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Yuste R. Breaking the neural code of a cnidarian: Learning principles of neuroscience from the "vulgar" Hydra. Curr Opin Neurobiol 2024; 86:102869. [PMID: 38552547 DOI: 10.1016/j.conb.2024.102869] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 02/04/2024] [Accepted: 03/07/2024] [Indexed: 06/11/2024]
Abstract
The cnidarian Hydra vulgaris is a small polyp with a nervous system of few hundred neurons belonging to a dozen cell types, organized in two nerve nets without cephalization or ganglia. Using this simple neural "chassis", Hydra can maintain a stable repertoire of behaviors, even performing complex fixed-action patterns, such as somersaulting and feeding. The ability to image the activity of Hydra's entire neural and muscle tissue has revealed that Hydra's nerve nets are divided into coactive ensembles of neurons, associated with specific movements. These ensembles can be activated by neuropeptides and interact using cross-inhibition circuits and implement integrate-to-threshold algorithms. In addition, Hydra's nervous system can self-assemble from dissociated cells in a stepwise modular architecture. Studies of Hydra and other cnidarians could enable the systematic deciphering of the neural basis of its behavior and help provide perspective on basic principles of neuroscience.
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Affiliation(s)
- Rafael Yuste
- Neurotechnology Center, Department of Biological Sciences, Columbia University, New York, NY 10027, USA.
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2
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Wiese J, Richards E, Kowalko JE, McGaugh SE. Loci associated with cave-derived traits concentrate in specific regions of the Mexican cavefish genome. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.29.587360. [PMID: 38585759 PMCID: PMC10996652 DOI: 10.1101/2024.03.29.587360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
A major goal of modern evolutionary biology is connecting phenotypic evolution with its underlying genetic basis. The Mexican cavefish (Astyanax mexicanus), a characin fish species comprised of a surface ecotype and a cave-derived ecotype, is well suited as a model to study the genetic mechanisms underlying adaptation to extreme environments. Here we map 206 previously published quantitative trait loci (QTL) for cave-derived traits in A. mexicanus to the newest version of the surface fish genome assembly, AstMex3. This analysis revealed that QTL cluster in the genome more than expected by chance, and this clustering is not explained by the distribution of genes in the genome. To investigate whether certain characteristics of the genome facilitate phenotypic evolution, we tested whether genomic characteristics, such as highly mutagenic CpG sites, are reliable predictors of the sites of trait evolution but did not find any significant trends. Finally, we combined the QTL map with previously collected expression and selection data to identify a list of 36 candidate genes that may underlie the repeated evolution of cave phenotypes, including rgrb which is predicted to be involved in phototransduction. We found this gene has disrupted exons in all non-hybrid cave populations but intact reading frames in surface fish. Overall, our results suggest specific "evolutionary hotspots" in the genome may play significant roles in driving adaptation to the cave environment in Astyanax mexicanus and demonstrate how this compiled dataset can facilitate our understanding of the genetic basis of repeated evolution in the Mexican cavefish.
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Affiliation(s)
- Jonathan Wiese
- Department of Ecology, Evolution, and Behavior, University of Minnesota, St. Paul, MN
| | - Emilie Richards
- Department of Ecology, Evolution, and Behavior, University of Minnesota, St. Paul, MN
| | | | - Suzanne E McGaugh
- Department of Ecology, Evolution, and Behavior, University of Minnesota, St. Paul, MN
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3
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Sachkova MY. Evolutionary origin of the nervous system from Ctenophora prospective. Evol Dev 2024:e12472. [PMID: 38390763 DOI: 10.1111/ede.12472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 02/09/2024] [Accepted: 02/10/2024] [Indexed: 02/24/2024]
Abstract
Nervous system is one of the key adaptations underlying the evolutionary success of the majority of animal groups. Ctenophores (or comb jellies) are gelatinous marine invertebrates that were probably the first lineage to diverge from the rest of animals. Due to the key phylogenetic position and multiple unique adaptations, the noncentralized nervous system of comb jellies has been in the center of the debate around the origin of the nervous system in the animal kingdom and whether it happened only once or twice. Here, we discuss the latest findings in ctenophore neuroscience and multiple challenges on the way to build a clear evolutionary picture of the origin of the nervous system.
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Affiliation(s)
- Maria Y Sachkova
- School of Biological Sciences, University of Bristol, Bristol, UK
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4
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Cherry AL, Wheeler MJ, Mathisova K, Di Miceli M. In silico analyses of the involvement of GPR55, CB1R and TRPV1: response to THC, contribution to temporal lobe epilepsy, structural modeling and updated evolution. Front Neuroinform 2024; 18:1294939. [PMID: 38404644 PMCID: PMC10894036 DOI: 10.3389/fninf.2024.1294939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 01/19/2024] [Indexed: 02/27/2024] Open
Abstract
Introduction The endocannabinoid (eCB) system is named after the discovery that endogenous cannabinoids bind to the same receptors as the phytochemical compounds found in Cannabis. While endogenous cannabinoids include anandamide (AEA) and 2-arachidonoylglycerol (2-AG), exogenous phytocannabinoids include Δ-9 tetrahydrocannabinol (THC) and cannabidiol (CBD). These compounds finely tune neurotransmission following synapse activation, via retrograde signaling that activates cannabinoid receptor 1 (CB1R) and/or transient receptor potential cation channel subfamily V member 1 (TRPV1). Recently, the eCB system has been linked to several neurological diseases, such as neuro-ocular abnormalities, pain insensitivity, migraine, epilepsy, addiction and neurodevelopmental disorders. In the current study, we aim to: (i) highlight a potential link between the eCB system and neurological disorders, (ii) assess if THC exposure alters the expression of eCB-related genes, and (iii) identify evolutionary-conserved residues in CB1R or TRPV1 in light of their function. Methods To address this, we used several bioinformatic approaches, such as transcriptomic (Gene Expression Omnibus), protein-protein (STRING), phylogenic (BLASTP, MEGA) and structural (Phyre2, AutoDock, Vina, PyMol) analyzes. Results Using RNA sequencing datasets, we did not observe any dysregulation of eCB-related transcripts in major depressive disorders, bipolar disorder or schizophrenia in the anterior cingulate cortex, nucleus accumbens or dorsolateral striatum. Following in vivo THC exposure in adolescent mice, GPR55 was significantly upregulated in neurons from the ventral tegmental area, while other transcripts involved in the eCB system were not affected by THC exposure. Our results also suggest that THC likely induces neuroinflammation following in vitro application on mice microglia. Significant downregulation of TPRV1 occurred in the hippocampi of mice in which a model of temporal lobe epilepsy was induced, confirming previous observations. In addition, several transcriptomic dysregulations were observed in neurons of both epileptic mice and humans, which included transcripts involved in neuronal death. When scanning known interactions for transcripts involved in the eCB system (n = 12), we observed branching between the eCB system and neurophysiology, including proteins involved in the dopaminergic system. Our protein phylogenic analyzes revealed that CB1R forms a clade with CB2R, which is distinct from related paralogues such as sphingosine-1-phosphate, receptors, lysophosphatidic acid receptors and melanocortin receptors. As expected, several conserved residues were identified, which are crucial for CB1R receptor function. The anandamide-binding pocket seems to have appeared later in evolution. Similar results were observed for TRPV1, with conserved residues involved in receptor activation. Conclusion The current study found that GPR55 is upregulated in neurons following THC exposure, while TRPV1 is downregulated in temporal lobe epilepsy. Caution is advised when interpreting the present results, as we have employed secondary analyzes. Common ancestors for CB1R and TRPV1 diverged from jawless vertebrates during the late Ordovician, 450 million years ago. Conserved residues are identified, which mediate crucial receptor functions.
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Affiliation(s)
- Amy L. Cherry
- Worcester Biomedical Research Group, School of Science and the Environment, University of Worcester, Worcester, United Kingdom
| | - Michael J. Wheeler
- Sustainable Environments Research Group, School of Science and the Environment University of Worcester, Worcester, United Kingdom
| | - Karolina Mathisova
- School of Science and the Environment University of Worcester, Worcester, United Kingdom
| | - Mathieu Di Miceli
- Worcester Biomedical Research Group, School of Science and the Environment, University of Worcester, Worcester, United Kingdom
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5
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Amplatz K, Zieger E, Abed-Navandi D, Weissenbacher A, Wanninger A. Neuromuscular development in the emerging scyphozoan model system, Cassiopea xamachana: implications for the evolution of cnidarian nervous systems. Front Neurosci 2024; 17:1324980. [PMID: 38274504 PMCID: PMC10808518 DOI: 10.3389/fnins.2023.1324980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 12/18/2023] [Indexed: 01/27/2024] Open
Abstract
The scyphozoan Cassiopea xamachana is an emerging cnidarian model system for studying regeneration, animal-algae symbiotic relationships, and various aspects of evolutionary biology including the early emergence of animal nervous systems. Cassiopea has a life cycle similar to other scyphozoans, which includes the alternation between a sessile, asexual form (polyp) and a sexually reproducing stage, the medusa. The transition between the two forms is called strobilation, where the polyp releases a miniature medusa, the iconic ephyra, that subsequently develops into the adult medusa. In addition, Cassiopea polyps may reproduce asexually by budding off free-swimming so-called planuloid buds. While the development of planuloid buds and polyps has been studied in some detail, little is known about the ontogeny of the sexually produced planula larva. Using immunofluorescence labeling and confocal microscopy, we examined neuromuscular development during metamorphosis of the planula larva into the juvenile polyp in C. xamachana. For this purpose, we used tyrosinated α-tubulin-, FMRFamide- and serotonin-like immunoreactivity together with phalloidin labeling. Our results show a planula nervous system that consists of a basiectodermal neural plexus with mostly longitudinally oriented neurites. This neural meshwork is connected to sensory neurons in the superficial stratum of the ectoderm, which are exclusively localized in the aboral half of the larva. During settlement, this aborally concentrated nervous system of the planula is replaced completely by the orally concentrated nervous system of the polyp. Adult polyps show an extensive nerve net with a loose concentration around the oral disc. These findings are consistent with data from other scyphozoans and most likely constitute a conserved feature of scyphozoan discomedusae. Taken together, the data currently available suggest an aborally concentrated nervous system including sensory cells as part of the neural ground pattern of cnidarian planula larvae. The reorganization of the nervous system from anterior to posterior in planula-to-polyp metamorphosis most likely also constitutes an ancestral trait in cnidarian evolution.
