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Table S1 New PCR primers used in this study.

Table S2 Genotype at the markers specific to the canonical form of the duplication (+: SR genotype) and Trf2 copy number (estimated by real-time PCR) in West Africa, Uganda and E123 from Israel 2006. inline image chromosomes produce <70% female offspring on average but significantly more females than males.

Table S3 Population genetics analyses for the vermilion locus.

Table S4 Population differentiation at the vermilion locus (pairwise inline image).

Table S5 Population differentiation (pairwise inline image) for the SR duplication loci (Trf2 and org-1).

Table S6 Population differentiation (pairwise inline image) for the second drive element loci (NRG to Crag).

Table S7 Population genetics analyses for CG33181.

Table S8 Tajima's D in the studied populations (all X chromosomes included).

Table S9 Population genetics analyses for the SR duplication loci (Trf2 and org-1).

Table S10 Population genetics analyses for the second drive element loci (NRG to Crag).

Fig. S1 Phenotype of the X chromosomes, with the presence (filled diamonds) or absence (open diamonds) of the canonical form of the SR duplication as assessed by the four markers described in Material and methods.

Fig. S2 Estimates of the copy number of the Trf2 gene by real-time PCR in subsamples from Sao Tome, Uganda and Israel (see Table S2).

Fig. S3 Haplotype network of the Junction marker.

Fig. S4 Sequences of the different copies of rIST on the reference strain XSR6 chromosome.

Fig. S5 Haplotype network of the candidate region for the second drive element (extended haplotype along the four markers).

Fig. S6 Ratios of nucleotide diversity in SR chromosomes (inline image) to nucleotide diversity in ST chromosomes (inline image) along the drive region in the Middle East: (A) Israel (2000 and 2006 population samples) and (B) Egypt (2007 and 2012 population samples).

Fig. S7 Linkage disequilibrium between SNPs in extended haplotypes along the two drive elements in (A) SR (driving) chromosomes and (B) standard (ST) chromosomes.

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