1
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Baños H, Susko E, Roger AJ. Is Over-parameterization a Problem for Profile Mixture Models? Syst Biol 2024; 73:53-75. [PMID: 37843172 PMCID: PMC11129589 DOI: 10.1093/sysbio/syad063] [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: 02/18/2022] [Revised: 09/12/2023] [Accepted: 10/13/2023] [Indexed: 10/17/2023] Open
Abstract
Biochemical constraints on the admissible amino acids at specific sites in proteins lead to heterogeneity of the amino acid substitution process over sites in alignments. It is well known that phylogenetic models of protein sequence evolution that do not account for site heterogeneity are prone to long-branch attraction (LBA) artifacts. Profile mixture models were developed to model heterogeneity of preferred amino acids at sites via a finite distribution of site classes each with a distinct set of equilibrium amino acid frequencies. However, it is unknown whether the large number of parameters in such models associated with the many amino acid frequency vectors can adversely affect tree topology estimates because of over-parameterization. Here, we demonstrate theoretically that for long sequences, over-parameterization does not create problems for estimation with profile mixture models. Under mild conditions, tree, amino acid frequencies, and other model parameters converge to true values as sequence length increases, even when there are large numbers of components in the frequency profile distributions. Because large sample theory does not necessarily imply good behavior for shorter alignments we explore the performance of these models with short alignments simulated with tree topologies that are prone to LBA artifacts. We find that over-parameterization is not a problem for complex profile mixture models even when there are many amino acid frequency vectors. In fact, simple models with few site classes behave poorly. Interestingly, we also found that misspecification of the amino acid frequency vectors does not lead to increased LBA artifacts as long as the estimated cumulative distribution function of the amino acid frequencies at sites adequately approximates the true one. In contrast, misspecification of the amino acid exchangeability rates can severely negatively affect parameter estimation. Finally, we explore the effects of including in the profile mixture model an additional "F-class" representing the overall frequencies of amino acids in the data set. Surprisingly, the F-class does not help parameter estimation significantly and can decrease the probability of correct tree estimation, depending on the scenario, even though it tends to improve likelihood scores.
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Affiliation(s)
- Hector Baños
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
- Department of Mathematics and Statistics, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
- Institute for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
| | - Edward Susko
- Department of Mathematics and Statistics, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
- Institute for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
| | - Andrew J Roger
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
- Institute for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
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2
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Wang C, Chen X, Fang Z. Geometric morphometrics casts light on phylogenetic relevance of cephalopod beak morphological. J Morphol 2024; 285:e21691. [PMID: 38555512 DOI: 10.1002/jmor.21691] [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: 10/05/2023] [Revised: 03/11/2024] [Accepted: 03/19/2024] [Indexed: 04/02/2024]
Abstract
The feeding organ of cephalopod species, the beak, can be used to reveal important ecological information. In this study, geometric morphometric approaches were employed to investigate the phylogenetic relevance and classification effect of beak lateral profile shape. The two-dimensional beak morphologies of 1164 pairs of 24 species from 13 genera and five families were constructed, and their evolutionary relationships and taxonomic status were confirmed using geometric morphometrics and molecular biology approaches. We also assessed the phylogenetic signals of beak shape. The analysis results show shape variation in the beak mainly in the rostrum, hood, and lateral wall. The overall shape parameters (all PCs) of the upper and lower beak are more useful for species identification. The shapes of the upper and lower beak show a strong phylogenetic signal, and the phenogram based on the beak shape basically reflected the families' taxonomic positions. We also hypothesized that the shape variation in the beaks of cephalopods may be ascribed to genetic and environmental differences. In summary, beaks are a reliable material for the classification of cephalopod species. Geometric morphometric approaches are a powerful tool to reveal the identification, phylogenetic relevance and phenotypic diversity of beak shape in cephalopods.
