Table 1.

Comparison of substitution rates between transmission chains. Strict, strict molecular clock; relaxed, exponential relaxed molecular clock; constant, constant size; exponential, exponential growth; 95% CIs shown in brackets.

dataset	molecular clock model	coalescent model	marginal mean log likelihood	substitution rate (×10−5 mutations per nucleotide per day)
cow-to-cow (chain A)	strict	constant	−11493.09	2.27 (0.770–3.90)
	strict	exponential	−11492.27	2.26 (0.728–3.91)
	relaxed	exponential	−11493.55	1.94 (0.205–3.78)
	relaxed	constant	−11494.03	1.97 (0.313–3.76)
cow-to-cow (chain B)	strict	constant	−11605.52	2.86 (1.32–4.43)
	strict	exponential	−11603.95	2.91 (1.41–4.57)
	relaxed	exponential	−11598.06	3.21 (1.42–5.28)
	relaxed	constant	−11600.19	3.05 (1.15–4.95)
herd-to-herd (2007)	strict	constant	−11650.38	2.51 (1.43–3.74)
	strict	exponential	−11647.06	2.61 (1.45–3.87)
	relaxed	exponential	−11640.31	3.09 (1.59–4.82)
	relaxed	constant	−11644.21	2.97 (1.48–4.65)
herd-to-herd (2001)a	relaxed	exponential		2.26 (1.75–2.8)
herd-to-herd (2001)b	relaxed	constant		2.08 (0.574–3.51)

^aAdapted from [10].

^bAdapted from [11].