacy data from previous and existing projects, supply media information to data aggregators including iDigBio, and engage educators and students. We will support training workshops both on-site at participating institutions and national society meetings of scientists and educators.
Proposed research uses of data generated through oVert project include: 1) diagnose, describe, and infer patterns of relationships among both living and extinct vertebrates 2) test hypotheses of morphological evolution such as patterns of disparity, modularity, and phenotype-environment correlations 3) develop structure-function models for testing hypotheses about morphological adaptations related to, e.g., feeding and locomotion 4) explore intraspecific phenotypic diversity related to spatial variation and ontogenetic transformations 5) explore relationships between brain and nervous system anatomy and both sensory and musculoskeletal function.
Project Websites & Social Media
MorphoSource (on-line depository for digital anatomical data, including from oVert TCN): https://www.morphosource.org/
oVert FAQs: https://www.floridamuseum.ufl.edu/overt/
oVert on Twitter: https://twitter.com/hashtag/overttcn
oVert on YouTube: https://www.youtube.com/channel/UCdj7bJFeKk10WNmc5R0cq_A/featured
Presentations from "Integrating Institutional Archives with Disciplinary Web Repositories" (Duke University, January 23-24, 2020): https://www.idigbio.org/wiki/index.php/Integrating_Institutional_Archives_with_Disciplinary_Web_Repositories
Protocols & Workflows
Blackburn, David. Introduction to oVert. Museum of Comparative Zoology, Harvard University, March 2018. (condensed version). PDF
Boyer, D. oVert MorphoSource Uploading Guide. PDF
Stanley, Edward. Introduction to CT scanning. Computed Tomography in the Analysis of Natural History, Morphology, and Evolution Workshop, University of Texas, Arlington, January 2018. PDF
Stanley, Edward. X-ray basics. Computed Tomography in the Analysis of Natural History, Morphology, and Evolution Workshop, University of Texas, Arlington, January 2018. PDF
Stanley, Edward. CT scanning basics. Computed Tomography in the Analysis of Natural History, Morphology, and Evolution Workshop, University of Texas, Arlington, January 2018. PDF
Summers, Adam. How to Scan All Fishes. https://bit.ly/HowToScanAllFishes
oVert Reference Specimens on MorphoSource: https://www.morphosource.org/Detail/ProjectDetail/Show/project_id/477
MorphoSource Tutorials on YouTube: https://www.youtube.com/playlist?list=PLP5eOaQsoxJGGa8wx6PgFBgBUXMgx5unW
Project sponsor: University of Florida (NSF Award 1701714)
Principal Investigator (PI): David Blackburn
University of Florida (lead)
University of Florida
David C. Blackburn, lead PI, Florida Museum of Natural History, University of Florida (NSF Award 1701714)
Jonathan I. Bloch, CoPI, Florida Museum of Natural History, University of Florida
Gavin J.P. Naylor, CoPI, Florida Museum of Natural History , University of Florida
Edward L. Stanley, CoPI, Florida Museum of Natural History, University of Florida
Academy of Natural Sciences of Drexel University
Mark H. Sabaj, PI, Ichthyology, Academy of Natural Sciences of Drexel University (NSF Award 1701943)
California Academy of Sciences
Luiz A. Rocha, PI, Department of Ichthyology, California Academy of Sciences (NSF Award 1701870)
John (Jack) P. Dumbacher, CoPI, Department of Ornithology and Mammalogy, California Academy of Sciences
Casey B. Dillman, PI, Cornell University Museum of Vertebrates, Cornell University (NSF Award 1700908)
David W. Winkler, CoPI, Cornell University Museum of Vertebrates, Cornell University
Amy R. McCune, CoPI, Cornell University Museum of Vertebrates, Cornell University
William E. Bemis, CoPI, Cornell University Museum of Vertebrates, Cornell University
Douglas M. Boyer, CoPI on UF subaward, Department of Evolutionary Anthropology, Duke University
Field Museum of Natural History
John M. Bates, PI, Science and Education, Field Museum of Natural History (NSF Award 1702421 )
Alan Resetar, CoPI, Science and Education, Field Museum of Natural History
Ben D. Marks, CoPI, Science and Education, Field Museum of Natural History
James Hanken, PI, Museum of Comparative Zoology, Harvard University (NSF Award 1702263)
Louisiana State University & Agricultural and Mechanical College
Christopher C. Austin, PI, Museum of Natural Science, Louisiana State University & Agricultural and Mechanical College (NSF Award 1701402)
Jake Esselstyn, CoPI, Museum of Natural Science, Louisiana State University & Agricultural and Mechanical College
Texas A&M University
Kevin W. Conway, PI, Department of Wildlife and Fisheries Science and Biodiversity Research and Teaching Collections, Texas A&M University (NSF Award 1702442)
Heather L. Prestridge, CoPI, Department of Wildlife and Fisheries Science and Biodiversity Research and Teaching Collections, Texas A&M University
Sarah Potvin, CoPI, University Libraries, Texas A&M University
University of California, Berkeley
Carol L. Spencer, PI, Museum of Vertebrate Zoology, University of California, Berkeley (NSF Award 1701797)
Michelle S. Koo, CoPI, Museum of Vertebrate Zoology, University of California, Berkeley
University of California, San Diego, Scripps Institution of Oceanography
Philip A. Hastings, PI, Marine Vertebrate Collection, Scripps Institution of Oceanography, University of California San Diego (NSF Award 1701737)
Benjamin Frable, CoPI, Marine Vertebrate Collection, Scripps Institution of Oceanography, University of California San Diego
University of Chicago
Zhe-Xi Luo, CoPI, Research Associate in Integrative Research Center, and Department of Organismal Biology and Anatomy, University of Chicago
University of Kansas
Richard E. Glor, PI, Biodiversity Institute, University of Kansas (NSF Award 1701932)
A. Townsend Peterson, Co-PI, Biodiversity Institute, University of Kansas
Robert G. Moyle, CoPI, Biodiversity Institute, University of Kansas
University of Michigan
Daniel L. Rabosky, PI, UM Museum of Zoology, University of Michigan (NSF Award 1701713)
Priscilla K. Tucker, Co-PI, UM Museum of Zoology (Director), University of Michigan
Alison R. Davis Rabosky, Senior Personnel, UM Museum of Zoology, University of Michigan
Cody W. Thompson, Senior Personnel, UM Museum of Zoology, University of Michigan
University of Texas, Austin
David C. Cannatella, PI, Department of Integrative Biology, University of Texas, Austin (NSF Award 1701516)
Travis J. LaDuc, CoPI, Department of Integrative Biology, University of Texas, Austin
Dean Hendrickson, Senior Personnel, Department of Integrative Biology, University of Texas, Austin
University of Washington
Luke M. Tornabene, PI, Burke Museum of Natural History and Culture, University of Washington (NSF Award 1701665)
Sharlene Santana, CoPI, Burke Museum of Natural History and Culture, University of Washington
Adam P. Summers, CoPI, Friday Harbor Laboratories, University of Washington
Katherine Maslenikov, Senior Personnel, Burke Museum of Natural History and Culture, University of Washington
Virginia Institute of Marine Science
Sarah K. Huber, PI, Nunnally Ichthyology Collection, Virginia Institute of Marine Science (NSF Award 1702143)
Eric J. Hilton, CoPI, Nunnally Ichthyology Collection and Fisheries Science, Virginia Institute of Marine Science
Yale University, Peabody Museum of Natural History
Gregory J. Watkins-Colwell, PI, Peabody Museum of Natural History, Yale University (NSF Award 1701769)
Bhart-Anjan Bhullar, CoPI, Department of Geology & Geophysics, Peabody Museum of Natural History, Yale University
Unfunded Collaborating Institutions
Carnegie Museum of Natural History
Smithsonian National Museum of Natural History
Bardua, C., Fabre, A.C., Bon, M., Das, K., Stanley, E.L., Blackburn, D.C., & Goswami, A. (2020). Evolutionary integration of the frog cranium. Evolution, 74, 1200–1215.
