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Evolutionary Morphing

David F. Wiley, Nina Amenta, Dan A. Alcantara, Deboshmita Ghosh, Yong J Kil, Eric Delson, Will Harcourt-Smith, F. James Rohlf, Katherine St. John, Bernd Hamann, Ryosuke Motani, Steven Frost, Alfred L. Rosenberger, Lissa Tallman, Todd Disotell, and Rob O'Neill

Abstract

Image

We propose to develop software tools for the analysis, interpretation and visualization of three-dimensional shape data from living and extinct organisms, using the statistical framework of geometric morphometics. While this software will be widely useful in biology and paleontology, we plan to focus our work by concentrating on one significant problem: incorporating fossils into evolutionary trees. Evolutionary trees for groups of living species are usually estimated using DNA sequence data. Since this is usually not available for extinct species, we need to use morphology (the shapes of fossil and modern specimens) to decide how the extinct species should be included in a tree whose framework is based on molecular studies. Specifically, we plan to estimate a well-supported evolutionary tree for the mainly African papionin monkeys, an inherently interesting group that includes about as many extinct as living clusters of species. Our analysis will be based on a large existing database of three-dimensional data (mostly skull surfaces) at the American Museum of Natural History.

This end-to-end analysis project should produce research results at all levels. The interactive graphics, visualization and statistical analysis tools we propose are ever more widely needed as the amount of three-dimensional morphology data increases. We expect that the close interaction of geometric morphometrics and computer graphics will lead to new ideas about the representation of shape. We have new approaches to the problem of integrating morphology with molecular data in the study of evolution, which we hope will be successful and applicable in many parts of the tree of life. And with massive amounts of new data, new processing and analytic software, and new approaches to integrating morphology, we hope to be able to answer specific questions about the evolution of African monkeys, which have remained elusive up until now.

Our proposed work will have a variety of broader impacts beyond our own research agendas. A large part of the project will be done at Lehman College of CUNY, a minority-serving institution in the Bronx, and minority undergraduates are already involved in the research. The software tools we will develop are sorely needed and will become part of the scientific infrastructure and our visualizations will form a basis for sharing research in evolution with the general public.

AAAS/NSF Scientific Visualization Competition Entry

Below is our five-minute video submission into the non-interactive media category for which we won an honorable mention award.

Our press release.

Article in Science magazine.

IEEE Visualization 2005

Download the powerpoint presentation given at Vis (ZIP 53MB)

Below is our five-minute video submission that accompanies our Visualization 2005 paper. This video is a bit more technical than our NSF video above.

Images

Landmark Editor

Landmark was developed by the scientists at the Institute for Data Analysis and Visualization (IDAV) and the University of California, Davis. Working together with collaborators at the American Museum of Natural History, the team was able to build an easy to use tool for landmark editing and placement on geometric surfaces typically obtained via laser range scans.

The main purpose of Landmark is to easily place landmark points and semi-landmark points accurately and with high repeatability on complex surfaces for the purpose of registration, alignment, morphing, and computation of hypothetical ancestors in evolutionary trees.

Features include:

Coming soon...

We are currently working on:

Documentation

The Landmark documentation is provided in PDF format and demonstrates a tutorial for two crania surfaces. It can be downloaded seperately by the following link (it is included in the software distribution below):

Download Here (PDF 12.8MB)

Download

Landmark is currently only available for Microsoft Windows. Download a zipped installation from the following link:

Download Here (EXE 20MB)

Revisions

Current release is version 3.6

Project Collaborators

  1. Institute for Data Analysis and Visualization, University of California, Davis
  2. Department of Computer Science, University of California, Davis
  3. Department of Evolution and Ecology, Stony Brook University
  4. Ph.D. Program in Anthropology, City University of New York
  5. NYCEP (New York Consortium in Evolutionary Primatology)
  6. NYCEP Morphometrics Group
  7. Department of Anthropology, Lehman College/CUNY
  8. Division of Paleontology, American Museum of Natural History
  9. Department of Mathematics and Computer Science, Lehman College/CUNY
  10. Department of Anthropology, University of Oregon
  11. Department of Anthropology, Brooklyn College, CUNY
  12. Department of Anthropology, New York University
  13. Digital Arts Research Laboratory, Pratt Institute

Publications


This material is based upon work supported by the National Science Foundation under Grant No. SEI(SBE)-0513894. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.

Preliminary work of this material was supported by the National Science Foundation under Grant Nos. DEB-0121681/0121682, ACI-9982351, DEB-0212023, ACI-962034, and NIH/NSF P20 MH60975-06A2.

Copyright (C) 2002-2006 by David F. Wiley and the Institute of Data Analysis and Visualization (IDAV)