1
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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: 75] [Impact Index Per Article: 75.0] [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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2
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Bell IJ, Horn MS, Van Raay TJ. Bridging the gap between non-canonical and canonical Wnt signaling through Vangl2. Semin Cell Dev Biol 2021; 125:37-44. [PMID: 34736823 DOI: 10.1016/j.semcdb.2021.10.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 09/30/2021] [Accepted: 10/05/2021] [Indexed: 12/29/2022]
Abstract
Non-canonical Wnt signaling (encompassing Wnt/PCP and WntCa2+) has a dual identity in the literature. One stream of research investigates its role in antagonizing canonical Wnt/β-catenin signaling in cancer, typically through Ca2+, while the other stream investigates its effect on polarity in development, typically through Vangl2. Rarely do these topics intersect or overlap. What has become clear is that Wnt5a can mobilize intracellular calcium stores to inhibit Wnt/β-catenin in cancer cells but there is no evidence that Vangl2 is involved in this process. Conversely, Wnt5a can independently activate Vangl2 to affect polarity and migration but the role of calcium in this process is also limited. Further, Vangl2 has also been implicated in inhibiting Wnt/β-catenin signaling in development. The consensus is that a cell can differentiate between canonical and non-canonical Wnt signaling when presented with a choice, always choosing non-canonical at the expense of canonical Wnt signaling. However, these are rare events in vivo. Given the shared resources between non-canonical and canonical Wnt signaling it is perplexing that there is not more in vivo evidence for cross talk between these two pathways. In this review we discuss the intersection of non-canonical Wnt, with a focus on Wnt/PCP, and Wnt/β-catenin signaling in an attempt to shed some light on pathways that rarely meet at a crossroads in vivo.
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Affiliation(s)
- Ian James Bell
- Department of Molecular and Cellular Biology, University of Guelph, 50 Stone Rd. E, Guelph, ON, Canada N1G 2W1
| | - Matthew Sheldon Horn
- Department of Molecular and Cellular Biology, University of Guelph, 50 Stone Rd. E, Guelph, ON, Canada N1G 2W1
| | - Terence John Van Raay
- Department of Molecular and Cellular Biology, University of Guelph, 50 Stone Rd. E, Guelph, ON, Canada N1G 2W1.
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3
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Klug C, Kerr J, Lee MSY, Cloutier R. A late-surviving stem-ctenophore from the Late Devonian of Miguasha (Canada). Sci Rep 2021; 11:19039. [PMID: 34561497 PMCID: PMC8463547 DOI: 10.1038/s41598-021-98362-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 09/06/2021] [Indexed: 11/08/2022] Open
Abstract
Like other soft-bodied organisms, ctenophores (comb jellies) produce fossils only under exceptional taphonomic conditions. Here, we present the first record of a Late Devonian ctenophore from the Escuminac Formation from Miguasha in eastern Canada. Based on the 18-fold symmetry of this disc-shaped fossil, we assign it to the total-group Ctenophora. Our phylogenetic analyses suggest that the new taxon Daihuoides jakobvintheri gen. et sp. nov. falls near Cambrian stem ctenophores such as 'dinomischids' and 'scleroctenophorans'. Accordingly, Daihuoides is a Lazarus-taxon, which post-dates its older relatives by over 140 million years, and overlaps temporally with modern ctenophores, whose oldest representatives are known from the Early Devonian. Our analyses also indicate that the fossil record of ctenophores does not provide strong evidence for or against the phylogenomic hypothesis that ctenophores are sister to all other metazoans.
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Affiliation(s)
- Christian Klug
- Paläontologisches Institut und Museum, Universität Zürich, Karl-Schmid-Strasse 4, 8006, Zurich, Switzerland
| | - Johanne Kerr
- Parc national de Miguasha, 231 Route de Miguasha Ouest, Nouvelle, QC, G0C 2E0, Canada
| | - Michael S Y Lee
- College of Science and Engineering, Flinders University, Adelaide, SA, Australia
- Earth Sciences Section, South Australian Museum, Adelaide, SA, Australia
| | - Richard Cloutier
- Département de Biologie, Chimie et Géographie, Université du Québec à Rimouski, 300 allée des Ursulines, Rimouski, QC, G5L 3A1, Canada.
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4
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Xu NW, Townsend JP, Costello JH, Colin SP, Gemmell BJ, Dabiri JO. Developing Biohybrid Robotic Jellyfish ( Aurelia aurita) for Free-swimming Tests in the Laboratory and in the Field. Bio Protoc 2021; 11:e3974. [PMID: 33889668 PMCID: PMC8054175 DOI: 10.21769/bioprotoc.3974] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 01/28/2021] [Accepted: 01/31/2021] [Indexed: 11/02/2022] Open
Abstract
Biohybrid robotics is a growing field that incorporates both live tissues and engineered materials to build robots that address current limitations in robots, including high power consumption and low damage tolerance. One approach is to use microelectronics to enhance whole organisms, which has previously been achieved to control the locomotion of insects. However, the robotic control of jellyfish swimming offers additional advantages, with the potential to become a new ocean monitoring tool in conjunction with existing technologies. Here, we delineate protocols to build a self-contained swim controller using commercially available microelectronics, embed the device into live jellyfish, and calculate vertical swimming speeds in both laboratory conditions and coastal waters. Using these methods, we previously demonstrated enhanced swimming speeds up to threefold, compared to natural jellyfish swimming, in laboratory and in situ experiments. These results offered insights into both designing low-power robots and probing the structure-function of basal organisms. Future iterations of these biohybrid robotic jellyfish could be used for practical applications in ocean monitoring.
