Table 2 Summary statistics of nucleotide and haplotype variation and frequency distribution spectrum of polymorphism at analyzed genes in Scottish populations of Scots pine

Locus	L	Nucleotide diversity								ρ ^b (SE)	D ^c	H ^d	Haplotype diversity
			Non-synonymous		Silent ^a								N	H _d (SD)
		π	SNPs	π	SNP	π	π_West	π_South	π_East
dhn1	1071	0.0144	8 (4)	0.0044	54 (12)	0.0203	0.0215	0.0225	0.0158	0.0113 (0.0012)	0.039	−0.285	24	0.964 (0.014)
dhn2	442	0.0074	1	0.0024	7 (0)	0.0112	0.0107	0.0110	0.0113	0.0779 (0.0379)	1.968^1,2,*	0.458	11	0.888 (0.028)
dhn3	359	0.0198	10 (2)	0.0137	13 (2)	0.0291	0.0325	0.0226	0.0366	—	0.911	1.733	8	0.829 (0.03)
dhn7	362	0.0042	3 (1)	0.0042	4 (3)	0.0043	0.0033	0.0036	0.0061	—	−0.223	−2.339	6	0.711 (0.039)
dhy2PP	476	0.0101	5 (3)	0.0011	12 (2)	0.0244	0.0240	0.0223	0.0257	0.0680 (0.0228)	0.103	1.738	21	0.954 (0.015)
abaR	396	0.0048	5 (0)	0.0052	3 (2)	0.0043	0.0035	0.0048	0.0046	—	0.052	−2.323	10	0.755 (0.057)
a3iP2	861	0.0043	2 (2)	0.0008	12 (5)	0.0049	0.0051	0.0045	0.0054	0.0022 (0.0016)	0.360	−2.231	11	0.779 (0.052)
ccoaomt	563	0.0018	1 (1)	0.0000	5 (0)	0.0032	0.0011	0.0053	0.0038	—	−0.711	−0.746	5	0.348 (0.092)
chcs	330	0.0075	1 (1)	0.0008	12 (6)	0.0094	0.0066	0.0137	0.0088	—	−0.682	−1.267	9	0.766 (0.065)
erd3	583	0.0021	3 (3)	0.0006	7 (4)	0.0037	0.0036	0.0029	0.0046	—	−1.464^2,*	−1.351	9	0.73 (0.052)
lp3-1	430	0.0095	1 (1)	0.0004	12 (1)	0.0137	0.0107	0.0144	0.0135	0.0195 (0.0111)	0.944	1.175	20	0.955 (0.017)
lp3-3	309	0.0370	8 (0)	0.0177	18 (1)	0.0660	0.0692	0.0683	0.0676	0.0018 (0.0011)	2.846^1,2,***	1.600	19	0.949 (0.019)
Total	6182		48 (18)		159 (38)
Mean^e	515	0.0078		0.0031		0.0117	0.0111	0.0116	0.0124	0.0085 (0.0009)^f	0.118	−0.494	12.18	0.789 (0.042)

Abbreviations: L, length of sequence in base pairs excluding indels; H_d, haplotype diversity (standard deviation); N-number of haplotypes; SE, standard error; SNP, single-nucleotide polymorphism. Silent sites variation reported separately for west, south and east geographical groups, otherwise average values for all samples combined.
π-nucleotide diversity (Nei, 1987).
^aSynonymous and non-coding positions.
^bLeast-squares estimate of recombination parameter.
^cD test (Tajima, 1989).
^dH test (Fay and Wu, 2000).
^eAverage values at 11 loci excluding lp3-3.
^fEstimates based on informative sites at all loci, excluding lp3-3; ‘—’ not estimated because of the low number of informative sites.
^*Statistically significant values based on coalescence simulations (1) without recombination and (2) with average recombination rate at six loci ^*P<0.05; ^***P<0.01.

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