Phylogenomic Resolution of the Hemichordate and Echinoderm Clade
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Systema Naturae∗
Systema Naturae∗ c Alexey B. Shipunov v. 5.802 (June 29, 2008) 7 Regnum Monera [ Bacillus ] /Bacteria Subregnum Bacteria [ 6:8Bacillus ]1 Superphylum Posibacteria [ 6:2Bacillus ] stat.m. Phylum 1. Firmicutes [ 6Bacillus ]2 Classis 1(1). Thermotogae [ 5Thermotoga ] i.s. 2(2). Mollicutes [ 5Mycoplasma ] 3(3). Clostridia [ 5Clostridium ]3 4(4). Bacilli [ 5Bacillus ] 5(5). Symbiobacteres [ 5Symbiobacterium ] Phylum 2. Actinobacteria [ 6Actynomyces ] Classis 1(6). Actinobacteres [ 5Actinomyces ] Phylum 3. Hadobacteria [ 6Deinococcus ] sed.m. Classis 1(7). Hadobacteres [ 5Deinococcus ]4 Superphylum Negibacteria [ 6:2Rhodospirillum ] stat.m. Phylum 4. Chlorobacteria [ 6Chloroflexus ]5 Classis 1(8). Ktedonobacteres [ 5Ktedonobacter ] sed.m. 2(9). Thermomicrobia [ 5Thermomicrobium ] 3(10). Chloroflexi [ 5Chloroflexus ] ∗Only recent taxa. Viruses are not included. Abbreviations and signs: sed.m. (sedis mutabilis); stat.m. (status mutabilis): s., aut i. (superior, aut interior); i.s. (incertae sedis); sed.p. (sedis possibilis); s.str. (sensu stricto); s.l. (sensu lato); incl. (inclusum); excl. (exclusum); \quotes" for environmental groups; * (asterisk) for paraphyletic taxa; / (slash) at margins for major clades (\domains"). 1Incl. \Nanobacteria" i.s. et dubitativa, \OP11 group" i.s. 2Incl. \TM7" i.s., \OP9", \OP10". 3Incl. Dictyoglomi sed.m., Fusobacteria, Thermolithobacteria. 4= Deinococcus{Thermus. 5Incl. Thermobaculum i.s. 1 4(11). Dehalococcoidetes [ 5Dehalococcoides ] 5(12). Anaerolineae [ 5Anaerolinea ]6 Phylum 5. Cyanobacteria [ 6Nostoc ] Classis 1(13). Gloeobacteres [ 5Gloeobacter ] 2(14). Chroobacteres [ 5Chroococcus ]7 3(15). Hormogoneae [ 5Nostoc ] Phylum 6. Bacteroidobacteria [ 6Bacteroides ]8 Classis 1(16). Fibrobacteres [ 5Fibrobacter ] 2(17). Chlorobi [ 5Chlorobium ] 3(18). Salinibacteres [ 5Salinibacter ] 4(19). Bacteroidetes [ 5Bacteroides ]9 Phylum 7. Spirobacteria [ 6Spirochaeta ] Classis 1(20). Spirochaetes [ 5Spirochaeta ] s.l.10 Phylum 8. Planctobacteria [ 6Planctomyces ]11 Classis 1(21). -
Identical Genomic Organization of Two Hemichordate Hox Clusters
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Elsevier - Publisher Connector Current Biology 22, 2053–2058, November 6, 2012 ª2012 Elsevier Ltd All rights reserved http://dx.doi.org/10.1016/j.cub.2012.08.052 Report Identical Genomic Organization of Two Hemichordate Hox Clusters Robert Freeman,1,12 Tetsuro Ikuta,2,12 Michael Wu,3 [10] have similar organization to the hemichordate cluster, Ryo Koyanagi,2 Takeshi Kawashima,2 Kunifumi Tagawa,4 but with different posterior genes. These results provide Tom Humphreys,5 Guang-Chen Fang,6 Asao Fujiyama,7 genomic evidence for a well-ordered complex in the deutero- Hidetoshi Saiga,8 Christopher Lowe,9 Kim Worley,10 stome ancestor for the hox1–hox9/10 region, with the Jerry Jenkins,11 Jeremy Schmutz,11 Marc Kirschner,1 number and kind of posterior genes still to be elucidated. Daniel Rokhsar,3 Nori Satoh,2,* and John Gerhart3,* 1 Department of Systems Biology, Harvard Medical School, Results and Discussion Boston, MA 02114, USA 2 Marine Genomics Unit, Okinawa Institute of Science and Here we characterize the order, transcriptional orientation, and Technology Graduate University, Onna, clustering of the Hox genes of the genomes of two widely Okinawa 904-0495, Japan studied model hemichordates, Saccoglossus kowalevskii 3 Department of Molecular and Cell Biology, University of and Ptychodera flava [4, 11, 12], that represent two major California, Berkeley, Berkeley, CA 94720-3200, USA evolutionary branches of enteropneust hemichordates that 4 Marine Biological Laboratory, Graduate School of Science, diverged an estimated 400 million years ago (MYa) [13]: Hiroshima University, Onomichi, Hiroshima 722-0073, Japan Saccoglossus, of the direct developing harimaniids, and 5 Department of Cell and Molecular Biology, University of Ptychodera, of the indirect developing ptychoderids [14]. -
