Figure 4: Evolution of mutually exclusive splicing clusters.

(a) The Venn diagrams⁴⁸ show the number of clusters of MXEs shared between species and subsets of species groups. Species abbreviations are D. simulans (dsim), D. sechellia (dsec), D. melanogaster (dmel), D. yakuba (dyak), D. erecta (dere), D. ananassae (dana), D. pseudoobscura (dpse), D. persimilis (dper), D. willistoni (dwil), which are all part of the Sophophora branch, and D. virilis (dvir), D. mojavensis (dmoj) and D. grimshawi (dgri). (b) The gene structure of the D. melanogaster Cacophony gene is shown in comparison with its homologues in D. willistoni and Daphnia pulex. The D. melanogaster gene contains three clusters of MXEs. A forth cluster is present in D. willistoni, Daphnia and in other insects that had been lost in D. melanogaster. The respective corresponding exons are marked by dotted lines, and their sequences are shown in the alignment. (c) The gene structure of the D. melanogaster Ras opposite gene is shown in comparison with its homologues in D. willistoni and Pediculus humans corporis. The D. melanogaster gene consists of a single exon as do the homologues in dere, dsec and dyak. The introns of this gene must have been lost in the ancestor of the melanogaster subgroup branch. In contrast, the Ras opposite gene in D. willistoni is a multi-exon gene and contains a cluster of MXEs. This cluster of MXEs is also found in Pediculus and most of the other analysed insect species. The sequences of the MXEs as well as the corresponding region in the D. melanogaster protein are shown in the alignment. All transcripts in b and c are represented 5′ to 3′. Coloured big bars represent mutually exclusive exons. The darkest coloured bar is the exon that was included in the query sequence, whereas the lighter coloured bars represent identified MXEs. The higher the similarity between the candidate and the query exon, the darker the colour of the candidate (100% identity would result in the same color). The opacity of the colours of each alternative exon corresponds to the alignment score of the alternative exon to the original one.