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Appendix A Detailed molecular methods.

Table S1 Genetic diversity at 21 microsatellite loci for 6 populations of Daphnia pulex and Daphnia pulicaria with N, sample size; A, number of alleles; Ar, allelic richness (with rarefaction to 27 individuals); HO, observed heterozygosity; HE, expected heterozygosity; FIS, inbreeding coefficient; PHW, exact P-value for Hardy-Weinberg equilibrium; r, frequency of null alleles. Significant deviations are indicated in bold for sequential Bonferroni corrections (Rice 1989) and italic for the false discovery rate (FDR; Benjamini & Hochberg 1995). Site IDs in Table 1.

Table S2 Hierarchical amova analysis based on ND5 data for Daphnia pulex and Daphnia pulicaria populations. Comparisons were performed considering pond and lake population as groups. Significant fixation indices at < 0.05 are indicated with asterisks.

Table S3 Linkage disequilibrium between all pairs of loci in each Daphnia pulex and Daphnia pulicaria population. Significant P-values are given in bold for sequential Bonferroni corrections (Rice 1989) and italic for the false discovery rate (FDR; Benjamini & Hochberg 1995).

Table S4 Linkage disequilibrium between microsatellite loci and mitochondrial profiles in lake Daphnia. Clade A/B/D indicates an association (LD) between a given microsatellite locus and any mitochondrial profile (clades A, B or D); clade A/B, indicates LD between a microsatellite locus and either clade A or B (figure 2). Significant P-values are indicated in bold for sequential Bonferroni corrections (Rice 1989) and italic for the false discovery rate (FDR; Benjamini & Hochberg 1995).

Fig. S1 Unrooted statistical parsimony network of mitochondrial ND5 haplotypes of Daphnia pulex and Daphnia pulicaria isolates from the Panarctic clade (see Fig. 1). The network was estimated using TCS 1.0 (Clement et al. 2000) under the 95% statistical limits of parsimony using the algorithm of Templeton et al. (1992). Circles represent sampled haplotypes and the area of each circle is scaled to represent the relative frequency of a particular haplotype. Small dots on the branches represent single nucleotide difference between haplotypes and represent hypothetical (unsampled) haplotypes. The central haplotype of the network was found in both lakes and ponds. Boxes delineate clades that experienced habitat transition events.

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