Table 1

Base substitutions detected in extant and ancient cpDNA sequences of Norway spruce (Picea abies)

cpDNA region

CK

MD

B

D

TL

Li

LF

K2i

Variable position

88

107-126

77

78

82

168

196

197

206

154

157

115

133

114

Position total

424

443 - 462

629

630

634

834

872

873

882

1081

1084

1279

1297

1464

Seq. length

Rel. freq.

Extant haplotypes

Ht1.

√

√

C

12A + 5G

A

A

C

G

T

C

G

T

C

T

T

C

1551

0.103

Ht2.

√

√

C

11A + 6G

A

A

C

G

T

C

G

T

C

A

T

C

1551

0.259

Ht3.

√

√

C

11A + 6G

C

A

C

G

T

C

G

T

C

A

T

C

1551

0.103

Ht4.

√

√

C

10A + 6G

A

A

C

G

T

C

G

T

A

A

T

T

1550

0.017

Ht5.

√

√

C

13A + 5G

A

A

C

G

T

C

G

T

C

A

T

C

1552

0.034

Ht6.

√

√

C

12A + 5G

C

A

C

G

T

C

G

T

C

A

T

C

1551

0.034

Ht7.

√

√

C

10A + 6G

A

A

C

G

T

C

G

T

C

A

T

C

1550

0.017

Ht8.

√

√

C

12A + 5G

A

A

C

G

T

C

G

T

C

A

T

C

1551

0.379

Ht9.

√

√

T

12A + 4G + 3A + G

A

C

T

G

T

A

G

C

C

A

G

C

1554

0.017

Macrofossil haplotypes

Cone

√

C

A

C

G

T

C

G

A

T

C

901

S 3.

A

A

C

124

S 4.

T

A

237

S 8.

√

C

A

C

G

T

C

G

575

S 9.

√

C

10A + 7GA + 7G

G

T

C

G

A

T

C

990

S 10.

√

A

A

C

G

T

A

G

T

C

C

1016

S 502-S 545

C

12A + 5G

211

Fossil pollen haplotypes

P1.

C

10A + 6G

212

P2-P3.

C

A

C

124

P4-P11.

G

T

C

G

251

P12.

G

T

A

G

251

P13.

G

G

A

G

251

P14-P15.

√

136

P16-P17.

√

200

(√) successful amplification of the fragment with no variation in the sequence; length of concatenated sequences is shown on the right; rows below the name of the fragments indicate the nucleotide position in the single fragments and in the concatenated sequence, respectively; base substitutions in bold were found only in the fossil material; Ht: haplotype; S: seed; P: pollen

Magyari et al. BMC Evolutionary Biology 2011 11:66   doi:10.1186/1471-2148-11-66