Blackburn, D.C., R.M. Keeffe, M.C. Vallejo-Pareja, and J. Vélez-Juarbe. (2020). The earliest record of Caribbean frogs: a fossil coquí from Puerto Rico. Biology Letters, 16, 20190947.
Bock, A., Doraiswamy, H., Summers, A., & Silva, C. (2018). Topoangler: Interactive topology-based extraction of fishes. IEEE transactions on visualization and computer graphics, 24(1), 812-821.
Boyer, D.M. & Harrington, A.R. (2018). Scaling of bony canals for encephalic vessels in euarchontans: Implications for the role of the vertebral artery and brain metabolism. Journal of Human Evolution, 114, 85-101.
Boyer, D.M., and A.R. Harrington. (2019). New estimates of blood flow rates in the vertebral artery of euarchontans and their implications for encephalic blood flow scaling: a response to Seymour and Snelling (2019). Journal of Human Evolution, 128, 93–98.
Boyer, D.M., Yapuncich, G.S., Dunham, N.T., McNamara, A., Shapiro, L.J., Hieronymus, T.L., & Young, J.W. (2019). My branch is your branch: Talar morphology correlates with relative substrate size in platyrrhines at Tiputini Biodiversity Station, Ecuador. Journal of Human Evolution, 133, 23-31.
Buser, T.J., O.F. Boyd, Á. Cortés, C.M. Donatelli, M.A. Kolmann, J.L. Luparell, J.A. Pfeiffenberger, B.L. Sidlauskas, and A.P. Summers. (2020). The natural historian’s guide to the CT galaxy: step-by-step instructions for preparing and analyzing computed tomographic (CT) data using cross-platform, open access software. Integrative Organismal Biology, 2, obaa009.
Buser, T.J., Finnegan, D.L., Summers, A.P., & Kolmann, M.A. (2019). Have niche, will travel. New means of linking diet and ecomorphology reveals niche conservatism in freshwater cottoid fishes. Integrative Organismal Biology, 1, obz023.
Conway, K.W, King, C. D. Summers A.P. Kim, D. Hastings, P.A. Moore, G.I. Iglésias, S.P Erdmann, M.V., Short, G. Fujiwara, K. Trnski, T. Voelker, G. and Rüber L. (2020). Molecular phylogenetics of the clingfishes (Teleostei: Gobiesocidae) – Implications for Classification. Copeia, in press.
Conway, K.W., Mateos, M., & Vrijenhoek, R.C. (2019). A new species of the live-bearing fish genus Poeciliopsis from northern Mexico (Cyprinodontiformes, Poeciliidae). ZooKeys, 883, 91.
Conway, K.W., Moore, G.I., & Summers, A.P. (2019). A new genus and two new species of miniature clingfishes from temperate southern Australia (Teleostei, Gobiesocidae). ZooKeys, 864, 35.
Conway, K.W., Stewart, A.L., & Summers, A.P. (2018). A new species of sea urchin associating clingfish of the genus Delllichthys from New Zealand (Teleostei, Gobeisocidae). ZooKeys, 740, 77–95.
Conway, K.W., Stewart, A.L., & Summers, A.P. (2018). A new genus and species of clingfish from the Rangitāhua Kermadec Islands of New Zealand (Teleostei: Gobiesocidae). ZooKeys, 786, 75–104.
Corn, K.A., Farina, S.C., Summers, A.P., & Gibb, A.C. (2018). Effects of organism and substrate size on burial mechanics of English sole, Parophrys vetulus. Journal of Experimental Biology, 221, jeb176131.
Crawford, C.H., Z.S. Randall, P.B. Hart, L.M. Page, P. Chakrabarty, A. Suvarnaraksha, and B.E. Flammang. (2020). Skeletal and muscular pelvic morphology of hillstream loaches (Cypriniformes: Balitoridae). Journal of Morphology, DOI:10.1002/jmor.21247.
Early, C.M., R.C. Ridgely, and L.M. Witmer. (2020). Beyond endocasts: using predicted brain-structure volumes of extinct birds to assess neuroanatomical and behavioral inferences. Diversity, 12, 34.
Fabre, A.-C., Bardua, C., Bon, M., Clavel, J., Felice, R.N., Streicher, J.W., Bonnel, J., Stanley, E.L., Blackburn, D.C., & Goswami, A. (2020). Metamorphosis shapes cranial diversity and rate of evolution in salamanders. Nature Ecology & Evolution, https://doi.org/10.1038/s41559-020-1225-3.
Farina, S.C.,Knope, M.L., Corn, K.A., Summers, A.P., & Bemis, W.B. (2019). Functional coupling in the evolution of suction feeding and gill ventilation of sculpins (Perciformes: Cottoidei), Integrative and Comparative Biology, icz022.
