On conditioned reconstruction, gene content data, and the recovery of fusion genomes

Abstract

Conditioned reconstruction (CR)1 represents a new phylogenetic method that has been presented as a means of utilizing vast amounts of gene absence/presence data to reconstruct phylogenetic relationships and to directly study the inXuence of genome fusion on evolution (Lake and Rivera, 2004; Rivera and Lake, 2004; Simonson et al., 2005). In the Wrst direct application of CR, the results were stated to unambiguously support the role of an archaeal and eubacterial genome fusion event in the ancestry of the eukaryotic genome (McInerney and Wilkinson, 2005; Rivera and Lake, 2004; Simonson et al., 2005). In the present manuscript, we outline the basic components of CR, discuss the logic behind their application, and subsequently identify concerns with aspects of data interpretation and the current use of conditioning genomes and aligned networks in the study of genome fusion. Conditioned reconstruction begins with the selection of a conditioning genome (CG) that will represent the full set of orthologous genes coded during matrix development (Lake and Rivera, 2004). Strong emphasis has been placed on the strict use of relatively small genomes as conditioning genomes (Lake and Rivera, 2004). This recommendation is based on the observation that the use of relatively large conditioning genomes can induce an artifact referred to as “big genome attraction,” which can mislead phylogenetic inference. All other genomes that will be used in the analysis are scored for the absence or presence of a putative ortholog to each gene in the CG. Orthologs present in other genomes included in the