29.1 Chordates
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The Phylum Vertebrata: a Case for Zoological Recognition Naoki Irie1,2* , Noriyuki Satoh3 and Shigeru Kuratani4
Irie et al. Zoological Letters (2018) 4:32 https://doi.org/10.1186/s40851-018-0114-y REVIEW Open Access The phylum Vertebrata: a case for zoological recognition Naoki Irie1,2* , Noriyuki Satoh3 and Shigeru Kuratani4 Abstract The group Vertebrata is currently placed as a subphylum in the phylum Chordata, together with two other subphyla, Cephalochordata (lancelets) and Urochordata (ascidians). The past three decades, have seen extraordinary advances in zoological taxonomy and the time is now ripe for reassessing whether the subphylum position is truly appropriate for vertebrates, particularly in light of recent advances in molecular phylogeny, comparative genomics, and evolutionary developmental biology. Four lines of current research are discussed here. First, molecular phylogeny has demonstrated that Deuterostomia comprises Ambulacraria (Echinodermata and Hemichordata) and Chordata (Cephalochordata, Urochordata, and Vertebrata), each clade being recognized as a mutually comparable phylum. Second, comparative genomic studies show that vertebrates alone have experienced two rounds of whole-genome duplication, which makes the composition of their gene family unique. Third, comparative gene-expression profiling of vertebrate embryos favors an hourglass pattern of development, the most conserved stage of which is recognized as a phylotypic period characterized by the establishment of a body plan definitively associated with a phylum. This mid-embryonic conservation is supported robustly in vertebrates, but only weakly in chordates. Fourth, certain complex patterns of body plan formation (especially of the head, pharynx, and somites) are recognized throughout the vertebrates, but not in any other animal groups. For these reasons, we suggest that it is more appropriate to recognize vertebrates as an independent phylum, not as a subphylum of the phylum Chordata. -
A New Species of Yunnanozoan with Implications for Deuterostome
R EPORTS istry, K. S. Birdi, Ed. (CRC Press Inc., Boca Raton, FL, 23. L. H. Sperling, Polymeric Multicomponent Materials (grant EA/TU¨ BA-GEBI˙P/2001-1-1) and the Koc¸ Uni- 1997), chap. 9. (Wiley-Interscience, New York, 1997), chap. 6. versity Fiat Fund. 18. , G. McHale, M. I. Newton, Langmuir 18, 2636 24. J. Varga, in Polypropylene Structure, Blends and Com- Supporting Online Material (2002). posites, J. Karger-Kocsis, Ed. (Chapman and Hall, Lon- www.sciencemag.org/cgi/content/full/299/5611/1377/ 19. Materials and methods are available as supporting don, 1995), vol. 1, chap. 3. DC1 material on Science Online. 25. We thank A. Altay, M. A. Gu¨lgu¨n of Sabancı Univer- Materials and Methods 20. R. N. Wenzel, Ind. Eng. Chem. 28, 988 (1936). sity, and A. Alkan of Brisa for their help with SEM Figs. S1 and S2 21. A. B. D. Cassie, S. Baxter, Trans. Faraday Soc. 3, 16 (1944). measurements. A.L.D. acknowledges the financial References 22. R. A. Veselovsky, V. N. Kestelman, Adhesion of Poly- support of the Turkish Academy of Sciences in the mers (McGraw-Hill, New York, 2002), chap. 2. framework of the Young Scientist Award Program 11 September 2002; accepted 22 January 2003 and ventral units are rarely touching (Fig. 1, A New Species of Yunnanozoan G and H), suggesting that the entire anterior region could expand and contract in height. with Implications for The expansion would occur by an accommo- dation along the median zone and about an axis of rotation near the posterior of the units. -
Przedstawiciele Rodzaju Craniscus Dali, 1871 Z Górnego Oksfordu Bielaw I Wapienna Na Kujawach
Przedstawic iele rodza ju Craniscus Da li. 187 1 z górnego oksfordu Bielaw i Wapienna na Kujawach 75 Przedstawiciele rodzaju Craniscus Dali, 1871 z górnego oksfordu Bielaw i Wapienna na Kujawach Representatives of the genus Craniscus Dali, 1871, from the Upper Oxfordian of Bielawy and Wapienno in Kujawy area Cezary KRAWCZYŃSKI Instytut Geologii Pod stawowej. Wydziat Geologii. Un iwers ytet Warszawski. ul. Ż wirk i i Wigury 93. 