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. 2025 Aug 5;16(9):e00564-25. doi: 10.1128/mbio.00564-25

Fig 1.

Phylogenetic and PCA analyses of Histoplasma reveal Africa and Hcf as distinct monophyletic lineages. Strong bootstrap support validates major clades, with the first four principal components capturing most genetic variation between continental groups.

The partition of genetic diversity in Histoplasma shows that the Africa and Hcf lineages are differentiated monophyletic groups. (A) BUSCO tree showing the genealogical relationships between the different lineages of Histoplasma. Isolates collected in Africa belong to two groups, Africa and Hcf, both marked with black bars. T-3-1, a North American isolate, is marked with a blue circle. All the samples in the Africa lineage are newly sequenced with the exception of the two tips labeled with a red pentagon (Hc_duboisii-A and Hc_duboisii-B). The only isolate from Africa that clustered outside of the Africa and Hcf lineages clustered with mz5-like (a species described in reference 34) and is labeled with a yellow triangle. Numbers in the nodes show the bootstrap and concordance factors for each node. (B) The first two components (PCs) of a principal component analysis show differentiation of the African lineages with the rest of genetic clusters in Histoplasma and explain over 40% of the genetic variance. (C) PC3 and PC4 explain 29% of the variance. (D) Scree plot showing the contributions of each PC. Light tan bars show the value of the eigenvalues. Brown bars show the expected eigenvalues in a broken stick model, and the red dashed line shows the expected contributions of the eigenvalues in a uniform distribution model.