Table 2.

Genetic diversity within Miscanthus sacchariflorus and M. × giganteus collected in eastern Asia

DAPC group	No. of individuals	SNP diversity (D)	Mean extrapolated allelic richness*	Number of SNPs with minor allele frequency >0.05	N P	N P unique	Plastid Gini–Simpson index	Plastid Gini–Simpson index excluding Msi haplotypes
Yangtze diploids (ssp. lutarioriparius)	67	0.115	1.71	11 377	17	5	0.69 ± 0.06	0.69 ± 0.06
N China diploids	64	0.139	1.82	15 087	18	3	0.85 ± 0.03	0.85 ± 0.03
Korea/NE China/Russia diploids	256	0.141	1.89	14 778	20	9	0.85 ± 0.01	0.85 ± 0.01
N China/Korea/Russia tetraploids	139	0.133	1.94	14 648	19	7	0.79 ± 0.03	0.79 ± 0.03
S Japan tetraploids	120	0.139	1.89	15 509	20	6	0.75 ± 0.04	0.74 ± 0.04
N Japan tetraploids	76	0.134	1.80	14 249	9	2	0.46 ± 0.07	0.45 ± 0.07
Mxg (2x × 2x)	7	0.123	1.82	12 616	5	0	0.86 ± 0.10	0.86 ± 0.10
Mxg (4x × 2x)	30	0.187	1.86	18 897	9	0	0.77 ± 0.06	0.53 ± 0.13

Groupings are based on discriminant analysis of principal components (DAPC) for 34 605 RAD-seq SNPs (Fig. 2).

Msi, M. sinensis; Mxg, M. × giganteus; D, diversity, as calculated from expected heterozygosity of RAD-seq SNPs (allele frequencies were estimated from read count data using the R package polyfreqs for tetraploid and triploid groups, and directly from genotypes called with UNEAK for diploid groups; standard error of D = 0.001 for each group); N_P, number of plastid haplotypes; N_{P unique}, number of plastid haplotypes unique to each group.

*Standard error of 0.001 or 0.002 for each group for allelic richness.