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Affiliation(s)
- Chao Wang
- College of Marine living Resource Sciences and Management, Shanghai Ocean University, Shanghai, China
| | - Xinjun Chen
- College of Marine living Resource Sciences and Management, Shanghai Ocean University, Shanghai, China
- National Engineering Research Center for Oceanic Fisheries, Shanghai Ocean University, Shanghai, China
- Key Laboratory of Sustainable Exploitation of Oceanic Fisheries Resources, Ministry of Education, Shanghai Ocean University, Shanghai, China
- Key Laboratory of Oceanic Fisheries Exploration, Ministry of Agriculture and Rural Affairs, Shanghai, China
- Scientific Observing and Experimental Station of Oceanic Fishery Resources, Ministry of Agriculture and Rural Affairs, Shanghai, China
| | - Zhou Fang
- College of Marine living Resource Sciences and Management, Shanghai Ocean University, Shanghai, China
- National Engineering Research Center for Oceanic Fisheries, Shanghai Ocean University, Shanghai, China
- Key Laboratory of Sustainable Exploitation of Oceanic Fisheries Resources, Ministry of Education, Shanghai Ocean University, Shanghai, China
- Key Laboratory of Oceanic Fisheries Exploration, Ministry of Agriculture and Rural Affairs, Shanghai, China
- Scientific Observing and Experimental Station of Oceanic Fishery Resources, Ministry of Agriculture and Rural Affairs, Shanghai, China
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3
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Fan F, Pei L, Jiang L, Ye Y, Liu Y, Liu B. Gene Rearrangements in the Mitochondrial Genome of Gonatopsis borealis and Onychoteuthis compacta Reveal Their Phylogenetic Implications for Oegopsida. Biochem Genet 2024:10.1007/s10528-024-10707-7. [PMID: 38466493 DOI: 10.1007/s10528-024-10707-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Accepted: 01/16/2024] [Indexed: 03/13/2024]
Abstract
The complete mitochondrial genome provides crucial information for comprehending gene rearrangement, molecular evolution, and phylogenetic analysis. Here, we have determined the complete mitogenome sequence of Gonatopsis borealis and Onychoteuthis compacta for the first time. Their genome sizes were 20,148 bp and 20,491 bp, respectively, including 18 protein-coding genes, COI-COIII, ATP6, and ATP8 are duplicated, 23 transfer RNA genes, and 2 ribosomal RNA (rRNA) genes (12S and 16S rRNA). Specifically, the overall A+T content is 70.69% and 72.67%. It shows a significant AT bias. The whole mitogenomes indicate positive AT skew (0.070 and 0.062). Furthermore, the gene order has been rearranged within Oegopsida. The tandem duplication random loss model was determined as most likely to explain the observed gene rearrangements. Phylogenetic analysis was performed, and the result tree was found to be consistent with the morphological identification classification. Estimation of divergence time for 35 species showed that the main differentiation of Oegopsida occurred in 140.70 Mya. These results will help to better understand the gene rearrangements and evolution of G. borealis and O. compacta and lay a foundation for further phylogeny genetic studies of Oegopsida.
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Affiliation(s)
- Fan Fan
- National Engineering Research Center of Marine Facilities Aquaculture, Zhejiang Ocean University, Zhoushan, 316022, China
| | - Liyi Pei
- National Engineering Research Center of Marine Facilities Aquaculture, Zhejiang Ocean University, Zhoushan, 316022, China
| | - Lihua Jiang
- National Engineering Research Center of Marine Facilities Aquaculture, Zhejiang Ocean University, Zhoushan, 316022, China.
| | - Yingying Ye
- National Engineering Research Center of Marine Facilities Aquaculture, Zhejiang Ocean University, Zhoushan, 316022, China
| | - Yifan Liu
- National Engineering Research Center of Marine Facilities Aquaculture, Zhejiang Ocean University, Zhoushan, 316022, China
| | - Bilin Liu
- College of Marine Sciences, Shanghai Ocean University, Shanghai, 201306, China
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4
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Albertin CB, Katz PS. Evolution of cephalopod nervous systems. Curr Biol 2023; 33:R1087-R1091. [PMID: 37875089 PMCID: PMC10792511 DOI: 10.1016/j.cub.2023.08.092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2023]
Abstract
Giant brains have independently evolved twice on this planet, in vertebrates and in cephalopods (Figure 1A). Thus, the brains and nervous systems of cephalopods provide an important counterpoint to vertebrates in the search for generalities of brain organization and function. Their mere existence disproves various hypotheses proposed to explain the evolution of the mind and the human brain, such as cognition and large brains evolved only in long-lived animals with complex social systems and parental care, none of which is true of cephalopods. Therefore, it is worthwhile to review what is known about the evolution of cephalopod nervous systems to consider how it informs our understanding of general principles of brain evolution.