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Affiliation(s)
- Klara Amplatz
- Department of Evolutionary Biology, University of Vienna, Vienna, Austria
| | - Elisabeth Zieger
- Department of Evolutionary Biology, University of Vienna, Vienna, Austria
| | - Daniel Abed-Navandi
- Department of Evolutionary Biology, University of Vienna, Vienna, Austria
- Haus des Meeres, Vienna, Austria
| | | | - Andreas Wanninger
- Department of Evolutionary Biology, University of Vienna, Vienna, Austria
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6
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Hsiao J, Deng LC, Moroz LL, Chalasani SH, Edsinger E. Ocean to Tree: Leveraging Single-Molecule RNA-Seq to Repair Genome Gene Models and Improve Phylogenomic Analysis of Gene and Species Evolution. Methods Mol Biol 2024; 2757:461-490. [PMID: 38668979 PMCID: PMC11112408 DOI: 10.1007/978-1-0716-3642-8_19] [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] [Indexed: 05/16/2024]
Abstract
Understanding gene evolution across genomes and organisms, including ctenophores, can provide unexpected biological insights. It enables powerful integrative approaches that leverage sequence diversity to advance biomedicine. Sequencing and bioinformatic tools can be inexpensive and user-friendly, but numerous options and coding can intimidate new users. Distinct challenges exist in working with data from diverse species but may go unrecognized by researchers accustomed to gold-standard genomes. Here, we provide a high-level workflow and detailed pipeline to enable animal collection, single-molecule sequencing, and phylogenomic analysis of gene and species evolution. As a demonstration, we focus on (1) PacBio RNA-seq of the genome-sequenced ctenophore Mnemiopsis leidyi, (2) diversity and evolution of the mechanosensitive ion channel Piezo in genetic models and basal-branching animals, and (3) associated challenges and solutions to working with diverse species and genomes, including gene model updating and repair using single-molecule RNA-seq. We provide a Python Jupyter Notebook version of our pipeline (GitHub Repository: Ctenophore-Ocean-To-Tree-2023 https://github.com/000generic/Ctenophore-Ocean-To-Tree-2023 ) that can be run for free in the Google Colab cloud to replicate our findings or modified for specific or greater use. Our protocol enables users to design new sequencing projects in ctenophores, marine invertebrates, or other novel organisms. It provides a simple, comprehensive platform that can ease new user entry into running their evolutionary sequence analyses.
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Affiliation(s)
- Jan Hsiao
- Molecular Neurobiology Laboratory, Salk Institute for Biological Study, La Jolla, CA 92037
| | - Lola Chenxi Deng
- Molecular Neurobiology Laboratory, Salk Institute for Biological Study, La Jolla, CA 92037
| | - Leonid L. Moroz
- Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, FL, 32080
- Department of Neuroscience and McKnight Brain Institute, University of Florida, Gainesville, FL32611
| | - Sreekanth H. Chalasani
- Molecular Neurobiology Laboratory, Salk Institute for Biological Study, La Jolla, CA 92037
| | - Eric Edsinger
- Molecular Neurobiology Laboratory, Salk Institute for Biological Study, La Jolla, CA 92037
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7
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Nanglu K, de Carle D, Cullen TM, Anderson EB, Arif S, Castañeda RA, Chang LM, Iwama RE, Fellin E, Manglicmot RC, Massey MD, Astudillo‐Clavijo V. The nature of science: The fundamental role of natural history in ecology, evolution, conservation, and education. Ecol Evol 2023; 13:e10621. [PMID: 37877102 PMCID: PMC10591213 DOI: 10.1002/ece3.10621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 09/20/2023] [Accepted: 09/27/2023] [Indexed: 10/26/2023] Open
Abstract
There is a contemporary trend in many major research institutions to de-emphasize the importance of natural history education in favor of theoretical, laboratory, or simulation-based research programs. This may take the form of removing biodiversity and field courses from the curriculum and the sometimes subtle maligning of natural history research as a "lesser" branch of science. Additional threats include massive funding cuts to natural history museums and the maintenance of their collections, the extirpation of taxonomists across disciplines, and a critical under-appreciation of the role that natural history data (and other forms of observational data, including Indigenous knowledge) play in the scientific process. In this paper, we demonstrate that natural history knowledge is integral to any competitive science program through a comprehensive review of the ways in which they continue to shape modern theory and the public perception of science. We do so by reviewing how natural history research has guided the disciplines of ecology, evolution, and conservation and how natural history data are crucial for effective education programs and public policy. We underscore these insights with contemporary case studies, including: how understanding the dynamics of evolutionary radiation relies on natural history data; methods for extracting novel data from museum specimens; insights provided by multi-decade natural history programs; and how natural history is the most logical venue for creating an informed and scientifically literate society. We conclude with recommendations aimed at students, university faculty, and administrators for integrating and supporting natural history in their mandates. Fundamentally, we are all interested in understanding the natural world, but we can often fall into the habit of abstracting our research away from its natural contexts and complexities. Doing so risks losing sight of entire vistas of new questions and insights in favor of an over-emphasis on simulated or overly controlled studies.
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Affiliation(s)
- Karma Nanglu
- Museum of Comparative Zoology and Department of Organismic and Evolutionary BiologyHarvard UniversityCambridgeMassachusettsUSA
| | - Danielle de Carle
- Department of Ecology and Evolutionary BiologyUniversity of TorontoTorontoOntarioCanada
- Department of Invertebrate ZoologyRoyal Ontario MuseumTorontoOntarioCanada
| | - Thomas M. Cullen
- Department of GeosciencesAuburn UniversityAuburnAlabamaUSA
- Negaunee Integrative Research CenterField Museum of Natural HistoryChicagoIllinoisUSA
| | - Erika B. Anderson
- The HunterianUniversity of GlasgowGlasgowUK
- Department of Earth and SpaceRoyal Ontario MuseumTorontoOntarioCanada
| | - Suchinta Arif
- Department of BiologyDalhousie UniversityHalifaxNova ScotiaCanada
| | - Rowshyra A. Castañeda
- Ecosystems and Ocean SciencesPacific Region, Fisheries and Oceans CanadaSidneyBritish ColumbiaCanada
| | | | - Rafael Eiji Iwama
- Departamento de Genética e Biologia Evolutiva, Instituto de BiociênciasUniversidade de São PauloSão PauloBrazil
| | - Erica Fellin
- Department of BiologyMcGill UniversityMontrealQuebecCanada
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8
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Schultz DT, Haddock SHD, Bredeson JV, Green RE, Simakov O, Rokhsar DS. Ancient gene linkages support ctenophores as sister to other animals. Nature 2023; 618:110-117. [PMID: 37198475 PMCID: PMC10232365 DOI: 10.1038/s41586-023-05936-6] [Citation(s) in RCA: 65] [Impact Index Per Article: 65.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Accepted: 03/09/2023] [Indexed: 05/19/2023]
Abstract
A central question in evolutionary biology is whether sponges or ctenophores (comb jellies) are the sister group to all other animals. These alternative phylogenetic hypotheses imply different scenarios for the evolution of complex neural systems and other animal-specific traits1-6. Conventional phylogenetic approaches based on morphological characters and increasingly extensive gene sequence collections have not been able to definitively answer this question7-11. Here we develop chromosome-scale gene linkage, also known as synteny, as a phylogenetic character for resolving this question12. We report new chromosome-scale genomes for a ctenophore and two marine sponges, and for three unicellular relatives of animals (a choanoflagellate, a filasterean amoeba and an ichthyosporean) that serve as outgroups for phylogenetic analysis. We find ancient syntenies that are conserved between animals and their close unicellular relatives. Ctenophores and unicellular eukaryotes share ancestral metazoan patterns, whereas sponges, bilaterians, and cnidarians share derived chromosomal rearrangements. Conserved syntenic characters unite sponges with bilaterians, cnidarians, and placozoans in a monophyletic clade to the exclusion of ctenophores, placing ctenophores as the sister group to all other animals. The patterns of synteny shared by sponges, bilaterians, and cnidarians are the result of rare and irreversible chromosome fusion-and-mixing events that provide robust and unambiguous phylogenetic support for the ctenophore-sister hypothesis. These findings provide a new framework for resolving deep, recalcitrant phylogenetic problems and have implications for our understanding of animal evolution.
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Affiliation(s)
- Darrin T Schultz
- Department of Neuroscience and Developmental Biology, University of Vienna, Vienna, Austria.
- Monterey Bay Aquarium Research Institute, Moss Landing, CA, USA.
- Department of Biomolecular Engineering and Bioinformatics, University of California, Santa Cruz, CA, USA.
| | - Steven H D Haddock
- Monterey Bay Aquarium Research Institute, Moss Landing, CA, USA
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA, USA
| | - Jessen V Bredeson
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Richard E Green
- Department of Biomolecular Engineering and Bioinformatics, University of California, Santa Cruz, CA, USA
| | - Oleg Simakov
- Department of Neuroscience and Developmental Biology, University of Vienna, Vienna, Austria.
| | - Daniel S Rokhsar
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA.
- Molecular Genetics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Japan.
- Chan Zuckerberg Biohub, San Francisco, CA, USA.
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9
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Chromosomal comparisons reveal comb jellies as the sister group to all other animals. Nature 2023:10.1038/d41586-023-00807-6. [PMID: 37198465 DOI: 10.1038/d41586-023-00807-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
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10
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Kimbara R, Kohtsuka H, Miura T. Differences of Sucker Formation Processes Depending on Benthic or Pelagic Posthatching Lifestyles in Two Octopus Species. THE BIOLOGICAL BULLETIN 2023; 244:82-93. [PMID: 37725699 DOI: 10.1086/726772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/21/2023]
Abstract
AbstractMorphologies of animal appendages are highly diversified depending on animal lifestyles. In cephalopods (Mollusca, Cephalopoda), an individual possesses multiple arms that contribute to elaborate behaviors, and suckers on them enable various arm functions. In octopus hatchlings, arm and sucker morphologies can be divided into two different types due to alternative posthatching lifestyles, that is, pelagic or benthic lifestyles, although the underlying developmental differences have yet to be elucidated. In this study, therefore, detailed developmental processes of arms and suckers were observed during embryogenesis in two different octopus species, Octopus parvus and Amphioctopus fangsiao, showing pelagic and benthic posthatching lifestyles, respectively. In O. parvus, sucker formation stopped at a relatively early stage in which three suckers on an arm were produced. In addition, at late embryonic stages, cell proliferation was hardly detected in whole arms, while in A. fangsiao, sucker production continued throughout embryogenesis and cell proliferation also remained active in whole arms even in the late stages. Therefore, although further investigations in other octopus species are required, it is suggested that in octopus evolution, the developmental program of suckers has been modified in accordance with the acquisition of a novel lifestyle.
