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.

背景：须鲸（baleen whales）是一类体型庞大且高度特化的海洋哺乳动物类群。研究者已通过其基因组解析其复杂的演化历史，并阐明其得以达到这般体型的分子机制。但目前仍有诸多未解之谜，尤其是有关鳁鲸（rorqual）的早期适应性辐射演化，以及癌症抗性与其海量细胞之间的相互作用机制。小露脊鲸（pygmy right whale）是须鲸类中体型最小且最难以观测的物种，其体长仅为近亲的一小部分，同时是该灭绝类群中唯一现存的物种。这一分类地位使得小露脊鲸基因组成为解析须鲸复杂演化起源的理想研究对象，因其可打破原本指向鳁鲸辐射演化的长支系结构。除此之外，该物种的基因组数据还有助于探究大型鲸类的癌症抗性机制，因为小露脊鲸无需像其他大型鳁鲸和露脊鲸那样依赖此类抗性机制。
结果：本研究首次构建了该物种的从头组装（de novo）基因组，并验证了其在系统基因组学（phylogenomics）与癌症研究中的应用潜力。为此，我们基于全基因组比对片段构建了多物种溯祖树，并定量分析了鳁鲸早期演化过程中的基因渐渗（introgression）水平。此外，通过对大、小体型须鲸的全基因组选择压力进行比较分析，我们鉴定出一组保守的候选基因，其可能与癌症抗性存在关联。
结论：本研究结果表明，鳁鲸的演化过程最符合“硬多歧支+快速辐射演化+高水平基因渐渗”的模型。不同大型鲸类之间不存在共有受正选择的基因，这一结果支持了此前提出的假说：须鲸的体型巨型化及其伴随的癌症抗性均为趋同演化的结果。