Ferry, L.A., E.W. Paig-Tran, A.P. Summers, and K.F. Liem. (2019). Extreme premaxillary protrusion in the king-of-the-salmon, Trachipterus altivelis. Journal of Morphology, 280, 1865–1870.
Fried, P., Woodward, J., Brown, D., Harvell, D., & Hanken, J. (2020). 3D scanning of antique glass by combining photography and computed tomography. Digital Applications in Archaeology and Cultural Heritage, 18, e00147.
Griffing, A.H., Sanger, T.J., Daza, J.D., Nielsen, S.V., Pinto, B.J., Stanley, E.L., & Gamble, T. (2019). Embryonic development of a parthenogenetic vertebrate, the mourning gecko (Lepidodactylus lugubris). Developmental Dynamics, 248, 1070–1090.
Hall, K.C., Hundt, P.J., Swenson, J.D., Summers, A.P., & Crow, K.D. (2018). The evolution of underwater flight: The redistribution of pectoral fin rays, in manta rays and their relatives (Myliobatidae). Journal of Morphology, 279,1155–1170.
Harrington, A.R., Kuzawa, C.W., & Boyer, D.M. (2019). Carotid foramen size in the human skull tracks developmental changes in cerebral blood flow and brain metabolism. American Journal of Physical Anthropology, 169, 161–169.
Hastings, P. A., Eytan, R. and Summers, A.P. (2020). A new species of Acanthemblemaria from the Caribbean coast of South America with notes on Acanthemblemaria johnsoni (Teleostei: Chaenopsidae). Zootaxa, 4816, 209–216.
Hedrick, B.P., Heberling, J.M., Meineke, E.K., Turner, K.G., Grassa, C.J., Park, D.S., Kennedy, J., Clarke, J.A., Cook, J.A., Blackburn, D.C. & Edwards, S.V. (2020). Digitization and the future of natural history collections. BioScience, 70, 243–251.
Hilton, E.J., G.J. Watkins-Colwell, & S.K. Huber. (2020). The expanding role of natural history collections. Copeia, in press.
Hoke, K.L., Adkins-Regan, E., Bass, A.H., McCune, A.R., & Wolfner, M.F. (2019). Co-opting evo-devo concepts for new insights into mechanisms of behavioural diversity. Journal of Experimental Biology, 222, jeb190058.
Hongjamrassilp, W., Summers, A.P., & Hastings, P.A. (2018). Heterochrony in fringeheads (Neoclinus) and amplification of an extraordinary aggressive display in the Sarcastic Fringehead (Teleostei: Blenniiformes). Journal of Morphology, 279, 626–635.
Huie, J.M., Summers, A.P., & Kolmann, M.A. (2019). Body shape separates guilds of rheophilic herbivores (Myleinae: Serrasalmidae) better than feeding morphology. Proceedings of the Academy of Natural Sciences of Philadelphia, 166, 1-15.
Huie, J.M., Thacker, C., & Tornabene, L. (2019). Co‐evolution of cleaning and feeding morphology in the western Atlantic and eastern Pacific gobies. Evolution, 74, 419–433.
Hulsey, C.D., K.E. Cohen, Z. Johanson, N. Karagic, A. Meyer, C.T. Miller, A. Sadier, A.P. Summers, and G.J. Fraser. (2020). Grand challenges in comparative tooth biology. Integrative & Comparative Biology, in press. https://doi.org/10.1093/icb/icaa038
Keeffe, R., and D.C. Blackburn. (2020). Comparative morphology of the humerus in forward-burrowing frogs. Biological Journal of the Linnean Society, in press.
Kolmann, M.A. K.E. Cohen, K. Bemis, A.P. Summers, Adam, F. Irish, and L.P. Hernandez (2019). Tooth and consequences: heterodonty and dental replacement in piranhas and pacus (Serrasalmidae). Evolution and Development, 21, 247-262.
Kolmann, M.A., Huie, J.M., Evans, K., & Summers, A.P. (2018). Specialized specialists and the narrow niche fallacy: a tale of scale-feeding fishes. Royal Society Open Science, 5, 171581.
Kruppert, S., Chu, F., Stewart, M.C., Schmitz, L., & Summers, A.P. (2020) Ontogeny and potential function of poacher armor (Actinopterygii: Agonidae). Journal of Morphology, in press. DOI: 10.1002/jmor.21223.
Leão, M.D.V., Carvalho, T.P., Reis, R.E., & Wosiacki, W.B. (2019). A new species of Pseudobunocephalus Friel, 2008 (Siluriformes: Aspredinidae) from the lower Tocantins and Mearim river drainages, North and Northeast of Brazil. Zootaxa, 4586, 109–126.
Lewis, Z.R., Dorantes, J.A., & Hanken, J. (2018). Expression of a novel surfactant protein gene is associated with sites of extrapulmonary respiration in a lungless salamander. Proceedings of the Royal Society B, 285, 20181589.
Lundberg, J.G., Hendrickson, D.A., Luckenbill, K.R. & Arce, M. (2017). Satan's skeleton revealed: a tomographic and comparative osteology of Satan eurystomus, the subterranean Widemouth Blindcat (Siluriformes, Ictaluridae). Proceedings of the Academy of Natural Sciences of Philadelphia, 165, 117-173.
Luparell. J.L., A.P. Summers, and T.J Buser. (2019). Digitizing North America’s fishes. American Currents, 44,14-16.
Marramà, G., & Carnevale, G. (2017). The relationships of "Gasteroclupea branisai" Signeux, 1964, a freshwater double-armored herring (Clupeomorpha, Ellimmicthyiformes) from the Late Cretaceous-Paleocene of South America. Historical Biology, 29, 904-917.
Matthews, T., Keeffe, R., & Blackburn, D.C. (2019) An identification guide to fossil frog assemblages of southern Africa based on ilia of extant taxa. Zoologischer Anzeiger, 283, 46–57.
Page, L.M., J.M. Pfeiffer, S. Suksri, Z.S. Randall, and D.A. Boyd (2020). Variation in the Arrow Loach, Nemacheilus masyae (Cypriniformes: Nemacheilidae), in mainland southeast Asia with description of a new species. Copeia, 108, 392–402.
Page, L.M., Ray, B.C., Tongnunui, S., Boyd, D.A., & Randall, Z.S. (2019). Garra surinbinnani, a new species of labeonine from the Mae Khlong basin of Thailand (Teleostei: Cyprinidae). Ichthyological Exploration of Freshwaters, 1–15. http://doi.org/10.23788/IEF-1117.
