Fig. S1 STRUCTURE results, showing the ln probability of the data for different numbers of clusters (K) in a) Erigeron lemmonii and b) Erigeron arisolius.
Table S1. Number of alleles (A) and allelic richness (AR) for each locus and each population of E. lemmonii and E. arisolius.
LE-1 / AR-1 / AR-2 / AR-3 / AR-4 / AR-5 / AR-6Locus / A / AR / A / AR / A / AR / A / AR / A / AR / A / AR / A / AR
Elem3-2 / 4 / 3.998 / 10 / 4.84 / 7 / 4.652 / 9 / 5.155 / 6 / 3.761 / 11 / 4.731 / 14 / 5.716
Elem4-1 / 4 / 3.534 / 5 / 3.197 / 4 / 3.493 / 5 / 4.354 / 9 / 3.743 / 6 / 3.849 / 6 / 3.725
Elem4-3 / 2 / 2 / 10 / 5.631 / 9 / 5.739 / 8 / 5.972 / 14 / 4.888 / 8 / 5.356 / 7 / 5.403
Eari4-1 / 7 / 5.451 / 8 / 5.349 / 7 / 5.164 / 7 / 4.472 / 6 / 4.113 / 7 / 4.849 / 8 / 4.298
Eari4-5 / 28 / 23.80 / 9 / 6.046 / 10 / 6.403 / 11 / 6.809 / 9 / 6.175 / 12 / 6.186 / 9 / 5.985
Loci used only for E. lemmonii:
Elem3-1 / 3 / 3 / - / - / - / - / - / - / - / - / - / - / - / -
Elem4-2 / 2 / 2 / - / - / - / - / - / - / - / - / - / - / - / -
Elem4-4 / 3 / 2.509 / - / - / - / - / - / - / - / - / - / - / - / -
Elem4-5 / 5 / 5 / - / - / - / - / - / - / - / - / - / - / - / -
Eari3-3 / 13 / 12.049 / - / - / - / - / - / - / - / - / - / - / - / -
Loci used only for E. arisolius:
Elem3-3 / - / - / 4 / 3.17 / 4 / 3.195 / 4 / 2.81 / 9 / 2.545 / 3 / 2.871 / 5 / 3.566
Eari4-4 / - / - / 10 / 7.25 / 13 / 8.161 / 14 / 7.614 / 9 / 6.429 / 12 / 6.264 / 9 / 6.41
Eari4-6 / - / - / 14 / 7.949 / 13 / 7.2 / 13 / 7.507 / 14 / 8.13 / 15 / 7.913 / 14 / 7.717
Eari4-7 / - / - / 13 / 8.125 / 8 / 6.77 / 10 / 7.148 / 6 / 4.638 / 8 / 8 / 14 / 8.448
Eari4-8 / - / - / 6 / 4.4 / 7 / 5.099 / 6 / 4.908 / 6 / 4.672 / 5 / 4.287 / 6 / 4.433
Eari4-10 / - / - / 14 / 7.534 / 10 / 8.387 / 13 / 7.267 / 10 / 7.603 / 12 / 7.314 / 13 / 7.925
Eari4-12 / - / - / 10 / 6.466 / 11 / 7.15 / 10 / 5.942 / 9 / 6.385 / 11 / 5.92 / 13 / 7.325
Table S2. Comparison of allelic richness of Erigeron lemmonii and E. arisolius using a common sample size, including only the five loci common to both species in the analysis.
LE-1 / AR-1 / AR-2 / AR-3 / AR-4 / AR-5 / AR-6 / All E. arisoliusEari41 / 3.292 / 5.927 / 5.711 / 4.81 / 4.647 / 5.296 / 4.727
Elem41 / 2.31 / 3.532 / 4 / 4.761 / 4 / 4.466 / 4.33
Elem32 / 3.302 / 5.904 / 5.538 / 6.079 / 4.565 / 5.684 / 6.997
Eari45 / 7.858 / 6.797 / 7.264 / 7.788 / 7.139 / 7.133 / 6.685
Elem43 / 2 / 6.459 / 6.452 / 6.636 / 5.281 / 5.87 / 5.961
Average across loci / 3.7524 / 5.7238 / 5.793 / 6.0148 / 5.1264 / 5.6898 / 5.74 / 5.68
Table S3. Inbreeding coefficient (without null alleles taken into account; FISA), expected (HE) and observed heterozygosity (HO), and loci at which populations demonstrate significant (P<0.05) heterozyote deficiencies (shaded) for each locus and each population of E. lemmonii and E. arisolius.
