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mec12530-sup-0001-FigS1-S5.docWord document1060K

Fig. S1 Neighbor-Net phylogenetic networks of mtDNA and Wolbachia haplotypes

Fig. S2 Maximum Likelihood tree of D. melanogaster mitochondria sequences. Included are the 91 lines from this paper, 20 additional sequences available on GenBank and a new assembly of short read sequences from a Canton-S line.

Fig. S3 Maximum Likelihood tree of mitochondrial COI sequences from this paper and Nunes et al. (2008b).

Fig. S4 Mitochondrial haplotype network

Fig. S5 Mitochondrial phylogenetic tree constructed with BEAST

mec12530-sup-0002_TableS1-S5.xlsapplication/msexcel250K

Table S1 Summary of reads mapped to the wMel and mtDNA references for each line.

Table S2 Summary of identified wMel SNPs.

Table S3 Summary of identified indels in wMel.

Table S4 Summary of identified mtDNA SNPs. SNP positions are given relative to the D. melanogaster mitochondrial reference sequence (NC_001709).

Table S5 Summary of identified indels in mtDNA.

mec12530-sup-0003-AppendixS1.txtplain text document2KAppendix S1 Perl script used for nucleotide diversity (π) calculations.

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