Table 1.

Summary of findings from Bayesian phylogenetic inference for major Shigella lineages.

Species	Lineage	TMRCA of SEA isolates (95% HPD lower – 95% HPD upper)	Substitution model	Clock model	Demogra-phic model	Substitution rate (95% HPD lower – 95% HPD upper)
Shigella flexneri	1	1974.43 (1972.36 – 1976.5)	TVM	Random local	BSk	6.65 (6.1 – 7.25) x 10−7
	2.1	1978.79 (1977.26 – 1980.57)	K3P	Random local	BSk	7.58 (6.4 – 8.7) x 10−7
	2.2	1948.69 (1942.15 – 1955.3)	TVM	Strict	BSk	7.52 (6.7 – 8.31) x 10−7
	3Xv	1988.81 (1987.79 – 1990.04)	TVM	Random local	Constant	8.60 (7.5 – 9.6) x 10−7
	3.1	1978.66 (1977.74 – 1979.62)	TVM	Random local	BSk	7.98 (7.4 – 8.56) x 10−7
	3.2	1979.58 (1977.11 – 1982.29)	TVM	Random local	BSk	8.85 (8.02 – 9.61) x 10−7
	4	NA	NA	NA	NA	NA
	7	1400.09 (1236.37 – 1589.93)	TVM	Strict	Constant	1.40 (1.00 – 1.78) x 10−7
	8	1932.57 (1915.11 – 1953.65)	TVM	Random local	BSk	3.66 (2.78 – 4.49) x 10−7
Shigella sonnei	Lin1	1869.93 (1834.41 – 1911.2)	TVM	Random local	Constant	3.84 (3.04 – 4.63) x 10−7
	earlySEA	1979.36 (1978.62 – 1980.19)	TVM	Random local	BSk	8.89 (7.63 – 10.2) x 10−7
	Global 3.1	1975.95 (1972.07 – 1980.45)	TVM	Random local	BSk	5.42 (4.81 – 6.04) x 10−7
	Global 3.2	1985.71 (1984 – 1986.05)	TVM	Random local	BSk	7.99 (7.25 – 8.7) x 10−7

The table details the estimation of major parameters, including the estimated TMRCA (time to most recent common ancestor) of isolates in Southeast Asia and its 95% high posterior density (95% HPD), the substitution rate (in substitutions per site per year) and its 95% HPD, as well as the molecular clock and demographic models utilised. For each lineage, the results are summarised across three independent BEAST runs, and the most appropriate evolutionary models were chosen based on Bayes factor comparison.

TVM Transversion model, K3P Kimura-3-parameters model, BSk Bayesian Skyline