Table 5

Polymorphism Within Regions and Sites for RISP.

Outcrop

Site

Alleles

Hap. #

Nonsyn¹

Syn

Silent

Indel #

π_syn²

π_tot-sil

π_total

Taj-D³

FW-H⁴

R⁵

R_m⁶

Santa Cruz

SCN

8

3

0

2

5

1

0.00346

0.00093

0.00069

-1.60⁺

-1.54

0

0

LH

6

2

0

0

0

1

0

0

0

N/A

N/A

-

-

Total

16

6

0

2

5

2

0.00198

0.00053

0.00040

0

0

Avg.

0.00173

0.00047

0.00035

Palos Verdes

PVL

8

3

0

2

15

2

0.00574

0.00639

0.00449

1.20

-3.14

0.0028

0

AB1

8

4

0

0

5

2

0

0.00189

0.00134

0.34

-1.50

0.0004

0

IP

8

6

0

2

8

3

0.00348

0.00228

0.00162

-0.86

1.71

0.0011

0

RP1

8

5

0

1

4

1

0.00294

0.00106

0.00075

-1.03

-0.21

-

0

Total

32

17

0

5

24

4

0.00745

0.00568

0.00404

0.15

-4.19⁺

0.0075

1

Avg.

0.00304

0.00291

0.00205

La Jolla

LJP1

8

8

0

1

17

4

0.00170

0.00431

0.00315

-0.89

-5.36*

0.0743

1

LJS

8

8

0

1

20

3

0.00167

0.00642

0.00462

0.07

-0.29

0.1166

5

BR

10

6

0

0

18

5

0

0.00430

0.00315

-0.71

-5.24*

0.0009

5

Total

26

22

0

2

33

7

0.00367

0.00720

0.00425

-0.68

-2.46

0.0514

9

Avg.

0.00112

0.00501

0.00364

Point Loma

SD

6

4

0

0

7

0

0

0.00236

0.00173

-0.25

-4.53*

-

-

¹The number of non-synonymous (nonsyn), synonymous (syn), and the combined non-coding and synonymous (silent).

²Average number of pairwise differences between sequences within a population for non-synonymous (π_non-syn), synonymous (π_syn), combined synonymous and non-coding (π_tot-sil), and all (π_total) sites.

³Tajima's D value, none were significant, but an ⁺ indicates 0.05 < P < 0.1.

⁴Fay and Wu's H value with significance indicated by an * (P < 0.05), and ⁺ indicating 0.05 < P < 0.1.

⁵Recombination parameter (R) could not be estimated for some sites (-).

⁶Minimum number of recombination events (R_m) could not be estimated for some sites (-).

Willett and Ladner BMC Evolutionary Biology 2009 9:139   doi:10.1186/1471-2148-9-139