02-089 Warszaw a; e-mail : c.kra [email protected] Key words: Craniidae, Craniscus, Inarticulated Brachiopods, Upper Jurassic, Poland. ABSTRACT: The presented paper contains a detailed description of four species of the genus Craniscus DalI, 1871, found in the Upper Oxfordian of Bielawy and Wapienno quarries, Kujawy area. Three of them: Craniscus bipartitus (Munster, 1837), Craniscus antiquior (Jelly, 1843) and Craniscus corallinus (Quenstedt, 1852) have already been described from Poland, the fourth, however - Craniscus tripartitus (Munster, 1840) , had only been known from the Lower Oxfordian of North Bavaria. The Craniscus specimens come from slope deposits of sponge-microbialitic bioherm. This is indicated by the fact that almost all specimens are dorsal valves, separated posthumously from ventral valves. The condition of some specimens and the rock lithology suggests, that the deposition was very violent in some cases and brachiopods were buried alive. The studied material is relatively well-preserved, which alIowes an accurate reading of the location of muscle scal's. WSTĘP BUDOWA GEOLOGICZNA I STRATYGRAFIA Praca niniejsza zawiera opis czterech gatunków W kamieniołomach Wapienno i Bielawy eksplo kranii z rodzaju Craniscus Dall, 1871, znalezionych atowane są wapienie biohermy gąbkowo-mikrobial w osadach górnego oksfordu odsłoniętych w kamie itowej oraz jej skłonu, które stanowią fragment niołomach Wapienno i Bielawy (fig. -
Brains of Primitive Chordates 439
Brains of Primitive Chordates 439 Brains of Primitive Chordates J C Glover, University of Oslo, Oslo, Norway although providing a more direct link to the evolu- B Fritzsch, Creighton University, Omaha, NE, USA tionary clock, is nevertheless hampered by differing ã 2009 Elsevier Ltd. All rights reserved. rates of evolution, both among species and among genes, and a still largely deficient fossil record. Until recently, it was widely accepted, both on morpholog- ical and molecular grounds, that cephalochordates Introduction and craniates were sister taxons, with urochordates Craniates (which include the sister taxa vertebrata being more distant craniate relatives and with hemi- and hyperotreti, or hagfishes) represent the most chordates being more closely related to echinoderms complex organisms in the chordate phylum, particu- (Figure 1(a)). The molecular data only weakly sup- larly with respect to the organization and function of ported a coherent chordate taxon, however, indicat- the central nervous system. How brain complexity ing that apparent morphological similarities among has arisen during evolution is one of the most chordates are imposed on deep divisions among the fascinating questions facing modern science, and it extant deuterostome taxa. Recent analysis of a sub- speaks directly to the more philosophical question stantially larger number of genes has reversed the of what makes us human. Considerable interest has positions of cephalochordates and urochordates, pro- therefore been directed toward understanding the moting the latter to the most closely related craniate genetic and developmental underpinnings of nervous relatives (Figure 1(b)). system organization in our more ‘primitive’ chordate relatives, in the search for the origins of the vertebrate Comparative Appearance of Brains, brain in a common chordate ancestor. -
The Origins of Chordate Larvae Donald I Williamson* Marine Biology, University of Liverpool, Liverpool L69 7ZB, United Kingdom
lopmen ve ta e l B Williamson, Cell Dev Biol 2012, 1:1 D io & l l o l g DOI: 10.4172/2168-9296.1000101 e y C Cell & Developmental Biology ISSN: 2168-9296 Research Article Open Access The Origins of Chordate Larvae Donald I Williamson* Marine Biology, University of Liverpool, Liverpool L69 7ZB, United Kingdom Abstract The larval transfer hypothesis states that larvae originated as adults in other taxa and their genomes were transferred by hybridization. It contests the view that larvae and corresponding adults evolved from common ancestors. The present paper reviews the life histories of chordates, and it interprets them in terms of the larval transfer hypothesis. It is the first paper to apply the hypothesis to craniates. I claim that the larvae of tunicates were acquired from adult larvaceans, the larvae of lampreys from adult cephalochordates, the larvae of lungfishes from adult craniate tadpoles, and the larvae of ray-finned fishes from other ray-finned fishes in different families. The occurrence of larvae in some fishes and their absence in others is correlated with reproductive behavior. Adult amphibians evolved from adult fishes, but larval amphibians did not evolve from either adult or larval fishes. I submit that [1] early amphibians had no larvae and that several families of urodeles and one subfamily of anurans have retained direct development, [2] the tadpole larvae of anurans and urodeles were acquired separately from different Mesozoic adult tadpoles, and [3] the post-tadpole larvae of salamanders were acquired from adults of other urodeles. Reptiles, birds and mammals probably evolved from amphibians that never acquired larvae. -