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11
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Haas E, Kim Y, Stanley D. Why can insects not biosynthesize cholesterol? ARCHIVES OF INSECT BIOCHEMISTRY AND PHYSIOLOGY 2023; 112:e21983. [PMID: 36372906 DOI: 10.1002/arch.21983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 10/21/2022] [Accepted: 10/24/2022] [Indexed: 06/16/2023]
Abstract
Two aspects of insect lipid biochemistry differ from the mammalian background. In one aspect, nearly a hundred years ago scientists demonstrated that the polyunsaturated fatty acid (PUFAs), linoleic acid (LA; 18:2n-6) is an essential nutrient in the diets of all mammals that have been studied in that regard. An unknown number of insect species are able to biosynthesize LA de novo. Some species take the biosynthesized LA into fatty acid elongation/desaturation pathways to produce other PUFAs, 18:3n-6, 20:3n-6 and 20:4n-6. A couple of species use the de novo produced LA to biosynthesize prostaglandins and other eicosanoids, short-lived signal moieties that mediate important physiological actions in immunity and reproduction. Insects differ from mammals, also, in their lack of genes that encode enzymes acting in biosynthesis of cholesterol. Insects require dietary cholesterol to meet their cellular, physiological, developmental, and reproductive needs. Looking at a broader view of invertebrate biochemistry, most protostomes lost all or most genes involved in cholesterol biosynthesis. The massive gene loss occurred during the Ediacaran Period, which lasted 96 million years, from the end of the Cryogenian Period (635 million years ago; MYA) to the beginning of the Cambrian Period (538.6 MYA). The key point here is that the inability to biosynthesize cholesterol is not limited to insects; it occured in most protostomes. We address the protostome need and benefits of acquiring exogenous sterols.
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Affiliation(s)
- Eric Haas
- Department of Chemistry and Biochemistry, Creighton University, Omaha, Nebraska, USA
| | - Yonggyun Kim
- Department of Plant Medicals, College of Life Sciences, Andong National University, Andong, Republic of Korea
| | - David Stanley
- Biological Control of Insect Research Laboratory, USDA-Agricultural Research Service, Columbia, Missouri, USA
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12
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McCarthy CGP, Mulhair PO, Siu-Ting K, Creevey CJ, O’Connell MJ. Improving Orthologous Signal and Model Fit in Datasets Addressing the Root of the Animal Phylogeny. Mol Biol Evol 2023; 40:6989790. [PMID: 36649189 PMCID: PMC9848061 DOI: 10.1093/molbev/msac276] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 12/19/2022] [Accepted: 12/23/2022] [Indexed: 01/18/2023] Open
Abstract
There is conflicting evidence as to whether Porifera (sponges) or Ctenophora (comb jellies) comprise the root of the animal phylogeny. Support for either a Porifera-sister or Ctenophore-sister tree has been extensively examined in the context of model selection, taxon sampling, and outgroup selection. The influence of dataset construction is comparatively understudied. We re-examine five animal phylogeny datasets that have supported either root hypothesis using an approach designed to enrich orthologous signal in phylogenomic datasets. We find that many component orthogroups in animal datasets fail to recover major lineages as monophyletic with the exception of Ctenophora, regardless of the supported root. Enriching these datasets to retain orthogroups recovering ≥3 major lineages reduces dataset size by up to 50% while retaining underlying phylogenetic information and taxon sampling. Site-heterogeneous phylogenomic analysis of these enriched datasets recovers both Porifera-sister and Ctenophora-sister positions, even with additional constraints on outgroup sampling. Two datasets which previously supported Ctenophora-sister support Porifera-sister upon enrichment. All enriched datasets display improved model fitness under posterior predictive analysis. While not conclusively rooting animals at either Porifera or Ctenophora, we do see an increase in signal for Porifera-sister and a decrease in signal for Ctenophore-sister when data are filtered for orthologous signal. Our results indicate that dataset size and construction as well as model fit influence animal root inference.
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Affiliation(s)
| | | | - Karen Siu-Ting
- Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast, Belfast BT9 5DL, United Kingdom
| | - Christopher J Creevey
- Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast, Belfast BT9 5DL, United Kingdom
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13
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The premetazoan ancestry of the synaptic toolkit and appearance of first neurons. Essays Biochem 2022; 66:781-795. [PMID: 36205407 DOI: 10.1042/ebc20220042] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 08/31/2022] [Accepted: 09/13/2022] [Indexed: 12/13/2022]
Abstract
Neurons, especially when coupled with muscles, allow animals to interact with and navigate through their environment in ways unique to life on earth. Found in all major animal lineages except sponges and placozoans, nervous systems range widely in organization and complexity, with neurons possibly representing the most diverse cell-type. This diversity has led to much debate over the evolutionary origin of neurons as well as synapses, which allow for the directed transmission of information. The broad phylogenetic distribution of neurons and presence of many of the defining components outside of animals suggests an early origin of this cell type, potentially in the time between the first animal and the last common ancestor of extant animals. Here, we highlight the occurrence and function of key aspects of neurons outside of animals as well as recent findings from non-bilaterian animals in order to make predictions about when and how the first neuron(s) arose during animal evolution and their relationship to those found in extant lineages. With advancing technologies in single cell transcriptomics and proteomics as well as expanding functional techniques in non-bilaterian animals and the close relatives of animals, it is an exciting time to begin unraveling the complex evolutionary history of this fascinating animal cell type.
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Puzakov MV, Puzakova LV, Ulupova YN. Differential Activity of Genes with IS630/TC1/MARINER Transposon Fragments in the Genome of the Ctenophore Mnemiopsis leidyi. MOLECULAR GENETICS, MICROBIOLOGY AND VIROLOGY 2022. [DOI: 10.3103/s089141682204005x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/22/2023]
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15
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Sachkova MY. Neuropeptides at the origin of neurons. Nat Ecol Evol 2022; 6:1410-1411. [PMID: 35941203 DOI: 10.1038/s41559-022-01828-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Maria Y Sachkova
- Sars International Centre for Marine Molecular Biology, University of Bergen, Bergen, Norway.
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16
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Deppisch P, Helfrich-Förster C, Senthilan PR. The Gain and Loss of Cryptochrome/Photolyase Family Members during Evolution. Genes (Basel) 2022; 13:genes13091613. [PMID: 36140781 PMCID: PMC9498864 DOI: 10.3390/genes13091613] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 09/02/2022] [Accepted: 09/05/2022] [Indexed: 11/20/2022] Open
Abstract
The cryptochrome/photolyase (CRY/PL) family represents an ancient group of proteins fulfilling two fundamental functions. While photolyases repair UV-induced DNA damages, cryptochromes mainly influence the circadian clock. In this study, we took advantage of the large number of already sequenced and annotated genes available in databases and systematically searched for the protein sequences of CRY/PL family members in all taxonomic groups primarily focusing on metazoans and limiting the number of species per taxonomic order to five. Using BLASTP searches and subsequent phylogenetic tree and motif analyses, we identified five distinct photolyases (CPDI, CPDII, CPDIII, 6-4 photolyase, and the plant photolyase PPL) and six cryptochrome subfamilies (DASH-CRY, mammalian-type MCRY, Drosophila-type DCRY, cnidarian-specific ACRY, plant-specific PCRY, and the putative magnetoreceptor CRY4. Manually assigning the CRY/PL subfamilies to the species studied, we have noted that over evolutionary history, an initial increase of various CRY/PL subfamilies was followed by a decrease and specialization. Thus, in more primitive organisms (e.g., bacteria, archaea, simple eukaryotes, and in basal metazoans), we find relatively few CRY/PL members. As species become more evolved (e.g., cnidarians, mollusks, echinoderms, etc.), the CRY/PL repertoire also increases, whereas it appears to decrease again in more recent organisms (humans, fruit flies, etc.). Moreover, our study indicates that all cryptochromes, although largely active in the circadian clock, arose independently from different photolyases, explaining their different modes of action.
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17
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Martynov AV, Korshunova TA. Renewed perspectives on the sedentary-pelagic last common bilaterian ancestor. CONTRIBUTIONS TO ZOOLOGY 2022. [DOI: 10.1163/18759866-bja10034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Abstract
Various evaluations of the last common bilaterian ancestor (lcba) currently suggest that it resembled either a microscopic, non-segmented motile adult; or, on the contrary, a complex segmented adult motile urbilaterian. These fundamental inconsistencies remain largely unexplained. A majority of multidisciplinary data regarding sedentary adult ancestral bilaterian organization is overlooked. The sedentary-pelagic model is supported now by a number of novel developmental, paleontological and molecular phylogenetic data: (1) data in support of sedentary sponges, in the adult stage, as sister to all other Metazoa; (2) a similarity of molecular developmental pathways in both adults and larvae across sedentary sponges, cnidarians, and bilaterians; (3) a cnidarian-bilaterian relationship, including a unique sharing of a bona fide Hox-gene cluster, of which the evolutionary appearance does not connect directly to a bilaterian motile organization; (4) the presence of sedentary and tube-dwelling representatives of the main bilaterian clades in the early Cambrian; (5) an absence of definite taxonomic attribution of Ediacaran taxa reconstructed as motile to any true bilaterian phyla; (6) a similarity of tube morphology (and the clear presence of a protoconch-like apical structure of the Ediacaran sedentary Cloudinidae) among shells of the early Cambrian, and later true bilaterians, such as semi-sedentary hyoliths and motile molluscs; (7) recent data that provide growing evidence for a complex urbilaterian, despite a continuous molecular phylogenetic controversy. The present review compares the main existing models and reconciles the sedentary model of an urbilaterian and the model of a larva-like lcba with a unified sedentary(adult)-pelagic(larva) model of the lcba.
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Affiliation(s)
- Alexander V. Martynov
- Zoological Museum, Moscow State University, Bolshaya Nikitskaya Str. 6, 125009 Moscow, Russia,
| | - Tatiana A. Korshunova
- Koltzov Institute of Developmental Biology RAS, 26 Vavilova Str., 119334 Moscow, Russia
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18
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Lamarca AP, Mello B, Schrago CG. The performance of outgroup-free rooting under evolutionary radiations. Mol Phylogenet Evol 2022; 169:107434. [PMID: 35143961 DOI: 10.1016/j.ympev.2022.107434] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 01/07/2022] [Accepted: 01/25/2022] [Indexed: 11/18/2022]
Abstract
Tree rooting implies a temporal dimension to phylogenies. Only after defining the position of the root node is that the ancestral-descendant relationship between branches can be fully deduced. Rooting has been usually carried out by employing evolutionarily close outgroup lineages, which is a drawback when these lineages are unavailable or unknown. Alternatively, outgroup-free rooting methods were proposed, which rely on the constancy of evolutionary rates to varying degrees. In this work we analyzed the performance of two of these methods, the midpoint rooting (MPR) and the minimal ancestor deviation (MAD), in rooting topologies evolved under challenging scenarios of fast evolutionary radiations derived from empirical data, characterized by short internal branches near the crown node. Considering all branch length combinations investigated, both methods exhibited average success rates below 50%, although MAD slightly outperformed MPR. Moreover, tree balance significantly impacted the relative performance of the methods. We found that, in four-taxa unrooted trees, the outcome of whether both methodologies will correctly root the tree can be roughly predicted by two simple dimensionless metrics: the coefficient of variation of the external branch lengths, and the ratio between the internal branch length to the total sum of branch lengths, which were employed to devise a general linear model that allowed calculating the probability of correct placing the root node for any four-taxa tree. We predicted that the performance of both outgroup-free rooting methods on loci representing the placental mammal radiation ranged between 50% and 75%.