Paluh, D.J., Stanley, E.L., & Blackburn, D.C. (2020). Evolution of hyperossification expands skull diversity in frogs. Proceedings of the National Academy of Sciences USA, 117, 8554-8562.
Parra Olea, G., M.G. Garcia-Castillo, S.M. Rovito, J. Maisano, J. Hanken, & D.B. Wake. (2020). Descriptions of five new species of the salamander genus Chiropterotriton (Caudata: Plethodontidae) from eastern Mexico and the status of three currently recognized taxa. PeerJ, 8, e8800.
Prestridge, H.L., & Conway, K.L. (2019). TCWC – The Collection of Fishes at the Biodiversity Research and Teaching Collections, Texas A&M University. Boletim Sociedade Brasileira de Ictiologia, 129, 121-124.
Robins, R.H., Brown, M.E., & Crutchfield, R.A. (2020). Identification of acara (Cichlidae: Cichlasoma) established in Florida, USA. BioInvasions Record, 9(1), 133-145.
Rutledge, K.M., Summers, A.P., & Kolmann, M.A. (2019). Killing them softly: Ontogeny of jaw mechanics and stiffness in mollusk‐feeding freshwater stingrays. Journal of Morphology.
Sabaj, M.H. (2020). Codes for natural history collections in ichthyology and herpetology. Copeia, 108 (3), 593–669.
Stocker, M.R., Nesbitt, S.J., Kligman, B.T., Paluh, D.J., Marsh, A.D., Blackburn, D.C., & Parker, W.G. (2019). The earliest equatorial record of frogs from the Late Triassic of Arizona. Biology Letters, 15(2), 20180922.
Štrus, J., M. Tušek-Žnidarič, U. Repnik, A. Blejec, and A.P. Summers (2019) Microscopy of crustacean cuticle: formation of a flexible extracellular matrix in moulting sea slaters Ligia pallasii. Journal of the Marine Biological Association of the United Kingdom, 99, 857-865.
Vigle, G.O., Coloma, L.A., Santos, J.C., Hernandez-Nieto, S., Ortega-Andrade, H.M., Paluh, D.J., & Read, M. (2020). A new species of Leucostethus (Anura: Dendrobatidae) from the Cordillera Mache-Chindul in northwestern Ecuador, with comments on similar Colostethus and Hyloxalus. Zootaxa, 4896, 342–372.
Vijayakumar, S.P., Pyron, R.A., Dinesh, K.P., Torsekar, V.R., Srikanthan, A.N., Swamy, P., Stanley, E.L., Blackburn, D.C., & Shanker, K. (2019). A new ancient lineage of frog (Anura: Nyctibatrachidae: Astrobatrachinae subfam. nov.) endemic to the Western Ghats of Peninsular India. PeerJ, 7.
Watkins-Colwell, G.J., Love, K., Randall, Z., Boyer, D.M., Winchester, J.M., Stanley, E.L., & Blackburn, D.C. (2018). The Walking Dead: status report, data workflow and best practices of the oVert Thematic Collections Network. Biodiversity Information Science and Standards, 2, e26078.
Weinell, J.L., Paluh, D.J., Siler, C.D., & Brown, R.M. (2020). A new, miniaturized genus and species of snake (Lamprophiidae: Cyclocorinae) from the Philippines. Copeia, 108, 907–923.
Weinell, J.L., Paluh, D.J., Singh, A.L., Blackburn, D.C., & Brown, R.M. (2019). Myersophis alpestris (Myers' Mountain Snake. Reproduction. Herpetological Review, 50, 164-165.
Westeen, E.P., Durso, A.M., Grundler, M.C., Rabosky, D.L., & Rabosky, A.R. (2020). What makes a fang? Phylogenetic and ecological controls on tooth evolution in rear-fanged snakes. BMC Evolutionary Biology, 20, 80.
Yapuncich, G.S., Feng, H.J., Dunn, R.H., Seiffert, E.R., & Boyer, D.M. (2019). Vertical support use and primate origins. Scientific reports, 9, 1-10.
Yapuncich, G.S., A.D. Kemp, D.M. Griffith, J.T. Gladman, E. Ehmke, and D.M. Boyer. (2019). A digital collection of rare and endangered lemurs and other primates from the Duke Lemur Center. PLoS ONE, 14, e0219411.
Yopak, K.E., Carrier, J.C., & Summers, A.P. (2018). Imaging technologies in the field and laboratory. In Shark Research: Emerging Technologies and Applications for the Field and Laboratory. J.C. Carrier & M.R. Heithaus, eds.
Arce, H.M. & K. Innamorato. Anatomical variation of mandibular and hyoid musculature of Chiapas catfishes (Lacantunidae, Siluriformes). Joint Meeting of Ichthyologists and Herpetologists, Snowbird, UT. July 2019.
Blackburn, D.C. 3D Anatomical Data for All: The oVert Thematic Collection Network. Society of Integrative and Comparative Biology, San Francisco, CA. January 2018.
Blackburn, D.C. Digital specimens and the future of natural history collections. North American Meeting of Tomography for Scientific Advancement (ToScA), Gainesville, FL. March 2019.
Blackburn, D.C. Digital specimens and the future of natural history collections. Congresso Brasileiro de Herpetologia, Campinas, Brazil. July 2019.
Blackburn, D.C. Blackburn, D.C. Digital specimens and the future of natural history collections. Museum of Vertebrate Zoology, University of California-Berkeley. October 2020. https://www.youtube.com/watch?v=8-4fG_oSxNg
Blackburn, D., C. Austin, W. Bemis, D. Cannatella, K. Conway, A. Davis Rabosky, C. Dillman, B. Frable, R. Glor, J. Hanken, P. Hastings, D. Hendrickson, E. Hilton, S. Huber, M. Koo, T. LaDuc, K. Maslenikov, A. McCune, H. Prestridge, D. Rabosky, Z. Randall, A. Resetar, L. Rocha, M. Sabaj, C. Spencer, A. Summers, L. Tornabene, G. Watkins- Colwell, L. Welton, E. Stanley. The oVert Thematic Collections Network. Joint Meeting of Ichthyologists and Herpetologists, Rochester, NY. July 2018.
Blackburn, D.C., J.I. Bloch, Z. Luo, E.L. Stanley, O. Takano. The oVert thematic collections network: 3D anatomical data for nearly every living vertebrate genus. Society of Vertebrate Paleontology, Albuquerque, NM. October 2018.
