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Figure S1. Sketch of the wing markings of Anopheles pretoriensis collected from the Comoros Islands.

Figure S2. Sampling from atypical peridomestic larval habitats on the island of Grande Comore: Top-cisterns (Bouni), Bottom-indoor water drum (Boeindi).

Figure S3. Pairwise FST values for sites within islands (above diagonal) and geographic distances (below the diagonal).

Figure S4. Mitochondrial ND5 haplotype network based on trimmed length (665 bp) sequences detected in this study combined with published sequences from East Africa (Besansky et al. 1997; Lehmann et al. 1997; Donnelly et al. 2001, 2004).

Figure S5. Elevation map for Grande Comore.

Table S1. Location and habitat characteristics of Anopheles on the Bijagós archipelago.

Table S2. Location and habitat characteristics of Aedes and other genera on the Bijagós archipelago.

Table S3. Location and habitat characteristics of Culex and other genera on the Bijagós archipelago.

Table S4. Location and habitat characteristics of Aedes mosquitoes collected in Comoros islands.

Table S5. Location and habitat characteristics of Culex mosquitoes collected in Comoros islands.

Table S6. Location and habitat characteristics of Anopheles mosquitoes collected in Comoros islands.

Table S7. Location and habitat characteristics of Eretmapodites and other mosquitoes collected in Comoros islands.

Table S8. Locus specific pairwise FST values for Tanzania-Comoros island comparisons, with significant values after Bonferoni correction underlined.

Table S9. Frequency of full length ND5 haplotypes by sampling location.

Table S10. Haplotype numbers from Fig. S4 and their corresponding haplotype designations by Besansky and Genbank accession numbers.

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