Table 1

Summary statistics for loci Cox1, Ras, ITS, β-tubulin and Avr3a from P. infestans in the Northern Andean region and worldwide.

GEOGRAPHIC

REGION

LOCUS

Sequences

(N) a

Length

(bp)

Segregating SITES

GENETIC

VARIABILITY

(Segregating Sites/Length)

πb

θ

SITE c

N Haplotypes

HDd


NORTHERN ANDEAN (Colombia and Venezuela)

Cox1

73

669

1

0.15

0.0004

0.0003

2

0.3

Ras

85

765

3

0.39

0.0008

0.0008

2

0.21

β-tub

90

815

14

1.72

0.0015

0.0036

11

0.47

Avr3a

80

444

12

2.70

0.0017

0.0055

4

0.12


Central Andes (Antioquia)

Cox1

17

669

0

0

0

0

1

0

Ras

18

765

0

0

0

0

1

0

β-tub

20

815

4

0.49

0.0012

0.0014

4

0.56

Avr3a

16

444

0

0

0

0

1

0


Eastern Andes (Boyacá Cundinamarca)

Cox1

35

669

1

0

0.00009

0.0004

2

0.057

Ras

35

765

0

0

0

0

1

0

β-tub

36

815

2

0.24

0.0002

0.0006

3

0.16

Avr3a

35

444

1

0.22

0.0001

0.0005

2

0.057


Southwestern Andes (Nariño)

Cox1

10

669

1

0.15

0.0005

0.0005

2

0.36

Ras

12

765

0

0

0

0

1

0

β-tub

21

815

12

1.47

0.004

0.004

9

0.843

Avr3a

17

444

11

2.48

0.007

0.007

3

0.412


Venezuela

Cox1

11

669

1

0.15

0.0003

0.0005

2

0.182

Ras

20

765

3

0.39

0.0021

0.0011

2

0.526

β-tub

13

815

1

0.13

0.0002

0.0004

2

0.154

Avr3a

12

444

0

0

0

0

1

0


REST OF THE WORLD

Cox1

69

669

4

0.59

0.0097

0.0012

5

0.574

Ras

166

766

13

1.69

0.0031

0.0029

12

0.583

β-tub

13

815

2

0.24

0.0011

0.0008

3

0.59

Avr3a

8

444

4

0.9

0.0046

0.0035

3

0.607

Cox1

142

669

4

0.59

0.00078

0.0011

5

0.473


WORLDWIDE

Ras

251

766

13

1.69

0.0024

0.0028

13

0.482

β-tub

103

815

14

1.71

0.0016

0.0033

11

0.544

Avr3a

88

444

12

2.7

0.002

0.0054

6

0.174


a Numbers represent sequences and can exceed the numbers of strains due to heterozygous individuals

b π = Nucleotide Diversity

c θ SITE = Watterson's Theta per site

d HD = Haplotype diversity

Colombia and Venezuela are designated NA; the rest of the world, corresponding to available sequences from other geographical origins, is designated R; and worldwide, corresponding to the combination of the two previous designations, is labeled W (W = NA +R).

Cárdenas et al. BMC Genetics 2011 12:23   doi:10.1186/1471-2156-12-23

Open Data