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Affiliation(s)
- Nicole W. Xu
- Department of Bioengineering, Stanford University, Stanford, CA, USA
- Graduate Aerospace Laboratories (GALCIT), California Institute of Technology, Pasadena, CA, USA
| | - James P. Townsend
- Marine Biological Laboratory, Woods Hole, MA, USA
- Department of Biology, Providence College, Providence, RI, USA
| | - John H. Costello
- Marine Biological Laboratory, Woods Hole, MA, USA
- Department of Biology, Providence College, Providence, RI, USA
| | - Sean P. Colin
- Marine Biological Laboratory, Woods Hole, MA, USA
- Department of Marine Biology and Environmental Science, Roger Williams University, Bristol, RI, USA
| | - Brad J. Gemmell
- Department of Integrative Biology, University of South Florida, Tampa, FL, USA
| | - John O. Dabiri
- Graduate Aerospace Laboratories (GALCIT), California Institute of Technology, Pasadena, CA, USA
- Department of Mechanical Engineering, California Institute of Technology, Pasadena, CA, USA
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5
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Kulkarni A, Lopez DH, Extavour CG. Shared Cell Biological Functions May Underlie Pleiotropy of Molecular Interactions in the Germ Lines and Nervous Systems of Animals. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.00215] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
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6
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Norekian TP, Moroz LL. Comparative neuroanatomy of ctenophores: Neural and muscular systems in
Euplokamis dunlapae
and related species. J Comp Neurol 2019; 528:481-501. [DOI: 10.1002/cne.24770] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2019] [Revised: 09/03/2019] [Accepted: 09/04/2019] [Indexed: 01/20/2023]
Affiliation(s)
- Tigran P. Norekian
- Whitney Laboratory for Marine Bioscience University of Florida St. Augustine Florida
- Friday Harbor Laboratories University of Washington Friday Harbor Washington
- Institute of Higher Nervous Activity and Neurophysiology Russian Academy of Sciences Moscow Russia
| | - Leonid L. Moroz
- Whitney Laboratory for Marine Bioscience University of Florida St. Augustine Florida
- Department of Neuroscience and McKnight Brain Institute University of Florida Gainesville Florida
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7
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Nadhira A, Sutton MD, Botting JP, Muir LA, Gueriau P, King A, Briggs DEG, Siveter DJ, Siveter DJ. Three-dimensionally preserved soft tissues and calcareous hexactins in a Silurian sponge: implications for early sponge evolution. ROYAL SOCIETY OPEN SCIENCE 2019; 6:190911. [PMID: 31417767 PMCID: PMC6689616 DOI: 10.1098/rsos.190911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Accepted: 07/09/2019] [Indexed: 06/10/2023]
Abstract
Sponges (Porifera), as one of the earliest-branching animal phyla, are crucial for understanding early metazoan phylogeny. Recent studies of Lower Palaeozoic sponges have revealed a variety of character states and combinations unknown in extant taxa, challenging our views of early sponge morphology. The Herefordshire Konservat-Lagerstätte yields an abundant, diverse sponge fauna with three-dimensional preservation of spicules and soft tissue. Carduispongia pedicula gen. et sp. nov. possesses a single layer of hexactine spicules arranged in a regular orthogonal network. This spicule type and arrangement is characteristic of the reticulosans, which have traditionally been interpreted as early members of the extant siliceous Class Hexactinellida. However, the unusual preservation of the spicules of C. pedicula reveals an originally calcareous composition, which would be diagnostic of the living Class Calcarea. The soft tissue architecture closely resembles the complex sylleibid or leuconid structure seen in some modern calcareans and homoscleromorphs. This combination of features strongly supports a skeletal continuum between primitive calcareans and hexactinellid siliceans, indicating that the last common ancestor of Porifera was a spiculate, solitary, vasiform animal with a thin skeletal wall.