Bemis, K.E. & E.J. Hilton. Tooth development, attachment and replacement in the longnose lancefish, Alepisaurus ferox. Society of Intergrative and Comparative Biology, Tampa, FL. January 2019.
Bemis, K.E., J. Tyler, E. Stanley, E.J. Hilton. Dentition of living and fossil porcupinefishes (Tetraodontiformes: Diodontidae) studied using CT scanning: implication for systematics of isolated fossil jaws. Joint Meeting of Ichthyologists and Herpetologists, Snowbird, UT. July 2019.
Bemis, W.E., K.E. Bemis, J. Tyler, E.J. Hilton. Comparative anatomy and ontogeny of ocean sunfishes (Tetraodontiformes: Tetraodontoidea: Molidae). Joint Meeting of Ichthyologists and Herpetologists, Snowbird, UT. July 2019.
Boyer, D.M., J.M. Winchester, S. Mukherjee, T. McGeary, T. Ryan, D.C. Blackburn. Deposit your data, build a virtual museum: MorphoSource. Society of Vertebrate Paleontology, Albuquerque, NM. October 2018.
Buser, T., B. Sidlauskas, A. Summers. 2D or not 2D? Testing the utility of 2D vs 3D landmarks in geometric morphometrics of the sculpin subfamily Oligocottinae. Joint Meeting of Ichthyologists and Herpetologists, Rochester, NY. July 2018.
Crawford, C., Z. Randall, B. Flammang. These Fins Were Made for Walking: Tetrapodal Morphology of Balitorid Fishes. Joint Meeting of Ichthyologists and Herpetologists, Rochester, NY. July 2018.
Dillman, C.B. Natural history collections as repositories of evolutionary change. Joint Meeting of Ichthyologists and Herpetologists, Snowbird, UT. July 2019.
Early, C.M., J. Bates, S. Baumgart, K. Love, A.T. Peterson, H.L. Prestridge, M. Robbins, G.J. Watkins-Colwell, E.L. Stanley, D.C. Blackburn. Information gaps in digital databases as identified by a multi-institution initiative to digitize avian specimens. iDigBio Digital Data in Biodiversity Conference, New Haven, CT. June 2019.
Early, C.M., A.C. Morhardt, T.P. Cleland, C.M. Milensky, H.F. James. Optimizing diceCT staining protocols to mitigate potential degradation of museum specimens. International Congress of Vertebrate Morphology, Prague, Czech Republic. July 2019.
Evans, A.J., C.D. De Santana, C.B. Dillman. Comparison of Sexually Dimorphic Snout and Tooth Morphology in Sternarchogiton nattereri and Sternarchorhynchus roseni (Gymnotiformes: Apteronotidae). Joint Meeting of Ichthyologists and Herpetologists, Rochester, NY. July 2018.
Gardner, J. & L. Tornabene. Iodine-based contrast-enhancing staining methods for visualization of soft tissues of snailfishes (Family: Liparidae) through CT-Scanning. Joint Meeting of Ichthyologists and Herpetologists, Rochester, NY. July 2018.
Gardner, J. & L. Tornabene. Rolling the dice: diffusible iodine-based contrast-enhanced computed tomography (diceCT) methods for visualization of soft tissues. Annual Meeting of the Gilbert Ichthyological Society, Blue River, OR. October 2018.
Hall, K.C., Hundt, P., Swenson, J., Summers, A., Crow, K.D. The evolution of underwater flight in manta rays and their relatives (Myliobatidae). Experimental Biology, San Diego, CA. April 2018.
Hanken, J. The advent of digital technology and its promise for biodiversity research. iDigBio Digital Data in Biodiversity Research Conference, Berkeley, CA. June 2018.
Hilton, E.J. Fishes and the new golden age of morphology. Gilbert Ichthyological Society, Blue River, OR. October 2018.
Hofmann, M. Web-based delivery and volume visualization of 30TB of high resolution tomography data. 24th International Conference on 3D Web Technology, Los Angeles, CA. July 2019.
Huber, S., K. Maslenikov, A. Williston, E. Hilton, A. Summers, D. Blackburn. oVert Deep Dive: Ontogenetic Series of Fishes. Joint Meeting of Ichthyologists and Herpetologists, Rochester, NY. July 2018.
Jasulevicz, R. & A. Bauer. A Bolder Shoulder: Pectoral Girdle Morphology in Geckos. Joint Meeting of Ichthyologists and Herpetologists, Rochester, NY. July 2018.
Keeffe, R. & D. Blackburn. Comparative Morphology of the Forelimb and Pectoral Girdle in Forward-Burrowing Frogs. Joint Meeting of Ichthyologists and Herpetologists, Rochester, NY. July 2018.
Keeffe, R.M. & D.C. Blackburn. Characterizing forward-burrowing frogs with pectoral girdle and humerus morphology. Society for Integrative and Comparative Biology, Tampa, FL. January 2019.
Keeffe, R.M. & D.C. Blackburn. Comparative morphology of the forelimb and pectoral girdle in forward-burrowing frogs. International Congress of Vertebrate Morphology, Prague, Czech Republic. July 2019.
Moreira, C.R. & K.W. Conway. Do freshwater hatchetfishes (Characiformes: Gasteropelecidae) hear with the top of their heads? Joint Meeting of Ichthyologists and Herpetologists, Snowbird, UT. July 2019.
Olsen, A. & E. Brainerd. An Ancient Throat Expansion Mechanism Functions as an 11-Bar Linkage in Channel Catfish. Joint Meeting of Ichthyologists and Herpetologists, Rochester, NY. July 2018.
Owens, H. & E. Stanley. Anatomy of Sexual Parasitism in Triplewart Sea-Devils (Cryptosaras couesii). Joint Meeting of Ichthyologists and Herpetologists, Rochester, NY. July 2018.
Paluh, D., E. Stanley, D. Blackburn. Convergent Evolution and Function of Hyperossification in Frogs. Joint Meeting of Ichthyologists and Herpetologists, Rochester, NY. July 2018.
Paluh, D.J., L.A. Coloma, D.C. Blackburn. Evolutionary lability in life history, morphology, and performance in Andean marsupial frogs. Society for Integrative and Comparative Biology, Tampa, FL. January 2019.
Randall, Z. oVert: lessons learned from high-throughput scanning across the fishes tree of life. North American Meeting of Tomography for Scientific Advancement (ToScA), Gainesville, FL. March 2019.
