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Table 3 Details of nucleotide diversity and neutrality tests for candidate genes in the wild collection

From: Molecular ecology and selection in the drought-related Asr gene polymorphisms in wild and cultivated common bean (Phaseolus vulgaris L.)

Gene

Set

Population

P(C)

h

S

Ts

Tv

Ka

Ks

ω

Ï€ (E-3)

S.D. π (E-3)

θw(E-3)

S.D. θW(E-3)

TD

DT 95% C.I.

p-value DT

R2

p-value R2

Max. K

Asr 1

Exon

Global

0.95

3

3

3

  

3

0.0

2.2

0.6

2.4

1.5

−0.22

−1.72

2.07

0.47

1.1

0.46

2

M

0.85

3

3

3

  

3

0.0

2.2

1.1

3.4

2.2

−1.18

−1.45

1.72

0.08

1.3

<0,001

2

G

0.75

2

2

2

  

2

0.0

1.9

1.3

2.8

2.1

−1.24

−1.24

1.65

<0,001

3.5

0.87

2

E

0.67

2

2

2

  

2

0.0

2.7

1.6

3.3

2.6

−0.97

−0.97

1.46

0.46

4.0

0.85

2

Intron

Global

0.95

3

2

1

1

   

3.9

1.0

4.2

3.1

−0.16

−1.49

2.09

0.48

1.1

0.36

2

M

0.86

2

1

 

1

   

4.1

1.0

2.9

2.9

0.95

−1.46

1.48

0.68

2.3

0.33

1

G

0.75

2

1

 

1

   

2.5

1.7

3.6

3.6

−1.01

−1.01

1.34

0.52

3.5

0.50

1

Asr 2

Global

Global

0.97

4

3

 

3

 

1

0.0

4.1

0.3

2.6

1.2

2.18

0.97

−1.62

<0,001

2.0

0.97

4

M

0.94

3

3

 

3

 

1

0.0

4.0

0.4

2.5

1.4

1.43

0.94

−1.74

1.92

1.9

0.92

4

G

0.78

2

3

 

3

   

4.1

1.0

3.0

2.0

1.60

0.91

−1.45

1.73

2.7

0.85

3

C

0.78

3

3

 

3

   

4.3

0.7

3.0

2.0

1.85

0.99

−1.45

1.73

2.8

0.93

3

A

0.91

3

3

 

3

   

2.5

0.9

2.8

1.4

0.48

0.72

−1.73

2.02

1.6

0.69

3

Exon

Global

0.97

2

1

 

1

 

1

0.0

0.7

0.3

1.1

1.1

−0.46

0.49

−1.06

1.78

0.6

0.28

1

M

0.94

2

1

 

1

 

1

0.0

0.3

0.3

1.4

1.4

−1.14

0.28

−1.14

1.64

1.7

0.69

1

UTR

Global

0.97

3

2

 

2

   

23.1

1.3

9.8

6.0

1.61

0.99

−1.57

1.96

2.4

0.99

3

M

0.94

2

2

 

2

   

23.7

1.9

11.8

7.4

2.32

0.99

−1.73

2.14

2.5

0.99

3

G

0.78

2

2

 

2

   

25.5

5.9

18.4

12.4

1.60

0.92

−1.45

1.86

2.7

0.88

3

C

0.78

2

2

 

2

   

26.6

4.2

18.4

12.4

1.85

0.98

−1.45

1.73

2.8

0.93

3

  

A

0.91

2

2

 

2

   

15.7

5.3

17.7

8.4

0.48

0.73

−1.73

1.87

0.16

0.65

0.03

  1. h: number of haplotypes, S: number of polymorphic sites.
  2. Populations M: Mesoamerican, G: Guatemala, C: Colombia, E: Peru and Ecuador, A: Andean.
  3. P(C): Probability of having captured the deepest coalescent event.
  4. π: nucleotide diversity Ts: Transitions, Tv: Transversions, ω: Non synonymous, synonymous substitution ratio (Ka/Ks) (Only for protein coding regions).
  5. TD: Tajima’s D, θw: Theta of Watterson (per site, from S), S.D.: Standard deviation.
  6. p-Value: probability estimator ≠ 0 as determined by coalescent simulation.
  7. R2: Ramos-Onsins & Rozas’ R2 (tests population growth), Max. K: Maximum number of nucleotide differences between any two sequences.
  8. Empty cells: No applicable data (when h = 0).
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BMC Genomic Data

ISSN: 2730-6844

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