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heterozygous (WS, middle) or Sitka spruce (SS, bottom). The frequency of observed genotypes are indicated on the right of the panel.

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(1)

Supporting Information – Figs S1 and S2

Figure S1 - Genomic clines for all loci indicating locus-specific patterns of introgression using the genome-wide estimate of admixture (hybrid index: 0=white spruce, 1=Sitka spruce) to estimate the probability of observing a particular genotype at that locus, P- values are provided in the right corner of the observed data under a model of neutral introgression. The 95% confidence envelope of the probability of the homozygous white spruce genotype (dark green) and the heterozygous genotype (light green) are based on 1000 neutral parametric simulations. Fitted genomic clines are observed for the

homozygous white spruce genotype (solid line) and heterozygous genotype (dashed line), while open circles indicate observed genotypes; either white spruce (WW, top),

heterozygous (WS, middle) or Sitka spruce (SS, bottom). The frequency of observed genotypes are indicated on the right of the panel.

Published in "New Phytologist 197(3): 927–938 , 2013"

which should be cited to refer to this work.

(2)

Hybrid index

Pr(genotype)

0_10112.contig2.C2.

P= 0

463 158 34

0.0 0.5 1.0

0.0 0 .5 1.0

Hybrid index

Pr(genotype)

0_10754.contig2.C1.

P= 1

655 0 0

0.0 0.5 1.0

0.0 0 .5 1.0

Hybrid index

Pr(genotype)

0_12681.contig2.C2.

P= 0

603 51 1

0.0 0.5 1.0

0.0 0 .5 1.0

Hybrid index

Pr(genotype)

0_13680.contig2.C1.

P= 0

535 101 19

0.0 0.5 1.0

0.0 0 .5 1.0

Hybrid index

Pr(genotype)

0_13680.contig2.NC P= 0.002

468 153 34

0.0 0.5 1.0

0.0 0 .5 1.0

Hybrid index

Pr(genotype)

0_14976.contig2.NC1 P= 0.4

627 27 1

0.0 0.5 1.0

0.0 0 .5 1.0

Pr(genotype)

0_15075.contig2.C2.

P= 0

5 66 584

0.0 0.5 1.0

0.0 0 .5 1.0 Pr(genotype)

0_16142.contig2.C1.

P= 0

560 82 13

0.0 0.5 1.0

0.0 0 .5 1.0 Pr(genotype)

0_17017.contig2.C1.

P= 0

473 132 50

0.0 0.5 1.0

0.0 0 .5 1.0

(3)

Hybrid index

Pr(genotype)

0_17017.contig2.NC1 P= 0

472 134 49

0.0 0.5 1.0

0.0 0 .5 1.0

Hybrid index

Pr(genotype)

0_17238.contig2.NC1 P= 0.113

462 172 21

0.0 0.5 1.0

0.0 0 .5 1.0

Hybrid index

Pr(genotype)

100_316_NS P= 0

376 231 48

0.0 0.5 1.0

0.0 0 .5 1.0

Hybrid index

Pr(genotype)

103_455_NS P= 0

75 307 273

0.0 0.5 1.0

0.0 0 .5 1.0

Hybrid index

Pr(genotype)

114_248_S P= 0.217

367 238 50

0.0 0.5 1.0

0.0 0 .5 1.0

Hybrid index

Pr(genotype)

124_495_S P= 0.812

282 278 95

0.0 0.5 1.0

0.0 0 .5 1.0

Pr(genotype)

125_312_S P= 0

521 101 33

0.0 0.5 1.0

0.0 0 .5 1.0 Pr(genotype)

127_273_S P= 0

501 139 15

0.0 0.5 1.0

0.0 0 .5 1.0 Pr(genotype)

13_496_NS P= 0.108

308 273 74

0.0 0.5 1.0

0.0 0 .5 1.0

(4)

Hybrid index

Pr(genotype)

13_632_S P= 0.006

205 297 153

0.0 0.5 1.0

0.0 0 .5 1.0

Hybrid index

Pr(genotype)

132_78_S P= 0

345 247 63

0.0 0.5 1.0

0.0 0 .5 1.0

Hybrid index

Pr(genotype)

133_39_S P= 0.046

536 112 7

0.0 0.5 1.0

0.0 0 .5 1.0

Hybrid index

Pr(genotype)

133_418_S P= 0

52 272 331

0.0 0.5 1.0

0.0 0 .5 1.0

Hybrid index

Pr(genotype)

133_553_NS P= 0

347 249 59

0.0 0.5 1.0

0.0 0 .5 1.0

Hybrid index

Pr(genotype)

135_122_NS P= 0

82 276 297

0.0 0.5 1.0

0.0 0 .5 1.0

Pr(genotype)

14_248_NS P= 0

166 313 176

0.0 0.5 1.0

0.0 0 .5 1.0 Pr(genotype)

14_301_NS P= 0

162 315 178

0.0 0.5 1.0

0.0 0 .5 1.0 Pr(genotype)

141_349_S P= 0

473 174 8

0.0 0.5 1.0

0.0 0 .5 1.0

(5)

Hybrid index

Pr(genotype)

144_441_S P= 0

350 184 121

0.0 0.5 1.0

0.0 0 .5 1.0

Hybrid index

Pr(genotype)

162_199_S P= 0

135 299 221

0.0 0.5 1.0

0.0 0 .5 1.0

Hybrid index

Pr(genotype)

164_465_S P= 0

263 284 108

0.0 0.5 1.0

0.0 0 .5 1.0

Hybrid index

Pr(genotype)

169_375_NS P= 0.005

512 121 22

0.0 0.5 1.0

0.0 0 .5 1.0

Hybrid index

Pr(genotype)

179_114_S P= 0

70 260 325

0.0 0.5 1.0

0.0 0 .5 1.0

Hybrid index

Pr(genotype)

179_319_NS P= 0

110 310 235

0.0 0.5 1.0

0.0 0 .5 1.0

Pr(genotype)

179_699_S P= 0

248 297 110

0.0 0.5 1.0

0.0 0 .5 1.0 Pr(genotype)

19_567_S P= 0.001

82 326 247

0.0 0.5 1.0

0.0 0 .5 1.0 Pr(genotype)

191_162_S P= 0

483 156 16

0.0 0.5 1.0

0.0 0 .5 1.0

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