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Table 1 Diversity parameters and neutrality test for the resequenced regions of TYR, TYRP1 and DCT

From: Complex signatures of selection for the melanogenic loci TYR, TYRP1 and DCT in humans

 

Pygmies

Senegal

Australian Ab.

Chinese

Europeans

Melanoma

Number of segregating sites, S:

DCT

6

4

4

4

4

4

TYR

5

8

5

7

6

7

TYRP1

11

21

5

3

6

4

Number of Haplotypes, h:

DCT

9

6

4

4

5

6

TYR

9

7

7

7

8

10

TYRP1

13

12

4

4

7

5

Haplotype diversity, Hd (SD):

DCT

0.79 (0.09)

0.82(0.05)

0.66(0.12)

0.28 (0.13)

0.70 (0.07)

0.74 (0.07)

TYR

0.89 (0.04)

0.77 (0.06)

0.88 (0.06)

0.85 (0.06)

0.70 (0.1)

0.88 (0.05)

TYRP1

0.93 (0.04)

0.94 (0.03)

0.71 (0.08)

0.36 (0.13)

0.71 (0.08)

0.57 (0.12)

Nucleotide diversity, Pi (SD) (*10 -4 )

DCT

3.8 (0.7)

3.1 (0.3)

3 (0.7)

1.2 (0.6)

3.5 (0.4)

3.5 (0.5)

TYR

5 (5)

3.8 (0.8)

4.9 (0.6)

5.5 (0.7)

3.8 (0.1)

5.4 (0.8)

TYRP1

7 (1)

6 (1)

4 (1)

1 (0)

4 (1)

2 (1)

Theta (per site) from S, Theta-W (SD a ) (*10 -4 )

DCT

4.1 (1.7)

2.7 (1.4)

3.1 (1.5)

2.8 (1.4)

2.7 (1.3)

2.7 (1.4)

TYR

3.8 (1.7)

6.1 (2.2)

4.3 (1.9)

5.3 (2)

4.5 (1.8)

5.3 (2)

TYRP1

6 (2)

12 (3)

3 (1)

2 (1)

3 (1)

2 (1)

Average number of nucleotide differences, k:

DCT

1.574

1.253

1.231

0.489

1.446

1.421

TYR

1.832

1.4

1.802

2.032

1.403

1.989

TYRP1

3.268

2.963

1.890

0.389

1.827

1.289

Tajima's D value

DCT

-0.221

0.321

-0.071

-1.638

0.892

0.754

TYR

0.917

-1.278

0.506

0.098

-0.458

0.027

TYRP1

0.192

-1.906

0.700

-1.447

0.341

0.416

Tajima's D, p (D <= D obs)

DCT

0.39b(0.37)c

0.67b(0.59)c

0.52b(-)c

0.04b(0.03)c

0.84b(0.65)c

0.8b(0.62)c

TYR

0.86b(0.79)c

0.04b(0.02)c

0.73b(-)c

0.57b(0.39)c

0.33b(0.21)c

0.54b(0.38)c

TYRP1

0.64b(0.49)c

1e-3b,d(1e-3)c,d

0.8b(-)c

0.09b(0.04)c

0.67b(0.44)c

0.69b(0.5)c

DHEW (HEW) p-values

DCT

0.19 (0.26)

0.68 (0.73)

0.20 (0.22)

4e-3e (5e-3f)

0.63 (0.32)

0.57 (0.20)

TYR

0.75 (0.81)

0.33 (0.43)

0.62 (0.69)

0.27 (0.12)

0.1 (3e-3f)

0.52 (0.63)

TYRP1

0.87 (0.91)

0.61 (0.72)

0.76 (0.82)

0.28 (0.33)

0.4 (0.03)

0.44 (0.03)

  1. a assuming free recombination.
  2. b using the standard neutral model in DnaSP.
  3. c using a demography-corrected neutral model.
  4. d significant after multiple test correction, at an FDR of 5%.
  5. e significant after multiple test correction, at an FDR of 8%.
  6. f significant after multiple test correction, at an FDR of 6%.