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Supplementary Table 4. Evidence for site-specific changes in ... - PLOS

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Sites with higher. dN/dS in. Idiomarina? Proportion of sites with higher dN/dS in Idiomarina. (dN/dS > 1 in bold). Glycolysis. Pgi. 166 yes*. 0.0066 (lower) yes***.

Supplementary Table 4. Evidence for site-specific changes in dN/dS in Idiomarina genes. Test A: Selection on Idiomarina

Test B: Site-specific selection on Idiomarina

Different dN/dS in Idiomarina ?

Sites with higher dN/dS in Idiomarina?

Proportion of sites with higher dN/dS in Idiomarina (dN/dS > 1 in bold)

yes*** yes*** yes*** yes*** yes*** yes***

0.40 0.18 0.08 0.26 0.30 0.75

yes* yes*** yes*** yes**

0.07 0.23 0.16 0.45

Pathway

Gene

COG

Glycolysis

Pgi Fbp Eno TpiA Pfk NagE

166 158 148 149 205 2190

yes* yes** yes*** yes* yes* no

dN/dS in Idiomarina (relative to other lineages) 0.0066 (lower) 0.0022 (lower) 0.0017 (lower) 0.0056 (lower) 0.0038 (lower) 0.0185

Phenylalanine biosynthesis

AroQ AroB AroE PheA

757 337 169 77

yes* no no no

0.0028 (lower) 0.0044 0.0055 0.0115

Likelihood ratio test:

* P 50 substitutions per site), perhaps explaining the relatively low average values of dN/dS. In Test B, Model 4 is compared to Model 3 in a likelihood ratio test (compare 2(L4 – L3) to χ2 distribution with degrees of freedom = # parameters in Model 4 – Model 3). For all 10 genes, this test supports sites under different selection in Idiomarina. In all cases, there is at least on site category with higher dN/dS in Idiomarina than other lineages. We performed a final test to determine whether there were some sites in Idiomarina with dN/dS > 1. In this test, we compared Model 4 to Model 5 in a likelihood ratio test (compare 2(L4 – L5) to χ2 distribution with degrees of freedom = # parameters in Model 4 – Model 5). For genes with significant evidence (P < 0.05) for sites with dN/dS > 1, the proportion of sites with elevated dN/dS in Idiomarina (far right column) is shown in bold.