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Published on: April 2, 2013
Phylogenetic incongruence arising from fragmented speciation in enteric bacteria
Adam C Retchless1, Jeffrey G Lawrence
1Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA.
Summary
Phylogenetic incongruence in Escherichia, Salmonella, and Citrobacter suggests ancestral recombination, not ongoing processes. This indicates a gradual decrease in genome-wide recombination rates over evolutionary time.
Area of Science:
- Evolutionary biology
- Genomics
- Phylogenetics
Background:
- Phylogenetic relationships are typically assumed to be unambiguous, with genes evolving cohesively.
- Incongruence between gene phylogenies is often attributed to individual gene evolutionary quirks.
Purpose of the Study:
- To investigate substantial phylogenetic incongruence observed among orthologous genes in Escherichia, Salmonella, and Citrobacter.
- To determine the underlying cause of this incongruence and its implications for evolutionary history.
Main Methods:
- Comparative phylogenetic analysis of orthologous genes across Escherichia coli, E. fergusonii, and E. albertii.
- Statistical assessment of conflicting phylogenetic topologies.
- Genomic analysis of phylogenetically informative sites to identify recombination patterns.
Main Results:
- Significant incongruence was detected between gene phylogenies, strongly suggesting recombination as the cause.
- Recombination events were inferred to span several kilobases on the genome.
- Analysis of more distant taxa showed consensus, indicating that recombination occurred in ancestral populations.
Conclusions:
- Conflicting gene phylogenies reflect ancestral recombination, not ongoing processes.
- Gradual decrease in genome-wide recombination rates, with locus-specific variation, explains pluralistic evolutionary relationships in descendant taxa.
- Instantaneous speciation models are less likely given the required ancestral population diversity.
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