Genome wide evolutionary analyses reveal serotype specific patterns of positive selection in selected Salmonella serotypes

Table 4 Evidence of recombination among genes with evidence for positive selection

Test for positive selection^a	No. of genes with evidence for positive selection and no evidence for recombination	No. of genes with evidence for positive selection that show evidence of recombination with^b				Total no. of genes with evidence for positive selection and recombination^c
		GENECONV	Max-χ²	PHI	NSS
TO	5	12	7	3	4	13
Ch#	8	11	10	1	3	11
Ty#	16	4	3	0	3	5
Tym#	7	4	4	0	1	4
Pty#	5	8	7	1	2	8

^aTO = overall test; Ch# = Choleraesuis branch specific test; Ty# = Typhi branch specific test; Tym# = Typhimurium branch specific test; Pty# = Paratyphi A branch specific test
^bBased on our preliminary analysis, among 3316 orthologous genes, 81 genes showed evidence of positive selection in at least one test. Among 81 genes, 32 genes also showed evidence of recombination with at least one of the four recombination tests used in our study. Statistical analysis showed that genes evidence of recombination were more likely to be under positive selection (P < 0.0001; chi-square test). Therefore, we excluded the 270 genes with evidence of recombination from our final positive selection analysis.
^cThis column lists the number of genes that show evidence for recombination and positive selection in a given test (e.g., TO); since many genes showed evidence of recombination in > 1 recombination test, the total number of genes in this column is lower than the sum of the numbers in a given row. While a total of 32 genes showed evidence of recombination and positive selection, the sum of the numbers in this column is > 32 as some genes showed evidence of positive selection in two tests.

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