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Affiliation(s)
- Caroline B Albertin
- Eugene Bell Center, Marine Biological Laboratory, Woods Hole, MA 02543, USA.
| | - Paul S Katz
- Department of Biology, Neuroscience and Behavior Graduate Program, University of Massachusetts Amherst, Amherst, MA 01003, USA.
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5
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Aristide L, Fernández R. Genomic Insights into Mollusk Terrestrialization: Parallel and Convergent Gene Family Expansions as Key Facilitators in Out-of-the-Sea Transitions. Genome Biol Evol 2023; 15:evad176. [PMID: 37793176 PMCID: PMC10581543 DOI: 10.1093/gbe/evad176] [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: 08/11/2023] [Revised: 09/08/2023] [Accepted: 09/28/2023] [Indexed: 10/06/2023] Open
Abstract
Animals abandoned their marine niche and successfully adapted to life on land multiple times throughout evolution, providing a rare opportunity to study the mechanisms driving large scale macroevolutionary convergence. However, the genomic factors underlying this process remain largely unknown. Here, we investigate the macroevolutionary dynamics of gene repertoire evolution during repeated transitions out of the sea in mollusks, a lineage that has transitioned to freshwater and terrestrial environments multiple independent times. Through phylogenomics and phylogenetic comparative methods, we examine ∼100 genomic data sets encompassing all major molluskan lineages. We introduce a conceptual framework for identifying and analyzing parallel and convergent evolution at the orthogroup level (groups of genes derived from a single ancestral gene in the species in question) and explore the extent of these mechanisms. Despite deep temporal divergences, we found that parallel expansions of ancient gene families played a major role in facilitating adaptation to nonmarine habitats, highlighting the relevance of the preexisting genomic toolkit in facilitating adaptation to new environments. The expanded functions primarily involve metabolic, osmoregulatory, and defense-related systems. We further found functionally convergent lineage-exclusive gene gains, while family contractions appear to be driven by neutral processes. Also, genomic innovations likely contributed to fuel independent habitat transitions. Overall, our study reveals that various mechanisms of gene repertoire evolution-parallelism, convergence, and innovation-can simultaneously contribute to major evolutionary transitions. Our results provide a genome-wide gene repertoire atlas of molluskan terrestrialization that paves the way toward further understanding the functional and evolutionary bases of this process.
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Affiliation(s)
- Leandro Aristide
- Metazoa Phylogenomics Laboratory Biodiversity Program, Institute of Evolutionary Biology (Spanish Research Council-University Pompeu Fabra), BarcelonaSpain
| | - Rosa Fernández
- Metazoa Phylogenomics Laboratory Biodiversity Program, Institute of Evolutionary Biology (Spanish Research Council-University Pompeu Fabra), BarcelonaSpain
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6
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Klug C, Hoffmann R, Tischlinger H, Fuchs D, Pohle A, Rowe A, Rouget I, Kruta I. 'Arm brains' (axial nerves) of Jurassic coleoids and the evolution of coleoid neuroanatomy. SWISS JOURNAL OF PALAEONTOLOGY 2023; 142:22. [PMID: 37780806 PMCID: PMC10533608 DOI: 10.1186/s13358-023-00285-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 08/11/2023] [Indexed: 10/03/2023]
Abstract
Although patchy, the fossil record of coleoids bears a wealth of information on their soft part anatomy. Here, we describe remains of the axial nerve cord from both decabrachian (Acanthoteuthis, Belemnotheutis, Chondroteuthis) and octobrachian (Plesioteuthis, Proteroctopus, Vampyronassa) coleoids from the Jurassic. We discuss some hypotheses reflecting on possible evolutionary drivers behind the neuroanatomical differentiation of the coleoid arm crown. We also propose some hypotheses on potential links between habitat depth, mode of life and the evolution of the Coleoidea. Supplementary Information The online version contains supplementary material available at 10.1186/s13358-023-00285-3.
