Table 2 Details of the sequenced fragments and polymorphisms indices found in analysed salmonid fish populations. Overlapping loci from the same gene have been combined as one index. Details of these SNPs have been included the sequences submitted to GenBank with the accession numbers [GenBank:DQ834848–DQ834885].

S. salar

U2A' (ii and iv)

Ssa

609

14

529/80

0

-

SS-II (i and ii)

Ssa

540

15

403/137

0

-

HMG-1 (ii)

Omy

505

15

475/30

0

-

TGF-beta (i and ii)

Omy

791

15

489/302

1

3.2

HMG-1 (iii)

Omy

540

15

394/146

0

-

Ran1 (iii)

Ssa

501

10

416/85

3

16.6

sGnRH (ii)

Ssa

562

15

481/81

0

-

GDF-8

Ssa

497

11

497/0

2

11.0

FGF6 (ii)

Omy

557

11

483/74

2

9.9

Vtg (ii)

Omy

447

15

277/170

0

-

ras-1(ii)

Omy

536

5

536/0

0

-

tnfa (ii)

Omy

522

13

462/60

0

-

IL-1 beta 2

Omy

399

10

399/0

1

7.1

RAG-1

Omy

563

15

563/0

0

-

c-myc

Omy

578

15

328/250

1

4.4

D(2)R

Omy

483

14

483/0

0

-

IgMh

Sal

518

15

518/0

2

9.7

rps24

Tru

776 ^c

11

unknown

5

17.5

CCBL1

Tru

298 ^d

4

unknown

0

-

epn ^b

Cca

359 ^e

5

unknown

0

-

epn(2) ^b

Cca

297 ^f

9

unknown

0

-

ssg(i)

Dre

470 ^g

15

unknown

1

5.4

EF1a

Dre

729 ^h

5

unknown

1

4.8

hox

Dre

834 ^h

9

unknown

0

-

12 911

11.7 ⁱ

7 700/1 448 ^j

19

3.99

S. trutta

SS-II (ii)

Ssa

385

5

353/32

1

9.2

tap2A (ii)

Ssa

367

5

238/129

6 ^k

57.8

HMG-1 (iii)

Omy

540

4

394/146

0

-

TGF-beta (ii)

Omy

487

5

336/151

2

14.5

tnfa (ii)

Omy

514

4

454/60

6 ^l

45.0

2293

4.6 ⁱ

1775/518

15

24.1

T. thymallus

SS-II (i)

Ssa

525

5

416/109

5

33.7

U2A' (ii)

Ssa

373

5

327/46

4

37.9

TGF-beta (i and ii)

Omy

743

5

441/302

3

14.3

RAG-1

Omy

376

5

376/0

2

18.8

2017

5 ⁱ

1560/457

14

24.5

S. alpinus

SS-II (ii)

Ssa

354

5

322/32

0

-

HMG-1 (iii)

Omy

524

5

378/146

2

13.5

tnfa (ii)

Omy

512

5

452/60

0

-

1390

5 ⁱ

1152/238

2

5.1