PSB 2004 Tutorial

PSB 2004

Network (Reticulated) Evolution: Biology, Models, and Algorithms

C. Randal Linder, Bernard M.E. Moret, and Tandy Warnow


This tutorial will present the state of knowledge in biology regarding reticulate evolution, review the proposed models for evolutionary networks, relate classical tree reconstruction to network reconstruction, introduce recent computational work in the latter, and identify some of the main challenges in data collection, modeling, and algorithm design that will have to be overcome in order to produce accurate simulation and reconstruction software. The tutorial will also address other evolutionary processes that can give the appearance of reticulation even though their underlying nature is tree-like. Finally, a computer lab will be conducted to demonstrate software currently available for detecting reticulation and recombination and to show how the evolutionary processes differ from one another.

Attendees will learn the extent to which reticulation impacts evolution and, in particular, what effect reticulation has on diseases, crops, and the environment; they will appreciate the main challenges involved in modeling and reconstructing network evolution and be brought up-to-date on the state-of-the-art in computational methods for detecting reticulation and recombination, assessing reconstructed networks, and attempting computational reconstructions.

Biographical Sketches

C. Randal Linder is Associate Professor of Integrative Biology in the School of Biological Sciences at the University of Texas. His research, funded under 5 separate NSF grants, focuses on two areas in biology: phylogenetics, with special emphasis on reticulate evolution, and the evolutionary significance of oil composition in seeds. His lab is developing benchmark biological systems that can be used to validate methods for reconstructing reticulate evolution. Dr. Linder has published papers on a wide variety of topics in evolutionary biology, has extensive experience lecturing on these topics, and has won the U. of Texas Teaching Excellence award.

Bernard M.E. Moret is Professor of Computer Science and of Electrical and Computer Engineering at the University of New Mexico. His research, funded under 6 separate NSF grants, a Sloan Foundation award, and an IBM grant, is aimed at developing high-performance methods for phylogenetic reconstruction (see He leads a group of 15 institutions (including Berkeley, San Diego, Austin, and Yale) on a very large, 5-year NSF project to develop a computational infrastructure to support attempts to reconstruct the Tree of Life. He has taught at UNM for 23 years, developed two dozen senior and graduate classes in algorithms and experimentation, won every department, college, and university teaching award, authored two textbooks, and given invited lecture series on algorithm engineering, phylogenetic reconstruction, and high-performance computing.

Tandy Warnow is Professor of Computer Sciences at the University of Texas in Austin, where she codirects the Center for Computational Biology and Bioinformatics. She is a past NSF Young Presidential Investigator and Packard Fellow. She has pursued research in algorithms for phylogenetic reconstruction for over a dozen years, including applications in linguistics (see http:/// She is funded by a number of NSF grants from both Computer Science and Biology. Prof. Warnow has taught classes in algorithms and computational biology for 10 years at U. of Pennsylvania, U. of Arizona, and U. of Texas, designed graduate seminars in computational biology, given invited lecture series in numerous workshops around the world, and recently co-taught a tutorial on phylogenetic methods (at ISMB'99).

The three lecturers are frequent collaborators; in particular, all three are jointly funded by the NSF to study network reconstruction.

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