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Affiliation(s)
- Christian Klug
- Paläontologisches Institut und Museum, Universität Zürich, Karl-Schmid-Strasse 4, 8006 Zurich, Switzerland
| | - René Hoffmann
- Institute of Geology, Mineralogy, & Geophysics, Ruhr-Universität Bochum, 44801 Bochum, Germany
| | - Helmut Tischlinger
- 85134 Stammham, Germany
- Jura-Museum Eichstätt, Willibaldsburg, 85072 Eichstätt, Germany
| | - Dirk Fuchs
- SNSB-Bayerische Staatssammlung für Paläontologie und Geologie, Richard-Wagner-Straße 10, 80333 Munich, Germany
| | - Alexander Pohle
- Paläontologisches Institut und Museum, Universität Zürich, Karl-Schmid-Strasse 4, 8006 Zurich, Switzerland
- Institute of Geology, Mineralogy, & Geophysics, Ruhr-Universität Bochum, 44801 Bochum, Germany
| | - Alison Rowe
- Centre de recherche en paléontologie - Paris, Sorbonne Université-MNHN-CNRS-CR2P, 4 Pl. Jussieu, 75005 Paris, France
| | - Isabelle Rouget
- Centre de recherche en paléontologie - Paris, Sorbonne Université-MNHN-CNRS-CR2P, 4 Pl. Jussieu, 75005 Paris, France
| | - Isabelle Kruta
- Centre de recherche en paléontologie - Paris, Sorbonne Université-MNHN-CNRS-CR2P, 4 Pl. Jussieu, 75005 Paris, France
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7
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Chung WS, López-Galán A, Kurniawan ND, Marshall NJ. The brain structure and the neural network features of the diurnal cuttlefish Sepia plangon. iScience 2023; 26:105846. [PMID: 36624840 PMCID: PMC9823234 DOI: 10.1016/j.isci.2022.105846] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 12/02/2022] [Accepted: 12/19/2022] [Indexed: 12/24/2022] Open
Abstract
Cuttlefish are known for their rapid changes of appearance enabling camouflage and con-specific communication for mating or agonistic display. However, interpretation of their sophisticated behaviors and responsible brain areas is based on the better-studied squid brain atlas. Here we present the first detailed description of the neuroanatomical features of a tropical and diurnal cuttlefish, Sepia plangon, coupled with observations on ontogenetic changes in its visual and learning centers using a suite of MRI-based techniques and histology. We then make comparisons to a loliginid squid, treating it as a 'baseline', and also to other cuttlefish species to help construct a connectivity map of the cuttlefish brain. Differences in brain anatomy and the previously unknown neural connections associated with camouflage, motor control and chemosensory function are described. These findings link brain heterogeneity to ecological niches and lifestyle, feeding hypotheses and evolutionary history, and provide a timely, new technology update to older literature.
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Affiliation(s)
- Wen-Sung Chung
- Queensland Brain Institute, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Alejandra López-Galán
- Queensland Brain Institute, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Nyoman D. Kurniawan
- Centre for Advanced Imaging, The University of Queensland, St Lucia, QLD 4072, Australia
| | - N. Justin Marshall
- Queensland Brain Institute, The University of Queensland, St Lucia, QLD 4072, Australia
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8
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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: 2] [Impact Index Per Article: 1.0] [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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Finding a home for the ram’s horn squid: phylogenomic analyses support Spirula spirula (Cephalopoda: Decapodiformes) as a close relative of Oegopsida. ORG DIVERS EVOL 2022. [DOI: 10.1007/s13127-022-00583-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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10
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Drerup C. The behavioural ecology of Sepiolidae (Cephalopoda: Sepiolida): a review. MOLLUSCAN RESEARCH 2022. [DOI: 10.1080/13235818.2022.2107503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
Affiliation(s)
- Christian Drerup
- Marine Behavioural Ecology Group, Department of Zoology, University of Cambridge, Cambridge, United Kingdom
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11
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Exceptional soft-tissue preservation of Jurassic Vampyronassa rhodanica provides new insights on the evolution and palaeoecology of vampyroteuthids. Sci Rep 2022; 12:8292. [PMID: 35739131 PMCID: PMC9225997 DOI: 10.1038/s41598-022-12269-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 04/26/2022] [Indexed: 11/27/2022] Open
Abstract
Although soft tissues of coleoid cephalopods record key evolutionary adaptations, they are rarely preserved in the fossil record. This prevents meaningful comparative analyses between extant and fossil forms, as well as the development of a relative timescale for morphological innovations. However, unique 3-D soft tissue preservation of Vampyronassa rhodanica (Vampyromorpha) from the Jurassic Lagerstätte of La Voulte-sur-Rhône (Ardèche, France) provides unparalleled opportunities for the observation of these tissues in the oldest likely relative of extant Vampyroteuthis infernalis. Synchrotron X-ray microtomography and reconstruction of V. rhodanica allowed, for the first time, a high-resolution re-examination of external and internal morphology, and comparison with other fossil and extant species, including V. infernalis. The new data obtained demonstrate that some key V. infernalis characters, such as its unique type of sucker attachment, were already present in Jurassic taxa. Nonetheless, compared with the extant form, which is considered to be an opportunistic detritivore and zooplanktivore, many characters in V. rhodanica indicate a pelagic predatory lifestyle. The contrast in trophic niches between the two taxa is consistent with the hypothesis that these forms diversified in continental shelf environments prior to the appearance of adaptations in the Oligocene leading to their modern deep-sea mode of life.