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Affiliation(s)
- Ardianty Nadhira
- Department of Earth Sciences and Engineering, Imperial College London, London SW7 2BP, UK
| | - Mark D. Sutton
- Department of Earth Sciences and Engineering, Imperial College London, London SW7 2BP, UK
| | - Joseph P. Botting
- Nanjing Institute of Geology and Palaeontology, 39 East Beijing Road, Nanjing 210008, People's Republic of China
- Department of Natural Sciences, Amgueddfa Cymru—National Museum Wales, Cathays Park, Cardiff CF10 3NP, UK
| | - Lucy A. Muir
- Department of Natural Sciences, Amgueddfa Cymru—National Museum Wales, Cathays Park, Cardiff CF10 3NP, UK
| | - Pierre Gueriau
- IPANEMA, CNRS, Ministère de la Culture, UVSQ, USR 3461, Université Paris-Saclay, 91192 Gif-sur-Yvette, France
- Institute of Earth Sciences, University of Lausanne, Géopolis, CH-1015 Lausanne, Switzerland
| | - Andrew King
- SOLEIL synchrotron, 91192 Gif-sur-Yvette, France
| | - Derek E. G. Briggs
- Department of Geology & Geophysics, and Yale Peabody Museum of Natural History, Yale University, PO Box 208109, New Haven, CT 06520-8109, USA
| | - David J. Siveter
- School of Geography, Geology and the Environment, University of Leicester, Leicester LE1 7RH, UK
| | - Derek J. Siveter
- Earth Collections, University Museum of Natural History, Oxford OX1 3PW, UK
- Department of Earth Sciences, University of Oxford, South Parks Road, Oxford OX1 3AN, UK
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8
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Zhao Y, Vinther J, Parry LA, Wei F, Green E, Pisani D, Hou X, Edgecombe GD, Cong P. Cambrian Sessile, Suspension Feeding Stem-Group Ctenophores and Evolution of the Comb Jelly Body Plan. Curr Biol 2019; 29:1112-1125.e2. [PMID: 30905603 DOI: 10.1016/j.cub.2019.02.036] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Revised: 11/10/2018] [Accepted: 02/14/2019] [Indexed: 12/22/2022]
Abstract
The origin of ctenophores (comb jellies) is obscured by their controversial phylogenetic position, with recent phylogenomic analyses resolving either sponges or ctenophores as the sister group of all other animals. Fossil taxa can provide morphological evidence that may elucidate the origins of derived characters and shared ancestries among divergent taxa, providing a means to "break" long branches in phylogenetic trees. Here we describe new fossil material from the early Cambrian Chengjiang Biota, Yunnan Province, China, including the putative cnidarian Xianguangia, the new taxon Daihua sanqiong gen et sp. nov., and Dinomischus venustus, informally referred to as "dinomischids" here. "Dinomischids" possess a basal calyx encircled by 18 tentacles that surround the mouth. The tentacles carry pinnules, each with a row of stiff filamentous structures interpreted as very large compound cilia of a size otherwise only known in ctenophores. Together with the Cambrian tulip animal Siphusauctum and the armored Cambrian scleroctenophores, they exhibit anatomies that trace ctenophores to a sessile, polypoid stem lineage. This body plan resembles the polypoid, tentaculate morphology of cnidarians, including a blind gastric cavity partitioned by mesenteries. We propose that comb rows are derived from tentacles with paired sets of pinnules that each bear a row of compound cilia. The scleroctenophores exhibit paired comb rows, also observed in Siphusauctum, in addition to an organic skeleton, shared as well by Dinomischus, Daihua, and Xianguangia. We formulate a hypothesis in which ctenophores evolved from sessile, polypoid suspension feeders, sharing similarities with cnidarians that suggest either a close relationship between these two phyla, a striking pattern of early convergent evolution, or an ancestral condition for either metazoans or eumetazoans.
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Affiliation(s)
- Yang Zhao
- Yunnan Key Laboratory for Palaeobiology, Yunnan University, Kunming 650091, China; MEC International Joint Laboratory for Palaeobiology and Palaeoenvironment, Yunnan University, Kunming 650091, China
| | - Jakob Vinther
- School of Earth Sciences, University of Bristol, Wills Memorial Building, Queens Road, Bristol BS8 1RJ, UK; School of Biological Sciences, University of Bristol, Life Sciences, Building, 24 Tyndall Avenue, Bristol BS8 1TQ, UK.
| | - Luke A Parry
- School of Earth Sciences, University of Bristol, Wills Memorial Building, Queens Road, Bristol BS8 1RJ, UK; Department of Earth Sciences, The Natural History Museum, Cromwell Road, London SW7 5BD, UK; Palaeobiology Section, Department of Natural History, Royal Ontario Museum, Toronto, ON M5S 2C6, Canada; Yale Institute for Biosphere Studies, Yale University, New Haven, CT, USA
| | - Fan Wei
- Yunnan Key Laboratory for Palaeobiology, Yunnan University, Kunming 650091, China; MEC International Joint Laboratory for Palaeobiology and Palaeoenvironment, Yunnan University, Kunming 650091, China
| | - Emily Green
- School of Earth Sciences, University of Bristol, Wills Memorial Building, Queens Road, Bristol BS8 1RJ, UK
| | - Davide Pisani
- School of Earth Sciences, University of Bristol, Wills Memorial Building, Queens Road, Bristol BS8 1RJ, UK; School of Biological Sciences, University of Bristol, Life Sciences, Building, 24 Tyndall Avenue, Bristol BS8 1TQ, UK
| | - Xianguang Hou
- Yunnan Key Laboratory for Palaeobiology, Yunnan University, Kunming 650091, China; MEC International Joint Laboratory for Palaeobiology and Palaeoenvironment, Yunnan University, Kunming 650091, China
| | - Gregory D Edgecombe
- MEC International Joint Laboratory for Palaeobiology and Palaeoenvironment, Yunnan University, Kunming 650091, China; Department of Earth Sciences, The Natural History Museum, Cromwell Road, London SW7 5BD, UK
| | - Peiyun Cong
- Yunnan Key Laboratory for Palaeobiology, Yunnan University, Kunming 650091, China; MEC International Joint Laboratory for Palaeobiology and Palaeoenvironment, Yunnan University, Kunming 650091, China; Department of Earth Sciences, The Natural History Museum, Cromwell Road, London SW7 5BD, UK.
