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Table 4 Alphabet size and performance.

From: Detecting coevolution without phylogenetic trees? Tree-ignorant metrics of coevolution perform as well as tree-aware metrics

(A) Tetrapod Myoglobin

Method

A1

A2

A3

A4

A5

 

Ï„

p-value

Ï„

p-value

Ï„

p-value

Ï„

p-value

Ï„

p-value

MI

-0.20

4.8 × 10-1

0.42

1.1 × 10-1

0.16

6.0 × 10-1

-0.33

2.2 × 10-1

0.24

3.8 × 10-1

NMI

-0.29

2.9 × 10-1

0.24

3.8 × 10-1

0.24

3.8 × 10-1

0.16

6.0 × 10-1

0.56

2.9 × 10-3

RMI

0.11

7.3 × 10-1

0.33

2.2 × 10-1

-0.51

4.7 × 10-3

-0.02

1.0

0.64

9.1 × 10-3

SCA8

-0.24

3.8 × 10-1

0.78

9.5 × 10-34*

0.56

2.9 × 10-3

-0.02

1.0

0.87

1.2 × 10-34*

MIp

0.16

6.0 × 10-1

0.47

7.3 × 10-2

0.29

2.9 × 10-1

-0.11

7.3 × 10-1

0.78

9.5 × 10-34 *

AS

-0.02

1.0

0.64

9.1 × 10-3

0.29

2.9 × 10-1

-0.47

7.3 × 10-2

0.07

8.6 × 10-1

G7

0.16

6.0 × 10-1

0.64

9.1 × 10-3

0.33

2.2 × 10-1

0.42

1.1 × 10-1

0.47

7.3 × 10-2

(B) Randomized Tetrapod Myoglobin

Method

A1

A2

A3

A4

A5

 

Ï„

p-value

Ï„

p-value

Ï„

p-value

Ï„

p-value

Ï„

p-value

MI

-0.38

1.6 × 10-1

-0.29

2.9 × 10-1

-0.07

8.6 × 10-1

0.16

6.0 × 10-1

0.60

1.7 × 10-3

NMI

-0.29

2.9 × 10-1

-0.16

6.0 × 10-1

-0.47

7.3 × 10-2

-0.07

8.6 × 10-1

0.16

6.0 × 10-1

RMI

-0.38

1.6 × 10-1

-0.29

2.9 × 10-1

-0.11

7.3 × 10-1

-0.16

6.0 × 10-1

0.56

2.9 × 10-3

SCA8

-0.73

2 2 × 10-3

-0.69

4.7 × 10-3

-0.60

1.7 × 10-3

-0.64

9.1 × 10-3

0.07

8.6 × 10-1

MIp

-0.38

1.6 × 10-1

-0.69

4.7 × 10-3

-0.42

1.1 × 10-1

-0.11

7.3 × 10-1

0.29

2.9 × 10-1

AS

-0.56

2.9 × 10-3

-0.42

1.1 × 10-1

-0.38

1.6 × 10-1

-0.38

1.6 × 10-1

-0.24

3.8 × 10-1

G7

0.60

1.7 × 10-3

0.29

2.9 × 10-1

-0.29

2.9 × 10-1

0.56

2.9 × 10-3

0.20

4.8 × 10-1

(C) Chordate Myosin

Method

A1

A2

A3

A4

A5

 

Ï„

p-value

Ï„

p-value

Ï„

p-value

Ï„

p-value

Ï„

p-value

MI

0.78

9.5 × 10-34*

0.78

9.5 × 10-34*

0.64

9.1 × 10-3

0.60

1.7 × 10-3

0.82

3.6 × 10-34*

NMI

0.69

4.7 × 10-3

0.78

9.5 × 10-34*

0.56

2.9 × 10-3

0.29

2.9 × 10-1

0.82

3.6 × 10-34*

RMI

0.29

2.9 × 10-1

0.29

2.9 × 10-1

-0.07

8.6 × 10-1

-0.51

4.7 × 10-3

0.60

1.7 × 10-3

SCA6

0.56

2.9 × 10-3

0.20

4.8 × 10-1

0.16

6.0 × 10-1

-0.07

8.6 × 10-1

0.16

6.0 × 10-1

MIp

0.78

9.5 × 10-34*

0.78

9.5 × 10-34*

0.69

4:7 × 10-3

0.60

1.7 × 10-3

0.73

2.2 × 10-3

AS

-0.16

6.0 × 10-1

0.29

2.9 × 10-1

0.73

2:2 × 10-3

0.42

1.1 × 10-1

0.29

2.9 × 10-1

(D) Randomized Chordate Myosin

Method

A1

A2

A3

A4

A5

 

Ï„

p-value

Ï„

p-value

Ï„

p-value

Ï„

p-value

Ï„

p-value

MI

-0.51

4.7 × 10-3

-0.33

2.2 × 10-1

-0.07

8.6 × 10-1

0.16

6.0 × 10-1

-0.16

6.0 × 10-1

NMI

-0.20

4.8 × 10-1

-0.78

9.5 × 10-34*

-0.29

2.9 × 10-1

0.51

4.7 × 10-3

0.20

4.8 × 10-1

RMI

-0.33

2.2 × 10-1

-0.60

1.7 × 10-3

-0.24

3.8 × 10-1

0.16

6.0 × 10-1

-0.11

7.3 × 10-1

SCA6

-0.16

6.0 × 10-1

-0.56

2.9 × 10-3

-0.60

1.7 × 10-3

0.20

4.8 × 10-1

-0.24

3.8 × 10-1

MIp

-0.29

2.9 × 10-1

-0.47

7.3 × 10-2

-0.64

9.1 × 10-3

0.38

1.6 × 10-1

-0.51

4.7 × 10-3

AS

0.20

4.8 × 10-1

0.20

4.8 × 10-1

-0.11

7.3 × 10-1

0.02

1.0

-0.11

7.3 × 10-1

  1. For each of the five heuristically defined alphabets, Kendall correlation coefficients (τ) and corresponding p-values are provided to illustrate the relationship between performance rank and alphabet size. Bolded values highlight p-values = 0.05, and starred values indicated p-values significant after adjustment for multiple comparisons (A-B Bonferroni-adjusted α = 0.0014, C-D Bonferroni-adjusted α = 0.0017). Tau range: [-1., 1.]. A positive τ value indicates a positive correlation (i.e., increased alphabet size is associated with increased performance), and a negative τ value indicates a negative correlation (i.e., decreased alphabet size is associated with increased performance).
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BMC Ecology and Evolution

ISSN: 2730-7182

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