Apr 8, 2015

Phylogenetic tree inference from local gene content

BioRxiv : the Preprint Server for Biology
Galina GlazkoArcady Mushegian

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 resist...Continue Reading

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Mentioned in this Paper

Genome
Genes
Trees (plant)
Reconstructive Surgical Procedures
Phylogenetic Analysis
Comparative Genomic Analysis
Firmicutes
Chromosomes
Biniou protein, Drosophila
Horizontal

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