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Table 1 Maximum likelihood tests of selection on Chs, Chi, F3h, F3’h, Dfr, and Ans using HyPhy

From: The factors affecting the evolution of the anthocyanin biosynthesis pathway genes in monocot and dicot plant species

Gene

Model

â„– of parameters

Ln L

ω

Chs

Global

33

−7585.83

ω = 0.036

Local

59

−7532.90**

 

Class (monocots vs dicots)

35

−7583.59

ωm = 0.035, ωd = 0.039

Pollination (pollinators vs no-pollinators)

36

−7577.00**

ωp = 0.099, ωnp = 0.042

Regulation (color-dep vs color-indep)

35

−7582.90

ωcd = 0.051, ωcid = 0.035

Chi

Global

33

−4367.90

ω = 0.121

Local

59

−4349.01**

 

Class (monocots vs dicots)

35

−4366.33

ωm = 0.163, ωd = 0.104

Pollination (pollinators vs no-pollinators)

36

−4362.81*

ωp = 0.102, ωnp = 0.173

Regulation (color-dep vs color-indep)

35

−4367.80

ωcd = 0.136, ωcid = 0.119

F3h

Global

33

−5750.13

ω = 0.061

Local

59

−5685.06**

 

Class (monocots vs dicots)

35

−5731.97**

ωm = 0.125, ωd = 0.034

Pollination (pollinators vs no-pollinators)

36

−5717.46**

ωp = 0.058, ωnp = 0.117

Regulation (color-dep vs color-indep)

35

−5723.24**

ωcd = 0.127, ωcid = 0.032

F3’h

Global

33

−10,269.21

ω = 0.085

Local

59

−10,230.12**

 

Class (monocots vs dicots)

35

−10,257.69**

ωm = 0.120, ωd = 0.065

Pollination (pollinators vs no-pollinators)

36

−10,259.64**

ωp = 0.068, ωnp = 0.112

Regulation (color-dep vs color-indep)

No data

Dfr

Global

33

−6728.67

ω = 0.095

Local

59

−6661.18**

 

Class (monocots vs dicots)

35

−6701.70**

ωm = 0.201, ωd = 0.061

Pollination (pollinators vs no-pollinators)

36

−6703.59**

ωp = 0.114, ωnp = 0.161

Regulation (color-dep vs color-indep)

35

−6722.73*

ωcd = 0.098, ωcid = 0.107

Ans

Global

33

−7629.37

ω = 0.094

Local

59

−7547.03**

 

Class (monocots vs dicots)

35

−7588.21**

ωm = 0.219, ωd = 0.049

Pollination (pollinators vs no-pollinators)

36

−7585.99**

ωp = 0.067, ωnp = 0.196

Regulation (color-dep vs color-indep)

35

−7626.46

ωcd = 0.087, ωcid = 0.106

  1. Three factors were tested: plant classes (two separate ω were calculated for monocotyledonous and dicotyledonous plant species, ωm/ωd); pollination type (the ω for the plant species pollinated by pollinators was calculated separately from the plant species pollinated without attracting pollinators, ωp/ωnp); regulation pattern (the plant species were combined based on color-dependent and color-independent ABP gene regulation, ωcd/ωind). Significant improvement in the likelihood in comparison with the one-ratio model (Global) is indicated with asterisks: **p < 0.001, *p < 0.05