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Updated: Aug 30, 2026

Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations
Published on: December 7, 2021
Application of phylogeny reconstruction and character-evolution analysis to inferring patterns of directional
1Department of Veterinary Pathobiology, College of Veterinary Medicine, University of Illinois, 2001 South Lincoln Avenue, Urbana, IL 61820, USA. tlgoldbe@uiuc.edu
Abstract:
I used phylogenetic analyses to reconstruct patterns of directional interspecific transmission during a pseudorabies virus outbreak in Illinois, USA, in 1989. Isolates were recovered from five species: cattle, sheep, goats, pigs, and raccoons (Procyon lotor). I generated DNA sequences for 16 isolates of pseudorabies virus at the glycoprotein C gene, from which I constructed phylogenetic trees. I then used these trees, in combination with parsimony-based analyses of character evolution, to infer the frequency and direction of interspecific transmission events. Comparing inferred frequencies and directions of transmission to null expectations based on 10,000 random trees indicated a significant excess of transmission events from pigs to pigs and a corresponding lack of transmission events from non-porcine species. These results are concordant with the know biology and natural history of pseudorabies virus, and they demonstrate that retrospective phylogeny reconstruction and analyses of character evolution can be used to investigate the transmission ecology of pathogens.
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