Genomics / Proteomics
Bailey, C. Donovan , Fain, Mathew G. , Houde, Peter .
Conditioned reconstruction and the recovery of fusion genomes.
CONDITIONED reconstruction represents a new phylogenetic method specifically designed to use gene presence/absence (PA) data to study divergent and reticulate evolutionary events. In the first direct application of conditioned reconstruction, the results were stated to unambiguously support the role of an archaeal and eubacterial genome fusion event (a form of highly divergent hybridization) in the ancestry of the eukaryotic genome. We outline the basic components of the methods that comprise conditioned reconstruction, discuss the logic behind their application, and use simulated genome evolution to identify concerns with aspects of data interpretation and the current use of conditioning genomes and aligned networks to investigate genome fusion. The simultaneous analysis of all available characters and the use of existing consensus techniques (e.g., Adams) recover fusion genomes in situations where the current application of conditioned reconstruction can fail. The results also demonstrate that the phylogenetic position of a conditioning genome(s), relative to putative fusion genomes, can be as great a consideration as the number of genes in the conditioning genome. These factors represent important considerations for those using conditioned reconstruction with gene PA data or anyone thinking of extrapolating such an approach to other classes of PA characters derived from genomic data (e.g., AFLP or array-based fragment screening).[c.e.:srb]
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1 - New Mexico State University, Department of Biology, Po Box 30001, Department 3Af, Las Cruces, New Mexico, 88003-8001, USA
2 - University of New Mexico, Department of Biology, 167 Castetter Hall, Albuquerque, New Mexico, 87131, USA
Presentation Type: Oral Paper:Papers for Topics
Date: Tuesday, August 1st, 2006
Time: 3:30 PM