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D'Aniello S, Bertrand S, Escriva H. Amphioxus as a model to study the evolution of development in chordates. eLife 2023; 12:e87028. [PMID: 37721204 PMCID: PMC10506793 DOI: 10.7554/elife.87028] [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: 02/20/2023] [Accepted: 08/10/2023] [Indexed: 09/19/2023] Open
Abstract
Cephalochordates and tunicates represent the only two groups of invertebrate chordates, and extant cephalochordates - commonly known as amphioxus or lancelets - are considered the best proxy for the chordate ancestor, from which they split around 520 million years ago. Amphioxus has been an important organism in the fields of zoology and embryology since the 18th century, and the morphological and genomic simplicity of cephalochordates (compared to vertebrates) makes amphioxus an attractive model for studying chordate biology at the cellular and molecular levels. Here we describe the life cycle of amphioxus, and discuss the natural histories and habitats of the different species of amphioxus. We also describe their use as laboratory animal models, and discuss the techniques that have been developed to study different aspects of amphioxus.
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Affiliation(s)
- Salvatore D'Aniello
- Biology and Evolution of Marine Organisms (BEOM), Stazione Zoologica Anton DohrnNapoliItaly
| | - Stephanie Bertrand
- Sorbonne Université, CNRS, Biologie Intégrative des Organismes Marins (BIOM), Observatoire OcéanologiqueBanyuls-sur-MerFrance
| | - Hector Escriva
- Sorbonne Université, CNRS, Biologie Intégrative des Organismes Marins (BIOM), Observatoire OcéanologiqueBanyuls-sur-MerFrance
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Brasó-Vives M, Marlétaz F, Echchiki A, Mantica F, Acemel RD, Gómez-Skarmeta JL, Hartasánchez DA, Le Targa L, Pontarotti P, Tena JJ, Maeso I, Escriva H, Irimia M, Robinson-Rechavi M. Parallel evolution of amphioxus and vertebrate small-scale gene duplications. Genome Biol 2022; 23:243. [PMID: 36401278 PMCID: PMC9673378 DOI: 10.1186/s13059-022-02808-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 10/31/2022] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Amphioxus are non-vertebrate chordates characterized by a slow morphological and molecular evolution. They share the basic chordate body-plan and genome organization with vertebrates but lack their 2R whole-genome duplications and their developmental complexity. For these reasons, amphioxus are frequently used as an outgroup to study vertebrate genome evolution and Evo-Devo. Aside from whole-genome duplications, genes continuously duplicate on a smaller scale. Small-scale duplicated genes can be found in both amphioxus and vertebrate genomes, while only the vertebrate genomes have duplicated genes product of their 2R whole-genome duplications. Here, we explore the history of small-scale gene duplications in the amphioxus lineage and compare it to small- and large-scale gene duplication history in vertebrates. RESULTS We present a study of the European amphioxus (Branchiostoma lanceolatum) gene duplications thanks to a new, high-quality genome reference. We find that, despite its overall slow molecular evolution, the amphioxus lineage has had a history of small-scale duplications similar to the one observed in vertebrates. We find parallel gene duplication profiles between amphioxus and vertebrates and conserved functional constraints in gene duplication. Moreover, amphioxus gene duplicates show levels of expression and patterns of functional specialization similar to the ones observed in vertebrate duplicated genes. We also find strong conservation of gene synteny between two distant amphioxus species, B. lanceolatum and B. floridae, with two major chromosomal rearrangements. CONCLUSIONS In contrast to their slower molecular and morphological evolution, amphioxus' small-scale gene duplication history resembles that of the vertebrate lineage both in quantitative and in functional terms.
