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Figure 1 | BMC Evolutionary Biology

Figure 1

From: Declining transition/transversion ratios through time reveal limitations to the accuracy of nucleotide substitution models

Figure 1

Estimates of key parameters plotted against root-node age for 10 representative viruses. (A) ti/tv, (B) d N /d S , (C) shape parameter α of the Γ-distribution, and (D) CG-content. The symbols represent the different viruses: African swine fever virus (ASFV), Barley yellow dwarf virus (BYDV), GPCR gene of Capripoxivirus (CaPV), CP gene of Cereal yellow dwarf virus (CYDV), Dengue virus type 4 (DENV-4), Ebolavirus (EBOV), Hepatitis B virus (HBV), HIV-1, Rabies virus (RABV), and HIV-2 and some closely related SIV lineages (HIV-2 + SIV). Black symbols correspond to the complete data sets, while red symbols correspond to the reduced-age data sets in which we removed the most divergent lineages. Lines show the differences in the estimates between the complete and the reduced-age data sets, and do not represent regressions. Dashed lines correspond to estimates that are not considered to differ between the complete and reduced-age data sets, which is assessed by estimating the parameters with random subsamples of the data (see Additional file 2: Table S2).

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