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Affiliation(s)
| | - Beatriz Mello
- Department of Genetics, Federal University of Rio de Janeiro, RJ, Brazil
| | - Carlos G Schrago
- Department of Genetics, Federal University of Rio de Janeiro, RJ, Brazil.
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19
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Parry LA, Lerosey-Aubril R, Weaver JC, Ortega-Hernández J. Cambrian comb jellies from Utah illuminate the early evolution of nervous and sensory systems in ctenophores. iScience 2021; 24:102943. [PMID: 34522849 PMCID: PMC8426560 DOI: 10.1016/j.isci.2021.102943] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 06/01/2021] [Accepted: 07/30/2021] [Indexed: 12/11/2022] Open
Abstract
Ctenophores are a group of predatory macroinvertebrates whose controversial phylogenetic position has prompted several competing hypotheses regarding the evolution of animal organ systems. Although ctenophores date back at least to the Cambrian, they have a poor fossil record due to their gelatinous bodies. Here, we describe two ctenophore species from the Cambrian of Utah, which illuminate the early evolution of nervous and sensory features in the phylum. Thalassostaphylos elegans has 16 comb rows, an oral skirt, and an apical organ with polar fields. Ctenorhabdotus campanelliformis has 24 comb rows, an oral skirt, an apical organ enclosed by a capsule and neurological tissues preserved as carbonaceous films. These are concentrated around the apical organ and ciliated furrows, which connect to a circumoral nerve ring via longitudinal axons. C. campanelliformis deviates from the neuroanatomy of living ctenophores and demonstrates a substantial complexity in the nervous system of Cambrian ctenophores. Two species of rare fossil ctenophores are described from the Cambrian of Utah Fossil ctenophores preserve remains of nervous tissue and sensory structures Neurological structures include an oral nerve ring and giant longitudinal axons Cambrian ctenophores had a more complex neuroanatomy than living species
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Affiliation(s)
- Luke A Parry
- Department of Earth Sciences, University of Oxford, 3 South Parks Road, Oxford, OX1 3AN, UK.,Department of Geology and Geophysics, Yale University, 210 Whitney Avenue, New Haven, CT 06511, USA
| | - Rudy Lerosey-Aubril
- Museum of Comparative Zoology and Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA
| | - James C Weaver
- Wyss Institute for Biologically Inspired Engineering, Harvard University, 60 Oxford Street, Cambridge, MA 02138, USA
| | - Javier Ortega-Hernández
- Museum of Comparative Zoology and Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA
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20
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Puzakov MV, Puzakova LV, Cheresiz SV, Sang Y. The IS630/Tc1/mariner transposons in three ctenophore genomes. Mol Phylogenet Evol 2021; 163:107231. [PMID: 34133948 DOI: 10.1016/j.ympev.2021.107231] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 05/31/2021] [Accepted: 06/11/2021] [Indexed: 10/21/2022]
Abstract
Transposable elements (TEs) exert a significant effect on the structure and functioning of the genomes and also serve as a source of the new genes. The study of the TE diversity and evolution in different taxa is indispensable for the fundamental understanding of their roles in the genomes. IS630/Tc1/mariner (ITm) transposable elements represent the most prevalent and diverse group of DNA transposons. In this work, we studied the diversity, evolutionary dynamics and the phylogenetic relationships of the ITm transposons found in three ctenophore species: Mnemiopsis leidyi, Pleurobrachia bachei, Beroe ovata. We identified 29 ITm transposons, seven of which possess the terminal inverted repeats (TIRs) and an intact transposase, and, thus, are, presumably, active. Four other ITm transposons have the features of domesticated TEs. According to the results of the phylogenetic analysis, the ITm transposons of the ctenophores represent five groups - MLE/DD34D, TLE/DD34-38E, mosquito/DD37E, Visiror/DD41D and pogo/DDxD. Pogo/DDxD superfamily turnes out to be the most diverse and prevalent, since it accounts for more than 40% of the TEs identified. The data obtained in this research will fill the gap of knowledge of the diversity and evolution of the ITm transposons in the multicellular genomes and will lay the ground for the study of the TE effects on the evolution of the ctenophores.
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Affiliation(s)
- Mikhail V Puzakov
- A.O. Kovalevsky Institute of Biology of the Southern Seas of RAS, Nakhimov av., 2, Sevastopol 299011, Russia.
| | - Ludmila V Puzakova
- A.O. Kovalevsky Institute of Biology of the Southern Seas of RAS, Nakhimov av., 2, Sevastopol 299011, Russia
| | - Sergey V Cheresiz
- V. Zelman Institute for Medicine and Psychology, Novosibirsk State University, Pirogova st., 1, Novosibirsk 630090, Russia; State Scientific Research Institute of Physiology and Basic Medicine, P.O. Box 237, Novosibirsk 630117, Russia
| | - Yatong Sang
- College of Animal Science & Technology, Yangzhou University, Yangzhou, Jiangsu 225009, China
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21
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Edgar A, Mitchell DG, Martindale MQ. Whole-Body Regeneration in the Lobate Ctenophore Mnemiopsis leidyi. Genes (Basel) 2021; 12:genes12060867. [PMID: 34198839 PMCID: PMC8228598 DOI: 10.3390/genes12060867] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 06/01/2021] [Accepted: 06/02/2021] [Indexed: 01/28/2023] Open
Abstract
Ctenophores (a.k.a. comb jellies) are one of the earliest branching extant metazoan phyla. Adult regenerative ability varies greatly within the group, with platyctenes undergoing both sexual and asexual reproduction by fission while others in the genus Beroe having completely lost the ability to replace missing body parts. We focus on the unique regenerative aspects of the lobate ctenophore, Mnemiopsis leidyi, which has become a popular model for its rapid wound healing and tissue replacement, optical clarity, and sequenced genome. M. leidyi’s highly mosaic, stereotyped development has been leveraged to reveal the polar coordinate system that directs whole-body regeneration as well as lineage restriction of replacement cells in various regenerating organs. Several cell signaling pathways known to function in regeneration in other animals are absent from the ctenophore’s genome. Further research will either reveal ancient principles of the regenerative process common to all animals or reveal novel solutions to the stability of cell fates and whole-body regeneration.
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22
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Moroz LL, Romanova DY, Kohn AB. Neural versus alternative integrative systems: molecular insights into origins of neurotransmitters. Philos Trans R Soc Lond B Biol Sci 2021; 376:20190762. [PMID: 33550949 PMCID: PMC7935107 DOI: 10.1098/rstb.2019.0762] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/23/2020] [Indexed: 12/18/2022] Open
Abstract
Transmitter signalling is the universal chemical language of any nervous system, but little is known about its early evolution. Here, we summarize data about the distribution and functions of neurotransmitter systems in basal metazoans as well as outline hypotheses of their origins. We explore the scenario that neurons arose from genetically different populations of secretory cells capable of volume chemical transmission and integration of behaviours without canonical synapses. The closest representation of this primordial organization is currently found in Placozoa, disk-like animals with the simplest known cell composition but complex behaviours. We propose that injury-related signalling was the evolutionary predecessor for integrative functions of early transmitters such as nitric oxide, ATP, protons, glutamate and small peptides. By contrast, acetylcholine, dopamine, noradrenaline, octopamine, serotonin and histamine were recruited as canonical neurotransmitters relatively later in animal evolution, only in bilaterians. Ligand-gated ion channels often preceded the establishment of novel neurotransmitter systems. Moreover, lineage-specific diversification of neurotransmitter receptors occurred in parallel within Cnidaria and several bilaterian lineages, including acoels. In summary, ancestral diversification of secretory signal molecules provides unique chemical microenvironments for behaviour-driven innovations that pave the way to complex brain functions and elementary cognition. This article is part of the theme issue 'Basal cognition: multicellularity, neurons and the cognitive lens'.
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Affiliation(s)
- Leonid L. Moroz
- Department of Neuroscience, McKnight Brain Institute and Whitney laboratory, University of Florida, 9505 Ocean shore Blvd, St Augustine, FL 32080, USA
| | - Daria Y. Romanova
- Laboratory of Cellular Neurobiology of Learning, Institute of Higher Nervous Activity and Neurophysiology of RAS, 5A Butlerova Street, Moscow 117485, Russia
| | - Andrea B. Kohn
- Department of Neuroscience, McKnight Brain Institute and Whitney laboratory, University of Florida, 9505 Ocean shore Blvd, St Augustine, FL 32080, USA
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23
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Abstract
The Ediacara Biota preserves the oldest fossil evidence of abundant, complex metazoans. Despite their significance, assigning individual taxa to specific phylogenetic groups has proved problematic. To better understand these forms, we identify developmentally controlled characters in representative taxa from the Ediacaran White Sea assemblage and compare them with the regulatory tools underlying similar traits in modern organisms. This analysis demonstrates that the genetic pathways for multicellularity, axial polarity, musculature, and a nervous system were likely present in some of these early animals. Equally meaningful is the absence of evidence for major differentiation of macroscopic body units, including distinct organs, localized sensory machinery or appendages. Together these traits help to better constrain the phylogenetic position of several key Ediacara taxa and inform our views of early metazoan evolution. An apparent lack of heads with concentrated sensory machinery or ventral nerve cords in such taxa supports the hypothesis that these evolved independently in disparate bilaterian clades.
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Affiliation(s)
- Scott D Evans
- Department of Paleobiology MRC-121, National Museum of Natural History, Washington, DC 20013-7012, USA
| | - Mary L Droser
- Department of Earth and Planetary Sciences, University of California, Riverside, CA 92521, USA
| | - Douglas H Erwin
- Department of Paleobiology MRC-121, National Museum of Natural History, Washington, DC 20013-7012, USA
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24
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Mendel HC, Kaas Q, Muttenthaler M. Neuropeptide signalling systems - An underexplored target for venom drug discovery. Biochem Pharmacol 2020; 181:114129. [PMID: 32619425 PMCID: PMC7116218 DOI: 10.1016/j.bcp.2020.114129] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 06/22/2020] [Accepted: 06/23/2020] [Indexed: 01/06/2023]
Abstract
Neuropeptides are signalling molecules mainly secreted from neurons that act as neurotransmitters or peptide hormones to affect physiological processes and modulate behaviours. In humans, neuropeptides are implicated in numerous diseases and understanding their role in physiological processes and pathologies is important for therapeutic development. Teasing apart the (patho)physiology of neuropeptides remains difficult due to ligand and receptor promiscuity and the complexity of the signalling pathways. The current approach relies on a pharmacological toolbox of agonists and antagonists displaying high selectivity for independent receptor subtypes, with the caveat that only few selective ligands have been discovered or developed. Animal venoms represent an underexplored source for novel receptor subtype-selective ligands that could aid in dissecting human neuropeptide signalling systems. Multiple endogenous-like neuropeptides as well as peptides acting on neuropeptide receptors are present in venoms. In this review, we summarise current knowledge on neuropeptides and discuss venoms as a source for ligands targeting neuropeptide signalling systems.
