Abstract
Background Complete genome sequences provide many new characters suitable for studying phylogenetic relationships. The limitations of the single sequence-based phylogenetic reconstruction prompted the efforts to build trees based on genome-wide properties, such as the fraction of shared orthologous genes or conservation of adjoining gene pairs. Gene content-based phylogenies, however, have their own biases: most notably, differential losses and horizontal transfers of genes interfere with phylogenetic signal, each in their own way, and special measures need to be taken to eliminate these types of noise.
Results We expand the repertoire of genome-wide traits available for phylogeny building, by developing a practical approach for measuring local gene conservation in two genomes. We counted the number of orthologous genes shared by chromosomal neighborhoods (“bins”), and built the phylogeny of 63 prokaryotic genomes on this basis. The tree correctly resolved all well-established clades, and also suggested the monophily of firmicutes, which tend to be split in other genome-based trees.
Conclusions Our measure of local gene order conservation extracts strong phylogenetic signal. This new measure appears to be substantially resistant to the observed instances of gene loss and horizontal transfer, two evolutionary forces which can cause systematic biases in the genome-based phylogenies.
