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Chen Z, Baeza JA, Chen C, Gonzalez MT, González VL, Greve C, Kocot KM, Arbizu PM, Moles J, Schell T, Schwabe E, Sun J, Wong NLWS, Yap-Chiongco M, Sigwart JD. A genome-based phylogeny for Mollusca is concordant with fossils and morphology. Science 2025; 387:1001-1007. [PMID: 40014700 DOI: 10.1126/science.ads0215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2024] [Accepted: 12/05/2024] [Indexed: 03/01/2025]
Abstract
Extreme morphological disparity within Mollusca has long confounded efforts to reconstruct a stable backbone phylogeny for the phylum. Familiar molluscan groups-gastropods, bivalves, and cephalopods-each represent a diverse radiation with myriad morphological, ecological, and behavioral adaptations. The phylum further encompasses many more unfamiliar experiments in animal body-plan evolution. In this work, we reconstructed the phylogeny for living Mollusca on the basis of metazoan BUSCO (Benchmarking Universal Single-Copy Orthologs) genes extracted from 77 (13 new) genomes, including multiple members of all eight classes with two high-quality genome assemblies for monoplacophorans. Our analyses confirm a phylogeny proposed from morphology and show widespread genomic variation. The flexibility of the molluscan genome likely explains both historic challenges with their genomes and their evolutionary success.
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Affiliation(s)
- Zeyuan Chen
- Senckenberg Research Institute and Natural History Museum Frankfurt, Frankfurt am Main, Germany
| | - J Antonio Baeza
- Department of Biological Sciences, Clemson University, Clemson, SC, USA
- Departamento de Biologia Marina, Universidad Catolica del Norte, Coquimbo, Chile
| | - Chong Chen
- X-STAR, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Maria Teresa Gonzalez
- Instituto Ciencias Naturales "Alexander von Humboldt," Universidad de Antofagasta, FACIMAR, Antofagasta, Chile
| | - Vanessa Liz González
- Informatics and Data Science Center, Smithsonian Institution National Museum of Natural History, Washington, DC, USA
| | - Carola Greve
- Senckenberg Research Institute and Natural History Museum Frankfurt, Frankfurt am Main, Germany
- LOEWE Centre for Translational Biodiversity Genomics, Frankfurt, Germany
| | - Kevin M Kocot
- Department of Biological Sciences, University of Alabama, Tuscaloosa, AL, USA
- Alabama Museum of Natural History, University of Alabama, Tuscaloosa, AL, USA
| | - Pedro Martinez Arbizu
- German Center for Marine Biodiversity Research, Senckenberg am Meer, Wilhelmshaven, Germany
| | - Juan Moles
- Department of Evolutionary Biology, Ecology, and Environmental Sciences, University of Barcelona, Faculty of Biology, Barcelona, Spain
- Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
| | - Tilman Schell
- Senckenberg Research Institute and Natural History Museum Frankfurt, Frankfurt am Main, Germany
- LOEWE Centre for Translational Biodiversity Genomics, Frankfurt, Germany
| | | | - Jin Sun
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
| | - Nur Leena W S Wong
- International Institute of Aquaculture and Aquatic Sciences, Universiti Putra Malaysia, Port Dickson, Malaysia
| | - Meghan Yap-Chiongco
- Department of Biological Sciences, University of Alabama, Tuscaloosa, AL, USA
| | - Julia D Sigwart
- Senckenberg Research Institute and Natural History Museum Frankfurt, Frankfurt am Main, Germany
- Institute of Ecology, Evolution and Diversity, Goethe University, Frankfurt, Germany
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2
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Xavier JC, Golikov AV, Queirós JP, Perales-Raya C, Rosas-Luis R, Abreu J, Bello G, Bustamante P, Capaz JC, Dimkovikj VH, González AF, Guímaro H, Guerra-Marrero A, Gomes-Pereira JN, Hernández-Urcera J, Kubodera T, Laptikhovsky V, Lefkaditou E, Lishchenko F, Luna A, Liu B, Pierce GJ, Pissarra V, Reveillac E, Romanov EV, Rosa R, Roscian M, Rose-Mann L, Rouget I, Sánchez P, Sánchez-Márquez A, Seixas S, Souquet L, Varela J, Vidal EAG, Cherel Y. The significance of cephalopod beaks as a research tool: An update. Front Physiol 2022; 13:1038064. [PMID: 36467695 PMCID: PMC9716703 DOI: 10.3389/fphys.2022.1038064] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 10/25/2022] [Indexed: 11/17/2022] Open