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Affiliation(s)
- Helen C Mendel
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
| | - Quentin Kaas
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
| | - Markus Muttenthaler
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia; University of Vienna, Faculty of Chemistry, Institute of Biological Chemistry, Vienna, Austria.
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25
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Williams EA. Function and Distribution of the Wamide Neuropeptide Superfamily in Metazoans. Front Endocrinol (Lausanne) 2020; 11:344. [PMID: 32547494 PMCID: PMC7270403 DOI: 10.3389/fendo.2020.00344] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/16/2020] [Accepted: 05/01/2020] [Indexed: 01/19/2023] Open
Abstract
The Wamide neuropeptide superfamily is of interest due to its distinctive functions in regulating life cycle transitions, metamorphic hormone signaling, and several aspects of digestive system function, from gut muscle contraction to satiety and fat storage. Due to variation among researchers in naming conventions, a global view of Wamide signaling in animals in terms of conservation or diversification of function is currently lacking. Here, I summarize the phylogenetic distribution of Wamide neuropeptides based on current data and describe recent findings in the areas of Wamide receptors and biological functions. Common trends that emerge across Cnidarians and protostomes are the presence of multiple Wamide receptors within a single organism, and the fact that Wamide signaling likely functions across an extensive variety of biological systems, including visual, circadian, and reproductive systems. Important areas of focus for future research are the further identification of Wamide-receptor pairs, confirmation of the phylogenetic distribution of Wamides through largescale sequencing and mass spectrometry, and assignment of different functions to specific subsets of Wamide-expressing neurons. More extensive study of Wamide signaling throughout larval development in a greater number of phyla is also important in order to understand the role of Wamides in hormonal regulation. Defining the evolution and function of neuropeptide signaling in animal nervous systems will benefit from an increased understanding of Wamide function and signaling mechanisms in a wider variety of organisms, beyond the traditional model systems.
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26
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Martinez P, Sprecher SG. Of Circuits and Brains: The Origin and Diversification of Neural Architectures. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.00082] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
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27
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Rey S, Zalc B, Klämbt C. Evolution of glial wrapping: A new hypothesis. Dev Neurobiol 2020; 81:453-463. [PMID: 32133794 DOI: 10.1002/dneu.22739] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 01/16/2020] [Accepted: 02/27/2020] [Indexed: 12/12/2022]
Abstract
Animals are able to move and react in numerous ways to external stimuli. Thus, environmental stimuli need to be detected, information must be processed and finally an output decision must be transmitted to the musculature to get the animal moving. All these processes depend on the nervous system which comprises an intricate neuronal network and many glial cells. In the last decades, a neurono-centric view on nervous system function channeled most of the scientific interest toward the analysis of neurons and neuronal functions. Neurons appeared early in animal evolution and the main principles of neuronal function from synaptic transmission to propagation of action potentials are conserved during evolution. In contrast, not much is known on the evolution of glial cells that were initially considered merely as static support cells. Although it is now accepted that glial cells have an equally important contribution as their neuronal counterpart to nervous system function, their evolutionary origin is unknown. Did glial cells appear several times during evolution? What were the first roles glial cells had to fulfil in the nervous system? What triggered the formation of the amazing diversity of glial morphologies and functions? Is there a possible mechanism that might explain the appearance of complex structures such as myelin in vertebrates? Here, we postulate a common evolutionary origin of glia and depict a number of selective forces that might have paved the way from a simple supporting cell to a wrapping and myelin forming glial cell.
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Affiliation(s)
- Simone Rey
- Institut für Neuro- und Verhaltensbiologie, Universität Münster, Münster, Germany
| | - Bernard Zalc
- Institut du Cerveau et de la Moelle Épinière, GH Pitié-Salpêtrière, Sorbonne Université, Inserm, CNRS, Paris, France
| | - Christian Klämbt
- Institut für Neuro- und Verhaltensbiologie, Universität Münster, Münster, Germany
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28
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Malakhov VV, Bogomolova EV, Kuzmina TV, Temereva EN. Evolution of Metazoan Life Cycles and the Origin of Pelagic Larvae. Russ J Dev Biol 2020. [DOI: 10.1134/s1062360419060043] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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29
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Guijarro-Clarke C, Holland PWH, Paps J. Widespread patterns of gene loss in the evolution of the animal kingdom. Nat Ecol Evol 2020; 4:519-523. [PMID: 32094540 DOI: 10.1038/s41559-020-1129-2] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 01/28/2020] [Indexed: 11/09/2022]
Abstract
The animal kingdom shows an astonishing diversity, the product of over 550 million years of animal evolution. The current wealth of genome sequence data offers an opportunity to better understand the genomic basis of this diversity. Here we analyse a sampling of 102 whole genomes including >2.6 million protein sequences. We infer major genomic patterns associated with the variety of animal forms from the superphylum to phylum level. We show that a remarkable amount of gene loss occurred during the evolution of two major groups of bilaterian animals, Ecdysozoa and Deuterostomia, and further loss in several deuterostome lineages. Deuterostomes and protostomes also show large genome novelties. At the phylum level, flatworms, nematodes and tardigrades show the largest reduction of gene complement, alongside gene novelty. These findings paint a picture of evolution in the animal kingdom in which reductive evolution at the protein-coding level played a major role in shaping genome composition.
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Affiliation(s)
| | | | - Jordi Paps
- School of Biological Sciences, University of Essex, Colchester, UK. .,Department of Zoology, University of Oxford, Oxford, UK. .,School of Biological Sciences, University of Bristol, Bristol, UK.
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30
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A Screen for Gene Paralogies Delineating Evolutionary Branching Order of Early Metazoa. G3-GENES GENOMES GENETICS 2020; 10:811-826. [PMID: 31879283 PMCID: PMC7003098 DOI: 10.1534/g3.119.400951] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The evolutionary diversification of animals is one of Earth’s greatest marvels, yet its earliest steps are shrouded in mystery. Animals, the monophyletic clade known as Metazoa, evolved wildly divergent multicellular life strategies featuring ciliated sensory epithelia. In many lineages epithelial sensoria became coupled to increasingly complex nervous systems. Currently, different phylogenetic analyses of single-copy genes support mutually-exclusive possibilities that either Porifera or Ctenophora is sister to all other animals. Resolving this dilemma would advance the ecological and evolutionary understanding of the first animals and the evolution of nervous systems. Here we describe a comparative phylogenetic approach based on gene duplications. We computationally identify and analyze gene families with early metazoan duplications using an approach that mitigates apparent gene loss resulting from the miscalling of paralogs. In the transmembrane channel-like (TMC) family of mechano-transducing channels, we find ancient duplications that define separate clades for Eumetazoa (Placozoa + Cnidaria + Bilateria) vs. Ctenophora, and one duplication that is shared only by Eumetazoa and Porifera. In the Max-like protein X (MLX and MLXIP) family of bHLH-ZIP regulators of metabolism, we find that all major lineages from Eumetazoa and Porifera (sponges) share a duplicated gene pair that is sister to the single-copy gene maintained in Ctenophora. These results suggest a new avenue for deducing deep phylogeny by choosing rather than avoiding ancient gene paralogies.
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31
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Lamarca AP, Schrago CG. Fast speciations and slow genes: uncovering the root of living canids. Biol J Linn Soc Lond 2019. [DOI: 10.1093/biolinnean/blz181] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Abstract
Despite ongoing efforts relying on computationally intensive tree-building methods and large datasets, the deeper phylogenetic relationships between living canid genera remain controversial. We demonstrate that this issue arises fundamentally from the uncertainty of root placement as a consequence of the short length of the branch connecting the major canid clades, which probably resulted from a fast radiation during the early diversification of extant Canidae. Using both nuclear and mitochondrial genes, we investigate the position of the canid root and its consistency by using three rooting methods. We find that mitochondrial genomes consistently retrieve a root node separating the tribe Canini from the remaining canids, whereas nuclear data mostly recover a root that places the Urocyon foxes as the sister lineage of living canids. We demonstrate that, to resolve the canid root, the nuclear segments sequenced so far are significantly less informative than mitochondrial genomes. We also propose that short intervals between speciations obscure the place of the true root, because methods are susceptible to stochastic error in the presence of short internal branches near the root.
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Affiliation(s)
- Alessandra P Lamarca
- Department of Genetics, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Carlos G Schrago
- Department of Genetics, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
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32
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Arnellos A, Keijzer F. Bodily Complexity: Integrated Multicellular Organizations for Contraction-Based Motility. Front Physiol 2019; 10:1268. [PMID: 31680996 PMCID: PMC6803425 DOI: 10.3389/fphys.2019.01268] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2019] [Accepted: 09/19/2019] [Indexed: 01/13/2023] Open
Abstract
Compared to other forms of multicellularity, the animal case is unique. Animals-barring some exceptions-consist of collections of cells that are connected and integrated to such an extent that these collectives act as unitary, large free-moving entities capable of sensing macroscopic properties and events. This animal configuration is so well-known that it is often taken as a natural one that 'must' have evolved, given environmental conditions that make large free-moving units 'obviously' adaptive. Here we question the seemingly evolutionary inevitableness of animals and introduce a thesis of bodily complexity: The multicellular organization characteristic for typical animals requires the integration of a multitude of intrinsic bodily features between its sensorimotor, physiological, and developmental aspects, and the related contraction-based tissue- and cellular-level events and processes. The evolutionary road toward this bodily complexity involves, we argue, various intermediate organizational steps that accompany and support the wider transition from cilia-based to contraction/muscle-based motility, and which remain insufficiently acknowledged. Here, we stress the crucial and specific role played by muscle-based and myoepithelial tissue contraction-acting as a physical platform for organizing both the multicellular transmission of mechanical forces and multicellular signaling-as key foundation of animal motility, sensing and maintenance, and development. We illustrate and discuss these bodily features in the context of the four basal animal phyla-Porifera, Ctenophores, Placozoans, and Cnidarians-that split off before the bilaterians, a supergroup that incorporates all complex animals.