"Lophophorates" Brachiopoda Echinodermata Asterozoa
Deuterostomes Bryozoa Phoronida "lophophorates" Brachiopoda Echinodermata Asterozoa Stelleroidea Asteroidea Ophiuroidea Echinozoa Holothuroidea Echinoidea Crinozoa Crinoidea Chaetognatha (arrow worms) Hemichordata (acorn worms) Chordata Urochordata (sea squirt) Cephalochordata (amphioxoius) Vertebrata PHYLUM CHAETOGNATHA (70 spp) Arrow worms Fossils from the Cambrium Carnivorous - link between small phytoplankton and larger zooplankton (1-15 cm long) Pharyngeal gill pores No notochord Peculiar origin for mesoderm (not strictly enterocoelous) Uncertain relationship with echinoderms PHYLUM HEMICHORDATA (120 spp) Acorn worms Pharyngeal gill pores No notochord (Stomochord cartilaginous and once thought homologous w/notochord) Tornaria larvae very similar to asteroidea Bipinnaria larvae CLASS ENTEROPNEUSTA (acorn worms) Marine, bottom dwellers CLASS PTEROBRANCHIA Colonial, sessile, filter feeding, tube dwellers Small (1-2 mm), "U" shaped gut, no gill slits PHYLUM CHORDATA Body segmented Axial notochord Dorsal hollow nerve chord Paired gill slits Post anal tail SUBPHYLUM UROCHORDATA Marine, sessile Body covered in a cellulose tunic ("Tunicates") Filter feeder (» 200 L/day) - perforated pharnx adapted for filtering & repiration Pharyngeal basket contractable - squirts water when exposed at low tide Hermaphrodites Tadpole larvae w/chordate characteristics (neoteny) CLASS ASCIDIACEA (sea squirt/tunicate - sessile) No excretory system Open circulatory system (can reverse blood flow) Endostyle - (homologous to thyroid of vertebrates) ciliated groove -
TREATISE TREATISE Paleo.Ku.Edu/Treatise
TREATISE TREATISE paleo.ku.edu/treatise For each fossil group, volumes describe and illustrate: morphological features; ontogeny; classification; geologic distribution; evolutionary trends and phylogeny; and All 53 volumes of the Treatise are now available as fully searchable pdf systematic descriptions. Each volume is fully indexed and files on CD, even out-of-print and superseded volumes! Also available contains a complete set of references, and there are many is the complete set of volumes, either on one DVD, or a set of 41 CDs, detailed illustrations and plates throughout the series. each decorated with a different fossil. See below for details. Complete set of 53 Treatise volumes Part B Single DVD or 41 CDs: $1850.00 Protoctista 1: Charophyta, vol. 1 Edited by Roger L. Kaesler, with coordinating author, Monique Feist, Porifera (Revised), vol. 2 Part F leading a team of international specialists, 2005 edited by Roger L. Kaesler; coordinating author, J. Keith Rigby, with First volume of Part B to be published, covering generally plantlike authors R. E. H. Reid, R.M. Finks, and J. Keith Rigby, 2003 Coelenterata, Supplement 1, Rugosa and Tabulata, vol. 1–2 autotrophic protoctists. Future volumes will cover the dinoflagellates, Second volume in the revision of Porifera. General features of the Porifera, edited by C. Teichert, coordinating author Dorothy Hill, 1981 silicoflagellates, ebredians, benthic calcareous algae, coccolithophorids, including glossary, references, and index. Introduction to Paleozoic corals and systematic descriptions for Rugosa; and diatoms. Included in the charophyte volume are introductory chapters 376 p., ISBN 0-8137-3130-5, $75.00, hard copy or CD introduction to and systematic descriptions for Tabulata. -
