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Figure S1. Mean hybrid index, separated by sex and chromosome, for all swarm replicates over all genotyped time points.

Figure S2. Fitted genomic clines for each locus, compared to null expectations, for the SD × PBJ swarms.

Figure S3. Fitted genomic clines for each locus, compared to null expectations, for the SD × SC swarms

Figure S4. Observed mean mitochondrial and nuclear hybrid index (HI; pure SD = 0) and cytonuclear mismatch for each swarm replicate, compared to distribution of mean values from 1000 simulated swarms.

Table S1. Pairs of markers in linkage disequilibrium at the FDR corrected P < 0.05.

Table S2. Probability of observed genotypic distributions, given a model of homogeneous admixture across the genome, for males and females separately.

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