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Affiliation(s)
- Argyris Arnellos
- IAS-Research Centre for Life, Mind & Society, Department of Logic and Philosophy of Science, University of the Basque Country, San Sebastián, Spain.,Department of Product and Systems Design Engineering, Complex Systems and Service Design Lab, University of the Aegean, Syros, Greece
| | - Fred Keijzer
- Department of Theoretical Philosophy, University of Groningen, Groningen, Netherlands
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Wong E, Mölter J, Anggono V, Degnan SM, Degnan BM. Co-expression of synaptic genes in the sponge Amphimedon queenslandica uncovers ancient neural submodules. Sci Rep 2019; 9:15781. [PMID: 31673079 PMCID: PMC6823388 DOI: 10.1038/s41598-019-51282-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Accepted: 09/28/2019] [Indexed: 12/13/2022] Open
Abstract
The synapse is a complex cellular module crucial to the functioning of neurons. It evolved largely through the exaptation of pre-existing smaller submodules, each of which are comprised of ancient sets of proteins that are conserved in modern animals and other eukaryotes. Although these ancient submodules themselves have non-neural roles, it has been hypothesized that they may mediate environmental sensing behaviors in aneural animals, such as sponges. Here we identify orthologues in the sponge Amphimedon queenslandica of genes encoding synaptic submodules in neural animals, and analyse their cell-type specific and developmental expression to determine their potential to be co-regulated. We find that genes comprising certain synaptic submodules, including those involved in vesicle trafficking, calcium-regulation and scaffolding of postsynaptic receptor clusters, are co-expressed in adult choanocytes and during metamorphosis. Although these submodules may contribute to sensory roles in this cell type and this life cycle stage, total synaptic gene co-expression profiles do not support the existence of a functional synapse in A. queenslandica. The lack of evidence for the co-regulation of genes necessary for pre- and post-synaptic functioning in A. queenslandica suggests that sponges, and perhaps the last common ancestor of sponges and other extant animals, had the ability to promulgate sensory inputs without complete synapse-like functionalities. The differential co-expression of multiple synaptic submodule genes in sponge choanocytes, which have sensory and feeding roles, however, is consistent with the metazoan ancestor minimally being able to undergo exo- and endocytosis in a controlled and localized manner.
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Affiliation(s)
- Eunice Wong
- School of Biological Sciences, University of Queensland, Brisbane, Queensland, 4072, Australia
| | - Jan Mölter
- Queensland Brain Institute, University of Queensland, Brisbane, Queensland, 4072, Australia
- School of Mathematics and Physics, University of Queensland, Brisbane, Queensland, 4072, Australia
| | - Victor Anggono
- Queensland Brain Institute, University of Queensland, Brisbane, Queensland, 4072, Australia
- Clem Jones Centre for Ageing Dementia Research, University of Queensland, Brisbane, Queensland, 4072, Australia
| | - Sandie M Degnan
- School of Biological Sciences, University of Queensland, Brisbane, Queensland, 4072, Australia
| | - Bernard M Degnan
- School of Biological Sciences, University of Queensland, Brisbane, Queensland, 4072, Australia.
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Martín-Durán JM, Hejnol A. A developmental perspective on the evolution of the nervous system. Dev Biol 2019; 475:181-192. [PMID: 31610146 DOI: 10.1016/j.ydbio.2019.10.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2017] [Revised: 06/02/2018] [Accepted: 10/04/2019] [Indexed: 12/20/2022]
Abstract
The evolution of nervous systems in animals has always fascinated biologists, and thus multiple evolutionary scenarios have been proposed to explain the appearance of neurons and complex neuronal centers. However, the absence of a robust phylogenetic framework for animal interrelationships, the lack of a mechanistic understanding of development, and a recapitulative view of animal ontogeny have traditionally limited these scenarios. Only recently, the integration of advanced molecular and morphological studies in a broad range of animals has allowed to trace the evolution of developmental and neuronal characters on a better-resolved animal phylogeny. This has falsified most traditional scenarios for nervous system evolution, paving the way for the emergence of new testable hypotheses. Here we summarize recent progress in studies of nervous system development in major animal lineages and formulate some of the arising questions. In particular, we focus on how lineage analyses of nervous system development and a comparative study of the expression of neural-related genes has influenced our understanding of the evolution of an elaborated central nervous system in Bilateria. We argue that a phylogeny-guided study of neural development combining thorough descriptive and functional analyses is key to establish more robust scenarios for the origin and evolution of animal nervous systems.
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Affiliation(s)
- José M Martín-Durán
- Sars International Centre for Marine Molecular Biology, University of Bergen, Thørmohlensgate 55, 5006, Bergen, Norway; School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, E1 4NS, London, UK.
| | - Andreas Hejnol
- Sars International Centre for Marine Molecular Biology, University of Bergen, Thørmohlensgate 55, 5006, Bergen, Norway.
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Hahn N, Büschgens L, Schwedhelm-Domeyer N, Bank S, Geurten BRH, Neugebauer P, Massih B, Göpfert MC, Heinrich R. The Orphan Cytokine Receptor CRLF3 Emerged With the Origin of the Nervous System and Is a Neuroprotective Erythropoietin Receptor in Locusts. Front Mol Neurosci 2019; 12:251. [PMID: 31680856 PMCID: PMC6797617 DOI: 10.3389/fnmol.2019.00251] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Accepted: 09/27/2019] [Indexed: 12/19/2022] Open
Abstract
The orphan cytokine receptor-like factor 3 (CRLF3) was identified as a neuroprotective erythropoietin receptor in locust neurons and emerged with the evolution of the eumetazoan nervous system. Human CRLF3 belongs to class I helical cytokine receptors that mediate pleiotropic cellular reactions to injury and diverse physiological challenges. It is expressed in various tissues including the central nervous system but its ligand remains unidentified. A CRLF3 ortholog in the holometabolous beetle Tribolium castaneum was recently shown to induce anti-apoptotic mechanisms upon stimulation with human recombinant erythropoietin. To test the hypothesis that CRLF3 represents an ancient cell-protective receptor for erythropoietin-like cytokines, we investigated its presence across metazoan species. Furthermore, we examined CRLF3 expression and function in the hemimetabolous insect Locusta migratoria. Phylogenetic analysis of CRLF3 sequences indicated that CRLF3 is absent in Porifera, Placozoa and Ctenophora, all lacking the traditional nervous system. However, it is present in all major eumetazoan groups ranging from cnidarians over protostomians to mammals. The CRLF3 sequence is highly conserved and abundant amongst vertebrates. In contrast, relatively few invertebrates express CRLF3 and these sequences show greater variability, suggesting frequent loss due to low functional importance. In L. migratoria, we identified the transcript Lm-crlf3 by RACE-PCR and detected its expression in locust brain, skeletal muscle and hemocytes. These findings correspond to the ubiquitous expression of crlf3 in mammalian tissues. We demonstrate that the sole addition of double-stranded RNA to the culture medium (called soaking RNA interference) specifically interferes with protein expression in locust primary brain cell cultures. This technique was used to knock down Lm-crlf3 expression and to abolish its physiological function. We confirmed that recombinant human erythropoietin rescues locust brain neurons from hypoxia-induced apoptosis and showed that this neuroprotective effect is absent after knocking down Lm-crlf3. Our results affirm the erythropoietin-induced neuroprotective function of CRLF3 in a second insect species from a different taxonomic group. They suggest that the phylogenetically conserved CRLF3 receptor may function as a cell protective receptor for erythropoietin or a structurally related cytokine also in other animals including vertebrate and mammalian species.
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Affiliation(s)
- Nina Hahn
- Department of Cellular Neurobiology, Institute for Zoology and Anthropology, Georg-August University of Göttingen, Göttingen, Germany
| | - Luca Büschgens
- Department of Cellular Neurobiology, Institute for Zoology and Anthropology, Georg-August University of Göttingen, Göttingen, Germany
| | - Nicola Schwedhelm-Domeyer
- Department of Cellular Neurobiology, Institute for Zoology and Anthropology, Georg-August University of Göttingen, Göttingen, Germany
| | - Sarah Bank
- Department of Animal Evolution and Biodiversity, Institute for Zoology & Anthropology, Georg-August University of Göttingen, Göttingen, Germany
| | - Bart R H Geurten
- Department of Cellular Neurobiology, Institute for Zoology and Anthropology, Georg-August University of Göttingen, Göttingen, Germany
| | - Pia Neugebauer
- Department of Cellular Neurobiology, Institute for Zoology and Anthropology, Georg-August University of Göttingen, Göttingen, Germany
| | - Bita Massih
- Department of Cellular Neurobiology, Institute for Zoology and Anthropology, Georg-August University of Göttingen, Göttingen, Germany
| | - Martin C Göpfert
- Department of Cellular Neurobiology, Institute for Zoology and Anthropology, Georg-August University of Göttingen, Göttingen, Germany
| | - Ralf Heinrich
- Department of Cellular Neurobiology, Institute for Zoology and Anthropology, Georg-August University of Göttingen, Göttingen, Germany
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Puzakov MV, Puzakova LV. leidyi Is a New Group of DD41D Transposons in Mnemiopsis leidyi Genome. RUSS J GENET+ 2019. [DOI: 10.1134/s1022795419070123] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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37
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Alzugaray ME, Bruno MC, Villalobos Sambucaro MJ, Ronderos JR. The Evolutionary History of The Orexin/Allatotropin GPCR Family: from Placozoa and Cnidaria to Vertebrata. Sci Rep 2019; 9:10217. [PMID: 31308431 PMCID: PMC6629687 DOI: 10.1038/s41598-019-46712-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Accepted: 07/04/2019] [Indexed: 12/14/2022] Open
Abstract
Peptidic messengers constitute a highly diversified group of intercellular messengers widely distributed in nature that regulate a great number of physiological processes in Metazoa. Being crucial for life, it seem that they have appeared in the ancestral group from which Metazoa evolved, and were highly conserved along the evolutionary process. Peptides act mainly through G-protein coupled receptors (GPCRs), a family of transmembrane molecules. GPCRs are also widely distributed in nature being present in metazoan, but also in Choanoflagellata and Fungi. Among GPCRs, the Allatotropin/Orexin (AT/Ox) family is particularly characterized by the presence of the DRW motif in the second intracellular loop (IC Loop 2), and seems to be present in Cnidaria, Placozoa and in Bilateria, suggesting that it was present in the common ancestor of Metazoa. Looking for the evolutionary history of this GPCRs we searched for corresponding sequences in public databases. Our results suggest that AT/Ox receptors were highly conserved along evolutionary process, and that they are characterized by the presence of the E/DRWYAI motif at the IC Loop 2. Phylogenetic analyses show that AT/Ox family of receptors reflects evolutionary relationships that agree with current phylogenetic understanding in Actinopterygii and Sauropsida, including also the largely discussed position of Testudines.
