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Using Avida to test the effects of natural selection on phylogenetic reconstruction methods

Hagstrom, George I. and Hang, Dehua H. and Ofria, Charles and Torng, Eric (2004) Using Avida to test the effects of natural selection on phylogenetic reconstruction methods. Artificial Life, 10 (2). pp. 157-166. ISSN 1064-5462. http://resolver.caltech.edu/CaltechAUTHORS:HAGal04

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Abstract

Phylogenetic trees group organisms by their ancestral relationships. There are a number of distinct algorithms used to reconstruct these trees from molecular sequence data, but different methods sometimes give conflicting results. Since there are few precisely known phylogenies, simulations are typically used to test the quality of reconstruction algorithms. These simulations randomly evolve strings of symbols to produce a tree, and then the algorithms are run with the tree leaves as inputs. Here we use Avida to test two widely used reconstruction methods, which gives us the chance to observe the effect of natural selection on tree reconstruction. We find that if the organisms undergo natural selection between branch points, the methods will be successful even on very large time scales. However, these algorithms often falter when selection is absent.


Item Type:Article
Related URLs:
URLURL TypeDescription
http://dx.doi.org/10.1162/106454604773563586DOIUNSPECIFIED
http://www.mitpressjournals.org/doi/abs/10.1162/106454604773563586PublisherUNSPECIFIED
Additional Information:© 2004 Massachusetts Institute of Technology. Posted Online March 11, 2006. We thank C. Adami, D. A. Drummond, R.E. Lenski, D. Wagenaar, and C. O. Wilke for discussions. This work was supported in part by the National Science Foundation’s Biocomplexity Program under Contract No. DEB-9981397. All data was obtained on a cluster of 160 processors at Michigan State University, supported by the NSF under the aforementioned contract. GIH acknowledges a Caltech SURF fellowship.
Funders:
Funding AgencyGrant Number
NSF Biocomplexity ProgramDEB-9981397
Caltech SURFUNSPECIFIED
Subject Keywords:phylogeny reconstruction; digital evolution; molecular clock; natural selection; Avida
Record Number:CaltechAUTHORS:HAGal04
Persistent URL:http://resolver.caltech.edu/CaltechAUTHORS:HAGal04
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:13452
Collection:CaltechAUTHORS
Deposited By: Tony Diaz
Deposited On:10 Jul 2009 17:03
Last Modified:26 Dec 2012 10:50

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