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SPECIAL PUBLICATION 6 the Effects of Marine Debris Caused by the Great Japan Tsunami of 2011
PICES SPECIAL PUBLICATION 6 The Effects of Marine Debris Caused by the Great Japan Tsunami of 2011 Editors: Cathryn Clarke Murray, Thomas W. Therriault, Hideaki Maki, and Nancy Wallace Authors: Stephen Ambagis, Rebecca Barnard, Alexander Bychkov, Deborah A. Carlton, James T. Carlton, Miguel Castrence, Andrew Chang, John W. Chapman, Anne Chung, Kristine Davidson, Ruth DiMaria, Jonathan B. Geller, Reva Gillman, Jan Hafner, Gayle I. Hansen, Takeaki Hanyuda, Stacey Havard, Hirofumi Hinata, Vanessa Hodes, Atsuhiko Isobe, Shin’ichiro Kako, Masafumi Kamachi, Tomoya Kataoka, Hisatsugu Kato, Hiroshi Kawai, Erica Keppel, Kristen Larson, Lauran Liggan, Sandra Lindstrom, Sherry Lippiatt, Katrina Lohan, Amy MacFadyen, Hideaki Maki, Michelle Marraffini, Nikolai Maximenko, Megan I. McCuller, Amber Meadows, Jessica A. Miller, Kirsten Moy, Cathryn Clarke Murray, Brian Neilson, Jocelyn C. Nelson, Katherine Newcomer, Michio Otani, Gregory M. Ruiz, Danielle Scriven, Brian P. Steves, Thomas W. Therriault, Brianna Tracy, Nancy C. Treneman, Nancy Wallace, and Taichi Yonezawa. Technical Editor: Rosalie Rutka Please cite this publication as: The views expressed in this volume are those of the participating scientists. Contributions were edited for Clarke Murray, C., Therriault, T.W., Maki, H., and Wallace, N. brevity, relevance, language, and style and any errors that [Eds.] 2019. The Effects of Marine Debris Caused by the were introduced were done so inadvertently. Great Japan Tsunami of 2011, PICES Special Publication 6, 278 pp. Published by: Project Designer: North Pacific Marine Science Organization (PICES) Lori Waters, Waters Biomedical Communications c/o Institute of Ocean Sciences Victoria, BC, Canada P.O. Box 6000, Sidney, BC, Canada V8L 4B2 Feedback: www.pices.int Comments on this volume are welcome and can be sent This publication is based on a report submitted to the via email to: [email protected] Ministry of the Environment, Government of Japan, in June 2017. -
Marine Species Distributions: from Data to Predictive Models
Marine Species Distributions: From data to predictive models Samuel Bosch Promoter: Prof. Dr. Olivier De Clerck Thesis submitted in partial fulfilment of the requirements for the degree of Doctor (PhD) in Science – Biology Academic year 2016-2017 Members of the examination committee Prof. Dr. Olivier De Clerck - Ghent University (Promoter)* Prof. Dr. Tom Moens – Ghent University (Chairman) Prof. Dr. Elie Verleyen – Ghent University (Secretary) Prof. Dr. Frederik Leliaert – Botanic Garden Meise / Ghent University Dr. Tom Webb – University of Sheffield Dr. Lennert Tyberghein - Vlaams Instituut voor de Zee * non-voting members Financial support This thesis was funded by the ERANET INVASIVES project (EU FP7 SEAS-ERA/INVASIVES SD/ER/010) and by VLIZ as part of the Flemish contribution to the LifeWatch ESFRI. Table of contents Chapter 1 General Introduction 7 Chapter 2 Fishing for data and sorting the catch: assessing the 25 data quality, completeness and fitness for use of data in marine biogeographic databases Chapter 3 sdmpredictors: an R package for species distribution 49 modelling predictor datasets Chapter 4 In search of relevant predictors for marine species 61 distribution modelling using the MarineSPEED benchmark dataset Chapter 5 Spatio-temporal patterns of introduced seaweeds in 97 European waters, a critical review Chapter 6 A risk assessment of aquarium trade introductions of 119 seaweed in European waters Chapter 7 Modelling the past, present and future distribution of 147 invasive seaweeds in Europe Chapter 8 General discussion 179 References 193 Summary 225 Samenvatting 229 Acknowledgements 233 Chapter 1 General Introduction 8 | C h a p t e r 1 Species distribution modelling Throughout most of human history knowledge of species diversity and their respective distributions was an essential skill for survival and civilization. -