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Affiliation(s)
- María Eugenia Alzugaray
- Cátedra de Histología y Embriología Animal, Facultad de Ciencias Naturales y Museo, Universidad Nacional de La Plata (FCNyM-UNLP), La Plata, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - María Cecilia Bruno
- Cátedra de Histología y Embriología Animal, Facultad de Ciencias Naturales y Museo, Universidad Nacional de La Plata (FCNyM-UNLP), La Plata, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - María José Villalobos Sambucaro
- Cátedra de Histología y Embriología Animal, Facultad de Ciencias Naturales y Museo, Universidad Nacional de La Plata (FCNyM-UNLP), La Plata, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Jorge Rafael Ronderos
- Cátedra de Histología y Embriología Animal, Facultad de Ciencias Naturales y Museo, Universidad Nacional de La Plata (FCNyM-UNLP), La Plata, Argentina.
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de Oliveira AL, Calcino A, Wanninger A. Ancient origins of arthropod moulting pathway components. eLife 2019; 8:46113. [PMID: 31266593 PMCID: PMC6660194 DOI: 10.7554/elife.46113] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Accepted: 06/27/2019] [Indexed: 12/25/2022] Open
Abstract
Ecdysis (moulting) is the defining character of Ecdysoza (arthropods, nematodes and related phyla). Despite superficial similarities, the signalling cascade underlying moulting differs between Panarthropoda and the remaining ecdysozoans. Here, we reconstruct the evolution of major components of the ecdysis pathway. Its key elements evolved much earlier than previously thought and are present in non-moulting lophotrochozoans and deuterostomes. Eclosion hormone (EH) and bursicon originated prior to the cnidarian-bilaterian split, whereas ecdysis-triggering hormone (ETH) and crustacean cardioactive peptide (CCAP) evolved in the bilaterian last common ancestor (LCA). Identification of EH, CCAP and bursicon in Onychophora and EH, ETH and CCAP in Tardigrada suggests that the pathway was present in the panarthropod LCA. Trunk, an ancient extracellular signalling molecule and a well-established paralog of the insect peptide prothoracicotropic hormone (PTTH), is present in the non-bilaterian ctenophore Mnemiopsis leidyi. This constitutes the first case of a ctenophore signalling peptide with homology to a neuropeptide. Animals such as insects, crabs and spiders belong to one of the most species-rich animal groups, called the arthropods. These animals have exoskeletons, which are hard, external coverings that support their bodies. Arthropods shed their exoskeletons as they grow, a process called ecdysis or moulting, and this behaviour is controlled by a set of hormones and small protein-like molecules called neuropeptides that allow communication between neurons. Other animals, such as roundworms, also moult; and together with arthropods they are classified into a group called the Ecdysozoa. Since moulting is a common behaviour in ecdysozoans, it was previously assumed that its signalling components had evolved in the common ancestor of roundworms and arthropods, although differences in the moulting machinery between both groups exist. Here, De Oliveira et al. investigate the evolutionary origins of the arthropod moulting machinery and find that some of the hormones and neuropeptides involved appeared long before the arthropods themselves. Database searches showed that important hormones and neuropeptides involved in arthropod moulting can be found in diverse animal groups, such as jellyfish, molluscs and starfish, confirming that these molecules evolved before the last common ancestor of roundworms and arthropods. These animals must therefore use the hormones and neuropeptides in many processes unrelated to moulting. De Oliveira et al. also found that roundworms have lost most of these molecules, and that moulting in these animals must be driven by a different complement of hormones and neuropeptides. These results invite research into the role of moulting hormones and neuropeptides in animals outside the Ecdysozoa. They also show that signalling pathways and the processes they regulate are highly adaptable: two animals can use the same hormone in entirely different processes, but conversely, the same behaviour may be regulated by different molecules depending on the animal. This means that the evolution of a process and the evolution of its regulation can be decoupled, a finding that has important implications for the study of signalling pathways and their evolution.
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Affiliation(s)
- André Luiz de Oliveira
- Department of Integrative Zoology, Faculty of Life Sciences, University of Vienna, Vienna, Austria
| | - Andrew Calcino
- Department of Integrative Zoology, Faculty of Life Sciences, University of Vienna, Vienna, Austria
| | - Andreas Wanninger
- Department of Integrative Zoology, Faculty of Life Sciences, University of Vienna, Vienna, Austria
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39
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Abstract
Genome sequence data from a range of animal species are raising questions about the origins of glutamate receptors.
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Affiliation(s)
- Mark L Mayer
- National Institute for Neurological Disorders and Stroke, Bethesda, United States
| | - Timothy Jegla
- Department of Biology, Pennsylvania State University, University Park, United States.,Huck Institute for the Life Sciences, Pennsylvania State University, University Park, United States
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40
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Babonis LS, DeBiasse MB, Francis WR, Christianson LM, Moss AG, Haddock SHD, Martindale MQ, Ryan JF. Integrating Embryonic Development and Evolutionary History to Characterize Tentacle-Specific Cell Types in a Ctenophore. Mol Biol Evol 2018; 35:2940-2956. [PMID: 30169705 PMCID: PMC6278862 DOI: 10.1093/molbev/msy171] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The origin of novel traits can promote expansion into new niches and drive speciation. Ctenophores (comb jellies) are unified by their possession of a novel cell type: the colloblast, an adhesive cell found only in the tentacles. Although colloblast-laden tentacles are fundamental for prey capture among ctenophores, some species have tentacles lacking colloblasts and others have lost their tentacles completely. We used transcriptomes from 36 ctenophore species to identify gene losses that occurred specifically in lineages lacking colloblasts and tentacles. We cross-referenced these colloblast- and tentacle-specific candidate genes with temporal RNA-Seq during embryogenesis in Mnemiopsis leidyi and found that both sets of candidates are preferentially expressed during tentacle morphogenesis. We also demonstrate significant upregulation of candidates from both data sets in the tentacle bulb of adults. Both sets of candidates were enriched for an N-terminal signal peptide and protein domains associated with secretion; among tentacle candidates we also identified orthologs of cnidarian toxin proteins, presenting tantalizing evidence that ctenophore tentacles may secrete toxins along with their adhesive. Finally, using cell lineage tracing, we demonstrate that colloblasts and neurons share a common progenitor, suggesting the evolution of colloblasts involved co-option of a neurosecretory gene regulatory network. Together these data offer an initial glimpse into the genetic architecture underlying ctenophore cell-type diversity.
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Affiliation(s)
- Leslie S Babonis
- Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, FL
| | - Melissa B DeBiasse
- Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, FL
| | - Warren R Francis
- Monterey Bay Aquarium Research Institute (MBARI), Moss Landing, CA
| | | | - Anthony G Moss
- Department of Biological Sciences, Auburn University, Auburn, AL
| | | | - Mark Q Martindale
- Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, FL
| | - Joseph F Ryan
- Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, FL
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41
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High Cell Diversity and Complex Peptidergic Signaling Underlie Placozoan Behavior. Curr Biol 2018; 28:3495-3501.e2. [DOI: 10.1016/j.cub.2018.08.067] [Citation(s) in RCA: 66] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2018] [Revised: 07/20/2018] [Accepted: 08/31/2018] [Indexed: 12/17/2022]
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42
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Evolution of the bilaterian mouth and anus. Nat Ecol Evol 2018; 2:1358-1376. [PMID: 30135501 DOI: 10.1038/s41559-018-0641-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Revised: 06/26/2018] [Accepted: 07/11/2018] [Indexed: 12/17/2022]
Abstract
It is widely held that the bilaterian tubular gut with mouth and anus evolved from a simple gut with one major gastric opening. However, there is no consensus on how this happened. Did the single gastric opening evolve into a mouth, with the anus forming elsewhere in the body (protostomy), or did it evolve into an anus, with the mouth forming elsewhere (deuterostomy), or did it evolve into both mouth and anus (amphistomy)? These questions are addressed by the comparison of developmental fates of the blastopore, the opening of the embryonic gut, in diverse animals that live today. Here we review comparative data on the identity and fate of blastoporal tissue, investigate how the formation of the through-gut relates to the major body axes, and discuss to what extent evolutionary scenarios are consistent with these data. Available evidence indicates that stem bilaterians had a slit-like gastric opening that was partially closed in subsequent evolution, leaving open the anus and most likely also the mouth, which would favour amphistomy. We discuss remaining difficulties, and outline directions for future research.
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43
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Abstract
The origin of animals, one of the major transitions in evolution, remains mysterious. Many key aspects of animal evolution can be reconstructed by comparing living species within a robust phylogenetic framework. However, uncertainty remains regarding the evolutionary relationships between two ancient animal lineages - sponges and ctenophores - and the remaining animal phyla. Comparative morphology and some phylogenomic analyses support the view that sponges represent the sister lineage to the rest of the animals, while other phylogenomic analyses support ctenophores, a phylum of carnivorous, gelatinous marine organisms, as the sister lineage. Here, we explore why different studies yield different answers and discuss the implications of the two alternative hypotheses for understanding the origin of animals. Reconstruction of ancient evolutionary radiations is devilishly difficult and will likely require broader sampling of sponge and ctenophore genomes, improved analytical strategies and critical analyses of the phylogenetic distribution and molecular mechanisms underlying apparently conserved traits. Rather than staking out positions in favor of the ctenophores-sister or the sponges-sister hypothesis, we submit that research programs aimed at understanding the biology of the first animals should instead embrace the uncertainty surrounding early animal evolution in their experimental designs.
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Sebé-Pedrós A, Chomsky E, Pang K, Lara-Astiaso D, Gaiti F, Mukamel Z, Amit I, Hejnol A, Degnan BM, Tanay A. Early metazoan cell type diversity and the evolution of multicellular gene regulation. Nat Ecol Evol 2018; 2:1176-1188. [PMID: 29942020 PMCID: PMC6040636 DOI: 10.1038/s41559-018-0575-6] [Citation(s) in RCA: 151] [Impact Index Per Article: 25.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Accepted: 05/09/2018] [Indexed: 12/11/2022]
Abstract
A hallmark of metazoan evolution is the emergence of genomic mechanisms that implement cell type-specific functions. However, the evolution of metazoan cell types and their underlying gene regulatory programs remain largely uncharacterized. Here, we use whole-organism single-cell RNA-seq to map cell type-specific transcription in Porifera (sponges), Ctenophora (comb jellies) and Placozoa species. We describe the repertoires of cell types in these non-bilaterian animals, uncovering diverse instances of previously unknown molecular signatures, such as multiple types of peptidergic cells in Placozoa. Analysis of the regulatory programs of these cell types reveal variable levels of complexity. In placozoans and poriferans, sequence motifs in the promoters are predictive of cell type-specific programs. In contrast, the generation of a higher diversity of cell types in ctenophores is associated to lower specificity of promoter sequences and to the existence of distal regulatory elements. Our findings demonstrate that metazoan cell types can be defined by networks of TFs and proximal promoters, and indicate that further genome regulatory complexity may be required for more diverse cell type repertoires.
