The genome of the pygmy right whale illuminates the evolution of rorquals
Abstract 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 rem...
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| Format: | Article |
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BMC
2023-04-01
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| Series: | BMC Biology |
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| Online Access: | https://doi.org/10.1186/s12915-023-01579-1 |
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| author | Magnus Wolf Konstantin Zapf Deepak Kumar Gupta Michael Hiller Úlfur Árnason Axel Janke |
| author_facet | Magnus Wolf Konstantin Zapf Deepak Kumar Gupta Michael Hiller Úlfur Árnason Axel Janke |
| author_sort | Magnus Wolf |
| collection | DOAJ |
| description | Abstract 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. |
| first_indexed | 2024-04-09T17:44:38Z |
| format | Article |
| id | doaj.art-0f961fa09c5845d0896a3b53624ffd1d |
| institution | Directory Open Access Journal |
| issn | 1741-7007 |
| language | English |
| last_indexed | 2024-04-09T17:44:38Z |
| publishDate | 2023-04-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Biology |
| spelling | doaj.art-0f961fa09c5845d0896a3b53624ffd1d2023-04-16T11:25:08ZengBMCBMC Biology1741-70072023-04-0121111810.1186/s12915-023-01579-1The genome of the pygmy right whale illuminates the evolution of rorqualsMagnus Wolf0Konstantin Zapf1Deepak Kumar Gupta2Michael Hiller3Úlfur Árnason4Axel Janke5Senckenberg Biodiversity and Climate Research Centre (BiK-F)Senckenberg Biodiversity and Climate Research Centre (BiK-F)LOEWE-Centre for Translational Biodiversity Genomics (TBG), Senckenberg Nature Research SocietySenckenberg Biodiversity and Climate Research Centre (BiK-F)Department of Clinical Sciences Lund, Lund UniversitySenckenberg Biodiversity and Climate Research Centre (BiK-F)Abstract 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.https://doi.org/10.1186/s12915-023-01579-1Pygmy right whaleCaperea marginataWhole-genome sequencingPhylogenomicsRorqualsPositive selection |
| spellingShingle | Magnus Wolf Konstantin Zapf Deepak Kumar Gupta Michael Hiller Úlfur Árnason Axel Janke The genome of the pygmy right whale illuminates the evolution of rorquals BMC Biology Pygmy right whale Caperea marginata Whole-genome sequencing Phylogenomics Rorquals Positive selection |
| title | The genome of the pygmy right whale illuminates the evolution of rorquals |
| title_full | The genome of the pygmy right whale illuminates the evolution of rorquals |
| title_fullStr | The genome of the pygmy right whale illuminates the evolution of rorquals |
| title_full_unstemmed | The genome of the pygmy right whale illuminates the evolution of rorquals |
| title_short | The genome of the pygmy right whale illuminates the evolution of rorquals |
| title_sort | genome of the pygmy right whale illuminates the evolution of rorquals |
| topic | Pygmy right whale Caperea marginata Whole-genome sequencing Phylogenomics Rorquals Positive selection |
| url | https://doi.org/10.1186/s12915-023-01579-1 |
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