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12
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Roscian M, Herrel A, Zaharias P, Cornette R, Fernandez V, Kruta I, Cherel Y, Rouget I. Every hooked beak is maintained by a prey: ecological signal in cephalopod beak shape. Funct Ecol 2022. [DOI: 10.1111/1365-2435.14098] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Marjorie Roscian
- UMR 7207 (MNHN‐CNRS‐Sorbonne Université), CR2P de Recherche en Paléontologie‐Paris, Département Origines et Évolution, Muséum National d’Histoire Naturelle Centre Paris France
- UMR 7179 C.N.R.S/M.N.H.N., Département Adaptations du Vivant, Bâtiment d’Anatomie Comparée, 55 rue Buffon, 75005 Paris France
| | - Anthony Herrel
- UMR 7179 C.N.R.S/M.N.H.N., Département Adaptations du Vivant, Bâtiment d’Anatomie Comparée, 55 rue Buffon, 75005 Paris France
| | | | - Raphaël Cornette
- UMR 7205 Institut de Systématique, Evolution, Biodiversité (CNRS, MNHN, UPMC, EPHE), Muséum national d’Histoire naturelle Paris France
| | - Vincent Fernandez
- Imaging and Analysis Centre, Natural History Museum, Cromwell Road, SW7 5BD, London, UK. fDepartment of Computer Science; University of Illinois Urbana‐Champaign Urbana IL USA
| | - Isabelle Kruta
- UMR 7207 (MNHN‐CNRS‐Sorbonne Université), CR2P de Recherche en Paléontologie‐Paris, Département Origines et Évolution, Muséum National d’Histoire Naturelle Centre Paris France
| | - Yves Cherel
- Centre d’Etudes Biologiques de Chizé, UMR7372 CNRS‐La Rochelle Université, 79360 Villiers‐en‐Bois France
| | - Isabelle Rouget
- UMR 7207 (MNHN‐CNRS‐Sorbonne Université), CR2P de Recherche en Paléontologie‐Paris, Département Origines et Évolution, Muséum National d’Histoire Naturelle Centre Paris France
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Genome and transcriptome mechanisms driving cephalopod evolution. Nat Commun 2022; 13:2427. [PMID: 35508532 PMCID: PMC9068888 DOI: 10.1038/s41467-022-29748-w] [Citation(s) in RCA: 50] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 03/28/2022] [Indexed: 11/27/2022] Open
Abstract
Cephalopods are known for their large nervous systems, complex behaviors and morphological innovations. To investigate the genomic underpinnings of these features, we assembled the chromosomes of the Boston market squid, Doryteuthis (Loligo) pealeii, and the California two-spot octopus, Octopus bimaculoides, and compared them with those of the Hawaiian bobtail squid, Euprymna scolopes. The genomes of the soft-bodied (coleoid) cephalopods are highly rearranged relative to other extant molluscs, indicating an intense, early burst of genome restructuring. The coleoid genomes feature multi-megabase, tandem arrays of genes associated with brain development and cephalopod-specific innovations. We find that a known coleoid hallmark, extensive A-to-I mRNA editing, displays two fundamentally distinct patterns: one exclusive to the nervous system and concentrated in genic sequences, the other widespread and directed toward repetitive elements. We conclude that coleoid novelty is mediated in part by substantial genome reorganization, gene family expansion, and tissue-dependent mRNA editing. “Cephalopods are known for their large nervous systems, complex behaviors, and morphological innovations. Here, the authors find that soft-bodied cephalopod genomes are more rearranged than other extant molluscs and that mRNA editing patterns are associated with the nervous system and repetitive elements”.