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9
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Renard E, Leys SP, Wörheide G, Borchiellini C. Understanding Animal Evolution: The Added Value of Sponge Transcriptomics and Genomics: The disconnect between gene content and body plan evolution. Bioessays 2018; 40:e1700237. [PMID: 30070368 DOI: 10.1002/bies.201700237] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Revised: 06/22/2018] [Indexed: 02/06/2023]
Abstract
Sponges are important but often-neglected organisms. The absence of classical animal traits (nerves, digestive tract, and muscles) makes sponges challenging for non-specialists to work with and has delayed getting high quality genomic data compared to other invertebrates. Yet analyses of sponge genomes and transcriptomes currently available have radically changed our understanding of animal evolution. Sponges are of prime evolutionary importance as one of the best candidates to form the sister group of all other animals, and genomic data are essential to understand the mechanisms that control animal evolution and diversity. Here we review the most significant outcomes of current genomic and transcriptomic analyses of sponges, and discuss limitations and future directions of sponge transcriptomic and genomic studies.
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Affiliation(s)
- Emmanuelle Renard
- Aix Marseille Univ., Univ Avignon, CNRS, IRD, UMR 7263, Mediterranean Institute of Marine and Continental Biodiversity and Ecology (IMBE), Station Marine d'Endoume, Marseille, France.,Aix Marseille Univ., CNRS, UMR 7288, IBDM, Marseille, France
| | - Sally P Leys
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta T6G 2E9, Canada
| | - Gert Wörheide
- Department of Earth and Environmental Sciences, Paleontology and Geobiology, Ludwig-Maximilians-Universität München, Richard-Wagner Straße 10, 80333 Munich, Germany.,GeoBio-Center, Ludwig-Maximilians-Universität München, Munich, Germany.,Bavarian State Collection for Paleontology and Geology, Munich, Germany
| | - Carole Borchiellini
- Aix Marseille Univ., Univ Avignon, CNRS, IRD, UMR 7263, Mediterranean Institute of Marine and Continental Biodiversity and Ecology (IMBE), Station Marine d'Endoume, Marseille, France
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10
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Kenny NJ, de Goeij JM, de Bakker DM, Whalen CG, Berezikov E, Riesgo A. Towards the identification of ancestrally shared regenerative mechanisms across the Metazoa: A Transcriptomic case study in the Demosponge Halisarca caerulea. Mar Genomics 2018; 37:135-147. [DOI: 10.1016/j.margen.2017.11.001] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Revised: 11/07/2017] [Accepted: 11/07/2017] [Indexed: 02/07/2023]
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11
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BluePharmTrain: Biology and Biotechnology of Marine Sponges. GRAND CHALLENGES IN MARINE BIOTECHNOLOGY 2018. [DOI: 10.1007/978-3-319-69075-9_13] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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12
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Evans SD, Droser ML, Gehling JG. Highly regulated growth and development of the Ediacara macrofossil Dickinsonia costata. PLoS One 2017; 12:e0176874. [PMID: 28520741 PMCID: PMC5435172 DOI: 10.1371/journal.pone.0176874] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Accepted: 04/18/2017] [Indexed: 11/21/2022] Open
Abstract
The Ediacara Biota represents the oldest fossil evidence for the appearance of animals but linking these taxa to specific clades has proved challenging. Dickinsonia is an abundant, apparently bilaterally symmetrical Ediacara fossil with uncertain affinities. We identified and measured key morphological features of over 900 specimens of Dickinsonia costata from the Ediacara Member, South Australia to characterize patterns in growth and morphology. Here we show that development in Dickinsonia costata was surprisingly highly regulated to maintain an ovoid shape via terminal addition and the predictable expansion of modules. This result, along with other characters found in Dickinsonia suggests that it does not belong within known animal groups, but that it utilized some of the developmental gene networks of bilaterians, a result predicted by gene sequencing of basal metazoans but previously unidentified in the fossil record. Dickinsonia thus represents an extinct clade located between sponges and the last common ancestor of Protostomes and Deuterostomes, and likely belongs within the Eumetazoa.
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Affiliation(s)
- Scott D. Evans
- Department of Earth Sciences, University of California at Riverside, Riverside, California, United States of America
- * E-mail:
| | - Mary L. Droser
- Department of Earth Sciences, University of California at Riverside, Riverside, California, United States of America
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13
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A Large and Consistent Phylogenomic Dataset Supports Sponges as the Sister Group to All Other Animals. Curr Biol 2017; 27:958-967. [PMID: 28318975 DOI: 10.1016/j.cub.2017.02.031] [Citation(s) in RCA: 283] [Impact Index Per Article: 40.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Revised: 02/07/2017] [Accepted: 02/13/2017] [Indexed: 01/11/2023]
Abstract
Resolving the early diversification of animal lineages has proven difficult, even using genome-scale datasets. Several phylogenomic studies have supported the classical scenario in which sponges (Porifera) are the sister group to all other animals ("Porifera-sister" hypothesis), consistent with a single origin of the gut, nerve cells, and muscle cells in the stem lineage of eumetazoans (bilaterians + ctenophores + cnidarians). In contrast, several other studies have recovered an alternative topology in which ctenophores are the sister group to all other animals (including sponges). The "Ctenophora-sister" hypothesis implies that eumetazoan-specific traits, such as neurons and muscle cells, either evolved once along the metazoan stem lineage and were then lost in sponges and placozoans or evolved at least twice independently in Ctenophora and in Cnidaria + Bilateria. Here, we report on our reconstruction of deep metazoan relationships using a 1,719-gene dataset with dense taxonomic sampling of non-bilaterian animals that was assembled using a semi-automated procedure, designed to reduce known error sources. Our dataset outperforms previous metazoan gene superalignments in terms of data quality and quantity. Analyses with a best-fitting site-heterogeneous evolutionary model provide strong statistical support for placing sponges as the sister-group to all other metazoans, with ctenophores emerging as the second-earliest branching animal lineage. Only those methodological settings that exacerbated long-branch attraction artifacts yielded Ctenophora-sister. These results show that methodological issues must be carefully addressed to tackle difficult phylogenetic questions and pave the road to a better understanding of how fundamental features of animal body plans have emerged.
