Complete genome sequences provide a case study for the evaluation of gene-tree thinking

Area of Science:

• Genomics
• Phylogenetics
• Bioinformatics

Background:

• This study investigates the gene-tree species-tree dichotomy using complete genome sequences from the bacterial genus Shewanella.
• Phylogenetic analyses were performed on datasets derived from 243 regions of collinear gene homology, including core Shewanella genes and genes with complete taxon sampling.

Discussion:

• Analysis of individual and concatenated genes, including sets of collinear genes, revealed a high number of unique phylogenetic topologies.
• No congruence was found between genes from collinear regions, and topologies derived from individual genes did not match concatenated results.

Key Insights:

• Maximum parsimony and maximum likelihood analyses of 55 collinear genes produced 164 unique topologies, none matching the concatenated gene tree.
• Analysis of 243 genes across the genome yielded 567 unique topologies, underscoring widespread incongruence.
• The findings challenge the assumption of the gene as a reliable phylogenetic unit without critical evaluation.

Outlook:

• Future molecular systematics research should critically assess the distinction between gene homology and character homology.
• This work contributes to understanding incongruence in phylogenetic analyses and the limitations of using individual genes as sole phylogenetic markers.