Evidence of microevolution of Salmonella Typhimurium during a series of egg-associated outbreaks linked to a single chicken farm

Table 3 Divergence dating analysis for outbreak-related S. Typhimurium 135@

	BEAST	Patho-O-Gen	Consensus values
Confidence	100 million iterations x 5 runs (ESS > 30,000)	R² = 0.71	-
Divergence date for all S . Typhimurium 135@	May 1996 [Jul 1986 - Nov 2001]	Mid 1997	1996-1997
Divergence date for S . Typhimurium 135@ farm clone	May 2004 [Sep 2002 - Mar 2005]	Early 2003	2003-2004
Substitution rate variable site^-1 day^-1	7.6 × 10^-6 [3.2 – 12.5 × 10^-6]	4.4 × 10^-6	4.4-7.6 × 10^-6
Substitution rate site^-1 year^-1	1.2 × 10^-6 [4.8 – 19 × 10^-7]	6.7 × 10^-7	6.7-12 × 10^-7
SNP year ^-1	5 [2–8]	3	3-5

Divergence and mutation rate estimates [95% highest posterior density intervals] from BEAST and Path-O-Gen analyses, and consensus values across these two methods. ESS, effective sample size; R², Pearson correlation between date of isolation and maximum likelihood tree branch length.

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