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14
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Mills DB, Canfield DE. A trophic framework for animal origins. GEOBIOLOGY 2017; 15:197-210. [PMID: 27686422 DOI: 10.1111/gbi.12216] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Accepted: 08/25/2016] [Indexed: 06/06/2023]
Abstract
Metazoans emerged in a microbial world and play a unique role in the biosphere as the only complex multicellular eukaryotes capable of phagocytosis. While the bodyplan and feeding mode of the last common metazoan ancestor remain unresolved, the earliest multicellular stem-metazoans likely subsisted on picoplankton (planktonic microbes 0.2-2 μm in diameter) and dissolved organic matter (DOM), similarly to modern sponges. Once multicellular stem-metazoans emerged, they conceivably modulated both the local availability of picoplankton, which they preferentially removed from the water column for feeding, and detrital particles 2-100 μm in diameter, which they expelled and deposited into the benthos as waste products. By influencing the availability of these heterotrophic food sources, the earliest multicellular stem-metazoans would have acted as ecosystem engineers, helping create the ecological conditions under which other metazoans, namely detritivores and non-sponge suspension feeders incapable of subsisting on picoplankton and DOM, could emerge and diversify. This early style of metazoan feeding, specifically the phagocytosis of small eukaryotic prey, could have also encouraged the evolution of larger, even multicellular, eukaryotic forms less prone to metazoan consumption. Therefore, the first multicellular stem-metazoans, through their feeding, arguably helped bridge the strictly microbial food webs of the Proterozoic Eon (2.5-0.541 billion years ago) to the more macroscopic, metazoan-sustaining food webs of the Phanerozoic Eon (0.541-0 billion years ago).
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Affiliation(s)
- D B Mills
- Department of Biology, Nordic Center for Earth Evolution, University of Southern Denmark, Odense, Denmark
| | - D E Canfield
- Department of Biology, Nordic Center for Earth Evolution, University of Southern Denmark, Odense, Denmark
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15
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Smith CL, Reese TS. Adherens Junctions Modulate Diffusion between Epithelial Cells in Trichoplax adhaerens. THE BIOLOGICAL BULLETIN 2016; 231:216-224. [PMID: 28048952 DOI: 10.1086/691069] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Trichoplax adhaerens is the sole named member of Placozoa, an ancient metazoan phylum. This coin-shaped animal glides on ventral cilia to find and digest algae on the substrate. It has only six cell types, all but two of which are incorporated into the epithelium that encloses it. The upper epithelium is thin, composed of a pavement of relatively large polygonal disks, each bearing a cilium. The lower epithelium is thick and composed primarily of narrow ciliated cells that power locomotion. Interspersed among these cells are two different secretory cells: one containing large lipophilic granules that, when released, lyse algae under the animal; the other, less abundant, is replete with smaller secretory granules containing neuropeptides. All cells within both epithelia are joined by adherens junctions that are stabilized by apical actin networks. Cells are held in place during shape changes or under osmotic stress, but dissociate in low calcium. Neither tight, septate, nor gap junctions are evident, leaving only the adherens junction to control the permeability of the epithelium. Small (<4 kDa) fluorescent dextrans introduced into artificial seawater readily penetrate into the animal between the cells. Larger dextrans enter slowly, except in animals treated with reduced calcium, indicating that the adherens junctions form a circumferential belt around each cell that impedes diffusion into the animal. During feeding, the limited permeability of the adherens junctions helps to confine material released from lysed algae within the narrow space under the animal, where it is absorbed by endocytosis.
