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Figure S1. Predicted mRNA secondary structure and accessibility of the miR-71 target site in the region of the Sdhd transcript flanking the M and I indel alleles.

Figure S2. Minority allele frequencies in contigs of Finland-derived sequences in M. cinxia transcriptome assembly 2.0 (Wheat et al. 2011).

Table S1. Summary of adult butterflies used for experiments associating Sdhd alleles with phenotypes.

Table S2. Sdhd genotype frequencies in samples from three distinct clades from Finland, France, and Spain.

Table S3. Analyses of Sdhd transcript abundance (N = 113) and SDH enzyme rate (N = 50).

Table S4. SDH enzyme activity in relation to 3′-UTR indel genotype a nonsynonymous polymorphism at amino acid 72.

Table S5. Factors affecting metabolic rate during consecutive 10-min episodes of continuously stimulated flight in two different gas mixtures (21% and 14% O2).

Table S6. Mitochondrial integrity in relation to physiological variables and Sdhd alleles.

Table S7. Factors affecting metabolic rate during 3-min episodes of continuously stimulated flight in two different gas mixtures (21% and 14% O2) presented in random order on consecutive days in a sample of 30 male and female butterflies from Spain.

Table S8. Factors related to flight endurance (total CO2 emitted) during the second flight in respirometry experiment 2.

Table S9. Tracheal morphogensis genes differentially expressed (P < 0.05) in Sdhd M vs. non-M butterflies (data from Wheat et al. 2011).

Table S10. Sequences for amplicons amplified from the cDNA of Melitaea cinxia butterflies in quantitative reverse transcriptase polymerase chain reaction (qRT-PCR) assays.

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