LE-1 / AR-1 / AR-2 / AR-3 / AR-4 / AR-5 / AR-6Locus / FISA / HE / HO / FISA / HE / HO / FISA / HE / HO / FISA / HE / HO / FISA / HE / HO / FISA / HE / HO / FISA / HE / HO
Loci used for both species:
Elem3-2 / 0 / 0.52 / 0.52 / -0.04 / 0.59 / 0.61 / 0.46 / 0.61 / 0.33 / 0.31 / 0.68 / 0.47 / -0.14 / 0.69 / 0.79 / -0.06 / 0.60 / 0.64 / 0.44 / 0.70 / 0.39
Elem4-1 / 0.21 / 0.48 / 0.38 / 0.39 / 0.54 / 0.33 / 0.29 / 0.52 / 0.38 / 0.57 / 0.67 / 0.30 / 0.15 / 0.83 / 0.73 / 0.41 / 0.52 / 0.31 / 0.65 / 0.49 / 0.18
Elem4-3 / 0.07 / 0.50 / 0.47 / 0.07 / 0.79 / 0.74 / 0.37 / 0.83 / 0.53 / 0.25 / 0.85 / 0.64 / 0.08 / 0.92 / 0.80 / 0.11 / 0.82 / 0.73 / 0.15 / 0.81 / 0.69
Eari4-1 / 0.05 / 0.59 / 0.56 / 0.04 / 0.82 / 0.78 / 0.21 / 0.80 / 0.63 / 0.24 / 0.77 / 0.59 / -0.14 / 0.69 / 0.79 / 0.04 / 0.79 / 0.76 / 0.16 / 0.75 / 0.63
Eari4-5 / 0.45 / 0.82 / 0.46 / 0.12 / 0.85 / 0.75 / 0.08 / 0.86 / 0.80 / 0.05 / 0.88 / 0.84 / 0.12 / 0.83 / 0.73 / 0.37 / 0.84 / 0.54 / 0.19 / 0.85 / 0.69
Loci used only for E. lemmonii:
Elem3-1 / 0.20 / 0.37 / 0.30 / - / - / - / - / - / - / - / - / - / - / - / - / - / - / - / - / - / -
Elem4-2 / 0.02 / 0.48 / 0.47 / - / - / - / - / - / - / - / - / - / - / - / - / - / - / - / - / - / -
Elem4-4 / 0.08 / 0.30 / 0.28 / - / - / - / - / - / - / - / - / - / - / - / - / - / - / - / - / - / -
Elem4-5 / 0.15 / 0.39 / 0.33 / - / - / - / - / - / - / - / - / - / - / - / - / - / - / - / - / - / -
Eari3-3 / 0.38 / 0.77 / 0.48 / - / - / - / - / - / - / - / - / - / - / - / - / - / - / - / - / - / -
Loci used only for E. arisolius:
Elem3-3 / - / - / - / 0.02 / 0.63 / 0.62 / 0.40 / 0.55 / 0.33 / 0.06 / 0.53 / 0.50 / -0.06 / 0.55 / 0.52 / 0.54 / 0.61 / 0.28 / 0.18 / 0.61 / 0.50
Eari4-4 / - / - / - / 0.03 / 0.90 / 0.88 / 0.06 / 0.92 / 0.87 / 0.10 / 0.90 / 0.82 / 0.08 / 0.87 / 0.80 / 0.10 / 0.85 / 0.77 / 0.08 / 0.86 / 0.79
Eari4-6 / - / - / - / 0.13 / 0.92 / 0.80 / 0.12 / 0.89 / 0.79 / 0.23 / 0.90 / 0.69 / 0.13 / 0.92 / 0.80 / 0.10 / 0.92 / 0.83 / -0.01 / 0.91 / 0.92
Eari4-7 / - / - / - / 0.28 / 0.92 / 0.67 / 0.13 / 0.89 / 0.78 / 0.45 / 0.89 / 0.50 / 0.71 / 0.67 / 0.20 / 0.48 / 0.92 / 0.50 / 0.22 / 0.93 / 0.73
Eari4-8 / - / - / - / -0.03 / 0.72 / 0.74 / 0.24 / 0.79 / 0.60 / 0.33 / 0.77 / 0.52 / -0.12 / 0.78 / 0.87 / 0.66 / 0.76 / 0.26 / 0.49 / 0.76 / 0.39
