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Figure S1. Dataset #1.1. Bayesian phylogenetic reconstruction based on sequence data for specimens for which mtDNA (cox1and nad4-3′) were sequenced for Bactrocera spp. in the current study.

Figure S2. Dataset 1.2. Phylogenetic reconstruction based on sequence data for specimens for which ribosomal DNA (ITS1 and ITS2) were sequenced for Bactrocera spp. in the current study.

Figure S3. Dataset 1.3. Phylogenetic reconstruction based on sequence data for specimens for which nuclear DNA (CAD gene) was sequenced for Bactrocera spp. in the current study.

Figure S4. Dataset 1.4. Phylogenetic reconstruction based on sequence data for specimens for which nuclear DNA (period gene) was sequenced for Bactrocera spp. in the current study.

Figure S5. Dataset #2. Phylogenetic reconstruction based on sequence data for specimens for which all six loci were sequenced for Bactrocera spp. in the current study (236 specimens, 3435 bp alignment).

Figure S6. Dataset #3. Phylogenetic reconstruction based on sequence data for specimens for which all six loci (cox1, nad4-3′, ITS1, ITS2, CAD and per) were sequenced for Bactrocera spp. in the current study.

Figure S7. Dataset #4. Phylogenetic reconstruction based on sequence data for specimens for which four loci were sequenced (cox1, nad4-3′, ITS1 and ITS2) for Bactrocera spp. in the current study (236 specimens, 2221 bp).

Figure S8. Dataset #5. Phylogenetic reconstruction based on sequence data for specimens for which at least two of four loci (cox1, nad4-3′, ITS1 and ITS2) were sequenced for Bactrocera spp. in the current study (315 specimens, 2221 bp).

jen12047-sup-0002-TableS1.pdfapplication/PDF113KTable S1. Collection and GenBank accession information for the samples included in this study.

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