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Digitization TCN: Digitizing Fossils to Enable New Syntheses in Biogeography - Creating a PALEONICHES

Paleoniches TCN
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Project Summary

Museum collections of fossils, along with their associated locality data, provide millions of records representing data on the temporal and geographic distribution of species in deep time. However, to reach their greatest scientific potential, these collections data need to be available on-line and in a format that facilitates quantitative biogeographic analyses. We will enter information about the age and precise location of fossil specimens from parts of several key paleontological collections into electronic databases. During this process improvements to computer programs for collections will be enhanced to allow paleontological specimens to be integrated with modern specimen data, thereby benefiting research on distribution of organisms over time. Our efforts will digitize nearly 450,000 specimens belonging to 900 species from several museums throughout the U.S. and will focus on three different time periods in the history of life: the Ordovician, Pennsylvanian, and Neogene. We will create on line digital atlases illustrating and describing these fossils and providing maps showing where they can be found. We will also create an 'app' so these atlases can be used on handheld devices out in the field.

The museum collections and fossils provide large amounts of data useful for studying what causes species to migrate, go extinct, or evolve over long time periods. They are of great relevance for considering how global change has and will continue to affect life on this planet. Our study will make these data available on line and accessible to scientists, facilitating many scientific analyses. The on-line and portable device digital atlases will be useful for educating amateur paleontologists and K-12 students about fossils both in classrooms and in the field. We will also provide training to students and scholars. This award is made as part of the National Resource for Digitization of Biological Collections through the Advancing Digitization of Biodiversity Collections program and all data resulting from this award will be available through the national resource (

Current Research

Proposed research:

  • Using Ecological Niche Modeling for analyzing neontological and paleontological data in biogeographic and ecological studies pertaining to:
    • the biotic effects of climate change,
    • changes to species associations in the face of changes in physical environment,
    • influences of abiotic and biotic factors on species distribution.
  • Determining species distributions from the Ordovician, the Pennsylvanian, and the Neogene time periods.

Thus far > 920,000 specimens have been databased and > 9,200 localities have been georeferenced. Further, these data have been shared/published with iDigBio and provided on line via institutional websites. We have created online digital atlases, [] , for more than 900 species from the time intervals studied. For each species ecological, stratigraphic, and taxonomic information is provided, along with images and geographic range maps. Our Digital Atlas of Ancient Life project is described in greater detail in an article in Palaeontologia Electronica in 2015 (18.2.3E:1-9). Our Digital Atlas of Ancient Life “App” is available at the Apple App Store for free download. Studies associated with the project have been published by the PIs in several journals including: Global Biogeography and Ecology; Journal of Biogeography; Paleobiology; and Proceedings of the Royal Society, Series B. A total of 9 graduate students (seven of them women), ten undergraduate students (eight of them women), and one female post-doctoral fellow received training and were supported by this project.

Project Websites & Social Media

Digital Atlas of Ancient Life

Citizen Science & Outreach Projects

Project Leadership

Project Sponsor: University of Kansas (NSF Award 1206757)

Principal Investigators (PIs): Bruce Lieberman (PI), Jonathan Hendricks (PI), Alycia Stigall (PI), James Beach (Co-PI), Una Farrell (Co-PI)

Project Collaborators

Map of Collaborating Institutions

Cincinnati Museum Center
Miami University of Ohio
Ohio University (NSF Award 1206750)
Paleontological Research Institution (NSF Award 1651208)
University of Florida, Florida Museum of Natural History
University of Kansas (NSF Award 1206757)

Protocols & Workflows


Bauer, J.E. and Stigall, A.L., 2016. A combined morphometric and phylogenetic revision of the Late Ordovician brachiopod genera Eochonetes and Thaerodonta. Journal of Paleontology, 90(5), pp.888-909.

Casey, Michelle M., and Bruce S. Lieberman. “Beyond Memorization: An Intermediate-Level Paleontology Activity That Integrates Anatomy, Ecology, and Macroevolutionary Theory Using Trilobites.” Evolution: Education and Outreach 7 (2014): 20. doi:10.1186/s12052-014-0020-5.

Hendricks, Jonathan R., Alycia L. Stigall, and Bruce S. Lieberman. “The Digital Atlas of Ancient Life: Delivering Information on Paleontology and Biogeography via the Web.” Palaeontologia Electronica 18.2.3E (2015): 1–9.

