Table 2.

Contingency Table Analysis for Puyacatengo

Puyacatengo Drainage
Data Included		Under Selection	Not Under Selection	Odds Ratio	P Value
All genes	DE	18	256	3.78547	<0.0001**
	Not DE	111	5,976
Nonsynonymous	DE	9	265	5.55329	<0.0001**
	Not DE	37	6,050
Synonymous	DE	9	265	2.75966	<0.0001**
	Not DE	74	6,013
Upregulated	DE	12	117	5.36051	<0.0001**
	Not DE	117	6,115
Downregulated	DE	6	139	2.13827	0.0737
	Not DE	123	6,093
Fixed	DE	2	272	4.96569	0.0787
	Not DE	9	6,078
Not fixed	DE	16	258	3.71287	<0.00001**
	Not DE	100	5,987

Note.—The leftmost column denotes the genes that are included in specific categories. “All genes” includes all differentially expressed genes in the “DE” category and all genes with at least one site under selection in the “Under selection” category. “Nonsynonymous” includes only genes containing at least one nonsynonymous site under selection in the “Under Selection” category. “Synonymous” includes only genes containing no nonsynonymous sites under selection in the “Under Selection” category. “Upregulated” includes only genes that were upregulated in the sulfidic population in the “DE” category. “Downregulated” includes only genes that were downregulated in the sulfidic population in the “DE” category. “Fixed” includes only genes that contained at least one fixed difference between sulfidic and nonsulfidic populations in the “Under selection” category. “Not fixed” includes only genes that did not contain any fixed differences, but had other sites under selection in the “Under Selection” category. The second through fourth columns from the left show the observed tables for each set of genes. The fifth column shows the odds ratio, and the last column shows the P value.

^*P value <0.05, **P value <0.005.