Phylogenetic Analysis of the mI Exon

We used the mI aa sequence in a tblastn BLAST search (Altschul et al. 1990) against the NCBI nucleotide collection (http://blast.ncbi.nlm.nih.gov) and recovered mI in the common housefly M. domestica (Scott et al. 2014) and the Mediterranean fruit fly C. capitata (http://www.hgsc.bcm.edu), but not in more distantly related species, such as the mosquitoes Anopheles gambiae and Aedes aegypti, the flour beetle Tribolium castaneum or the honey bee Apis mellifera. We used the same method to identify the mI exon in the genome of the tsetse fly G. morsitans (International Glossina Genome Initiative 2014), made available through VectorBase (Megy et al. 2012). To generate an alignment of the surrounding introns, we extended the sequences by including 50 nt on each side of the mI exon and aligned the sequences with MUSCLE (Edgar 2004). For the coding part of the alignment, we estimated dN/dS for the whole tree using codeml and standard settings (Yang 1997).