Eari4-10 / - / - / - / 0.60 / 0.90 / 0.36 / 0.42 / 0.94 / 0.56 / 0.47 / 0.89 / 0.47 / 0.46 / 0.91 / 0.50 / 0.65 / 0.89 / 0.32 / 0.30 / 0.91 / 0.64
Eari4-12 / - / - / - / 0.02 / 0.88 / 0.86 / 0.25 / 0.88 / 0.67 / -0.12 / 0.83 / 0.93 / 0.00 / 0.86 / 0.87 / 0.16 / 0.83 / 0.70 / 0.21 / 0.89 / 0.71
Table S4. Comparison of estimates of genetic diversity in Erigeron lemmonii and E. arisolius when all loci are included and when loci showing large frequencies of null alleles (n=2 in E. lemmonii and n=4 in E. arisolius) are removed.
Estimates including all loci / Estimates calculated without loci demonstrating large frequencies of null allelesSpecies / Population / n / A / HE / HO / FISA / A / HE / HO / FISA
E. lemmonii / LE-1 / 121 / 7.1 / 0.52 / 0.42 / 0.19 / 3.75 / 0.45 / 0.41 / 0.09
E. arisolius / AR-1 / 24 / 9.25 / 0.78 / 0.679 / 0.14 / 8.75 / 0.79 / 0.72 / 0.10
AR-2 / 21 / 8.58 / 0.78 / 0.605 / 0.24 / 8.88 / 0.78 / 0.62 / 0.22
AR-3 / 27 / 9.17 / 0.61 / 0.606 / 0.25 / 9.00 / 0.79 / 0.66 / 0.17
AR-4 / 15 / 7.33 / 0.75 / 0.663 / 0.12 / 9.88 / 0.75 / 0.66 / 0.05
AR-5 / 30 / 9.17 / 0.78 / 0.553 / 0.30 / 9.25 / 0.81 / 0.76 / 0.22
AR-6 / 30 / 9.83 / 0.79 / 0.606 / 0.24 / 8.88 / 0.77 / 0.64 / 0.20
E. arisolius mean / 8.89 / 0.75 / 0.62 / 0.22 / 9.10 / 0.78 / 0.68 / 0.16
n number of plants from each population included in the present analysis, A number of alleles per locus averaged across loci, AR allelic richness averaged across loci; HE expected heterozygosity, HO observed heterozygosity, FISA inbreeding coefficient as calculated without null alleles taken into account
Table S5. Results of Bottleneck analyses for each population. Values indicate the P-values of the one-tailed Wilcoxon signed rank test for heterozygote excess for each model for each population. Populations were determined to have undergone a recent bottleneck if significant results were obtained for tests using two or more mutation models.
ModelPopulation / 100% SMM / 100% IAM / 30% IAM / 20% IAM / 10% IAM
LE-1 / 0.95 / 0.04* / 0.16 / 0.26 / 0.61
AR-1 / 0.95 / 0.15 / 0.60 / 0.74 / 0.79
AR-2 / 0.68 / 0.05* / 0.10 / 0.13 / 0.21
AR-3 / 0.60 / 0.0006* / 0.10 / 0.10 / 0.15
AR-4 / 0.81 / 0.21 / 0.52 / 0.52 / 0.55
AR-5 / 0.87 / 0.10 / 0.37 / 0.45 / 0.69
AR-6 / 0.99 / 0.12 / 0.71 / 0.88 / 0.95
SMM, stepwise mutation model; IAM, infinite alleles model; TPM, two-phase mutation model; *P<0.05