Fig 2.

(A) Phylogenomic and pangenomic tree comparisons of Haemophilus and Aggregatibacter reference genomes cluster genomes into the same species-level groups. Rectangle color indicates species. The phylogenomic tree was constructed using maximum likelihood with concatenated single-copy core genes. The pangenomic tree was constructed using the gene frequencies present in each genome. Lines connect rectangles that represent the same genome. (B) Average nucleotide identity (ANI) comparison of Haemophilus and Aggregatibacter reference genomes included in the pangenome. ANI represents genome-level similarity at the nucleotide level between any two genomes and reveals distinct species, corroborating the results of pangenome clustering. Rectangle color indicates species, as in panel A. The color scale denotes genome percent similarity: 100% is red, 95% is white, and 90% and below is blue.