Tropical Marine Invertebrates CAS BI 569 Phylum Echinodermata by J
Tropical Marine Invertebrates CAS BI 569 Phylum Echinodermata by J. R. Finnerty Porifera Ctenophora Cnidaria Deuterostomia Ecdysozoa Lophotrochozoa Chordata Arthropoda Annelida Hemichordata Onychophora Mollusca Echinodermata *Nematoda *Platyhelminthes Acoelomorpha Calcispongia Silicispongiae PROTOSTOMIA Phylum Phylum Phylum CHORDATA ECHINODERMATA HEMICHORDATA Blastopore -> anus Radial / equal cleavage Coelom forms by enterocoely ! Protostome = blastopore contributes to the mouth blastopore mouth anus ! Deuterostome = blastopore becomes anus blastopore anus mouth Halocynthia, a tunicate (Urochordata) Coelom Formation Protostomes: Schizocoely Deuterostomes: Enterocoely Enterocoely in a sea star Axocoel (protocoel) Gives rise to small portion of water vascular system. Hydrocoel (mesocoel) Gives rise to water vascular system. Somatocoel (metacoel) Gives rise to lining of adult body cavity. Echinoderm Metamorphosis ECHINODERM FEATURES Water vascular system and tube feet Pentaradial symmetry Coelom formation by enterocoely Water Vascular System Tube Foot Tube Foot Locomotion ECHINODERM DIVERSITY Crinoidea Asteroidea Ophiuroidea Holothuroidea Echinoidea “sea lilies” “sea stars” “brittle stars” “sea cucumbers” “urchins, sand dollars” Group Form & Habit Habitat Ossicles Feeding Special Characteristics Crinoids 5-200 arms, stalked epifaunal Internal skeleton suspension mouth upward; mucous & Of each arm feeders secreting glands on sessile podia Ophiuroids usually 5 thin arms, epifaunal ossicles in arms deposit feeders act and appear like vertebrae -
Chlorophyta Is a Division of Green Algae, Informally Called
Chlorophyta is a division of green algae, informally waters of the Sargasso Sea. Many brown algae, such as called chlorophytes. The name is used in two very members of the order Fucales, commonly grow along different senses so that care is needed to determine the rocky seashores. Some members of the class are used as use by a particular author. In older classification food for humans. systems, it refers to a highly paraphyletic group of all Worldwide there are about 1500–2000 species of brown the green algae within the green plants (Viridiplantae), algae.[4] Some species are of sufficient commercial and thus includes about 7,000 species [4] [5] of mostly importance, such as Ascophyllum nodosum , that they aquatic photosynthetic eukaryotic organisms. Like the have become subjects of extensive research in their own land plants (bryophytes and tracheophytes), green algae right.[5] [4] contain chlorophylls a and b, and store food as starch Brown algae belong to a very large group, the in their plastids. Heterokontophyta, a eukaryotic group of organisms In newer classifications, it refers to one of the two distinguished most prominently by having chloroplasts clades making up the Viridiplantae, which are the surrounded by four membranes, suggesting an origin chlorophytes and the streptophytes or charophytes.[6][7] from a symbiotic relationship between a basal In this sense it includes only about 4,300 species.[3] eukaryote and another eukaryotic organism. Most brown algae contain the pigment fucoxanthin, which is responsible for the distinctive greenish-brown color that The red algae, or Rhodophyta ( / r o ʊ ˈ d ɒ f ɨ t ə / or / gives them their name. -
Development of the Annelid Axochord: Insights Into Notochord Evolution Antonella Lauri Et Al
