Table 2. Average genetic diversity within populations (H _S), total genetic diversity (H _T), three coefficients of population divergence for mtDNA (G _ST, N _ST and Jost’s D) and for cpDNA (G _ST, R _ST and Jost’s D ), and mismatch distribution test for Pinus yunnanensis.

	No. of						Mismatch distribution
	populations	H S (SE)	H T (SE)	G ST (SE)	N ST or R ST (SE)	Jost’s D	N	τ	P (SSD)	Raggedeness index
mtDNA
Species-wide	16	0.371 (0.068)	0.804 (0.036)	0.538 (0.091)	0.554 (0.091)	0.688 (0.016)	255	1.4	0.007	0.098**
Within groups†Group I	3	0.119 (0.067)	0.120 (0.063)	0.003 (0.062)	0.003 (0.062)	0 (0.016)	48	3.0	0.297	0.593
Group II	1	NC	NC	NC	NC	NC	NC	NC	NC	NC
Group III	1	NC	NC	NC	NC	NC	16	1.2	0.572	0.093
Group IV	1	NC	NC	NC	NC	NC	16	1.3	0.491	0.110
Group V	2	NC	NC	NC	NC	NC	32	1.7	0.111	0.124
Group VI	6	0.424 (0.075)	0.467 (0.077)	0.094 (NC)	0.066 (0.022)	0.076 (0.052)	95	1.8	0.518	0.140
Group VII	2	NC	NC	NC	NC	NC	32	3.0	0.184	0.452
Within ecotypes‡Py-eco1	3	0.119 (0.067)	0.120 (0.063)	0.003 (0.062)	0.003 (0.062)	0 (0.016)	48	3.0	0.299	0.593
Py-eco2	11	0.478 (0.076)	0.754 (0.074)	0.366 (0.110)	0.423 (0.116)	0.529 (0.038)	95	1.6	0.067	0.077
Py-eco3	2	NC	NC	NC	NC	NC	32	3.0	0.182	0.452
cpDNASpecies-wide	16	0.728 (0.058)	0.816 (0.053)	0.108 (0.030)	0.099 (0.026)	0.209 (0.049)	255	0.8	0.598	0.020
Within ecotypes‡Py-eco1	3	0.692 (0.225)	0.820 (0.173)	0.157 (0.228)	0.105 (0.262)	0.417 (0.140)	48	10.2	0.670	0.027
Py-eco2	11	0.812 (0.033)	0.870 (0.037)	0.067 (0.018)	0.132 (0.032)	0.138 (0.066)	95	2.0	0.689	0.030
Py-eco3	2	NC	NC	NC	NC	NC	32	3.0	0.617	0.202

SE, standard error; N, sample size; τ, expansion parameter; P _(SSD), SSD P-value; NC, not calculated due to low variation among populations;

^** P<0.01;

^†,Grouping follows the division resulting from mtDNA SAMOVA;

^‡, Grouping follows the division resulting from TwoStep niche clustering analysis.