Abstract
The use of cephalopod beaks in ecological and population dynamics studies has allowed major advances of our knowledge on the role of cephalopods in marine ecosystems in the last 60 years. Since the 1960's, with the pioneering research by Malcolm Clarke and colleagues, cephalopod beaks (also named jaws or mandibles) have been described to species level and their measurements have been shown to be related to cephalopod body size and mass, which permitted important information to be obtained on numerous biological and ecological aspects of cephalopods in marine ecosystems. In the last decade, a range of new techniques has been applied to cephalopod beaks, permitting new kinds of insight into cephalopod biology and ecology. The workshop on cephalopod beaks of the Cephalopod International Advisory Council Conference (Sesimbra, Portugal) in 2022 aimed to review the most recent scientific developments in this field and to identify future challenges, particularly in relation to taxonomy, age, growth, chemical composition (i.e., DNA, proteomics, stable isotopes, trace elements) and physical (i.e., structural) analyses. In terms of taxonomy, new techniques (e.g., 3D geometric morphometrics) for identifying cephalopods from their beaks are being developed with promising results, although the need for experts and reference collections of cephalopod beaks will continue. The use of beak microstructure for age and growth studies has been validated. Stable isotope analyses on beaks have proven to be an excellent technique to get valuable information on the ecology of cephalopods (namely habitat and trophic position). Trace element analyses is also possible using beaks, where concentrations are significantly lower than in other tissues (e.g., muscle, digestive gland, gills). Extracting DNA from beaks was only possible in one study so far. Protein analyses can also be made using cephalopod beaks. Future challenges in research using cephalopod beaks are also discussed.
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Affiliation(s)
- José C. Xavier
- Department of Life Sciences, Marine and Environmental Sciences Centre/ ARNET–Aquatic Research Network, University of Coimbra, Coimbra, Portugal
- British Antarctic Survey, Natural Environment Research Council, Cambridge, United Kingdom
| | | | - José P. Queirós
- Department of Life Sciences, Marine and Environmental Sciences Centre/ ARNET–Aquatic Research Network, University of Coimbra, Coimbra, Portugal
- British Antarctic Survey, Natural Environment Research Council, Cambridge, United Kingdom
| | | | | | - José Abreu
- Department of Life Sciences, Marine and Environmental Sciences Centre/ ARNET–Aquatic Research Network, University of Coimbra, Coimbra, Portugal
- British Antarctic Survey, Natural Environment Research Council, Cambridge, United Kingdom
| | | | - Paco Bustamante
- Littoral Environnement et Sociétés (LIENSs), UMR 7266 CNRS-La Rochelle Université, La Rochelle, France
- Institut Universitaire de France (IUF), Paris, France
| | - Juan C. Capaz
- Center of Marine Sciences, University of Algarve, Campus de Gambelas, Faro, Portugal
| | - Valerie H. Dimkovikj
- Department of Marine Science, Coastal Carolina University, Conway, SC, United States
| | | | - Hugo Guímaro
- Department of Life Sciences, Marine and Environmental Sciences Centre/ ARNET–Aquatic Research Network, University of Coimbra, Coimbra, Portugal
- British Antarctic Survey, Natural Environment Research Council, Cambridge, United Kingdom
| | - Airam Guerra-Marrero
- IU-ECOAQUA, University of Las Palmas de Gran Canaria, Edf. Ciencias Básicas, Campus de Tafira, Las Palmas de Gran Canaria, Spain
| | | | | | | | - Vladimir Laptikhovsky
- Centre for Environment, Fisheries and Aquaculture Science (CEFAS), Lowestoft, United Kingdom
| | | | - Fedor Lishchenko
- Laboratory for Ecology and Morphology of Marine Invertebrates, A.N. Severtsov Institute of Ecology and Evolution of the Russian Academy of Sciences, Moscow, Russia
| | - Amanda Luna