RESEARCH | REPORTS ORIGIN OF NOTOCHORD by double WMISH (Fig. 2, F to L). Although none of the genes were exclusively expressed in the annelid mesodermal midline, their combined Development of the annelid coexpression was unique to these cells (implying that mesodermal midline in annelids and chor- damesoderm in vertebrates are more similar to axochord: Insights into each other than to any other tissue). It is unlikely that the molecular similarity between annelid notochord evolution and vertebrate mesodermal midline is due to in- dependent co-option of a conserved gene cas- Antonella Lauri,1*† Thibaut Brunet,1* Mette Handberg-Thorsager,1,2‡ sette, because this would require either that this Antje H.L. Fischer,1§ Oleg Simakov,1 Patrick R. H. Steinmetz,1‖ Raju Tomer,1,2¶ cassette was active elsewhere in the body (which Philipp J. Keller,2 Detlev Arendt1,3# is not the case) or that multiple identical inde- pendent events of co-option occurred (which is The origin of chordates has been debated for more than a century, with one key issue being unparsimonious). As in vertebrates, the meso- the emergence of the notochord. In vertebrates, the notochord develops by convergence dermal midline resembles the neuroectodermal and extension of the chordamesoderm, a population of midline cells of unique molecular midline, which expresses foxD, foxA, netrin, slit, identity. We identify a population of mesodermal cells in a developing invertebrate, the marine and noggin (figs. S6 and S7) but not brachyury or annelid Platynereis dumerilii, that converges and extends toward the midline and expresses a twist. However, unlike in chicken (10), the an- notochord-specific combination of genes. -
Collin Et Al. Page 1 of 31 Unexpected Molecular and Morphological
Unexpected Molecular and Morphological Diversity of Hemichordate Larvae from the Neotropics Rachel Collin1*, Dagoberto E. Venera-Pontón1, Amy C. Driskell2, Kenneth S. Macdonald III2, Michael J. Boyle3 1Smithsonian Tropical Research Institute, Apartado Postal 0843-03092, Balboa Ancon, Panama. 2Laboratories of Analytical Biology, National Museum of Natural History, Smithsonian Institution, Washington DC, USA 3Smithsonian Marine Station, Fort Pierce, Florida *Corresponding author: e-mail: [email protected]; (202) 633-4700 x28766. Address for correspondence: STRI, Unit 9100, Box 0948, DPO AA 34002, USA. Invertebrate Biology Keywords: Tropical East Pacific, Panama, Caribbean, meroplankton, enteropneust, invertebrate, larval morphology Running Head: Neotropic Hemichordate Larval Diversity September 2019 Collin et al. Page 1 of 31 Abstract The diversity of tropical marine invertebrates is poorly documented, especially those groups for which collecting adults is difficult. We collected the planktonic tornaria larvae of hemichordates (acorn worms) to assess their hidden diversity in the Neotropics. Larvae were retrieved in plankton tows from waters of the Pacific and Caribbean coasts of Panama, followed by DNA barcoding of mitochondrial cytochrome c oxidase subunit I (COI) and 16S ribosomal DNA to estimate their diversity in the region. With moderate sampling efforts, we discovered 6 operational taxonomic units (OTUs) in the Bay of Panama on the Pacific coast, in contrast to the single species previously recorded for the entire Tropical Eastern Pacific. We found 8 OTUs in Bocas del Toro Province on the Caribbean coast, compared to 7 species documented from adults in the entire Caribbean. All OTUs differed from each other and from named acorn worm sequences in GenBank by >10% pairwise distance in COI and >2% in 16S. -