Treatise on Invertebrate Paleontology
PART H, Revised BRACHIOPODA VOLUMES 2 & 3: Linguliformea, Craniiformea, and Rhynchonelliformea (part) ALWYN WILLIAMS, S. J. CARLSON, C. H. C. BRUNTON, L. E. HOLMER, L. E. POPOV, MICHAL MERGL, J. R. LAURIE, M. G. BASSETT, L. R. M. COCKS, RONG JIA-YU, S. S. LAZAREV, R. E. GRANT, P. R. RACHEBOEUF, JIN YU-GAN, B. R. WARDLAW, D. A. T. HARPER, A. D. WRIGHT, and MADIS RUBEL CONTENTS INFORMATION ON TREATISE VOLUMES ...................................................................................... x EDITORIAL PREFACE .............................................................................................................. xi STRATIGRAPHIC DIVISIONS .................................................................................................. xxiv COORDINATING AUTHOR'S PREFACE (Alwyn Williams) ........................................................ xxv BRACHIOPOD CLASSIFICATION (Alwyn Williams, Sandra J. Carlson, and C. Howard C. Brunton) .................................. 1 Historical Review .............................................................................................................. 1 Basis for Classification ....................................................................................................... 5 Methods.......................................................................................................................... 5 Genealogies ....................................................................................................................... 6 Recent Brachiopods ....................................................................................................... -
Abstract Introduction
Marine and Freshwater Miscellanea III KEY TRAITS OF AMPHIOXUS SPECIES (CEPHALOCHORDATA) AND THE GOLT1 Daniel Pauly and Elaine Chu Sea Around Us, Institute for the Oceans and Fisheries University of British Columbia, Vancouver, B.C, Canada Email: [email protected] Abstract Major biological traits of amphioxus species (Cephalochordata) are presented with emphasis on the size reached by their 32 valid species in the genera Asymmetron (2 spp.), Branchiostoma (25 spp.), and Epigonichthys (5 spp.) and on related features, i.e., growth parameters and size at first maturity. Overall, these traits combined with features of their respiration, suggest that the cephalochordates conform to the Gill Oxygen Limitation Theory (GOLT), which relates the growth performance of water-breathing ectotherms to the surface area of their respiratory organ(s). Introduction The small fish-like animals know as ‘lancelet‘ or ‘amphioxius’ belong the subphylum Cephalochordata, which is either a sister group, or related to the ancestor of the vertebrate animals (see Garcia-Fernàndez and Benito-Gutierrez 2008). The cephalochordates consist of 3 families (the Asymmetronidae, Epigonichthyidae and Branchiostomidae), with one genus each, Asymmetron (2 spp.), Branchiostoma (24 spp.) and Epigonichthys (6 spp.), as detailed in Table 1 and SeaLifeBase (www.sealifebase.org). This contribution is to assemble some of the basic biological traits of lancelets (Figure 1), notably the maximum size each of their 34 species can reach, which is easily their most important attribute, though it is often ignored (Haldane 1926). Finally, reported lengths at first maturity of cephalochordates were related to the corresponding, population-specific maximum length, to test whether these animals mature as predicted by the Gill- Oxygen Limitation Theory (GOLT; see Pauly 2021a, 2021b). -
Alyssa Weinrauch