- Department of Ecology and Animal Biology, Faculty of Marine Sciences, University of Vigo, Vigo, Spain
| | - Bilin Liu
- College of Marine Sciences, Shanghai Ocean University, Shanghai, China
| | | | - Vasco Pissarra
- MARE—Marine and Environmental Sciences Centre/ARNET–Aquatic Research Network, Laboratório Marítimo da Guia, Faculdade de Ciências, Universidade de Lisboa, Cascais, Portugal
| | - Elodie Reveillac
- Littoral Environnement et Sociétés (LIENSs), UMR 7266 CNRS-La Rochelle Université, La Rochelle, France
| | - Evgeny V. Romanov
- Centre Technique de Recherche et de Valorisation des Milieux Aquatiques (CITEB), Le Port, Île de la Réunion, France
| | - Rui Rosa
- MARE—Marine and Environmental Sciences Centre/ARNET–Aquatic Research Network, Laboratório Marítimo da Guia, Faculdade de Ciências, Universidade de Lisboa, Cascais, Portugal
| | - Marjorie Roscian
- Centre de Recherche en Paléontologie-Paris (CR2P), CNRS, Sorbonne Université, Paris, France
| | - Lisa Rose-Mann
- University of South Florida, College of Marine Science, St. Petersburg, FL, United States
| | - Isabelle Rouget
- Centre de Recherche en Paléontologie-Paris (CR2P), CNRS, Sorbonne Université, Paris, France
| | - Pilar Sánchez
- Institut de Ciènces del Mar, CSIC, Psg. Marítim de la Barceloneta, Barcelona, Spain
| | | | - Sónia Seixas
- Department of Life Sciences, Marine and Environmental Sciences Centre/ ARNET–Aquatic Research Network, University of Coimbra, Coimbra, Portugal
- Universidade Aberta, Rua Escola Politécnica, Lisboa, Portugal
| | - Louise Souquet
- Department of Mechanical Engineering, Faculty of Engineering Science, University College London, London, United Kingdom
| | - Jaquelino Varela
- MARE—Marine and Environmental Sciences Centre/ARNET–Aquatic Research Network, Laboratório Marítimo da Guia, Faculdade de Ciências, Universidade de Lisboa, Cascais, Portugal
| | - Erica A. G. Vidal
- Center for Marine Studies—Federal University of Parana (UFPR), Pontal do Paraná, PR, Brazil
| | - Yves Cherel
- Centre d’Etudes Biologiques de Chizé, UMR 7372 du CNRS-La Rochelle Université, Villiers-en-Bois, France
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Fuchs D, Hoffmann R, Klug C. Evolutionary development of the cephalopod arm armature: a review. SWISS JOURNAL OF PALAEONTOLOGY 2021; 140:27. [PMID: 34956072 PMCID: PMC8688392 DOI: 10.1186/s13358-021-00241-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 11/11/2021] [Indexed: 06/14/2023]
Abstract
The cephalopod arm armature is certainly one of the most important morphological innovations responsible for the evolutionary success of the Cephalopoda. New palaeontological discoveries in the recent past afford to review and reassess origin and homology of suckers, sucker rings, hooks, and cirri. Since a priori character state reconstructions are still ambiguous, we suggest and discuss three different evolutionary scenarios. Each of them is based on the following assumptions: (1) Neocoleoidea uniting extant Decabrachia and Octobrachia is monophyletic (= proostracum-bearing coleoids); (2) extinct Belemnitida and Diplobelida are stem decabrachians; (3) proostracum-less coleoids (Hematitida, Donovaniconida, Aulacoceratida) represent stem-neocoleoids; (4) Ammonoidea and Bactritoidea are stem coleoids. We consider a scenario where belemnoid hooks derived from primitive suckers as well-supported. Regarding belemnoid hooks and suckers as homologues implies that belemnoid, oegopsid, and probably ammonoid arm hooks arose through parallel evolution. Our conclusions challenge the widespread opinion, whereupon belemnoid hooks evolved de novo, and instead support earlier ideas formulated by Sigurd von Boletzky.
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Affiliation(s)
- Dirk Fuchs
- Bayerische Staatssammlung für Paläontologie und Geologie, Richard-Wagner-Straße 10, 80333 Munich, Germany
| | - René Hoffmann
- Institute of Geology, Mineralogy, & Geophysics, Ruhr-Universität Bochum, 44801 Bochum, Germany
| | - Christian Klug
- Paläontologisches Institut und Museum, Universität Zürich, Karl-Schmid-Strasse 4, 8006 Zurich, Switzerland
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