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Table S1 Alleles and allele counts for six outlier loci in species-level comparisons (including HT0495, which was later discarded) and three representative loci that did not show a statistically significant reduction in variation in H. deserticola. For outlier loci, the alleles that are fixed or nearly fixed in H. deserticola are shown in bold.

Fig. S1 A) Unrooted neighbour-joining dendogram constructed using all 96 microsatellite 1 loci and containing all populations of Helianthus. Numbers represent bootstrap support after 1000 replicates. B) Rooted neighbor-joining tree constructed using 25 microsatellite loci derived from Helianthus annuus and containing only populations of H. annuus and H. deserticola. Pooled allele frequencies from H. petiolaris served as an outgroup. Numbers represent bootstrap support after 1000 replicates. C) Rooted neighbour-joining tree constructed using 16 microsatellite loci derived from Helianthus petiolaris and containing only populations of H. petiolaris and H. deserticola. Pooled allele frequencies from H. annuus served as an outgroup. Numbers represent bootstrap support after 1000 replicates.

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