Extended Data Fig. 5: Subtype deep branching and comparison of FBP and TBE using medium-sized HIV datasets.

As the taxa were randomly drawn from the full dataset, the supports and findings show some fluctuations. a, b, Trees obtained with two of the medium-sized datasets; branches with FBP > 70%: yellow dots; branches with TBE > 70%: blue dots; subtype clades: red stars, filled if support > 70% (see Methods and Fig. 1 legend for further details). c, Deep branching of the subtypes¹⁹ and supports obtained on the full dataset (see also Fig. 1). Rare subtypes (H, J and K) are absent in the medium-sized datasets, and the subtype clades are almost perfectly recovered (only one incorrect taxon in A clade for both trees). FBP supports are higher when using medium-sized datasets than when using the full dataset (for example, 58% and 99% for subtype B, versus 3% in Fig. 1). However, some subtype clades (for example, D) have moderate FBP support, though the clade matches the subtype perfectly. When using TBE, all subtype supports are higher than 95%. The deep branching is the same for all full and medium-sized datasets, and is identical to that found in a previous study¹⁹, but is not supported by FBP, whereas TBE is larger than 70% for every branch (or path in Fig. 1). Again, the Indian and East African sub-epidemics of subtype C are supported by TBE, but not by FBP.