The digestive physiology of the Pacific hagfish, Eptatretus stoutii by Alyssa Weinrauch A thesis submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Physiology, Cell and Developmental Biology Department of Biological Sciences University of Alberta © Alyssa Weinrauch, 2019 Abstract Hagfish are considered the oldest living representatives of the vertebrates and as such are of interest for studies in evolutionary biology. Moreover, hagfish occupy a unique trophic niche wherein they are active predators and benthic scavengers of a wide range of invertebrate and vertebrate prey, yet can tolerate nearly a year of fasting. Hagfish are also capable of acquiring nutrients across the integument in a manner similar to that of marine invertebrates, a hallmark of their position between the invertebrate and vertebrate lineages. Despite many interesting modes of feeding, relatively few studies have examined the digestive physiology of the hagfishes. Feeding and digestion cause many physiological perturbations, which result in elevated metabolic rate. I have characterised the increased metabolic demand (specific dynamic action) and determined that its peak in hagfish corresponds with the peak of acid-base alterations. Specifically, the rate of base efflux reaches a maximum 8 h post- feeding when the intestinal blood supply is significantly more alkaline. The offloading of base to the circulation (alkaline tide) is common of vertebrates that employ an acidic digestion in order to maintain cellular acid-base homeostasis. Likewise, the hagfishes employ a luminal acidification, despite lacking a stomach. I further investigated the cellular mechanisms responsible for hindgut luminal acidification and found that soluble adenylyl cyclase and cAMP are utilised to enhance proton secretion via proton-potassium exchangers (HKA), as is found in later-diverging vertebrates. -
Using Information in Taxonomists' Heads to Resolve Hagfish And
This article was downloaded by: [Max Planck Inst fuer Evolutionsbiologie] On: 03 September 2013, At: 07:01 Publisher: Taylor & Francis Informa Ltd Registered in England and Wales Registered Number: 1072954 Registered office: Mortimer House, 37-41 Mortimer Street, London W1T 3JH, UK Historical Biology: An International Journal of Paleobiology Publication details, including instructions for authors and subscription information: http://www.tandfonline.com/loi/ghbi20 Using information in taxonomists’ heads to resolve hagfish and lamprey relationships and recapitulate craniate–vertebrate phylogenetic history Maria Abou Chakra a , Brian Keith Hall b & Johnny Ricky Stone a b c d a Department of Biology , McMaster University , Hamilton , Canada b Department of Biology , Dalhousie University , Halifax , Canada c Origins Institute, McMaster University , Hamilton , Canada d SHARCNet, McMaster University , Hamilton , Canada Published online: 02 Sep 2013. To cite this article: Historical Biology (2013): Using information in taxonomists’ heads to resolve hagfish and lamprey relationships and recapitulate craniate–vertebrate phylogenetic history, Historical Biology: An International Journal of Paleobiology To link to this article: http://dx.doi.org/10.1080/08912963.2013.825792 PLEASE SCROLL DOWN FOR ARTICLE Taylor & Francis makes every effort to ensure the accuracy of all the information (the “Content”) contained in the publications on our platform. However, Taylor & Francis, our agents, and our licensors make no representations or warranties whatsoever as to the accuracy, completeness, or suitability for any purpose of the Content. Any opinions and views expressed in this publication are the opinions and views of the authors, and are not the views of or endorsed by Taylor & Francis. The accuracy of the Content should not be relied upon and should be independently verified with primary sources of information. -
Single Cell Chromatin Accessibility of the Developmental
bioRxiv preprint doi: https://doi.org/10.1101/2020.03.17.994954; this version posted March 19, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. Single cell chromatin accessibility of the developmental cephalochordate Dongsheng Chen1, Zhen Huang2,3, Xiangning Ding1,4, Zaoxu Xu1,4, Jixing Zhong1,4, Langchao Liang1,4, Luohao Xu5, Chaochao Cai1,4, Haoyu Wang1,4, Jiaying Qiu1,4, Jiacheng Zhu1,4, Xiaoling Wang1,4, Rong Xiang1,4, Weiying Wu1,4, Peiwen Ding1,4, Feiyue Wang1,4, Qikai Feng1,4, Si Zhou1, Yuting Yuan1, Wendi Wu1, Yanan Yan2,3, Yitao Zhou2,3, Duo Chen2,3, Guang Li6, Shida Zhu1, Fang Chen1,7, Qiujin Zhang2,3, Jihong Wu8,9,10,11 &Xun Xu1 1. BGI-shenzhen, Shenzhen 518083, China 2. Life Science College, Fujian Normal University 3. Key Laboratory of Special Marine Bio-resources Sustainable Utilization of Fujian Province, Fuzhou 350108, P. R. China 4. BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China 5. Department of Neuroscience and Developmental Biology, University of Vienna 6. State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiangan District, Xiamen, Fujian 361102, China 7. MGI, BGI-Shenzhen, Shenzhen 518083, China 8. Eye Institute, Eye and ENT Hospital, Shanghai Medical College, Fudan University, Shanghai, China 9. Shanghai Key Laboratory of Visual Impairment and Restoration, Science and Technology Commission of Shanghai Municipality, Shanghai, China 10. -