Lam, A. R., Stigall, A. L., & Matzke, N. J. (2018). Dispersal in the Ordovician: Speciation patterns and paleobiogeographic analyses of brachiopods and trilobites. Palaeogeography, Palaeoclimatology, Palaeoecology, 489, 147-165.doi:10.1016/j.palaeo.2017.10.006

Lieberman, B. S., and E. E. Saupe. Palaeoniches get stiches: analyses of niches informing macroevolutionary theory. Lethaia 49: (2016) 145-149.

Myers, Corinne E., Alycia L. Stigall, and Bruce S. Lieberman. “PaleoENM : Applying Ecological Niche Modeling to the Fossil Record.” Paleobiology 41, no. March (2015): 1–19. doi:10.1017/pab.2014.19.

Saupe, Erin E., Jonathan R. Hendricks, A Townsend Peterson, and Bruce S. Lieberman. “Climate Change and Marine Molluscs of the Western North Atlantic: Future Prospects and Perils.” Journal of Biogeography 41, no. 7 (2014): 1352–66. doi:10.1111/jbi.12289.

Saupe, Erin E., Jonathan R. Hendricks, Roger W. Portell, H.J. Dowsett, A. Haywood, Stephen J. Hunter, and Bruce S. Lieberman. “Macroevolutionary Consequences of Profound Climate Change on Niche Evolution in Marine Molluscs over the Past Three Million Years.” Proceedings of the Royal Society of London B: Biological Sciences 281, no. 1795 (2014): 1–9. doi:10.1098/rspb.2014.1995.

Saupe, Erin E., Huijie Qiao, Jonathan R. Hendricks, Roger W. Portell, Stephen J. Hunter, Jorge Soberón, and Bruce S. Lieberman. “Niche Breadth and Geographic Range Size as Determinants of Species Survival on Geological Time Scales.” Global Ecology and Biogeography 24, no. 10 (2015): 1159–69. doi:10.1111/geb.12333.

Stigall, Alycia L. "The Impact of Invasive Species on Speciation: Lessons from the Fossil Record." Species and Speciation in the Fossil Record (2016): 340.

Stigall, Alycia L., Jennifer E. Bauer, Adriane R. Lam, and David F. Wright. "Biotic immigration events, speciation, and the accumulation of biodiversity in the fossil record." Global and Planetary Change (2016).

Stigall, Alycia L., Danielle E. Dani, Sara R. Helfrich, and Aaron J. Sickel. "Using observations of fossils to reconstruct ancient environments." Science Scope 39, no. 2 (2015): 10-16.

Trubovitz, Sarah, and Alycia L. Stigall. "Synchronous diversification of Laurentian and Baltic rhynchonelliform brachiopods: Implications for regional versus global triggers of the Great Ordovician Biodiversification Event." Geology 44, no. 9 (2016): 743-746.

Professional Presentations

iDigBio Summit V, 2015

Other project documentation


Digitization PEN: Paleoniches on the western Cincinnati arch, the Ordovician of Indiana

This project will make one of the key Ordovician fossil collections in the nation digitally accessible for research and public use. The Ordovician Period was the second greatest period in the history of animal life, about 485 to 444 million years ago. The diversity of life increased remarkably during the Ordovician Period until the mass extinction event at the end of the Period. The Indiana University Paleontology Collection has systematically documented fossil records of 10 million years leading up to the extinction, including a series of fossils that were collected in the early 1900s when a new railway grade was cut through Indiana's Ordovician rocks along Tanner's Creek near Cincinnati. The fossils in the Ordovician collection document the migration of ancient marine organisms in response to changing sea level, demonstrate evolutionary adaptation to changing environments, and reveal ecological interactions that help explain why some groups survived the extinction and others did not. Digitizing the collections makes this material accessible for large-scale quantitative scientific studies. Importantly, digitization also makes these incredible fossils available to students, teachers, and fossil enthusiasts in Indiana, across the nation, and around the world. This project will involve K-12 teachers in developing school curriculum exercises based on the fossils and on the digitization process. It will also engage the region's avocational paleontological community in the digitization initiative, giving them unprecedented access to the same fossil research collections used by scientists.

