Fig. S1.

Exact exon deletion boundaries are shared between related toothed whales. (A) The protein coding exons alignment from Fig. 2A,Top, and Fig. 2B are reproduced to tag five large deletions in the Mx genes in four toothed whales. Legend as in Fig. 2. (B) Diagram (not to scale) showing where the endpoints of each deletion land in the baleen minke whale genome with respect to the exons of each Mx gene. In particular, note here and in C how deletion 3 and deletion 5 respect the predetermined phylogeny: although both take out Mx2 exon 7, the intronic boundaries of deletion 3 are identical between bottlenose dolphin and orca (suggesting the loss happened in a common ancestor after its split from the Yangtze River dolphin lineage), whereas the intronic boundaries of the sperm whale deletion 5 of the same exon are different. (C) Base pair resolution alignment of the five deletions using genomic sequencing traces from bottlenose dolphin and orca and scaffolds from Yangtze River dolphin against regions of the minke whale assembly flanking each deletion. Red marks the location of each deletion. Note how the precise boundaries of deletions 1, 3, and 4 are shared between the different species, providing strong support for fixed ancestral loss events. Three dots denote that the respective minke whale read continues into the toothed whale deletion.