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OVert: Open Exploration of Vertebrate Diversity in 3D: Difference between revisions
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=== Project Websites & Social Media === | === Project Websites & Social Media === | ||
oVert | MorphoSource (on-line depository for digital anatomical data, including from oVert TCN): https://www.morphosource.org/ | ||
oVert | 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). [[media:OVert_30March2018.pdf | PDF]] <br> | |||
Boyer, D. oVert MorphoSource Uploading Guide. [[media:OVert_template_for_media_data_FIN_7-21-18.pdf | PDF]] <br> | |||
Stanley, Edward. Introduction to CT scanning. Computed Tomography in the Analysis of Natural History, Morphology, and Evolution Workshop, University of Texas, Arlington, January 2018. [[media:UTArlington_workshop_CT_intro.pdf | PDF]] <br> | |||
Stanley, Edward. X-ray basics. Computed Tomography in the Analysis of Natural History, Morphology, and Evolution Workshop, University of Texas, Arlington, January 2018. [[media:UTArlington_Workshop_Xray_basics.pdf | PDF]] <br> | |||
Stanley, Edward. CT scanning basics. Computed Tomography in the Analysis of Natural History, Morphology, and Evolution Workshop, University of Texas, Arlington, January 2018. [[media:UTArlington_Workshop_CT_basics.pdf | PDF]] <br> | |||
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 Leadership === | ||
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Bhart-Anjan Bhullar, CoPI, Department of Geology & Geophysics, Peabody Museum of Natural History, Yale University<br> | Bhart-Anjan Bhullar, CoPI, Department of Geology & Geophysics, Peabody Museum of Natural History, Yale University<br> | ||
=== | === 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.<br> | 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.<br> | ||
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.<br> | 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.<br> | ||
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.<br> | |||
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.<br> | |||
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.<br> | 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.<br> | ||
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. <br> | |||
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. <br> | |||
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.<br> | |||
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.<br> | 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.<br> | ||
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.<br> | |||
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.<br> | 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.<br> | ||
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.<br> | 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.<br> | ||
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.<br> | |||
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.<br> | |||
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.<br> | |||
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 === | === 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. <br> | Blackburn, D.C. 3D Anatomical Data for All: The oVert Thematic Collection Network. Society of Integrative and Comparative Biology, San Francisco, CA. January 2018. <br> | ||
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. <br> | |||
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. <br> | |||
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. <br> | |||
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. <br> | |||
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. <br> | |||
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. <br> | |||
Jasulevicz, R. & A. Bauer. A Bolder Shoulder: Pectoral Girdle Morphology in Geckos. Joint Meeting of Ichthyologists and Herpetologists, Rochester, NY. July 2018. <br> | |||
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. <br> | |||
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. <br> | |||
Owens, H. & E. Stanley. Anatomy of Sexual Parasitism in Triplewart Sea-Devils (''Cryptosaras couesii''). Joint Meeting of Ichthyologists and Herpetologists, Rochester, NY. July 2018. <br> | |||
Paluh, D., E. Stanley, D. Blackburn. Convergent Evolution and Function of Hyperossification in Frogs. Joint Meeting of Ichthyologists and Herpetologists, Rochester, NY. July 2018. <br> | |||
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. <br> | |||
Stanley, E., D. Paluh, D. Blackburn. Diversification of dermal armor in squamates. Joint Meeting of Ichthyologists and Herpetologists, Rochester, NY. July 2018. <br> | |||
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. <br> | |||
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. <br> | |||
=== Other project documentation === | === Other project documentation === | ||
Article in ''Science'': http://science.sciencemag.org/content/357/6353/742.summary | 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 [https://www.nsf.gov/awardsearch/showAward?AWD_ID=1802491 (NSF Award 1802491)] | |||
''Principal Investigators: [mailto:tapaleif@isu.edu Leif Tapanila] (PI), David Blackburn (Co-PI) | |||