Randall, Z., K. Love, E. Stanley, M. Sabaj, L. Page, D. Blackburn. oVert: Lessons learned for high-throughput scanning across the Fishes Tree of Life. Joint Meeting of Ichthyologists and Herpetologists, Snowbird, UT. July 2019.
Sheehy, C., L. Nuñez, M. Fedler, M. Nickerson, D. Blackburn. Progress in the Herpetology Collections at the Florida Museum of Natural History. Joint Meeting of Ichthyologists and Herpetologists, Rochester, NY. July 2018.
Singh, A.L., L.A. Gonzales, D.J. Paluh, D. C. Blackburn. Variation in the bony labyrinth (inner ear) of Anurans. International Congress of Vertebrate Morphology, Prague, Czech Republic. July 2019.
Singh, A.L., R.M. Keeffe, D.C. Blackburn. Tips and fits: tricks to 3D-puzzle making. Society for Integrative and Comparative Biology, Tampa, FL. January 2019.
Singh, A.L., R.M. Keeffe, D.C. Blackburn. Tips and fits: tricks to 3D-puzzle making. International Congress of Vertebrate Morphology, Prague, Czech Republic. July 2019.
Stanley, E.L., C.M. Early, D.J. Paluh, D.C. Blackburn. The oVert thematic collections network: 3D-anatomical data for nearly every living vertebrate genus. International Congress of Vertebrate Morphology, Prague, Czech Republic. July 2019.
Stanley, E., D. Paluh, D. Blackburn. Diversification of dermal armor in squamates. Joint Meeting of Ichthyologists and Herpetologists, Rochester, NY. July 2018.
Summers, A.P. How and why to scan all the vertebrates: open access data as a transformative tool. Experimental Biology, San Diego, CA. April 2018.
Takano, O.M., J.M. Bates, J.P. Dumbacher, B.D. Marks, R.G. Moyle, A.T. Peterson, J. Wieczorek, D.W. Winkler, H.F. James, D.W. Steadman, C.M. Eliason, E.L. Stanley, D.C. Blackburn. Inside the Birds of the World: CT-scanning fluid-preserved bird collections via the oVert Thematic Collections Network. American Ornithological Society, Tucson, AZ. April 2018.
Thompson, C.W., J.I. Bloch, D.M. Boyer, J.P. Dumbacher, J.A. Esselstyn, A.L. Hines, Z.-X. Luo, R.S. Nagesan, G.G. Pandelis, S.E. Santana, E.L. Stanley, P.K. Tucker, K.M. Winchester, D.C. Blackburn. oVert: a collaborative effort to produce 3D data for all vertebrate genera. American Society of Mammalogists, Washington, D.C. June 2019.
Watkins-Colwell, G.J., K. Love, Z. Randall, D.M. Boyer, J.M. Winchester, E.L. Stanley, D.C. Blackburn. The Walking Dead: status report, data workflow and best practices of the oVert Thematic Collections Network. Society for the Preservation of Natural History Collections, Dunedin, New Zealand. August 2018.
Zobek, C., C. Dillman, H. Greene. Comparative Adaptations for Skink Predation in the Genus Lampropeltis. Joint Meeting of Ichthyologists and Herpetologists, Rochester, NY. July 2018.
Other project documentation
Article in Science: http://science.sciencemag.org/content/357/6353/742.summary
Article about the oVert educators workshop: https://www.idigbio.org/content/overt-workshop-3d-vertebrates-museum-shelves-classrooms
Website from the oVert educators workshop, including learning activities: https://www.cpet.ufl.edu/teachers/ssi/ssi-2019/3d-vertebrates/
iDigBio Biodiversity Spotlight of oVert specimen: https://www.idigbio.org/content/june-2019-biodiversity-spotlight
QUBES lesson plan on "Origin and Diversity of Armor in Girdled Lizards": https://qubeshub.org/publications/1846/1
3D models on Sketchfab for education and outreach: https://sketchfab.com/ufherps
Digitization PEN: oMEGA - Online Metrology of Extant Giant Animals for the oVert TCN
This is a Partner to Existing Networks (PEN) award to the Idaho Museum of Natural History to partner with the Open Vertebrate (oVert) Thematic Collections Network (TCN). The oVert TCN is creating high-resolution three-dimensional (3D) data for internal anatomy across the diversity of vertebrate animals. Using computed tomography (CT) scanners at institutional collections across the US, more than 20,000 fluid-preserved specimens will be scanned and made available online for open public use. This PEN complements the oVert TCN program by including vertebrate animals too large to be preserved in fluid or scanned by conventional CT scanners. The oMEGA PEN will use portable surface scanners to provide high-resolution scans of skeletons of large vertebrate animals curated at Harvard, Berkeley, and California Academy of Sciences. The addition of large vertebrates, including whales and elephants, provides an important segment of the animal world to open access collections for researchers and educators. The process of creating this 3D resource will provide training for undergraduate students, and on-site workshops for collections staff. Skeletal models will support TCN activities in creating K-12 STEM lesson plans and 3D-printable resources for the classroom.
The digitized skeletons acquired in this PEN will help fill a major gap in the original TCN and support its research theme on the evolution of vertebrate morphological diversity. By virtue of their large size, vertebrates exceeding 250 kg define upper boundaries of size-dependent anatomical form and function, and therefore push the limits on development and physiology. These skeletal data will provide new opportunities to evaluate gigantism and the tendency of animal lineages toward ever-larger body size. Combined with the other oVert 3D specimens, the TCN's digital collection distributed through MorphoSource and iDigBio will inspire new research questions and provide the raw materials to test hypotheses in a broad range of biosciences.
