Supporting Data for: The genome of the pygmy right whale illuminates the evolution of rorquals

Background Baleen whales are a clade of gigantic and highly specialized
marine mammals. Their genomes have been used to investigate their complex
evolutionary history and to decipher the molecular mechanisms that allowed
them to reach these dimensions. However, many unanswered questions remain,
especially about the early radiation of rorquals and how cancer resistance
interplays with their huge number of cells. The pygmy right whale is the
smallest and most elusive among the baleen whales. It reaches only a
fraction of the body length compared to its relatives and it is the only
living member of an otherwise extinct family. This placement makes the
pygmy right whale genome an interesting target to update the complex
phylogenetic past of baleen whales, because it splits up an otherwise long
branch that leads to the radiation of rorquals. Apart from that, genomic
data of this species might help to investigate cancer resistance in large
whales, since these mechanisms are not as important for the pygmy right
whale as in other giant rorquals and right whales. Results Here, we
present a first de novo genome of the species and test its potential in
phylogenomics and cancer research. To do so, we constructed a
multi-species coalescent tree from fragments of a whole-genome alignment
and quantified the amount of introgression in the early evolution of
rorquals. Furthermore, a genome wide comparison of selection rates between
large and small bodied baleen whales revealed a small set of conserved
candidate genes with potential connections to cancer resistance.
Conclusions Our results suggest that the evolution of rorquals is best
described as a hard polytomy with a rapid radiation and high levels of
introgression. The lack of shared positive selected genes between
different large-bodied whale species supports a previously proposed
convergent evolution of gigantism and hence cancer resistance in baleen
whales.