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Affiliation(s)
- Marina Brasó-Vives
- grid.9851.50000 0001 2165 4204Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland ,grid.419765.80000 0001 2223 3006Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Ferdinand Marlétaz
- grid.83440.3b0000000121901201Department of Genetics, Evolution and Environment (GEE), University College London, London, UK
| | - Amina Echchiki
- grid.9851.50000 0001 2165 4204Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland ,grid.419765.80000 0001 2223 3006Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Federica Mantica
- grid.11478.3b0000 0004 1766 3695Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Rafael D. Acemel
- grid.15449.3d0000 0001 2200 2355Andalusian Centre for Developmental Biology (CABD), CSIC-Pablo Olavide University, Sevilla, Spain
| | - José L. Gómez-Skarmeta
- grid.15449.3d0000 0001 2200 2355Andalusian Centre for Developmental Biology (CABD), CSIC-Pablo Olavide University, Sevilla, Spain
| | - Diego A. Hartasánchez
- grid.9851.50000 0001 2165 4204Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
| | - Lorlane Le Targa
- IRD, APHM, MEPHI, Aix Marseille Université, Marseille, France ,grid.483853.10000 0004 0519 5986IHU-Méditerranée Infection, Marseille, France
| | - Pierre Pontarotti
- IRD, APHM, MEPHI, Aix Marseille Université, Marseille, France ,grid.483853.10000 0004 0519 5986IHU-Méditerranée Infection, Marseille, France ,grid.4444.00000 0001 2112 9282CNRS, Paris, France
| | - Juan J. Tena
- grid.15449.3d0000 0001 2200 2355Andalusian Centre for Developmental Biology (CABD), CSIC-Pablo Olavide University, Sevilla, Spain
| | - Ignacio Maeso
- grid.15449.3d0000 0001 2200 2355Andalusian Centre for Developmental Biology (CABD), CSIC-Pablo Olavide University, Sevilla, Spain ,grid.5841.80000 0004 1937 0247Department of Genetics, Microbiology and Statistics, University of Barcelona, Barcelona, Spain
| | - Hector Escriva
- grid.462844.80000 0001 2308 1657Biologie Intégrative des Organismes Marins, BIOM, CNRS-Sorbonne University, Banyuls-sur-Mer, France
| | - Manuel Irimia
- grid.11478.3b0000 0004 1766 3695Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Barcelona, Spain ,grid.5612.00000 0001 2172 2676Pompeu Fabra University (UPF), Barcelona, Spain ,grid.425902.80000 0000 9601 989XICREA, Barcelona, Spain
| | - Marc Robinson-Rechavi
- grid.9851.50000 0001 2165 4204Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland ,grid.419765.80000 0001 2223 3006Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
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Carvalho JE, Lahaye F, Yong LW, Croce JC, Escrivá H, Yu JK, Schubert M. An Updated Staging System for Cephalochordate Development: One Table Suits Them All. Front Cell Dev Biol 2021; 9:668006. [PMID: 34095136 PMCID: PMC8174843 DOI: 10.3389/fcell.2021.668006] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 03/31/2021] [Indexed: 12/17/2022] Open
Abstract
Chordates are divided into three subphyla: Vertebrata, Tunicata, and Cephalochordata. Phylogenetically, the Cephalochordata, more commonly known as lancelets or amphioxus, constitute the sister group of Vertebrata and Tunicata. Lancelets are small, benthic, marine filter feeders, and their roughly three dozen described species are divided into three genera: Branchiostoma, Epigonichthys, and Asymmetron. Due to their phylogenetic position and their stereotypical chordate morphology and genome architecture, lancelets are key models for understanding the evolutionary history of chordates. Lancelets have thus been studied by generations of scientists, with the first descriptions of adult anatomy and developmental morphology dating back to the 19th century. Today, several different lancelet species are used as laboratory models, predominantly for developmental, molecular and genomic studies. Surprisingly, however, a universal staging system and an unambiguous nomenclature for developing lancelets have not yet been adopted by the scientific community. In this work, we characterized the development of the European lancelet (Branchiostoma lanceolatum) using confocal microscopy and compiled a streamlined developmental staging system, from fertilization through larval life, including an unambiguous stage nomenclature. By tracing growth curves of the European lancelet reared at different temperatures, we were able to show that our staging system permitted an easy conversion of any developmental time into a specific stage name. Furthermore, comparisons of embryos and larvae from the European lancelet (B. lanceolatum), the Florida lancelet (Branchiostoma floridae), two Asian lancelets (Branchiostoma belcheri and Branchiostoma japonicum), and the Bahamas lancelet (Asymmetron lucayanum) demonstrated that our staging system could readily be applied to other lancelet species. Although the detailed staging description was carried out on developing B. lanceolatum, the comparisons with other lancelet species thus strongly suggested that both staging and nomenclature are applicable to all extant lancelets. We conclude that this description of embryonic and larval development will be of great use for the scientific community and that it should be adopted as the new standard for defining and naming developing lancelets. More generally, we anticipate that this work will facilitate future studies comparing representatives from different chordate lineages.
