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Table 2 Parameters utilized for Bayesian inference of evolution of the GH9 and CBM49 domains

From: Origin, evolution, and divergence of plant class C GH9 endoglucanases

Site

Model: Gamma

Subsitution rate = 1.0

Substitution model: WAG/ JTT

Gamma category count = 5

Shape: 1.537/ 0.813

Proportion invariant: NA/ 0.027

Clock

Model: Relaxed clock Log Normal

Number of Discrete Rates = − 1

Clock rate = 1.0

Calibrated Yule model

Birth rate = 1.0

Type (Full)

birthRate

Model: Gamma

Initial = 1.0 [−∞, ∞]

α = 1.0E − 03

β = 1.0E + 03

Mode:= Shape Scale

Offset = 0.0

gammaShape

Model: Gamma

Initial = 1.0 [−∞, ∞]

α = 1.0E − 03

β = 1.0E + 03

Mode: Shape Scale

Offset = 0.0

Population mean

Model: Exponential

Initial = 1.0 [−∞, ∞]

μ = 10.0

Offset = 0.0

Uncorrelated relaxed local clock mean

Model: Exponential

Initial = 1.0 [−∞, ∞]

μ = 10.0

Offset = 0.0

Uncorrelated relaxed local clock standard deviation

Model: Exponential

Initial = 1.0 [−∞, ∞]

σ = 0.3337

Offset = 0.0

Root

Parent of: Bacteria/ Vascular class C land plants

Monophyletic

Model: Log Normal

μ = 8.2/ 5.41

σ = 0.07/ 0.055

Offset = 0.0

2.5% Quantile = 3170/ 201Mya

97.5% Quantile = 4180/ 249Mya

Markov chain monte carlo

Chain length = 14,917,000 / 16,120,000

Pre Burnin = 4,200,000/ 2,130,000

Recording interval = 1000

  1. Abbreviations: GH9 Glycoside hydrolase 9, CBM49 Carbohydrate binding module 49, WAG Whelan and Goldman, JTT Jones, Taylor, and Thornton