Table 1 Selected genomic characters that were significantly (α=0.01) habitat-correlated in the BayesTraits tests under all conditions (for sulphoacetaldehyde acetyltransferase (EC 2.3.3.15) under most conditions), along with their overall type of evolution (as in Figure 2), sum of evolutionary rates estimated by BayesTraits indicating co-occurrence divided by overall sum of rates and percentage occurrences (on which the test is not based) in marine and non-marine strains

From: Phylogenomics of Rhodobacteraceae reveals evolutionary adaptation to marine and non-marine habitats

Feature

ID

Rate quotient

Marine

Non-marine

I. Lost in non-marine habitats

 Chloride channel protein

COG0038

0.834

96

32

 Ca2+/Na+ antiporter

COG0530

0.783

99

42

 NhaP-type Na+/H+ and K+/H+ antiporters

COG0025

0.829

76

21

 (S)-2-haloacid dehalogenase

EC 3.8.1.2

0.751

94

21

 Mercury (Hg) II reductase

EC 1.16.1.1

0.887

98

26

 Carbon monoxide dehydrogenase

EC 1.2.99.2

0.654

93

42

 Precorrin-8X methylmutase

EC 5.4.1.2

0.445

96

63

 Precorrin-4 C11-methyltransferase

EC 2.1.1.133

0.687

95

68

 Precorrin-6B methylase 2

COG2242

0.794

85

37

 Predicted cobalamin binding protein

COG5012

0.596

90

42

 Cobalamin biosynthesis protein CbiD

COG1903

0.774

38

5

 Choline-glycine betaine transporter

COG1292

0.733

98

69

II. Gained in marine habitats

 Ectoine synthase

EC 4.2.1.108

0.979

41

0

 Ectoine biosynthesis pathway

P101-PWY

0.954

38

0

 Betaine-homocysteine S-methyltransferase

EC 2.1.1.5

0.763

25

0

 Glycine betaine degradation

PWY-3661

0.883

94

74

 Gamma butyrobetaine dioxygenase

EC 1.14.11.1

0.969

48

0

 Trimethylamine-corrinoid protein Co-methyltransferase

EC 2.1.1.250

0.493

62

11

 Trimethylamine-N-oxide reductase

EC 1.6.6.9

0.891

12

5

 Probable taurine catabolism dioxygenase

COG2175

0.859

52

16

 Nitrile hydratase

EC 4.2.1.84

0.749

62

0

 Arylsulphatase

EC 3.1.6.1

0.752

61

11

 Precorrin-3B synthase

EC 1.14.13.83

0.596

47

37

Unclear whether lost or gained

 ABC-type tungstate transport system, periplasmic component

COG4662

0.567

70

5

 ABC-type tungstate transport system, permease component

COG2998

0.676

69

5

 Sulphoacetaldehyde acetyltransferase

EC 2.3.3.15

0.434

69

53

 Trimethylamine-N-oxide reductase (cytochrome c)

EC 1.7.2.3

0.763

34

26

III. Gained in non-marine habitats

 ABC-type sulphate transport system, permease component

COG4208

0.128

12

95

 ABC-type sulphate transport system, periplasmic component

COG1613

0.129

10

95

 ABC-type sulphate/molybdate transport systems, ATPase component

COG1118

0.13

10

95

 Formaldehyde oxidation pathway II (glutathione-dependent)

PWY-1801

0.412

8

58

 S-(hydroxymethyl)glutathione synthase

EC 4.4.1.22

0.372

8

63

 Taurine dehydrogenase

EC 1.4.99.2

0.154

4

37

 6-Phosphofructokinase

EC 2.7.1.11

0.398

16

58

  1. P-values differ depending on the underlying tree and strain sampling and are provided in the according sments. The characters are presence and absence of enzymes (as indicated by their EC number), COGs (as indicated by their COG number) and pathways (as indicated by their Metacyc IDs). Ancestral character-state reconstructions of the exemplary occurrences of (S)-2-haloacid dehalogenase (EC 3.8.1.2) for type I, ectoine synthase (EC 4.2.1.108) for type II and 6-phosphofructokinase (EC 2.7.1.11) for type III are depicted in Figure 2.
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