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Affiliation(s)
- Arnau Sebé-Pedrós
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel. .,Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel.
| | - Elad Chomsky
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel.,Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Kevin Pang
- Sars International Centre for Marine Molecular Biology, University of Bergen, Bergen, Norway
| | - David Lara-Astiaso
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Federico Gaiti
- School of Biological Sciences, University of Queensland, Brisbane, Queensland, Australia.,Department of Medicine, Weill Cornell Medicine and New York Genome Center, New York, NY, USA
| | - Zohar Mukamel
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel.,Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Ido Amit
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Andreas Hejnol
- Sars International Centre for Marine Molecular Biology, University of Bergen, Bergen, Norway
| | - Bernard M Degnan
- School of Biological Sciences, University of Queensland, Brisbane, Queensland, Australia
| | - Amos Tanay
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel. .,Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel.
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45
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Paps J. What Makes an Animal? The Molecular Quest for the Origin of the Animal Kingdom. Integr Comp Biol 2018; 58:654-665. [DOI: 10.1093/icb/icy036] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Jordi Paps
- School of Biological Sciences, University of Essex, Colchester, Essex CO4 3SQ, UK
- Department of Zoology, University of Oxford, Oxford OX1 3PS, UK
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46
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Reconstruction of the ancestral metazoan genome reveals an increase in genomic novelty. Nat Commun 2018; 9:1730. [PMID: 29712911 PMCID: PMC5928047 DOI: 10.1038/s41467-018-04136-5] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Accepted: 02/28/2018] [Indexed: 12/03/2022] Open
Abstract
Understanding the emergence of the Animal Kingdom is one of the major challenges of modern evolutionary biology. Many genomic changes took place along the evolutionary lineage that gave rise to the Metazoa. Recent research has revealed the role that co-option of old genes played during this transition, but the contribution of genomic novelty has not been fully assessed. Here, using extensive genome comparisons between metazoans and multiple outgroups, we infer the minimal protein-coding genome of the first animal, in addition to other eukaryotic ancestors, and estimate the proportion of novelties in these ancient genomes. Contrary to the prevailing view, this uncovers an unprecedented increase in the extent of genomic novelty during the origin of metazoans, and identifies 25 groups of metazoan-specific genes that are essential across the Animal Kingdom. We argue that internal genomic changes were as important as external factors in the emergence of animals. Animals, the Metazoa, co-opted numerous unicellular genes in their transition to multicellularity. Here, the authors use phylogenomic analyses to infer the genome composition of the ancestor of extant animals and show there was also a burst of novel gene groups associated with this transition.
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Elphick MR, Mirabeau O, Larhammar D. Evolution of neuropeptide signalling systems. ACTA ACUST UNITED AC 2018; 221:221/3/jeb151092. [PMID: 29440283 PMCID: PMC5818035 DOI: 10.1242/jeb.151092] [Citation(s) in RCA: 126] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Neuropeptides are a diverse class of neuronal signalling molecules that regulate physiological processes and behaviour in animals. However, determining the relationships and evolutionary origins of the heterogeneous assemblage of neuropeptides identified in a range of phyla has presented a huge challenge for comparative physiologists. Here, we review revolutionary insights into the evolution of neuropeptide signalling that have been obtained recently through comparative analysis of genome/transcriptome sequence data and by ‘deorphanisation’ of neuropeptide receptors. The evolutionary origins of at least 30 neuropeptide signalling systems have been traced to the common ancestor of protostomes and deuterostomes. Furthermore, two rounds of genome duplication gave rise to an expanded repertoire of neuropeptide signalling systems in the vertebrate lineage, enabling neofunctionalisation and/or subfunctionalisation, but with lineage-specific gene loss and/or additional gene or genome duplications generating complex patterns in the phylogenetic distribution of paralogous neuropeptide signalling systems. We are entering a new era in neuropeptide research where it has become feasible to compare the physiological roles of orthologous and paralogous neuropeptides in a wide range of phyla. Moreover, the ambitious mission to reconstruct the evolution of neuropeptide function in the animal kingdom now represents a tangible challenge for the future. Summary: A review of the revolutionary advances in our knowledge of the evolution of neuropeptide signalling systems that have been enabled by comparative genomics and neuropeptide receptor deorphanisation.
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Affiliation(s)
- Maurice R Elphick
- School of Biological & Chemical Sciences, Queen Mary University of London, London E1 4NS, UK
| | - Olivier Mirabeau
- Genetics and Biology of Cancers Unit, Institut Curie, INSERM U830, Paris Sciences et Lettres Research University, Paris 75005, France
| | - Dan Larhammar
- Department of Neuroscience, Science for Life Laboratory, Uppsala University, Box 593, 75124 Uppsala, Sweden
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Helm C, Karl A, Beckers P, Kaul-Strehlow S, Ulbricht E, Kourtesis I, Kuhrt H, Hausen H, Bartolomaeus T, Reichenbach A, Bleidorn C. Early evolution of radial glial cells in Bilateria. Proc Biol Sci 2018; 284:rspb.2017.0743. [PMID: 28724733 PMCID: PMC5543218 DOI: 10.1098/rspb.2017.0743] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Accepted: 06/13/2017] [Indexed: 12/13/2022] Open
Abstract
Bilaterians usually possess a central nervous system, composed of neurons and supportive cells called glial cells. Whereas neuronal cells are highly comparable in all these animals, glial cells apparently differ, and in deuterostomes, radial glial cells are found. These particular secretory glial cells may represent the archetype of all (macro) glial cells and have not been reported from protostomes so far. This has caused controversial discussions of whether glial cells represent a homologous bilaterian characteristic or whether they (and thus, centralized nervous systems) evolved convergently in the two main clades of bilaterians. By using histology, transmission electron microscopy, immunolabelling and whole-mount in situ hybridization, we show here that protostomes also possess radial glia-like cells, which are very likely to be homologous to those of deuterostomes. Moreover, our antibody staining indicates that the secretory character of radial glial cells is maintained throughout their various evolutionary adaptations. This implies an early evolution of radial glial cells in the last common ancestor of Protostomia and Deuterostomia. Furthermore, it suggests that an intraepidermal nervous system—composed of sensory cells, neurons and radial glial cells—was probably the plesiomorphic condition in the bilaterian ancestor.
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Affiliation(s)
- Conrad Helm
- Sars International Center for Marine Molecular Biology, University of Bergen, 5008 Bergen, Norway
| | - Anett Karl
- Paul-Flechsig-Institute for Brain Research, University of Leipzig, 04103 Leipzig, Germany.,Translational Center for Regenerative Medicine, University of Leipzig, 04103 Leipzig, Germany.,Carl-Ludwig-Institute for Physiology, University of Leipzig, 04103 Leipzig, Germany
| | - Patrick Beckers
- Institute of Evolutionary Biology and Ecology, University of Bonn, 53121 Bonn, Germany
| | | | - Elke Ulbricht
- Biotechnology Center, Technische Universität Dresden, 01307 Dresden, Germany
| | - Ioannis Kourtesis
- Sars International Center for Marine Molecular Biology, University of Bergen, 5008 Bergen, Norway
| | - Heidrun Kuhrt
- Paul-Flechsig-Institute for Brain Research, University of Leipzig, 04103 Leipzig, Germany
| | - Harald Hausen
- Sars International Center for Marine Molecular Biology, University of Bergen, 5008 Bergen, Norway
| | - Thomas Bartolomaeus
- Institute of Evolutionary Biology and Ecology, University of Bonn, 53121 Bonn, Germany
| | - Andreas Reichenbach
- Paul-Flechsig-Institute for Brain Research, University of Leipzig, 04103 Leipzig, Germany
| | - Christoph Bleidorn
- Museo Nacional de Ciencias Naturales, Spanish National Research Council (CSIC), 28006 Madrid, Spain
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Haen Whitmer KM. Model Systems for Exploring the Evolutionary Origins of the Nervous System. Results Probl Cell Differ 2018; 65:185-196. [PMID: 30083921 DOI: 10.1007/978-3-319-92486-1_10] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/10/2022]
Abstract
The development of nervous systems can be seen as one of the key transitions in animal evolution, allowing the efficient integration of sensory input and motor output and the expedient transmission of impulses over relatively long distances inside an organism. With the increased availability of genome sequences for animals at the base of the metazoan phylogenetic tree, two alternative hypotheses have been proposed regarding nervous system evolutionary origins, ultimately prompting a debate whether an enormously complicated system like the nervous system could have evolved more than once. This review summarizes what is currently known about nervous system origins, concentrating on the evolution of synapse components, with respect to phylogenetic knowledge of early diverging animal groups, comprising members of the Porifera, Ctenophora, Placozoa, and Cnidaria.
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Affiliation(s)
- Karri M Haen Whitmer
- Department of Genetics, Development & Cell Biology, Iowa State University, Ames, IA, USA.
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Yaghmaeian Salmani B, Monedero Cobeta I, Rakar J, Bauer S, Curt JR, Starkenberg A, Thor S. Evolutionarily conserved anterior expansion of the central nervous system promoted by a common PcG-Hox program. Development 2018. [DOI: 10.1242/dev.160747] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
A conserved feature of the central nervous system (CNS) is the prominent expansion of anterior regions (brain) when compared to posterior (nerve cord). The cellular and regulatory processes driving anterior CNS expansion are not well understood in any bilaterian species. Here, we address this expansion in Drosophila and mouse. We find that when compared to the nerve cord the brain, in both Drosophila and mouse, displays extended progenitor proliferation, more elaborate daughter cell proliferation and more rapid cell cycle speed. These features contribute to anterior CNS expansion in both species. With respect to genetic control, enhanced brain proliferation is severely reduced by ectopic Hox gene expression, by either Hox misexpression or by loss of Polycomb Group (PcG) function. Strikingly, in PcG mutants, early CNS proliferation appears unaffected, whereas subsequently, brain proliferation is severely reduced. Hence, a conserved PcG-Hox program promotes the anterior expansion of the CNS. The profound differences in proliferation and in the underlying genetic mechanisms between brain and nerve cord lend support to the emerging concept of separate evolutionary origins of these two CNS regions.
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Affiliation(s)
| | - Ignacio Monedero Cobeta
- Dept. of Clinical and Experimental Medicine, Linkoping University, SE-58185, Linkoping, Sweden
| | - Jonathan Rakar
- Dept. of Clinical and Experimental Medicine, Linkoping University, SE-58185, Linkoping, Sweden
| | - Susanne Bauer
- Dept. of Clinical and Experimental Medicine, Linkoping University, SE-58185, Linkoping, Sweden
| | - Jesús Rodriguez Curt
- Dept. of Clinical and Experimental Medicine, Linkoping University, SE-58185, Linkoping, Sweden
| | - Annika Starkenberg
- Dept. of Clinical and Experimental Medicine, Linkoping University, SE-58185, Linkoping, Sweden
| | - Stefan Thor
- Dept. of Clinical and Experimental Medicine, Linkoping University, SE-58185, Linkoping, Sweden
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