Supplementary Table S1. Summary Statistics of Nucleotide and Haplotype Variation, Neutrality

Supplementary Table S1. Summary statistics of nucleotide and haplotype variation, neutrality tests and recombination rate estimates at cold related genes in the north and south groups of Scots pine

Nucleotide diversity
Total / Nonsynonymous / Haplotype diversity
Locus / n / S /  / S /  / Da / Hb / R2c / ρd / N / Hd (SD)
dhn1 / North / 15 / 44 (15) / 0.0134 / 4 (2) / 0.0042 / 0.516 / 3.371 / 0.164 / 0.0050 (0.0008) / 12 / 0.962 (0.04)
South / 15 / 54 (9) / 0.0164 / 4 (0) / 0.0045 / 0.654 / 3.086 / 0.173*1 / 0.0101 (0.0009) / 15(+)***1,2 / 1 (0.024) (+)***1,2
dhn2 / North / 13 / 11 (6) / 0.0048 / 2 (1) / 0.0029 / -0.855 / -2.410 / 0.135 / -0.0022 (0.0016) / 5 / 0.538 (0.161) (-)*1
South / 14 / 11 (7) / 0.0040 / 2 (1) / 0.0019 / -1.262 / -3.429 / 0.119 / -0.0026 (0.0032) / 5 / 0.505 (0.158) (-)*1
dhn3 / North / 14 / 5 (1) / 0.0046 / 2 (1) / 0.0019 / 0.192 / -1.143 / 0.160 / 0.5281 (0.9099) / 6 / 0.868 (0.054) (+)*2
South / 14 / 8 (3) / 0.0059 / 3 (0) / 0.0041 / -0.608 / -0.703 / 0.126 / 0.0438 (0.0483) / 7 / 0.857 (0.74)
dhn4 / North / 15 / 2 (2) / 0.0012 / 1 (1) / 0.0008 / -1.491*1 / 0.248 / 0.249 / na / 2 / 0.133 (0.112)
South / 15 / 1 (0) / 0.0011 / 1 (0) / 0.0015 / -0.399 / -1,362*1,2 / 0.129 / na / 2 / 0.248 (0.131)
dhn5 / North / 15 / 2 (1) / 0.0009 / 0 (0) / 0.0000 / -1.002 / 0.209 / 0.139 / na / 3 / 0.362 (0.145)
South / 15 / 4 (3) / 0.0018 / 0 (0) / 0.0000 / -1.270 / 0.371 / 0.109*1 / na / 5(+)*2 / 0.562 (0.143)
dhn7 / North / 14 / 3 (1) / 0.0025 / 2 (1) / 0.0019 / -0.137 / -1.582 / 0.153 / na / 4 / 0.571 (0.132)
South / 14 / 3 (1) / 0.0030 / 2 (1) / 0.0028 / 0.433 / -0.923 / 0.178 / na / 3 / 0.538 (0.115)
dhn9 / North / 15 / 54 (22) / 0.0213 / 23 (12) / 0.0163 / 0.143 / -3.181 / 0.146 / 0.0034 (0.0006) / 11 / 0.952 (0.04)
South / 15 / 55 (19) / 0.0219 / 21 (6) / 0.0156 / 0.188 / -0.305 / 0.151 / 0.0033 (0.0005) / 12 / 0.962 (0.04)
ef / North / 15 / 3 (2) / 0.0006 / 0 (0) / 0.0000 / -1.317*1 / 0,457 / 0.171 / na / 3 / 0.362 (0.145)
South / 15 / 4 (3) / 0.0007 / 0 (0) / 0.0000 / -1.518*1 / 0,581 / 0.105*1 / na / 5(+)*2 / 0.562 (0.143)
lea / North / 15 / 21 (9) / 0.0047 / 1 (0) / 0.0012 / -0.304 / 0.514 / 0.128 / 0.0045 (0.0019) / 11(+)*2 / 0.952 (0.04) (+)*2
South / 15 / 15 (6) / 0.0033 / 2 (1) / 0.0014 / -0.201 / -2.105 / 0.128 / 0.0054 (0.0032) / 10(+)*2 / 0.914 (0.056)
lp3-2 / North / 14 / 28 (9) / 0.0134 / 7 (1) / 0.0096 / -0.524 / - / 0.118 / 0.0065 (0.0018) / 9 / 0.879 (0.079)
South / 13 / 25 (18) / 0.0087 / 7 (5) / 0.0059 / -1.647*1 / - / 0.099*1 / 0.0030 (0.0032) / 7 / 0.79 (0.109)
abaR / North / 15 / 10 (6) / 0.0058 / 8 (3) / 0.0067 / -1.109 / -1.305 / 0.103 / na / 9 / 0.886 (0.069)
South / 15 / 10 (4) / 0.0061 / 8 (3) / 0.0085 / -0.647 / -3.752*1 / 0.110 / na / 8 / 0.867 (0.067)
abaH / North / 10 / 15 (6) / 0.0074 / 2 (0) / 0.0025 / 0.085 / 0.533 / 0.156 / 0.0059 (0.0007) / 7 / 0.867 (0.107)
South / 12 / 17 (10) / 0.0069 / 2 (0) / 0.0031 / -0.368 / 1.778 / 0.136 / -0.0014 (0.0003) / 5 / 0.758 (0.093)
gst1 / North / 15 / 3 (2) / 0.0009 / 1 (1) / 0.0005 / -1.009 / - / 0.129 / na / 4 / 0.467 (0.148)
South / 12 / 2 (2) / 0.0005 / 0 (0) / 0.0000 / -1.451*1 / - / 0.186 / na / 3 / 0.318 (0.164)
gst2 / North / 9 / 4 (1) / 0.0046 / 2 (1) / 0.0050 / 0.385 / -0.722 / 0.191 / na / 4 / 0.778 (0.110)
South / 11 / 9 (5) / 0.0071 / 4 (2) / 0.0083 / -0.771 / -1.527 / 0.124 / na / 7 / 0.873 (0.089)
Average / North / 14 / 15 (6) / 0.0062 / 4 (2) / 0.0038 / -0.459 / -0.465 / 0.153 / 0.0043 (0.0005)e / 6.4 / 0.6841 (0.1)
South / 14 / 16 (6) / 0.0062 / 4 (1) / 0.0041 / -0.633 / -0.753 / 0.134 / 0.0064 (0.0005)e / 6.7 / 0.6967 (0.15)

n – haploid sample size; S – number of polymorphic sites (singleton);  – nucleotide diversity (Nei 1987); a Tajima’s D test (Tajima 1989),b Fay and Wu H test (Fay and Wu 2000); cR2 - Ramos-Onsins and Rozas test (2002); d - least-squares estimate of recombination parameter (standard error),e multilocus least-squares estimate of recombination parameter at seven loci (standard error), N – number of haplotypes, ‘-‘ no outgroup sequence available, na – not analysed.

*statistically significant values based on coalescent simulations with1locus specific or average ρ estimates from seven loci (see material and methods); 2based on coalescent simulations withno recombination (*P<0.05; ** P<0.01; ***P<0.001).