Project Sponsor: Idaho State University (NSF Award 1802491)
Principal Investigators: Leif Tapanila (PI), David Blackburn (Co-PI)
Functional Quantitative Characters for Ecology and Evolution (FuncQEE)
An award is made to Chicago State University to join the oVert Thematic Collection Network (TCN) as a Partner to an Existing Network (PEN). Computed tomography (CT) scanning will be used to provide 3D data relating to structural diversity for ca. 1,700 specimens of rodents. Rodents are among the most common but also among the most diverse mammals on the planet. They are found in virtually every terrestrial ecosystem, with species ranging from guinea pigs, to prairie dogs, kangaroo rats, flying squirrels, capybaras, lemmings, house mice, and sewer rats. Across this diversity, their bodies vary considerably in size and shape as they adapted to distinct habitats (e.g., Arctic tundra, grasslands, temperate and tropical forests), locomotion (e.g. terrestrial, arboreal, swimming, burrowing habits), feeding preferences (e.g., insectivores, granivores, herbivores, or generalists), and more. Given these vast differences, this project will provide 3D digitized data making it possible to examine and quantify the characters found in this radiation of diversity throughout the rodent tree of life. Undergraduate students at an MSI (Chicago State University) will be trained in CT-scan image processing
The project will generate computed tomography (CT) scans as a basis for 3D modeling of structural diversity for 1,700 specimens of rodents. Sampling will focus on less common species. The 3D data will be available to researchers and educators via MorphoSource. These data will enable studies on functional quantitative characters for ecology and evolution (FuncQEE) as well as studies and lessons ranging from physiology to biomedical applications. The project will bring together scientists and educators from Chicago State University, University of Michigan, University of New Mexico, University of Florida, and Sandia National Laboratory. Master's degree candidates and undergraduate students will receive training, including an effort to provide opportunities for underrepresented, first generation, and/or low-income students in science careers in cutting edge visualization and analytical approaches.
Project Sponsor: Chicago State University (NSF Award 1902105)
Principal Investigators: Noe de la Sancha (Principal Investigator), David Blackburn (co-PI), Cody Thompson (co-PI)
The oUTCT PEN: Outwardly Mobilizing the UTCT Vertebrate Archive for Research and Training
The University of Texas High-Resolution X-ray CT Facility (UTCT) was established in 1997 to make HRXCT - a direct descendant of medical CT - available to researchers in the natural sciences. Through this award, oUTCT will partner with the oVert (openVertebrate) project to make nearly nine terabytes of existing high-resolution X-ray computed tomographic (HRXCT) data publicly accessible, and to train the next generation of students in best practices for these data. Scientists from around the world have brought their most important and precious natural history specimens to UTCT to image and measure their interior features nondestructively. This application of HRXCT technology has been tremendously successful, resulting in the proliferation of scanners at institutions across the country. Over the course of two years, oUTCT will upload HRXCT data for 90 UTCT clients to MorphoSource. About 3000 specimen scans, representing nearly 1,500 fossil and extant vertebrate species, will be made available so they can be easily discovered and downloaded by everyone from scientists to artists to K-12 educators. This mobilization will be accomplished by undergraduate students employed at UTCT, who will learn the basics of HRXCT data acquisition and visualization as well as basic bioinformatics.
The UTCT datasets, acquired in part via dozens of NSF grants and cited more than 18,000 times in academic publications, remain in high demand due to their broad scope, high data quality, and historical significance. This demand has been fueled in part by the public-facing Digital Library of Morphology (DigiMorph.org), an NSF-funded project online since 2002 and housed at UTCT, which serves HRXCT-derived animations for more than 1,000 biological and paleontological specimens. In the oUTCT project, UTCT and DigiMorph will partner with oVert and iDigBio, both at the University of Florida, and the MorphoSource data repository at Duke University to make this unparalleled collection of HRXCT datasets more readily discoverable and more easily repurposed. As part of the educational outreach for this project, oUTCT will also provide training to the oVert community, which spans nearly 20 universities and academic institutions, to maximize the scientific impact of that project. The UTCT will host two short courses per year, cosponsored by oVert and iDigBio, to train students and scientists associated with oVert and MorphoSource in the fundamentals of HRXCT data acquisition, visualization, analysis, and long-term management. These activities will expand the impact of the original oVert project and maximize the return on NSF?s investment in it, UTCT, DigiMorph, iDigBio, and MorphoSource.
Project Sponsor: University of Texas at Austin (NSF Award 1902242)
Principal Investigators: Jessica Maisano (PI), David Blackburn (co-PI)
CryptoVert - Digitizing small-bodied cryptobenthic fishes for the oVertTCN
The Open Vertebrate thematic collections network (oVert) aims to create a digital resource of computed tomography (CT) scans across the vertebrate Tree of Life. This digital database allows researchers to quickly and efficiently study morphological patterns across all vertebrate groups. One of the most apparent differences among vertebrates is their body size, with some species obtaining large body sizes, while others remain very small even as mature adults. This Partner to Existing Networks (PEN) award will link the Natural History Museum of Los Angeles County with oVert to create a digital repository of data focusing on some of the world?s smallest vertebrates: cryptobenthic fishes. Fishes represent approximately half of the total vertebrate diversity, yet many groups remain understudied. Cryptobenthic fishes, which are small marine fishes that live in a variety of habitats, are one of these understudied groups and their importance in marine ecosystems is only beginning to be understood. This project will complement oVert taxonomically by focusing on an understudied vertebrate group, and methodologically by developing best practices for scanning very small organisms for both bony and soft-tissue anatomy. In addition to their research utility, these scans will be an excellent educational resource that will be incorporated into public museum displays and K-12 classroom lesson plans. Furthermore, processing of CT scans will train undergraduate students in skills that are used in a variety of professional disciplines.
Studying very small organisms comes with inherent challenges, and previous attempts to describe the internal anatomy of small vertebrates was only possible using destructive approaches. This project will focus on 17 different fish families that comprise the majority of cryptobenthic fishes using traditional CT scans to document the skeletal system and contrast-enhanced CT scans to reveal soft-tissue anatomy such as muscle, nervous, and circulatory systems. Cryptobenthic fishes fill a variety of functional ecosystem roles, and the bony and soft-tissue scans associated with this project will create the raw data necessary for researchers to understand how these minute fishes have adapted in different ways to their environment without damaging valuable museum specimens. In combination with CT scans completed by oVert and oVert partners, the products of this project will also be useful for researchers to identify general trends in vertebrate anatomical evolution associated with body size and will be a valuable resource for the development of new questions and hypotheses in a variety of scientific disciplines. Data will be shared with and made available through iDigBio.org and MorphoSource.org.
Principal Investigators: Willian Ludt (PI)
GalapaGateway: Unlocking Model Evolutionary Systems for Research and Education
The California Academy of Sciences (CAS) is home to the largest and most complete collection of scientific research specimens from the Galápagos Islands, the majority of which can only be accessed by a small number of researchers able to visit the museum. GalapaGateway is a Partnership to Existing Networks (PEN) award that compliments the Open Vertebrate Thematic Collections Network (oVert TCN). This PEN will produce and disseminate high resolution three-dimensional (3D) imagery of approximately 1300 vertebrate specimens of reptiles, birds, and mammals from the Galápagos Islands, thereby increasing accessibility to these historical specimens. Resulting 3D scans will be available free of charge on multiple platforms, including iDigBio, MorphoSource, SketchFab, and a dedicated CAS portal that links scans to specimen data, fieldnotes, and images. Physical 3D models of selected specimens, such as giant tortoises and Darwin?s finches, will be printed for use in education and public outreach at the CAS and at the Charles Darwin Foundation in the Galápagos Islands.