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Senatore A, Raiss H, Le P. Physiology and Evolution of Voltage-Gated Calcium Channels in Early Diverging Animal Phyla: Cnidaria, Placozoa, Porifera and Ctenophora. Front Physiol 2016; 7:481. [PMID: 27867359 PMCID: PMC5095125 DOI: 10.3389/fphys.2016.00481] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Accepted: 10/07/2016] [Indexed: 12/18/2022] Open
Abstract
Voltage-gated calcium (Cav) channels serve dual roles in the cell, where they can both depolarize the membrane potential for electrical excitability, and activate transient cytoplasmic Ca2+ signals. In animals, Cav channels play crucial roles including driving muscle contraction (excitation-contraction coupling), gene expression (excitation-transcription coupling), pre-synaptic and neuroendocrine exocytosis (excitation-secretion coupling), regulation of flagellar/ciliary beating, and regulation of cellular excitability, either directly or through modulation of other Ca2+-sensitive ion channels. In recent years, genome sequencing has provided significant insights into the molecular evolution of Cav channels. Furthermore, expanded gene datasets have permitted improved inference of the species phylogeny at the base of Metazoa, providing clearer insights into the evolution of complex animal traits which involve Cav channels, including the nervous system. For the various types of metazoan Cav channels, key properties that determine their cellular contribution include: Ion selectivity, pore gating, and, importantly, cytoplasmic protein-protein interactions that direct sub-cellular localization and functional complexing. It is unclear when these defining features, many of which are essential for nervous system function, evolved. In this review, we highlight some experimental observations that implicate Cav channels in the physiology and behavior of the most early-diverging animals from the phyla Cnidaria, Placozoa, Porifera, and Ctenophora. Given our limited understanding of the molecular biology of Cav channels in these basal animal lineages, we infer insights from better-studied vertebrate and invertebrate animals. We also highlight some apparently conserved cellular functions of Cav channels, which might have emerged very early on during metazoan evolution, or perhaps predated it.
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Affiliation(s)
- Adriano Senatore
- Department of Biology, University of Toronto Mississauga Mississauga, ON, Canada
| | - Hamad Raiss
- Department of Biology, University of Toronto Mississauga Mississauga, ON, Canada
| | - Phuong Le
- Department of Biology, University of Toronto Mississauga Mississauga, ON, Canada
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Revisiting the Phylogeny of the Animal Formins: Two New Subtypes, Relationships with Multiple Wing Hairs Proteins, and a Lost Human Formin. PLoS One 2016; 11:e0164067. [PMID: 27695129 PMCID: PMC5047451 DOI: 10.1371/journal.pone.0164067] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Accepted: 09/19/2016] [Indexed: 11/23/2022] Open
Abstract
Formins are a widespread family of eukaryotic cytoskeleton-organizing proteins. Many species encode multiple formin isoforms, and for animals, much of this reflects the presence of multiple conserved subtypes. Earlier phylogenetic analyses identified seven major formin subtypes in animals (DAAM, DIAPH, FHOD, FMN, FMNL, INF, and GRID2IP/delphilin), but left a handful of formins, particularly from nematodes, unassigned. In this new analysis drawing from genomic data from a wider range of taxa, nine formin subtypes are identified that encompass all the animal formins analyzed here. Included in this analysis are Multiple Wing Hairs proteins (MWH), which bear homology to formin N-terminal domains. Originally identified in Drosophila melanogaster and other arthropods, MWH-related proteins are also identified here in some nematodes (including Caenorhabditis elegans), and are shown to be related to a novel MWH-related formin (MWHF) subtype. One surprising result of this work is the discovery that a family of pleckstrin homology domain-containing formins (PHCFs) is represented in many vertebrates, but is strikingly absent from placental mammals. Consistent with a relatively recent loss of this formin, the human genome retains fragments of a defunct homologous formin gene.
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O'Malley MA. Histories of molecules: Reconciling the past. STUDIES IN HISTORY AND PHILOSOPHY OF SCIENCE 2016; 55:69-83. [PMID: 26774071 DOI: 10.1016/j.shpsa.2015.09.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2015] [Revised: 09/07/2015] [Accepted: 09/08/2015] [Indexed: 06/05/2023]
Abstract
Molecular data and methods have become centrally important to evolutionary analysis, largely because they have enabled global phylogenetic reconstructions of the relationships between organisms in the tree of life. Often, however, molecular stories conflict dramatically with morphology-based histories of lineages. The evolutionary origin of animal groups provides one such case. In other instances, different molecular analyses have so far proved irreconcilable. The ancient and major divergence of eukaryotes from prokaryotic ancestors is an example of this sort of problem. Efforts to overcome these conflicts highlight the role models play in phylogenetic reconstruction. One crucial model is the molecular clock; another is that of 'simple-to-complex' modification. I will examine animal and eukaryote evolution against a backdrop of increasing methodological sophistication in molecular phylogeny, and conclude with some reflections on the nature of historical science in the molecular era of phylogeny.
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Moroz LL, Kohn AB. Independent origins of neurons and synapses: insights from ctenophores. Philos Trans R Soc Lond B Biol Sci 2016; 371:20150041. [PMID: 26598724 PMCID: PMC4685580 DOI: 10.1098/rstb.2015.0041] [Citation(s) in RCA: 101] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/18/2015] [Indexed: 12/29/2022] Open
Abstract
There is more than one way to develop neuronal complexity, and animals frequently use different molecular toolkits to achieve similar functional outcomes. Genomics and metabolomics data from basal metazoans suggest that neural signalling evolved independently in ctenophores and cnidarians/bilaterians. This polygenesis hypothesis explains the lack of pan-neuronal and pan-synaptic genes across metazoans, including remarkable examples of lineage-specific evolution of neurogenic and signalling molecules as well as synaptic components. Sponges and placozoans are two lineages without neural and muscular systems. The possibility of secondary loss of neurons and synapses in the Porifera/Placozoa clades is a highly unlikely and less parsimonious scenario. We conclude that acetylcholine, serotonin, histamine, dopamine, octopamine and gamma-aminobutyric acid (GABA) were recruited as transmitters in the neural systems in cnidarian and bilaterian lineages. By contrast, ctenophores independently evolved numerous secretory peptides, indicating extensive adaptations within the clade and suggesting that early neural systems might be peptidergic. Comparative analysis of glutamate signalling also shows numerous lineage-specific innovations, implying the extensive use of this ubiquitous metabolite and intercellular messenger over the course of convergent and parallel evolution of mechanisms of intercellular communication. Therefore: (i) we view a neuron as a functional character but not a genetic character, and (ii) any given neural system cannot be considered as a single character because it is composed of different cell lineages with distinct genealogies, origins and evolutionary histories. Thus, when reconstructing the evolution of nervous systems, we ought to start with the identification of particular cell lineages by establishing distant neural homologies or examples of convergent evolution. In a corollary of the hypothesis of the independent origins of neurons, our analyses suggest that both electrical and chemical synapses evolved more than once.
