Table 3.

Testing for common ancestry of E6 and E7 on reduced dataset 2. The test was performed using the software Bali-Phy on the concatenated E6 and E7 amino acid sequences as well as on E6 and E7 separately. The log marginal likelihoods (P(data|M)) are indicated for the Common Ancestry (CA) model (H0) and the alternative Independent Origin (IO) models (H1–H7). The Bayes factor for CA is calculated as ΔBF = log [Prob(CA)] − log [Prob(IO)], such that positive values favour CA and negative values indicate IO.

	E6E7		E6		E7
model	P(data|M)	ΔBF	P(data|M)	ΔBF	P(data|M)	ΔBF
H0: (grey-blue-yellow-red-black-green)	−19083.055	0	−10847.336	0	−8106.947	0
H1: grey+(blue-yellow-red-black-green)	−19165.438	82.383	−10915.029	67.693	−8153.371	46.424
H2: grey+blue+(yellow-red-black-green)	−19406.063	323.008	−11020.832	173.496	−8281.371	174.424
H3: grey+blue+yellow+(red-black-green)	−19676.573	593.518	−11174.707	327.371	−8424.371	317.424
H4: grey+blue+yellow+red+(black-green)	−19921.623	838.568	−11306.744	459.408	−8539.261	432.314
H5: grey+blue+(red-black)+(green-yellow)	−19682.881	599.826	−13601.982	2754.646	−8411.536	304.589
H6: grey+blue+red+black+(green-yellow)	−19886.211	803.156	−13704.295	2856.959	−8511.299	404.352
H7: grey+blue+yellow+red+black+green	−20121.000	1037.945	−11412.956	565.620	−8642.184	535.237