The paleontological holdings that will be digitized through this project include macrofossils and thin sections that were collected along the entire Ordovician outcrop of the Kope, Dillsboro, and Whitewater Formations in Indiana. The species are closely tied to a series of well-documented measured sections that provide stratigraphic and sedimentological context. The material includes an extensive and unique series of bryozoan thin sections produced by E.R. Cumings and J.J. Galloway. This material adds substantially to the PaleoNICHES digitization initiative of the Cincinnati Arch by filling in its entire western flank. Inter-basin dispersals between the Cincinnati Arch and western epicontinental seas were mediated by rises and falls in sea level through the late Ordovician Period that iteratively flooded and exposed the transcontinental arch. Spatially and temporally resolved digital occurrences of complete faunas are used to study the timing of dispersal events and changes in ecological associations that were mediated by these eustatic changes. This project will utilize the stratigraphic and taxonomic backbone of the digitized collections from the Cincinnati Arch region to serve as a launchpad for engaging K-12 students and citizen scientists using the Notes from Nature transcription portal. This rich, interactive content will be generated for smartphone apps (including the Digital Atlas of Ancient Life) to expand the use of biological collections data into regional K-12 classrooms and online, via curated curricula hosted on iDigPaleo. High-quality specimen data and images will also be made available through iDigBio (

Project Sponsor: Indiana University (NSF Award 1702289)

Principal Investigators (PIs): Gary Motz (PI), P. David Polly (Co-PI), Claudia Johnson (Co-PI)

Digitization PEN: Targeted Digitization to Expand and Enhance the PALEONICHES TCN

The invertebrate and plant fossil collections of the University of Texas at Austin document geological research spanning the last 150 years. These four million fossils range in age from Precambrian to the Holocene, encompassing critical intervals of geologic time and geographic areas and certain well-studied organisms. Such huge collections are of little value unless the objects along with related documentation, images, and analytical data are digitized and made globally accessible. This project will connect digital data from these UT collections to institutions that are part of the Paleoniches TCN and ultimately to the national data resource ( The geologic "deep" time slots that have been selected are the Cambro-Ordovician, Pennsylvanian and Paleogene-Neogene. The major groups of organisms will be brachiopods, echinoderms, and molluscs. The digital record will link the specimen's scientific name to its collection site and geological time period. The collection site will be recorded in current and deep time geography, thus allowing the researcher to examine organisms from the perspective of distinct "plate" configurations. High quality multi-focus imagery with digitally embedded scales will provide researchers with a functional image that can be analyzed in open source software. The final data resource will provide a more robust database for future analytical studies on a broad range of topics within the history of life.

This data set will make visible long-term effects of major global changes in the distribution, migration, and extinction of organisms. Using a web interface that will allow for mobile platforms, this rich geological record will become available to researchers, educators, and the general public. The project will provide training for students. This award is made as part of the National Resource for Digitization of Biological Collections through the Advancing Digitization of Biological Collections program and all data resulting from this award will be available through the national resource (

Project Sponsor: University of Texas at Austin (NSF Award 1305070)

Principal Investigators (PIs): Ann Molineux (PI), James Sprinkle (Co-PI)

Digitization PEN: Increasing the Robustness of the Ordovician and Pennsylvanian Dataset of PALEONICHES-TCN

Invertebrate fossil collections hold millions of specimens that record the history of diversity and evolution of life on earth. Over 123,000 historically important specimens in the Yale Peabody Museum (YPM) will be recorded in a database with identification, geologic age, and the location of where the fossils were collected. The database, combined with similar databases from collaborating museums and those involved with the Paleoniches Thematic Collections Network, will show where animals lived over the course of hundreds of million years and help us understand how long-term climate change affected their distribution over time.

YPM will hold a workshop to teach other professionals how to database fossil collection locations through creation of an integrated data management infrastructure that allows researchers to view the objects on a map and analyze data. Those maps, along with information about some of the most important fossils, will become part of a multimedia educational cart for use in public exhibition areas. This project will rely on employment of undergraduate student workers who will gain experience in scientific and museum collections research. It will also provide internships for two students in the YPM EVOLUTIONS program (NSF GEO1108086: Track 1: GEOPATH: Geoscience Educational Opportunities Promoting Advancement to Higher Education), an afterschool program for underserved high school students from the New Haven, CT region. This award is made as part of the National Resource for Digitization of Biological Collections through the Advancing Digitization of Biological Collections program and all data resulting from this award will be available through the national resource (

Project Sponsor: Yale University (NSF Award 1304931)

Principal Investigator (PI): Derek Briggs