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14
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Mesozoic origin of coleoid cephalopods and their abrupt shifts of diversification patterns. Mol Phylogenet Evol 2021; 166:107331. [PMID: 34687843 DOI: 10.1016/j.ympev.2021.107331] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 09/25/2021] [Accepted: 10/18/2021] [Indexed: 11/22/2022]
Abstract
Coleoids are the most diverse group of cephalopod mollusks. While their origin is date during the Mesozoic, the diversification pattern is unknown. However, two hypotheses have been proposed. The first suggests an increasing diversification rate after the Cretaceous-Paleogene extinction event (K-Pg) as consequence of empty habitats left by the ammonites and belemnites. The second hypothesis proposes a mid-Cenozoic increase in diversification rate related to distributional changes during ice ages and biotic interactions. To test these hypotheses, we estimated a lineage through time (LTT) and the gamma-statistic along with model-based diversification rates. These analyses were conducted on a dated molecular phylogeny for coleoids that we reconstructed using five molecular markers (cytochrome b, 16S rRNA, cytochrome oxidase I, rhodopsin, and PAX-6). Our divergence time estimation suggests that coleoids originated in the Mesozoic Era (Middle Triassic) and that both main clades (Decapodiformes and Octopodiformes) diverged in the Cretaceous/Jurassic Period. The LTT, gamma statistic, and diversification rates inferred with the Bayesian Analysis of Macro-evolutionary Mixtures (BAMM), indicate an acceleration in diversification rate over time since the origin of coleoids. Additionally, BAMM allowed us to detect abrupt increases in diversification rate before and after the K-Pg boundary. Our results partially support both hypotheses as all analyses indicate that the coleoid diversification rate was increasing during the Cenozoic. However, our results also indicate increasing diversification rates before the K-Pg boundary. We propose that the radiation of coleoids has been shaped by an acceleration in diversification rate over time, including exceptional episodes of abrupt increases before and after the K-Pg boundary.
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15
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Fernández-Álvarez FÁ, Taite M, Vecchione M, Villanueva R, Allcock AL. A phylogenomic look into the systematics of oceanic squids (order Oegopsida). Zool J Linn Soc 2021. [DOI: 10.1093/zoolinnean/zlab069] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Abstract
Oceanic squids of the order Oegopsida are ecologically and economically important members of the pelagic environment. They are the most diverse group of cephalopods, with 24 families that are divergent morphologically. Despite their importance, knowledge of phylogenetic relationships among oegopsids is less than that among neritic cephalopods. Here, we provide the complete mitogenomes and the nuclear 18S and 28S ribosomal genes for 35 selected oceanic squids, which were generated using genome skimming. We performed maximum likelihood and Bayesian inference analyses that included 21 of the 24 oegopsid families. In our analyses, the architeuthid, chiroteuthid and enoploteuthid family groups, which have been proposed previously based on morphological and natural history characteristics, were retrieved as monophyletic. The morphologically divergent Cranchiidae formed a well-supported clade with families Ommastrephidae and Thysanoteuthidae, with a unique mitochondrial gene order. The family Lycoteuthidae was revealed as paraphyletic and contained Pyroteuthidae. Thus, the two lycoteuthid subfamilies are herein elevated to family level, increasing the number of oegopsid squid families to 25. In order to describe the diversity and evolutionary trends of oegopsid squids accurately, the superfamilies Architeuthoidea, Chiroteuthoidea, Cranchioidea and Enoploteuthoidea are resurrected from the literature, and the superfamilies Cycloteuthoidea, Octopoteuthoidea and Pholidoteuthoidea are proposed. The phylogenetic positions of Gonatidae, Histioteuthidae and Onychoteuthidae were not stable in our phylogenetic analyses and are not assigned to a superfamily. This study supports the utility of genome skimming to solve the phylogenetic relationships of oceanic squids.
