Table 1 Summary of diversity indexes and private SNPs in Eremurus species using SNPs identified across all species (‘species SNPs’)

Species	SNP dataset	N	Ne (SE)	I (SE)	Ho (SE)	He (SE)	Fis (SE)	P (%)	Heterozygous SNPs (%)	Private SNPs	Diagnostic SNPs
E. inderiensis	3002	6	1.044 (0.006)	0.060 (0.003)	0.011 (0.001)	0.042 (0.002)	0.654 (0.010)	9.79	0.94	163	20
E. kopet-daghensis		3	0.969 (0.006)	0.033 (0.003)	0.009 (0.001)	0.023 (0.002)	0.586 (0.012)	5.16	0.71	18	–
E. luteus		13	1.079 (0.006)	0.088 (0.004)	0.023 (0.002)	0.060 (0.003)	0.509 (0.009)	16.89	2.08	106	146
E. stenophyllus		13	1.164 (0.006)	0.138 (0.005)	0.053 (0.002)	0.094 (0.003)	0.361 (0.009)	25.35	5.41	82 (0;0)^a	410 (57;10)^a
E. olgae		17	1.129 (0.005)	0.111 (0.004)	0.038 (0.002)	0.074 (0.003)	0.368 (0.009)	22.29	3.78	82 (0;0)^a	410 (57;10)^a
E. persicus		8	0.880 (0.008)	0.039 (0.003)	0.008 (0.001)	0.027 (0.002)	0.557 (0.010)	7.26	0.70	467	54
E. spectabilis		26	1.124 (0.005)	0.106 (0.004)	0.030 (0.002)	0.071 (0.003)	0.450 (0.008)	22.52	2.94	28	87
Total		86	1.055 (0.002)	0.082 (0.001)	0.025 (0.001)	0.056 (0.001)	0.454 (0.004)	15.61	2.37	864	717

N number of accessions, Ne number of effective alleles, I Shannon’s information index, Ho observed heterozygosity, He expected heterozygosity, Fis fixation index, SE standard error, P percentage of polymorphic loci (%)
SNP dataset: number of SNPs in the dataset used to calculate the diversity indexes; heterozygous SNPs: percentage of heterozygous SNPs (%); private SNPs: number of SNPs fixed in one species (at a frequency of 100%) and absent in all other species; diagnostic SNPs: number of SNPs present in one species at a frequency below 100% and absent in all other species
E_S_62 and E_GH7 were not included in this analysis
^aThe two numbers in parentheses separated by a semi-colon correspond to the number of private/diagnostic SNPs recorded for E. stenophyllus (first number) and E. olgae (second number)

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