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Genty G, Sandoval-Castillo J, Beheregaray LB, Möller LM. Into the Blue: Exploring genetic mechanisms behind the evolution of baleen whales. Gene 2024; 929:148822. [PMID: 39103058 DOI: 10.1016/j.gene.2024.148822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Revised: 07/29/2024] [Accepted: 08/02/2024] [Indexed: 08/07/2024]
Abstract
Marine ecosystems are ideal for studying evolutionary adaptations involved in lineage diversification due to few physical barriers and reduced opportunities for strict allopatry compared to terrestrial ecosystems. Cetaceans (whales, dolphins, and porpoises) are a diverse group of mammals that successfully adapted to various habitats within the aquatic environment around 50 million years ago. While the overall adaptive transition from terrestrial to fully aquatic species is relatively well understood, the radiation of modern whales is still unclear. Here high-quality genomes derived from previously published data were used to identify genomic regions that potentially underpinned the diversification of baleen whales (Balaenopteridae). A robust molecular phylogeny was reconstructed based on 10,159 single copy and complete genes for eight mysticetes, seven odontocetes and two cetacean outgroups. Analysis of positive selection across 3,150 genes revealed that balaenopterids have undergone numerous idiosyncratic and convergent genomic variations that may explain their diversification. Genes associated with aging, survival and homeostasis were enriched in all species. Additionally, positive selection on genes involved in the immune system were disclosed for the two largest species, blue and fin whales. Such genes can potentially be ascribed to their morphological evolution, allowing them to attain greater length and increased cell number. Further evidence is presented about gene regions that might have contributed to the extensive anatomical changes shown by cetaceans, including adaptation to distinct environments and diets. This study contributes to our understanding of the genomic basis of diversification in baleen whales and the molecular changes linked to their adaptive radiation, thereby enhancing our understanding of cetacean evolution.
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Affiliation(s)
- Gabrielle Genty
- Cetacean Ecology, Behaviour and Evolution Lab, College of Science and Engineering, Flinders University, GPO Box 2100, Adelaide, SA 5001, Australia; Molecular Ecology Lab, College of Science and Engineering, Flinders University, GPO Box 2100, Adelaide, SA 5001, Australia.
| | - Jonathan Sandoval-Castillo
- Molecular Ecology Lab, College of Science and Engineering, Flinders University, GPO Box 2100, Adelaide, SA 5001, Australia
| | - Luciano B Beheregaray
- Molecular Ecology Lab, College of Science and Engineering, Flinders University, GPO Box 2100, Adelaide, SA 5001, Australia
| | - Luciana M Möller
- Cetacean Ecology, Behaviour and Evolution Lab, College of Science and Engineering, Flinders University, GPO Box 2100, Adelaide, SA 5001, Australia; Molecular Ecology Lab, College of Science and Engineering, Flinders University, GPO Box 2100, Adelaide, SA 5001, Australia
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Bisconti M, Bosselaers M, Locatelli C, Carnevale G, Lambert O. The tympanoperiotic complex of the blue whale, Balaenoptera musculus. Anat Rec (Hoboken) 2024; 307:3041-3070. [PMID: 38297482 DOI: 10.1002/ar.25393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 01/08/2024] [Accepted: 01/10/2024] [Indexed: 02/02/2024]
Abstract
The tympanoperiotic complex of a blue whale Balaenoptera musculus is described and compared to the homologous structures in the other extant and fossil baleen whale species. The periotic and the tympanic bulla represent informative anatomical regions in both functional and phylogenetic studies and for this reason a micro-CT scan of the bones was performed in order to better characterize their external aspect and to reconstruct the inner structures. In particular, the cochlea, the semicircular canals and associated portions of the periotic are reconstructed so that these structures may be used in phylogenetic analyses. We observed that the blue whale periotic is characterized by the presence of a strong dorsal protrusion which is posteriorly bordered by a previously undescribed morphological character that we name the posterotransverse fossa. The peculiar shape of the anterior process and the en echelon organization of the posterior foramina of the pars cochlearis are also described and compared. From a phylogenetic perspective, the blue whale is confirmed to be closely related to the fin whale, Balaenoptera physalus, but it is suggested, based on ear bone characters only, that it diverged before the other balaenopterid species in the phylogeny of Balaenopteridae. This placement supports a series of morphological observations suggesting that the extant blue whale was an early-diverging member of Balaenoptera. Our results help to decipher the evolutionary origin of the blue whale, the largest living animal, by allowing new and more detailed morphological analyses of the balaenopterid fossil record.
