Methods to examine trait evolution on trees: advancing the field
| PI(s): | Brian C O'Meara |
| Start Date: | 2007-11-01 |
| End Date: | 2009-07-31 |
| Keywords: | database, phylogenetics, genomics, comparative methods |
Examining the evolution of morphological, behavioral, geographical, genetic, biochemical, and physiological traits using methods that incorporate phylogenetic information has been an important area of growth in evolutionary biology for over two decades. As more methods are made available, the ability to test hypotheses and infer patterns of trait evolution becomes ever greater. However, the wide variety of methods in the literature and the limited communication between sub-disciplines in biology hampers method use and development. Broadly-applicable methods developed in one sub-discipline go unused in other sub-disciplines; biologists may not test certain hypotheses due to a perceived lack of relevant methods; and those who would develop methods to meet current needs have difficulty finding which areas require such work. I intend to develop and implement methods to help understand trait evolution, first identifying and communicating areas of need.This project has four main goals. 1) Describing extant methods: A database of existing phylogenetic methods for examining trait evolution, from fields of genomics, paleontology, and comparative biology, will be creating using information from the literature. 2) Identifying underdeveloped areas: use database above. These areas will be communicated through a publication targeted to a general audience and through a website featuring the database and searchable by input data type, software availability, significance criterion, and other factors. This will allow empiricists to find appropriate methods quickly and permit theoreticians, especially those from fields outside biology, to identify areas still needing development. 3) Develop new methods in some of these areas. 4) Implement these new methods in existing software and integrate this software into Mesquite and CIPRES/Kepler. By the end of this project, empiricists will more easily identify relevant techniques and software to answer their questions, methods still needing development will be publicized, and a subset of the areas needing development will have methods created and implemented.
Related products
Software and Datasets- Ben Bolker, Marguerite Butler, Peter Cowan, Steven Kembel, Thibaut Jombart, Aaron Mackey, Brian O'Meara, Damien de Vienne, David Orme, Derrick Zwickl, Francois Michonneau, Hilmar Lapp, Klaus Schliep. 2008. Phylobase. http://r-forge.r-project.org/projects/phylobase/
- Bolker et al. 2008. Phylobase. http://r-forge.r-project.org/projects/phylobase/ . A new R package produced at the R hackathon; my contribution was to help add the ability for R to read data and trees from Nexus files.
- Lewis, Holder, et al. 2008. Nexus Class Library. http://sourceforge.net/projects/ncl/ . I've been added as an author for relatively minor contributions to reading multiple Nexus blocks of the same type.
- O'Meara, B.C. 2008. Brownie 2.1 (used in manuscripts, source code available): http://www.brianomeara.info/brownie
- O'Meara, B.C. 2008. MrFisher. http://www.brianomeara.info/mrfisher
- O'Meara, B.C. 2008. TreEvo. http://r-forge.r-project.org/projects/treevo/
- TreeBase mirror: http://www.brianomeara.info/treebase
- Collar, D.C., B.C. O'Meara, P.C. Wainwright, and T.J. Near. (2009) Piscivory limits diversification of feeding morphology in Centrarchid fishes. Evolution. 63(6):1557-1573.
- Collar, D.C., B.C. O'Meara, P.C. Wainwright, and T.J. Near. 2009. Piscivory Limits Diversification of Feeding Morphology in Centrarchid Fishes. Evolution 63 (6) pp. 1557-1573
- McBride, C. S., J. R. Arguello, and B. C. O'Meara. 2007. Five Drosophila Genomes Reveal Nonneutral Evolution and the Signature of Host Specialization in the Chemoreceptor Superfamily. Genetics 177:1395. [Note that the paper is authored by McBride and Arguello, and I have a separately-authored appendix, but this is how the citation appears]
- O'Meara, B.C. A new heuristic method for joint species delimitation and species tree inference. [accepted, Systematic Biology]
- O'Meara, Brian. 2008. PhD Dissertation - Using Trees: Myrmecocystus Phylogeny and Character Evolution and New Methods for Investigating Trait Evolution and Species Delimitation. Available from Nature Precedings.
- O?Meara, Brian, Alfaro, Michael, Bell, Charles, Bolker, Benjamin, Butler, Marguerite, Cowan, Peter, de Vienne, Damien, Desper, Richard, Felsenstein, Joseph, Harmon, Luke, Heibl, Christoph, Hipp, Andrew, Hunt, Gene, Jombart, Thibaut, Kembel, Steve, Lapp, Hilmar, Loarie, Scott, Maddison, Wayne, Midford, Peter, Orme, David, Paradis, Emmanuel, Price, Sam, Rabosky, Dan, Sidlauskas, Brian, Smith, Stacey, Swofford, Dave, Vision, Todd, Waddell, Peter, Zanne, Amy, and Zwickl, Derrick. 2008. Comparative methods in R hackathon. Available from Nature Precedings.
