OVert: Open Exploration of Vertebrate Diversity in 3D

Digitization TCN: oVert: Open Exploration of Vertebrate Diversity in 3D

oVert TCN
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Project Summary

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.

Current Research

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

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 Leadership

Project sponsor: University of Florida (NSF Award 1701714)

Principal Investigator (PI): David Blackburn

Project Collaborators

Map of Collaborating Institutions

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
https://www.morphosource.org/Detail/ProjectDetail/Show/project_id/211

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
https://www.morphosource.org/Detail/ProjectDetail/Show/project_id/273

Cornell University

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

Duke 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

Harvard University

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

Luke J. Welton, 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
Richard E. Glor, 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
https://www.morphosource.org/Detail/ProjectDetail/Show/project_id/374

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
http://www.morphosource.org/Detail/ProjectDetail/Show/project_id/220

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

Publications

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., 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.

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 Kermadec Islands of New Zealand (Teleostei: Gobiesocidae). ZooKeys, 786, 75-104.

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.

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, https://doi.org/10.1002/jmor.20837.

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.

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.

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), 1-15.

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(1), 171581.

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(7), 904-917.

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(1), 117-173.

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.

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.

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.

Vijayakumar, S. P., Pyron, R. A., Dinesh, K. P., Torsekar, V. R., Srikanthan, A. N., Swamy, P., ... & 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.

Professional Presentations

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. 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.

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.

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.

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.

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.

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.

Stanley, E., D. Paluh, D. Blackburn. Diversification of dermal armor in squamates. Joint Meeting of Ichthyologists and Herpetologists, Rochester, NY. July 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.

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

PENs

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)