Postdoctoral Fellow
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.
Methods to examine trait evolution on trees: advancing the field
| PI(s): | Brian C O'Meara |
| Start Date: | 1-Nov-2007 |
| End Date: | 31-Jul-2009 |
| 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- O'Meara, B.C. 2008. Brownie 2.1. Brownie is a program for analyzing rates of continuous character evolution and looking for substantial rate differences in different parts of a tree using likelihood ratio tests and Akaike Information Criterion (AIC) statistics. It now also implements many other methods for examining trait evolution and methods for doing species delimitation. See below for info on downloading the program. http://www.brianomeara.info/brownie
- O'Meara, B.C. 2008. MrFisher. This program a slight modification of MrBayes to do simulated annealing maximum likelihood tree searches (Bayes is credited with inventing Bayesian statistics, Fisher with inventing likelihood).
- O'Meara, B.C. 2008. TreEvo. TreEvo (TREE + EVOlution) is an assortment of methods for understanding evolution using trees. It aims to be compatible and complementary with the wide assortment of existing packages in this area in R.
- Lewis, Holder, et al. 2008. Nexus Class Library. The Nexus Class Library (NCL) is a C++ library for interpreting data files created according to the NEXUS file format used in phylogenetic systematics and molecular evolution.
- Brian O'Meara (2008). TreeTapper. TreeTapper is a database of methods for using phylogenies to understand evolution. Status: well-developed database schema, work is ongoing on php scripts for adding content to the database and for displaying web pages.
Development site: http://treetapper.nescent.org
Source code: http://code.google.com/p/treetapper/
- RBrownie: an R package for testing hypotheses about rates of evolutionary change J. Conrad Stack, Luke J. Harmon and Brian O'Meara. RBrownie: an R package for testing hypotheses about rates of evolutionary change, Methods in Ecology and Evolution, volume 2, issue 6, pp. 660-662
- The iPlant collaborative: cyberinfrastructure for plant biology Goff SA, Vaughn M, McKay S, Lyons E, Stapleton AE, Gessler D, Matasci N, Wang L, Hanlon M, Lenards A, Muir A, Merchant N, Lowry S, Mock S, Helmke M, Kubach A, Narro M, Hopkins N, Micklos D, Hilgert U, Gonzales M, Jordan C, Skidmore E, Dooley R, Cazes J, McLay R, Lu Z, Pasternak S, Koesterke L, Piel WH, Grene R, Noutsos C, Gendler K, Feng X, Tang C, Lent M, Kim S-J, Kvilekval K, Manjunath BS, Tannen V, Stamatakis A, Sanderson M, Welch SM, Cranston KA, Soltis P, Soltis D, O'Meara B, Ane C, Brutnell T, Kleibenstein DJ, White JW, Leebens-Mack J, Donoghue MJ, Spalding EP, Vision TJ, Myers CR, Lowenthal D, Enquist BJ, Boyle B, Akoglu A, Andrews G, Ram S, Ware D, Stein L and Stanzione D (2011) The iPlant collaborative: cyberinfrastructure for plant biology. Front. Plant Sci. 2:34. doi: 10.3389/fpls.2011.00034
- Morphogenera, Monophyly, And Macroevolution Smith, S.A. and B.C. O'Meara (2009). Morphogenera, Monophyly, And Macroevolution. Proceedings Of The National Academy Of Sciences Of The United States Of America 106(36): E97-E98.
- B. C. O'Meara (2009) New Heuristic Methods for Joint Species Delimitation and Species Tree Inference, Systematic Biology, volume 59, issue 1, pp. 59-73
- Piscivory Limits Diversification of Feeding Morphology in Centrarchid Fishes 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.
- Comparative methods in R hackathon O'Meara, B., M. Alfaro, C. Bell, et al. (2008). Comparative methods in R hackathon. Nature Precedings.
- Using Trees: Myrmecocystus Phylogeny and Character Evolution and New Methods for Investigating Trait Evolution and Species Delimitation O'Meara, Brian (2008). Using trees: Myrmecocystus phylogeny and character evolution and new methods for investigating trait evolution and species delimitation. Nature Precedings.
- Five Drosophila Genomes Reveal Nonneutral Evolution and the Signature of Host Specialization in the Chemoreceptor Superfamily 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.