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Affiliation(s)
| | - Morag Taite
- Ryan Institute and School of Natural Sciences, National University of Ireland Galway, Galway, Ireland
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Penglais, Aberystwyth, Ceredigion, UK
| | - Michael Vecchione
- NOAA/NMFS National Systematics Laboratory, National Museum of Natural History, Washington, DC, USA
| | - Roger Villanueva
- Institut de Ciències del Mar (CSIC), Passeig Marítim 37–49, E-08003 Barcelona, Spain
| | - A Louise Allcock
- Ryan Institute and School of Natural Sciences, National University of Ireland Galway, Galway, Ireland
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16
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Shoshan Y, Liscovitch-Brauer N, Rosenthal JJC, Eisenberg E. Adaptive Proteome Diversification by Nonsynonymous A-to-I RNA Editing in Coleoid Cephalopods. Mol Biol Evol 2021; 38:3775-3788. [PMID: 34022057 PMCID: PMC8382921 DOI: 10.1093/molbev/msab154] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
RNA editing by the ADAR enzymes converts selected adenosines into inosines, biological mimics for guanosines. By doing so, it alters protein-coding sequences, resulting in novel protein products that diversify the proteome beyond its genomic blueprint. Recoding is exceptionally abundant in the neural tissues of coleoid cephalopods (octopuses, squids, and cuttlefishes), with an over-representation of nonsynonymous edits suggesting positive selection. However, the extent to which proteome diversification by recoding provides an adaptive advantage is not known. It was recently suggested that the role of evolutionarily conserved edits is to compensate for harmful genomic substitutions, and that there is no added value in having an editable codon as compared with a restoration of the preferred genomic allele. Here, we show that this hypothesis fails to explain the evolutionary dynamics of recoding sites in coleoids. Instead, our results indicate that a large fraction of the shared, strongly recoded, sites in coleoids have been selected for proteome diversification, meaning that the fitness of an editable A is higher than an uneditable A or a genomically encoded G.
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Affiliation(s)
- Yoav Shoshan
- Raymond and Beverly Sackler School of Physics and Astronomy, Tel Aviv University, Tel Aviv, Israel
| | - Noa Liscovitch-Brauer
- Raymond and Beverly Sackler School of Physics and Astronomy, Tel Aviv University, Tel Aviv, Israel
| | | | - Eli Eisenberg
- Raymond and Beverly Sackler School of Physics and Astronomy, Tel Aviv University, Tel Aviv, Israel
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17
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Sato N. A review of sperm storage methods and post-copulatory sexual selection in the Cephalopoda. Biol J Linn Soc Lond 2021. [DOI: 10.1093/biolinnean/blab096] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Abstract
In many animal phyla, females have a unique sperm storage organ (SSO). Post-copulatory sexual selection is a powerful driving force of SSO evolution. SSOs are generally considered to have evolved through sexual antagonistic coevolution between male genitalia and the SSO and/or cryptic female choice (CFC). In cephalopods, sperm transfer and fertilization are conducted through complex processes, and sperm storage methods show inter-species variation. In some species, males implant spermatangia superficially under the female skin, and then sperm released from the spermatangia are transferred into a seminal receptacle (SR). Deep-sea cephalopods, which lack a SR, have instead evolved a deep-implanting method by which the spermatangium is embedded deep in the musculature of the mantle wall of the female. In some species, the female stores whole spermatangia within a spermatangium pocket. Because the males of most species do not insert an intromittent organ into the female when transferring sperm, SSO evolution may have been influenced by CFC alone. This review summarizes the sperm storage methods and the mechanisms of post-copulatory sexual selection in cephalopods and it is proposed that these diverse methods evolved as adaptive mechanisms through post-copulatory sexual selection.
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Affiliation(s)
- Noriyosi Sato
- Applied Biological Science, Department of Fisheries, School of Marine Science and Technology, Tokai University, Orido 3-20-1 Shimizu Shizuoka, Japan
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18
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Sanchez G, Fernández-Álvarez FÁ, Taite M, Sugimoto C, Jolly J, Simakov O, Marlétaz F, Allcock L, Rokhsar DS. Phylogenomics illuminates the evolution of bobtail and bottletail squid (order Sepiolida). Commun Biol 2021; 4:819. [PMID: 34188187 PMCID: PMC8241861 DOI: 10.1038/s42003-021-02348-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 05/13/2021] [Indexed: 11/09/2022] Open
Abstract
Bobtail and bottletail squid are small cephalopods with striking anti-predatory defensive mechanisms, bioluminescence, and complex morphology; that inhabit nektobenthic and pelagic environments around the world's oceans. Yet, the evolution and diversification of these animals remain unclear. Here, we used shallow genome sequencing of thirty-two bobtail and bottletail squids to estimate their evolutionary relationships and divergence time. Our phylogenetic analyses show that each of Sepiadariidae, Sepiolidae, and the three subfamilies of the Sepiolidae are monophyletic. We found that the ancestor of the Sepiolinae very likely possessed a bilobed light organ with bacteriogenic luminescence. Sepiolinae forms a sister group to Rossinae and Heteroteuthinae, and split into Indo-Pacific and Atlantic-Mediterranean lineages. The origin of these lineages coincides with the end of the Tethys Sea and the separation of these regions during the Eocene and the beginning of the Oligocene. We demonstrated that sepiolids radiated after the Late Cretaceous and that major biogeographic events might have shaped their distribution and speciation.