Reinterpretation of the Enigmatic Ordovician Genus Bolboporites (Echinodermata)
Reinterpretation of the enigmatic Ordovician genus Bolboporites (Echinodermata). Emeric Gillet, Bertrand Lefebvre, Véronique Gardien, Emilie Steimetz, Christophe Durlet, Frédéric Marin To cite this version: Emeric Gillet, Bertrand Lefebvre, Véronique Gardien, Emilie Steimetz, Christophe Durlet, et al.. Reinterpretation of the enigmatic Ordovician genus Bolboporites (Echinodermata).. Zoosymposia, Magnolia Press, 2019, 15 (1), pp.44-70. 10.11646/zoosymposia.15.1.7. hal-02333918 HAL Id: hal-02333918 https://hal.archives-ouvertes.fr/hal-02333918 Submitted on 13 Nov 2020 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. 1 Reinterpretation of the Enigmatic Ordovician Genus Bolboporites 2 (Echinodermata) 3 4 EMERIC GILLET1, BERTRAND LEFEBVRE1,3, VERONIQUE GARDIEN1, EMILIE 5 STEIMETZ2, CHRISTOPHE DURLET2 & FREDERIC MARIN2 6 7 1 Université de Lyon, UCBL, ENSL, CNRS, UMR 5276 LGL-TPE, 2 rue Raphaël Dubois, F- 8 69622 Villeurbanne, France 9 2 Université de Bourgogne - Franche Comté, CNRS, UMR 6282 Biogéosciences, 6 boulevard 10 Gabriel, F-2100 Dijon, France 11 3 Corresponding author, E-mail: [email protected] 12 13 Abstract 14 Bolboporites is an enigmatic Ordovician cone-shaped fossil, the precise nature and systematic affinities of 15 which have been controversial over almost two centuries. -
Regulatory Circuit Rewiring and Functional Divergence of the Duplicate Admp Genes in Dorsoventral Axial Patterning
Developmental Biology 410 (2016) 108–118 Contents lists available at ScienceDirect Developmental Biology journal homepage: www.elsevier.com/locate/developmentalbiology Evolution of Developmental Control Mechanisms Regulatory circuit rewiring and functional divergence of the duplicate admp genes in dorsoventral axial patterning Yi-Cheng Chang a,b, Chih-Yu Pai a, Yi-Chih Chen a, Hsiu-Chi Ting a, Pedro Martinez c,d, Maximilian J. Telford e, Jr-Kai Yu a, Yi-Hsien Su a,b,n a Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan b Department of Bioscience and Biotechnology, National Taiwan Ocean University, Keelung, Taiwan c Department de Genètica, Universitat de Barcelona, Barcelona, Spain d Institució de Recerca I Estudis Avançats (ICREA), Barcelona, Spain e Department of Genetics, Evolution and Environment, University College London, London, UK article info abstract Article history: The spatially opposed expression of Antidorsalizing morphogenetic protein (Admp) and BMP signals Received 18 December 2015 controls dorsoventral (DV) polarity across Bilateria and hence represents an ancient regulatory circuit. Accepted 18 December 2015 Here, we show that in addition to the conserved admp1 that constitutes the ancient circuit, a second Available online 21 December 2015 admp gene (admp2) is present in Ambulacraria (EchinodermataþHemichordata) and two marine worms Keywords: belonging to Xenoturbellida and Acoelomorpha. The phylogenetic distribution implies that the two admp BMP genes were duplicated in the Bilaterian common ancestor and admp2 was subsequently lost in chordates Admp and protostomes. We show that the ambulacrarian admp1 and admp2 are under opposite transcriptional Sea urchin control by BMP signals and knockdown of Admps in sea urchins impaired their DV polarity. -
Zootaxa, a Taxonomic Revision of the Family Harrimaniidae (Hemichordata