Hemichordate Phylogeny: a Molecular, and Genomic Approach By
Hemichordate Phylogeny: A molecular, and genomic approach by Johanna Taylor Cannon A dissertation submitted to the Graduate Faculty of Auburn University in partial fulfillment of the requirements for the Degree of Doctor of Philosophy Auburn, Alabama May 4, 2014 Keywords: phylogeny, evolution, Hemichordata, bioinformatics, invertebrates Copyright 2014 by Johanna Taylor Cannon Approved by Kenneth M. Halanych, Chair, Professor of Biological Sciences Jason Bond, Associate Professor of Biological Sciences Leslie Goertzen, Associate Professor of Biological Sciences Scott Santos, Associate Professor of Biological Sciences Abstract The phylogenetic relationships within Hemichordata are significant for understanding the evolution of the deuterostomes. Hemichordates possess several important morphological structures in common with chordates, and they have been fixtures in hypotheses on chordate origins for over 100 years. However, current evidence points to a sister relationship between echinoderms and hemichordates, indicating that these chordate-like features were likely present in the last common ancestor of these groups. Therefore, Hemichordata should be highly informative for studying deuterostome character evolution. Despite their importance for understanding the evolution of chordate-like morphological and developmental features, relationships within hemichordates have been poorly studied. At present, Hemichordata is divided into two classes, the solitary, free-living enteropneust worms, and the colonial, tube- dwelling Pterobranchia. The objective of this dissertation is to elucidate the evolutionary relationships of Hemichordata using multiple datasets. Chapter 1 provides an introduction to Hemichordata and outlines the objectives for the dissertation research. Chapter 2 presents a molecular phylogeny of hemichordates based on nuclear ribosomal 18S rDNA and two mitochondrial genes. In this chapter, we suggest that deep-sea family Saxipendiidae is nested within Harrimaniidae, and Torquaratoridae is affiliated with Ptychoderidae. -
Molecular Investigation of the Cnidarian-Dinoflagellate Symbiosis
AN ABSTRACT OF THE DISSERTATION OF Laura Lynn Hauck for the degree of Doctor of Philosophy in Zoology presented on March 20, 2007. Title: Molecular Investigation of the Cnidarian-dinoflagellate Symbiosis and the Identification of Genes Differentially Expressed during Bleaching in the Coral Montipora capitata. Abstract approved: _________________________________________ Virginia M. Weis Cnidarians, such as anemones and corals, engage in an intracellular symbiosis with photosynthetic dinoflagellates. Corals form both the trophic and structural foundation of reef ecosystems. Despite their environmental importance, little is known about the molecular basis of this symbiosis. In this dissertation we explored the cnidarian- dinoflagellate symbiosis from two perspectives: 1) by examining the gene, CnidEF, which was thought to be induced during symbiosis, and 2) by profiling the gene expression patterns of a coral during the break down of symbiosis, which is called bleaching. The first chapter characterizes a novel EF-hand cDNA, CnidEF, from the anemone Anthopleura elegantissima. CnidEF was found to contain two EF-hand motifs. A combination of bioinformatic and molecular phylogenetic analyses were used to compare CnidEF to EF-hand proteins in other organisms. The closest homologues identified from these analyses were a luciferin binding protein involved in the bioluminescence of the anthozoan Renilla reniformis, and a sarcoplasmic calcium- binding protein involved in fluorescence of the annelid worm Nereis diversicolor. Northern blot analysis refuted link of the regulation of this gene to the symbiotic state. The second and third chapters of this dissertation are devoted to identifying those genes that are induced or repressed as a function of coral bleaching. In the first of these two studies we created a 2,304 feature custom DNA microarray platform from a cDNA subtracted library made from experimentally bleached Montipora capitata, which was then used for high-throughput screening of the subtracted library.