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Affiliation(s)
- Leonid L Moroz
- The Whitney Laboratory for Marine Bioscience, 9505 Ocean Shore Boulevard, St Augustine, FL 32080, USA Department of Neuroscience and McKnight Brain Institute, University of Florida, Gainesville, FL 32611, USA
| | - Andrea B Kohn
- The Whitney Laboratory for Marine Bioscience, 9505 Ocean Shore Boulevard, St Augustine, FL 32080, USA
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Liebeskind BJ, Hillis DM, Zakon HH, Hofmann HA. Complex Homology and the Evolution of Nervous Systems. Trends Ecol Evol 2015; 31:127-135. [PMID: 26746806 DOI: 10.1016/j.tree.2015.12.005] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Revised: 12/01/2015] [Accepted: 12/02/2015] [Indexed: 02/07/2023]
Abstract
We examine the complex evolution of animal nervous systems and discuss the ramifications of this complexity for inferring the nature of early animals. Although reconstructing the origins of nervous systems remains a central challenge in biology, and the phenotypic complexity of early animals remains controversial, a compelling picture is emerging. We now know that the nervous system and other key animal innovations contain a large degree of homoplasy, at least on the molecular level. Conflicting hypotheses about early nervous system evolution are due primarily to differences in the interpretation of this homoplasy. We highlight the need for explicit discussion of assumptions and discuss the limitations of current approaches for inferring ancient phenotypic states.
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Affiliation(s)
- Benjamin J Liebeskind
- Center for Systems and Synthetic Biology, University of Texas, Austin, TX 78712, USA; Institute for Cellular and Molecular Biology, University of Texas, Austin, TX 78712, USA; Center for Computational Biology and Bioinformatics, University of Texas, Austin, TX 78712.
| | - David M Hillis
- Institute for Cellular and Molecular Biology, University of Texas, Austin, TX 78712, USA; Center for Computational Biology and Bioinformatics, University of Texas, Austin, TX 78712; Department of Integrative Biology, University of Texas, Austin, TX 78712, USA
| | - Harold H Zakon
- Institute for Cellular and Molecular Biology, University of Texas, Austin, TX 78712, USA; Center for Computational Biology and Bioinformatics, University of Texas, Austin, TX 78712; Department of Integrative Biology, University of Texas, Austin, TX 78712, USA; Department of Neuroscience, University of Texas, Austin, TX 78712, USA; Institute for Neuroscience, University of Texas, Austin, TX 78712, USA; Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA 02543, USA
| | - Hans A Hofmann
- Institute for Cellular and Molecular Biology, University of Texas, Austin, TX 78712, USA; Center for Computational Biology and Bioinformatics, University of Texas, Austin, TX 78712; Department of Integrative Biology, University of Texas, Austin, TX 78712, USA; Department of Neuroscience, University of Texas, Austin, TX 78712, USA; Institute for Neuroscience, University of Texas, Austin, TX 78712, USA
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New animal phylogeny: future challenges for animal phylogeny in the age of phylogenomics. ORG DIVERS EVOL 2015. [DOI: 10.1007/s13127-015-0236-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Moroz LL. Biodiversity Meets Neuroscience: From the Sequencing Ship (Ship-Seq) to Deciphering Parallel Evolution of Neural Systems in Omic's Era. Integr Comp Biol 2015; 55:1005-17. [PMID: 26163680 DOI: 10.1093/icb/icv084] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
The origins of neural systems and centralized brains are one of the major transitions in evolution. These events might occur more than once over 570-600 million years. The convergent evolution of neural circuits is evident from a diversity of unique adaptive strategies implemented by ctenophores, cnidarians, acoels, molluscs, and basal deuterostomes. But, further integration of biodiversity research and neuroscience is required to decipher critical events leading to development of complex integrative and cognitive functions. Here, we outline reference species and interdisciplinary approaches in reconstructing the evolution of nervous systems. In the "omic" era, it is now possible to establish fully functional genomics laboratories aboard of oceanic ships and perform sequencing and real-time analyses of data at any oceanic location (named here as Ship-Seq). In doing so, fragile, rare, cryptic, and planktonic organisms, or even entire marine ecosystems, are becoming accessible directly to experimental and physiological analyses by modern analytical tools. Thus, we are now in a position to take full advantages from countless "experiments" Nature performed for us in the course of 3.5 billion years of biological evolution. Together with progress in computational and comparative genomics, evolutionary neuroscience, proteomic and developmental biology, a new surprising picture is emerging that reveals many ways of how nervous systems evolved. As a result, this symposium provides a unique opportunity to revisit old questions about the origins of biological complexity.