While the oVert TCN aims to scan a single representative of each vertebrate genus, this PEN will image multiple specimens per species to capture within-species variation. Variation within species of Galapagos animals was central to Darwin?s theory of evolution by natural selection and continues to serve as a textbook example for explaining these foundational concepts to students and the general public. Through a combination of computed tomography (CT) and structured light surface scanning, the GalapaGateway project will create morphological data and 3D models of multiple series of closely related taxa from across the Galápagos Archipelago, allowing for in-depth analysis of vertebrate morphology, variation, adaptation, and speciation. 3D surface scanning will be used on specimens too large for traditional CT-scanning machines. Producing these scans of iconic historical specimens from the Galápagos will facilitate a wide variety of academic inquiries, including research into morphology and allometry, development, taxonomy, and adaptive ecology and evolution.
Project Sponsor: California Academy of Sciences (NSF Award #2001435)
Principal Investigators: Lauren Scheinberg (PI), David Blackburn, Maureen Flannery (co-PIs)
oBird: 3D Photogrammetry of Museum Specimens for Phenomics across the Avian Tree of Life
The oBird project (for ?outside of the bird?) will create 3D digital models for nearly all living bird species for research and education. Preserved specimens in museum research collections are a record of Earth?s biodiversity and provide a baseline for assessing past and future environmental changes, planetary health, and for understanding how biodiversity arose and proliferated. Major efforts over the last several decades have sought to make museum records digital to facilitate their access and inclusion in large-scale research projects. Computerized tomography (CT) scans are an increasingly common way to make digital specimens, especially when the insides of the specimen have also been preserved, as with whole fish preserved in jars. However, with birds, CT scans will miss the color and arrangement of feathers, features of great importance to researchers and also appreciated by the public. oBird will create 3D digital models using a process called photogrammetry. Photogrammetry uses hundreds of photographs from all angles of a specimen to create realistic, interactive 3D virtual models in full, natural color. The 3D models from oBird will be free to access on the internet, facilitating research on the origins of bird diversity, including novel colors and pigments. The 3D models will also be incorporated into public displays on biodiversity in the new Anderson Center for Environmental Sciences at Occidental College as well as lesson plans for K-12 education.
As a partner project to the Open Vertebrate Thematic Collections Network (OVert TCN), oBird will extend OVert into the world of 3D photogrammetry, an emerging method in collections digitization that preserves the external features of specimens as interactive, 3D models. The project will increase genus-level coverage of avian diversity compared to OVert from 60% to 90%. The 3D photogrammetry technique involves taking hundreds of 2D photos of a whole, dried bird specimen on a rotating stand followed by processing with a novel, automated computational pipeline that generates a 3D model with minimal manual oversight. oBird will prioritize imaging the same species as OVert to provide paired external and internal anatomy across species. The 3D models will be hosted on MorphoSource, an open-access platform for storing and archiving 3D data, extending access to large-scale phenomic data in furtherance of the OVert research theme: the evolution of vertebrate morphological diversity. By providing natural-color data for 3D specimens, oBird will thus bring more accurate and realistic color analysis to research on plumage evolution, especially in the comparative context of an existing bird tree of life. New questions that will be enabled include research into the origins and evolution of bird plumage color and morphological novelty in beak dimensions and wing shape, enabling comparative evolutionary study of these important ecomorphological traits. oBird will integrate with a strong undergraduate research program in a large bird natural history collection at a small liberal arts college, providing training in digital technology and effects, biodiversity informatics, and museum collections.
Project Sponsor: Occidental Collect (NSF Award #2001652)
Principal Investigators: John McCormack (PI)
oMeso: Opening Mesoamerican Herpetofaunal Diversity to Whole Phenome Imaging
The oMeso project is a Partner to an Existing Network (PEN) award to the University of Colorado Museum of Natural History to join the openVertebrate (oVert) Thematic Content Network (TCN). oMeso expands upon oVert objectives by using 2D and 3D specimen imaging technologies to facilitate exploration of structural and functional diversity in Mesoamerican reptiles and amphibians. The unique ecology and geology of Mesoamerica has fostered the rapid evolution of multiple species adapted for a variety of habitats and life modes. Computed tomography (CT) scans of internal anatomy paired with high resolution photos of external traits will provide complimentary image datasets to create a novel resource for one of the world?s most hyperdiverse regions. Increased access to digital vouchers generated by oMeso will enable research spanning multiple disciplines, from evolutionary biology and ecology to biomechanics and conservation science. The project provides inclusive training opportunities for university students in curation, data dissemination, and cutting-edge museum technologies. Beyond its research value, the oMeso PEN aims to increase scientific literacy and public engagement around Mesoamerican herpetofaunal diversity through a year-long exhibit accompanied by a community lecture, K-12 programming, and open access lesson plans that incorporate project products.
oMeso will increase the taxonomic scope of the oVert TCN by adding 1100 species across 160 genera, additionally filling a phenotypic data gap in the digital biodiversity landscape pertaining to reptile and amphibian media. These data will broadly support analysis of the patterns and processes relating to evolution, adaptation, convergence, and comparative and functional morphology. Extensive regional sampling will drive investigations into ecomorphology along various environmental gradients, and targeting endemic species will uncover rare or cryptic phenotypes such as those belonging to narrowly distributed microhabitat specialists, endangered, threatened and extinct species, and miniaturized taxa found throughout Mesoamerica. oMeso will leverage existing oVert TCN workflows and digital infrastructure to optimize efficiency and standardize products. Roughly 10% of specimens will be prepared with contrast-enhancement to render soft tissue structures in scans. Resulting raw CT tomograms, 3D surface models, and photo-stacked images will be openly disseminated through MorphoSource and Arctos and integrate with iDigBio, linking project media to corresponding source specimen records and extended data products (e.g., genetic sequences, publications, symbionts). oMeso will bring together collaborators from the University of Colorado, the University of California, Berkeley, and the University of Florida, along with specimen contributions from seven museum institutions to develop this comprehensive and globally accessible whole phenome resource.
Project Sponsor: University of Colorado at Boulder (NSF Award #2001474)
Principal Investigators: Emily Braker