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Affiliation(s)
- Michelangelo Bisconti
- Dipartimento di Scienze della Terra, Università degli Studi di Torino, Torino, Italy
- Paleontology Department, San Diego Natural History Museum, San Diego, California, USA
| | - Mark Bosselaers
- D.O. Terre et Histoire de la Vie, Institut royal des Sciences naturelles de Belgique, Bruxelles, Belgium
| | - Camille Locatelli
- Service scientifique Patrimoine, Institut royal des Sciences naturelles de Belgique, Bruxelles, Belgium
| | - Giorgio Carnevale
- Dipartimento di Scienze della Terra, Università degli Studi di Torino, Torino, Italy
| | - Olivier Lambert
- D.O. Terre et Histoire de la Vie, Institut royal des Sciences naturelles de Belgique, Bruxelles, Belgium
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Wolf M, Greve C, Schell T, Janke A, Schmitt T, Pauls SU, Aspöck H, Aspöck U. The de novo genome of the Black-necked Snakefly (Venustoraphidia nigricollis Albarda, 1891): A resource to study the evolution of living fossils. J Hered 2024; 115:112-119. [PMID: 37988623 PMCID: PMC10838129 DOI: 10.1093/jhered/esad074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 11/15/2023] [Accepted: 11/21/2023] [Indexed: 11/23/2023] Open
Abstract
Snakeflies (Raphidioptera) are the smallest order of holometabolous insects that have kept their distinct and name-giving appearance since the Mesozoic, probably since the Jurassic, and possibly even since their emergence in the Carboniferous, more than 300 million years ago. Despite their interesting nature and numerous publications on their morphology, taxonomy, systematics, and biogeography, snakeflies have never received much attention from the general public, and only a few studies were devoted to their molecular biology. Due to this lack of molecular data, it is therefore unknown, if the conserved morphological nature of these living fossils translates to conserved genomic structures. Here, we present the first genome of the species and of the entire order of Raphidioptera. The final genome assembly has a total length of 669 Mbp and reached a high continuity with an N50 of 5.07 Mbp. Further quality controls also indicate a high completeness and no meaningful contamination. The newly generated data was used in a large-scaled phylogenetic analysis of snakeflies using shared orthologous sequences. Quartet score and gene concordance analyses revealed high amounts of conflicting signals within this group that might speak for substantial incomplete lineage sorting and introgression after their presumed re-radiation after the asteroid impact 66 million years ago. Overall, this reference genome will be a door-opening dataset for many future research applications, and we demonstrated its utility in a phylogenetic analysis that provides new insights into the evolution of this group of living fossils.
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Affiliation(s)
- Magnus Wolf
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Frankfurt am Main, Germany
- Institute for Ecology, Evolution and Diversity, Goethe University, Frankfurt am Main, Germany
| | - Carola Greve
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Frankfurt am Main, Germany
- LOEWE-Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt am Main, Germany
| | - Tilman Schell
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Frankfurt am Main, Germany
- LOEWE-Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt am Main, Germany
| | - Axel Janke
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Frankfurt am Main, Germany
- Institute for Ecology, Evolution and Diversity, Goethe University, Frankfurt am Main, Germany
- LOEWE-Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt am Main, Germany
| | - Thomas Schmitt
- Senckenberg German Entomological Institute, Müncheberg, Germany
- Entomology and Biogeography, Faculty of Science, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Steffen U Pauls
- LOEWE-Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt am Main, Germany
- Senckenberg Research Institute and Natural History Museum Frankfurt, Frankfurt am Main, Germany
- Institute of Insects Biotechnology, Justus-Liebig-University Giessen, Giessen, Germany
| | - Horst Aspöck
- Institute of Specific Prophylaxis and Tropical Medicine, Medical Parasitology, Medical University of Vienna (MUW), Vienna, Austria
| | - Ulrike Aspöck
- Department of Evolutionary Biology, University of Vienna, Vienna, Austria
- Department of Entomology, Natural History Museum Vienna, Vienna, Austria
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