NMITA – using an illustrated taxonomic database of living and fossil corals to expand bioinformatics education.

What is NMITA?

The Neogene Marine Biota of Tropical America (NMITA: pronounced na-me-tah) is a website and database that provides global access to Tropical American marine biodiversity data from the past 25 million years (http://nmita.iowa.uiowa.edu/). Developed through multiple grants from the National Science Foundation since 1998, NMITA was one of the earliest projects to bring together a database of multi-institutional biological specimen data and images that could be searched on-line and used in research and education in systematics, evolutionary paleontology, stratigrFigure 1. Example species page generated from the NMITA database.aphy, and biodiversity. Images and information on taxa were collected as part of two large multi-taxa fossil sampling programs: the Panama Paleontology Project (http://faculty.fiu.edu/~collinsl/pppabout.html) coordinated by the Smithsonian Tropical Research Institute in Panama; and the Neogene Paleontology of the northern Dominican Republic project (http://nmita.iowa.uiowa.edu/drprojct.htm) coordinated by the Natural History Museum in Basel, Switzerland.  Many researchers collected over one million specimens including bryozoans, corals (zooxanthellate and azooxanthellate), molluscs (gastropods and bivalves), benthic foraminifera, ostracodes, and fish otoliths. The fossil collections are housed at the U.S. National Museum of Natural History (https://naturalhistory.si.edu/) of the Smithsonian Institution in Washington, D.C. and at the Natural History Museum in Basel, Switzerland (https://www.nmbs.ch/home). NMITA contains thousands of specimen images and species occurrence records. Budd et al. 2008 provide an overview of the database structure and capabilities. The NMITA database and web servers are currently located in the Department of Earth and Environmental Sciences at the University of Iowa and are in the process of being transferred to the University of Miami for future development.

What can you do with NMITA?
Figure 2. Interactive map of fossils collecting localities in the central research area of the Rio Cana, Dominican Republic. Selecting a locality generates a page of information about locality details stratigraphy, and taxa collected (linked to species pages) as well as cross-referencing with information on the research area in full.
Visitors to the NMITA website can select taxa to receive conventional taxonomic information on authorship, synonyms, morphology, type specimens, and spatial and temporal distribution (Figure 1). Alternatively they may click on maps and stratigraphic columns to receive faunal lists for specific horizons (Figure 2). NMITA also contains online identification keys and illustrated glossaries of morphological terms.

The educational resources of NMITA are:

  • Florida Bay / Puerto Rico Field Trip Coral Lab: a guide for identifying common shallow water Caribbean reef corals in preparation for a field trip. It includes two identification tools that can be used to identify specimens based on morphologic characters.
  • Colonial Invertebrates: an introduction to sponges, stromatoporoids, corals, and bryozoans.
  • Maps and Faunal Lists: Explore collecting localities to determine which species were present during the last 25 million years in the Dominican Republic.
  • Paleoecology and Sedimentology of Ancient Coral Reefs in the Dominican Republic: a workshop guidebook (in English and Spanish) illustrating how studies of fossil reef systems, thousands to millions of years old, are relevant to addressing modern-day issues in reef conservation.Figure 3. Instructions for biodiversity bioinformatics Lesson 1 available on the NMITA website.
  • Missing 'links' in bioinformatics education: four inquiry-based biodiversity bioinformatics lessons for high school students, targeting National Science Education Standards, and college non-majors using NMITA (Nehm and Budd 2006).
    • Lesson 1: An introduction to biodiversity bioinformatics (Figure 3). This lesson uses NMITA to give an introduction to the overall structure of a bioinformatics database and the types of data that are contained within it, so that students can then gather larger amounts of data and answer specific questions about evolution and biodiversity. The lesson is a virtual journey to the Dominican Republic, a country located on the island of Hispañola in the Caribbean Sea. On the island students explore along the banks of the Rio Gurabo in the Cibao Valley, looking at the fossil corals that occur in the sedimentary rock layers that were formed when parts of the island were under the Caribbean Sea.
    • Lesson 2: Quantify coral reef biodiversity patterns. Students test hypotheses about coral biodiversity change through time by gathering data from the marine fossil corals and coral reefs that occur in different sedimentary rock layers and investigating the diversity of living coral reefs from the southwestern part of the Dominican Republic. Students collect coral reef biodiversity data from six different time periods (three samples from each) in order to determine if coral reef biodiversity has increased, decreased, or stayed the same over the past 20 million years in the Dominican Republic.
    • Lesson 3: Quantify reef coral ecological patterns using NMITA. Lesson 3 builds upon lessons 1 and 2 and explores ecological and morphological patterns of biodiversity change in the same coral reef samples. Students use NMITA to gather data on the morphology, or shape, of the living and fossil coral species and plot these changes through time.
    • Lesson 4: When did modern reef corals originate? Did all the living genera and species of corals appear recently, or many millions of years ago? Did the modern genera and species appear together or randomly through time? NMITA’s data on fossil reef corals, combined with data from living reefs, can be used to answer these questions. Students use NMITA to virtually collect coral reef biodiversity data from six different time periods in order to determine when, in geological time, modern reef coral biodiversity originated in the Dominican Republic.
  • Identification Tools: NMITA providFigure 4. Example NIT process.es both a polychotomous identification key and the dynamic NMITA Identification Tool (NIT) (http://nmita.iowa.uiowa.edu/idkeys.htm). The polychotomous key allows users to work through a sequence of characters to obtain an identification. NIT allows users to select multiple characters in table and check-box format (Figure 4). NIT is highly flexible in that users may select one or more characters and one or more states for each character, and the results show all species matching the selections with additional character states and links to dynamic species pages. Each character state is illustrated in a morphological glossary. The identification tools are easy to use in educational activities where students are given actual specimens or photographs of specimens to identify.     

Visit the NMITA website and explore the current resources, or contact the NMITA developers, via the author, for data sets, web services, and assistance with the NMITA educational tools.  

Budd, A. F., Adrain, T. S., Park, J. W., Klaus, J, S. and Johnson, K. G. 2008. The Neogene Marine Biota of Tropical America (“NMITA”) Database: Integrating data from the Dominican Republic Project. In Nehm, R. H. and Budd, A. F. (eds) Evolutionary Stasis and Change in the Dominican Republic Neogene. Topics in Geobiology 30: 301-310.
Nehm, R. H. and Budd, A. F. 2006. Missing Links in Bioinformatics Education: expanding students’ conceptions of bioinformatics using a biodiversity database of living & fossil reef corals. The American Biology Teacher, Online Publication, September 2006, p. 91-97.

Author: Tiffany Adrain, Collections Manager, University of Iowa Paleontology Repository, Department of Earth & Environmental Sciences, 115 Trowbridge Hall, Iowa City, Iowa 52242. Email: tiffany-adrain@uiowa.edu. Phone: 319 335 1822.