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Affiliation(s)
- Gustavo Sanchez
- Graduate School of Integrated Science for Life, Hiroshima University, Higashi Hiroshima, Hiroshima, Japan.,Molecular Genetics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
| | | | - Morag Taite
- Ryan Institute and School of Natural Sciences, National University of Ireland Galway, Galway, Ireland, UK
| | - Chikatoshi Sugimoto
- Molecular Genetics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
| | - Jeffrey Jolly
- Molecular Genetics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
| | - Oleg Simakov
- Department of Molecular Evolution and Development, University of Vienna, Vienna, Austria
| | - Ferdinand Marlétaz
- Department of Genetics, Evolution and Environment, Centre for Life's Origins and Evolution, University College London, London, UK
| | - Louise Allcock
- Ryan Institute and School of Natural Sciences, National University of Ireland Galway, Galway, Ireland, UK
| | - Daniel S Rokhsar
- Molecular Genetics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan. .,Department of Molecular and Cell Biology, Life Sciences Addition #3200, Berkeley, CA, USA. .,Chan-Zuckerberg BioHub, San Francisco, CA, USA.
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19
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Drerup C. First detailed description of the burying behaviour of a bottletail squid, Sepiadarium kochii Steenstrup, 1881. MOLLUSCAN RESEARCH 2021. [DOI: 10.1080/13235818.2021.1927464] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Christian Drerup
- Marine Behavioural Ecology Group, Department of Zoology, University of Cambridge, Cambridge, United Kingdom
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20
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Ponte G, Taite M, Borrelli L, Tarallo A, Allcock AL, Fiorito G. Cerebrotypes in Cephalopods: Brain Diversity and Its Correlation With Species Habits, Life History, and Physiological Adaptations. Front Neuroanat 2021; 14:565109. [PMID: 33603650 PMCID: PMC7884766 DOI: 10.3389/fnana.2020.565109] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Accepted: 12/30/2020] [Indexed: 12/01/2022] Open
Abstract
Here we analyze existing quantitative data available for cephalopod brains based on classical contributions by J.Z. Young and colleagues, to cite some. We relate the relative brain size of selected regions (area and/or lobe), with behavior, life history, ecology and distribution of several cephalopod species here considered. After hierarchical clustering we identify and describe ten clusters grouping 52 cephalopod species. This allows us to describe cerebrotypes, i.e., differences of brain composition in different species, as a sign of their adaptation to specific niches and/or clades in cephalopod molluscs for the first time. Similarity reflecting niche type has been found in vertebrates, and it is reasonable to assume that it could also occur in Cephalopoda. We also attempted a phylogenetic PCA using data by Lindgren et al. (2012) as input tree. However, due to the limited overlap in species considered, the final analysis was carried out on <30 species, thus reducing the impact of this approach. Nevertheless, our analysis suggests that the phylogenetic signal alone cannot be a justification for the grouping of species, although biased by the limited set of data available to us. Based on these preliminary findings, we can only hypothesize that brains evolved in cephalopods on the basis of different factors including phylogeny, possible development, and the third factor, i.e., life-style adaptations. Our results support the working hypothesis that the taxon evolved different sensorial and computational strategies to cope with the various environments (niches) occupied in the oceans. This study is novel for invertebrates, to the best of our knowledge.
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Affiliation(s)
- Giovanna Ponte
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Naples, Italy
| | - Morag Taite
- Department of Zoology, Ryan Institute, National University of Ireland Galway, Galway, Ireland
| | - Luciana Borrelli
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Naples, Italy
| | - Andrea Tarallo
- Department of Research Infrastructures for Marine Biological Resources (RIMAR), Stazione Zoologica Anton Dohrn, Naples, Italy
| | - A Louise Allcock
- Department of Zoology, Ryan Institute, National University of Ireland Galway, Galway, Ireland
| | - Graziano Fiorito
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Naples, Italy
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