Table 1 Models of codon substitution employed on the present analysis.

Sites

M7

Distribution of ω along sites follows a β distribution, no selection

7

2

p, q

Alignments of DEF- and GLO-like genes without basal angiosperm outgroup.

M8

β distribution where ω > 1. Implements BEB^b.

8

4

p₀, p, q, ω_s, where s = number of site categories

Branches

M0

one ω value for all branches

0

1

ω

Alignments of DEF- and GLO-like genes without basal angiosperm outgroup.

M2

n different ω values on n specified branches

0

User-specified

Different ω values corresponding to each of the user-specified groups of branches

Clades and sites

M1a

nearly neutral evolution

1

2

Clades 1 and 2: 0 < ω₀ < 1, ω₁ = 1

Alignment of orchid DEF-like genes from clades 1 and 2.

p ₀

MC

In site classes 2 and 3 selective pressure varies in different parts of the phylogeny. Implements BEB^b.

2

5

Clade 1: 0 < ω₀ < 1, ω₁ = 1, ω₂

Alignment of orchid DEF-like genes from clades 3 and 4.

Clade 2: 0 < ω₀ < 1, ω₁ = 1, ω₃

Alignment of Poales GLO-like genes from clades 1 and 2.

Proportions: p₀, p₁ ^c

M3

Assumes several site classes with independently estimated ω.

3

5

ω₀, ω₁, ω₂

Same datasets analyzed with M1a vs. MC.

Proportions: p₀, p₁,

MD

In site class 2, selective pressure is different on each clade.

3

6

Clade 1: ω₀, ω₁, ω_{2 Clade 1}

Clade 2: ω₀, ω₁, ω_{2 Clade 2}

Proportions: p₀, p₁ ^d

Branches and sites

MA1

Neutral or purifying selection on individual codons along specific clades.

4

3

Site class Background Foreground

Alignments of DEF- and GLO-like genes without basal angiosperm outgroup. Specific branches of the phylogenies were tested in separate analyses.

0

0 < ω₀ < 1

0 < ω₀ < 1

1

ω₁ = 1

ω₁ = 1

2a

0 < ω₀ < 1

ω₂ = 1

2b

ω₁ = 1

ω₂ = 1

Proportions: p₀, p₁ ^d

MA

Tests for positive selection on individual codons along specific clades. Implements BEB^b. Only foreground clades experience positive selection.

4

4

Site class Background Foreground

0

0 < ω₀ < 1

0 < ω₀ < 1

1

ω₁ = 1

ω₁ = 1

2a

0 < ω₀ < 1

ω₂>1

2b

ω₁ = 1

ω₂>1

Proportions: p₀, p₁ ^d