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Affiliation(s)
- Leonid L Moroz
- The Whitney Laboratory for Marine Bioscience and Department of Neuroscience and McKnight Brain Institute, University of Florida, 9505 Ocean Shore Blvd., St Augustine, FL 32080, USA
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Structure, Distribution, and Function of Neuronal/Synaptic Spinules and Related Invaginating Projections. Neuromolecular Med 2015; 17:211-40. [PMID: 26007200 DOI: 10.1007/s12017-015-8358-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2015] [Accepted: 05/08/2015] [Indexed: 10/23/2022]
Abstract
Neurons and especially their synapses often project long thin processes that can invaginate neighboring neuronal or glial cells. These "invaginating projections" can occur in almost any combination of postsynaptic, presynaptic, and glial processes. Invaginating projections provide a precise mechanism for one neuron to communicate or exchange material exclusively at a highly localized site on another neuron, e.g., to regulate synaptic plasticity. The best-known types are postsynaptic projections called "spinules" that invaginate into presynaptic terminals. Spinules seem to be most prevalent at large very active synapses. Here, we present a comprehensive review of all kinds of invaginating projections associated with both neurons in general and more specifically with synapses; we describe them in all animals including simple, basal metazoans. These structures may have evolved into more elaborate structures in some higher animal groups exhibiting greater synaptic plasticity. In addition to classic spinules and filopodial invaginations, we describe a variety of lesser-known structures such as amphid microvilli, spinules in giant mossy terminals and en marron/brush synapses, the highly specialized fish retinal spinules, the trophospongium, capitate projections, and fly gnarls, as well as examples in which the entire presynaptic or postsynaptic process is invaginated. These various invaginating projections have evolved to modify the function of a particular synapse, or to channel an effect to one specific synapse or neuron, without affecting those nearby. We discuss how they function in membrane recycling, nourishment, and cell signaling and explore how they might change in aging and disease.
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Whelan NV, Kocot KM, Halanych KM. Employing Phylogenomics to Resolve the Relationships among Cnidarians, Ctenophores, Sponges, Placozoans, and Bilaterians. Integr Comp Biol 2015; 55:1084-95. [PMID: 25972566 DOI: 10.1093/icb/icv037] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Despite an explosion in the amount of sequence data, phylogenomics has failed to settle controversy regarding some critical nodes on the animal tree of life. Understanding relationships among Bilateria, Ctenophora, Cnidaria, Placozoa, and Porifera is essential for studying how complex traits such as neurons, muscles, and gastrulation have evolved. Recent studies have cast doubt on the historical viewpoint that sponges are sister to all other animal lineages with recent studies recovering ctenophores as sister. However, the ctenophore-sister hypothesis has been criticized as unrealistic and caused by systematic error. We review past phylogenomic studies and potential causes of systematic error in an effort to identify areas that can be improved in future studies. Increased sampling of taxa, less missing data, and a priori removal of sequences and taxa that may cause systematic error in phylogenomic inference will likely be the most fruitful areas of focus when assembling future datasets. Ultimately, we foresee metazoan relationships being resolved with higher support in the near future, and we caution against dismissing novel hypotheses merely because they conflict with historical viewpoints of animal evolution.
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Affiliation(s)
- Nathan V Whelan
- *Department of Biological Sciences, Molette Biology Laboratory for Environmental and Climate Change Studies, Auburn University, 101 Life Sciences Building, Auburn, AL 36849, USA;
| | - Kevin M Kocot
- School of Biological Sciences, The University of Queensland, 325 Goddard Building, St Lucia, QLD 4101, Australia
| | - Kenneth M Halanych
- *Department of Biological Sciences, Molette Biology Laboratory for Environmental and Climate Change Studies, Auburn University, 101 Life Sciences Building, Auburn, AL 36849, USA
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Abstract
Elucidating relationships among early animal lineages has been difficult, and recent phylogenomic analyses place Ctenophora sister to all other extant animals, contrary to the traditional view of Porifera as the earliest-branching animal lineage. To date, phylogenetic support for either ctenophores or sponges as sister to other animals has been limited and inconsistent among studies. Lack of agreement among phylogenomic analyses using different data and methods obscures how complex traits, such as epithelia, neurons, and muscles evolved. A consensus view of animal evolution will not be accepted until datasets and methods converge on a single hypothesis of early metazoan relationships and putative sources of systematic error (e.g., long-branch attraction, compositional bias, poor model choice) are assessed. Here, we investigate possible causes of systematic error by expanding taxon sampling with eight novel transcriptomes, strictly enforcing orthology inference criteria, and progressively examining potential causes of systematic error while using both maximum-likelihood with robust data partitioning and Bayesian inference with a site-heterogeneous model. We identified ribosomal protein genes as possessing a conflicting signal compared with other genes, which caused some past studies to infer ctenophores and cnidarians as sister. Importantly, biases resulting from elevated compositional heterogeneity or elevated substitution rates are ruled out. Placement of ctenophores as sister to all other animals, and sponge monophyly, are strongly supported under multiple analyses, herein.
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