Fig 3. Examples of incompatibilities between species assignments and phylogenetic groupings.

(A) Genetic relationships of HIV-1 (red dots) with simian immunodeficiency viruses infecting chimpanzees (gray dots) and gorillas (black dots). HIV-1 strains are polyphyletic and cannot be assigned to a single species taxon without incorporating nonhuman viruses within the definition. (B) Genetic relationships of louping ill virus (LIV) with tick-borne encephalitis virus (TBEV) strains isolated in Europe and Asia, with the principal groups labeled. Although LIV (red dots) is assigned to the species Louping ill virus, it lies within the phylogenetic tree created by strains of TBEV that all belong to the species Tick-borne encephalitis virus. The current assignment of LIV as a species therefore logically prevents strains of TBEV being assigned into a single species if species were to remain monophyletic. Trees were constructed from maximum composite likelihood distances between nucleotide sequences of (A) the pol gene of HIV-1/SIV and (B) the complete coding sequence of TBEV and LIV. To investigate the robustness of branches, nucleotide positions were bootstrap resampled 100 times as implemented in the MEGA7 program [91]; branches with 70% or greater support are labeled. The HIV-1/SIV tree was rooted using the HIV-2 sequence, M31113; the TBEV/LIV tree was rooted using the closely related Omsk haemorrhagic fever virus sequence, AY193805. Both trees have been annotated with a scale bar indicating substitutions per site.