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Affiliation(s)
- João E Carvalho
- Laboratoire de Biologie du Développement de Villefranche-sur-Mer, Institut de la Mer de Villefranche, Sorbonne Université, CNRS, Villefranche-sur-Mer, France
| | - François Lahaye
- Laboratoire de Biologie du Développement de Villefranche-sur-Mer, Institut de la Mer de Villefranche, Sorbonne Université, CNRS, Villefranche-sur-Mer, France
| | - Luok Wen Yong
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan
| | - Jenifer C Croce
- Laboratoire de Biologie du Développement de Villefranche-sur-Mer, Institut de la Mer de Villefranche, Sorbonne Université, CNRS, Villefranche-sur-Mer, France
| | - Hector Escrivá
- Biologie Intégrative des Organismes Marins, Observatoire Océanologique, Sorbonne Université, CNRS, Banyuls-sur-Mer, France
| | - Jr-Kai Yu
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan.,Marine Research Station, Institute of Cellular and Organismic Biology, Academia Sinica, Yilan, Taiwan
| | - Michael Schubert
- Laboratoire de Biologie du Développement de Villefranche-sur-Mer, Institut de la Mer de Villefranche, Sorbonne Université, CNRS, Villefranche-sur-Mer, France
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Caccavale F, Osca D, D’Aniello S, Crocetta F. Molecular taxonomy confirms that the northeastern Atlantic and Mediterranean Sea harbor a single lancelet, Branchiostoma lanceolatum (Pallas, 1774) (Cephalochordata: Leptocardii: Branchiostomatidae). PLoS One 2021; 16:e0251358. [PMID: 33956890 PMCID: PMC8101936 DOI: 10.1371/journal.pone.0251358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 04/23/2021] [Indexed: 12/02/2022] Open
Abstract
Branchiostomatidae (lancelets or amphioxus) comprises about 30 species, several of which are well-established models in evolutionary development. Our zoological and ecological knowledge of the family is nonetheless limited. Despite evident differences can be found among known populations, the taxonomy of Branchiostoma lanceolatum (type species of the genus Branchiostoma) has never been investigated with modern methods through its range in the northeastern Atlantic and Mediterranean Sea. We address this via a multilocus molecular approach and comparing specimens collected from different European populations. Results obtained here confirm the presence of a single species inhabiting the range between the topotypical localities of B. lanceolatum (Atlantic Ocean) and of its junior synonym B. lubricum (Mediterranean Sea), without evincing geographical structure between populations. This suggests that environment most likely drives the characteristics observed in different geographic areas. The long larval phase and the slow mutation rate in lancelets may have played a key role in the evolutionary history of this iconic species.
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Affiliation(s)
- Filomena Caccavale
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn Napoli, Naples, Italy
| | - David Osca
- Department of Integrated Marine Ecology, Stazione Zoologica Anton Dohrn Napoli, Naples, Italy
| | - Salvatore D’Aniello
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn Napoli, Naples, Italy
| | - Fabio Crocetta
- Department of Integrated Marine Ecology, Stazione Zoologica Anton Dohrn Napoli, Naples, Italy
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Abstract
How vertebrates evolved from their invertebrate ancestors has long been a central topic of discussion in biology. Evolutionary developmental biology (evodevo) has provided a new tool-using gene expression patterns as phenotypic characters to infer homologies between body parts in distantly related organisms-to address this question. Combined with micro-anatomy and genomics, evodevo has provided convincing evidence that vertebrates evolved from an ancestral invertebrate chordate, in many respects resembling a modern amphioxus. The present review focuses on the role of evodevo in addressing two major questions of chordate evolution: (1) how the vertebrate brain evolved from the much simpler central nervous system (CNS) in of this ancestral chordate and (2) whether or not the head mesoderm of this ancestor was segmented.
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