Zootaxa 2408: 1–30 (2010) ISSN 1175-5326 (print edition) www.mapress.com/zootaxa/ Article ZOOTAXA Copyright © 2010 · Magnolia Press ISSN 1175-5334 (online edition) A taxonomic revision of the family Harrimaniidae (Hemichordata: Enteropneusta) with descriptions of seven species from the Eastern Pacific C. DELAND1, C. B. CAMERON1,6, K. P. RAO2,5, W. E. RITTER3,5 & T. H. BULLOCK4,5 1Sciences biologiques, Université de Montréal, C.P. 6128, Succ. Centre-ville, Montreal, QC, H3C 3J7, Canada 2Department of Zoology, Bangalore University, Bangalore, India 3Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, U.S.A. 4Scripps Institution of Oceanography and Department of Neurosciences, School of Medicine, University of California San Diego, La Jolla, California, U.S.A. 5Deceased 6Corresponding author. E-mail: [email protected] Abstract The family Harrimaniidae (Hemichordata: Enteropneusta) is revised on the basis of morphological characters. The number of harrimaniid genera is increased to nine by the addition of Horstia n. gen., Mesoglossus n. gen., Ritteria n. gen. and Saxipendium, a genus previously assigned to the monospecific family Saxipendiidae. The number of species is increased to 34, resulting from the description of five new species from the eastern Pacific — Horstia kincaidi, Mesoglossus intermedius, M. macginitiei, Protoglossus mackiei and Ritteria ambigua. A description is supplied for a sixth harrimaniid species, Stereobalanus willeyi Ritter & Davis, 1904, which previously had the status of a nomen nudum. Four harrimaniids previously assigned to the genus Saccoglossus are transfered to the genus Mesoglossus — M. bournei, M. caraibicus, M. gurneyi and M. pygmaeus, while Saccoglossus borealis is reassigned to the genus Harrimania. -
Analysis of the Complete Mitochondrial DNA Sequence of the Brachiopod Terebratulina Retusa Places Brachiopoda Within the Protostomes
See discussions, stats, and author profiles for this publication at: https://www.researchgate.net/publication/12415870 Analysis of the complete mitochondrial DNA sequence of the brachiopod Terebratulina retusa places Brachiopoda within the protostomes Article in Proceedings of the Royal Society B: Biological Sciences · November 1999 DOI: 10.1098/rspb.1999.0885 · Source: PubMed CITATIONS READS 83 50 2 authors, including: Martin Schlegel University of Leipzig 151 PUBLICATIONS 2,931 CITATIONS SEE PROFILE Some of the authors of this publication are also working on these related projects: Rare for a reason? Scale-dependence of factors influencing rarity and diversity of xylobiont beetles View project Bat diversity and vertical niche activity in the fluvial flood forest Leipzig View project All content following this page was uploaded by Martin Schlegel on 22 May 2014. The user has requested enhancement of the downloaded file. Analysis of the complete mitochondrial DNA sequence of the brachiopod Terebratulina retusa places Brachiopoda within the protostomes Alexandra Stechmann* and Martin Schlegel UniversitÌt Leipzig, Institut fÏr Zoologie/Spezielle Zoologie,Talstr. 33, 04103 Leipzig, Germany Brachiopod phylogeny is still a controversial subject. Analyses using nuclear 18SrRNA and mitochondrial 12SrDNA sequences place them within the protostomes but some recent interpretations of morphological data support a relationship with deuterostomes. In order to investigate brachiopod a¤nities within the metazoa further,we compared the gene arrangement on the brachiopod mitochondrial genome with several metazoan taxa. The complete (15 451bp) mitochondrial DNA (mtDNA) sequence of the articulate brachiopod Terebratulina retusa was determined from two overlapping long polymerase chain reaction products. All the genes are encoded on the same strand and gene order comparisons showed that only one major rearrangement is required to interconvert the T.retusa and Katharina tunicata (Mollusca: Polyplaco- phora) mitochondrial genomes.