Pseudoderbesia Eckloniae, Sp. Nov. (Bryopsidaceae, Ulvophyceae) from Western Australia
cryptogamie Algologie 2020 ● 41 ● 3 DIRECTEUR DE LA PUBLICATION : Bruno DAVID, Président du Muséum national d’Histoire naturelle RÉDACTEUR EN CHEF / EDITOR-IN-CHIEF : Line LE GALL ASSISTANT DE RÉDACTION / ASSISTANT EDITOR : Audrina NEVEU ([email protected]) MISE EN PAGE / PAGE LAYOUT : Audrina NEVEU RÉDACTEURS ASSOCIÉS / ASSOCIATE EDITORS Ecoevolutionary dynamics of algae in a changing world Stacy KRUEGER-HADFIELD Department of Biology, University of Alabama, 1300 University Blvd, Birmingham, AL 35294 (United States) Jana KULICHOVA Department of Botany, Charles University, Prague (Czech Repubwlic) Cecilia TOTTI Dipartimento di Scienze della Vita e dell’Ambiente, Università Politecnica delle Marche, Via Brecce Bianche, 60131 Ancona (Italy) Phylogenetic systematics, species delimitation & genetics of speciation Sylvain FAUGERON UMI3614 Evolutionary Biology and Ecology of Algae, Departamento de Ecología, Facultad de Ciencias Biologicas, Pontificia Universidad Catolica de Chile, Av. Bernardo O’Higgins 340, Santiago (Chile) Marie-Laure GUILLEMIN Instituto de Ciencias Ambientales y Evolutivas, Universidad Austral de Chile, Valdivia (Chile) Diana SARNO Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Napoli (Italy) Comparative evolutionary genomics of algae Nicolas BLOUIN Department of Molecular Biology, University of Wyoming, Dept. 3944, 1000 E University Ave, Laramie, WY 82071 (United States) Heroen VERBRUGGEN School of BioSciences, University of Melbourne, Victoria, 3010 (Australia) Algal physiology -
A Chronology of Middle Missouri Plains Village Sites
Smithsonian Institution Scholarly Press smithsonian contributions to botany • number 106 Smithsonian Institution Scholarly Press ConspectusA Chronology of the Benthic of MiddleMarine AlgaeMissouri of the Plains Gulf of California:Village Rhodophyta, Sites Phaeophyceae, and ChlorophytaBy Craig M. Johnson with contributions by StanleyJames A. N. Ahler, Norris, Herbert Luis Haas, E. and Aguilar-Rosas, Georges Bonani and Francisco F. Pedroche SERIES PUBLICATIONS OF THE SMITHSONIAN INSTITUTION Emphasis upon publication as a means of “diffusing knowledge” was expressed by the first Secretary of the Smithsonian. In his formal plan for the Institution, Joseph Henry outlined a program that included the following statement: “It is proposed to publish a series of reports, giving an account of the new discoveries in science, and of the changes made from year to year in all branches of knowledge.” This theme of basic research has been adhered to through the years by thousands of titles issued in series publications under the Smithsonian imprint, commencing with Smithsonian Contributions to Knowledge in 1848 and continuing with the following active series: Smithsonian Contributions to Anthropology Smithsonian Contributions to Botany Smithsonian Contributions to History and Technology Smithsonian Contributions to the Marine Sciences Smithsonian Contributions to Museum Conservation Smithsonian Contributions to Paleobiology Smithsonian Contributions to Zoology In these series, the Smithsonian Institution Scholarly Press (SISP) publishes small papers and -
New Record of Two Derbesia Species(Chlorophyta)
ISSN 1226-9999 (print) ISSN 2287-7851 (online) 150 Jae Woo An, Pil Joon Kang and Ki Wan Nam Korean J. Environ. Biol. 36(2) : 150~155 (2018) https://doi.org/10.11626/KJEB.2018.36.2.150 <Original article> New Record of Two Derbesia Species (Chlorophyta) in Korea Jae Woo An, Pil Joon Kang and Ki Wan Nam* Department of Marine Biology, Pukyong National University, Busan 48513, Republic of Korea Abstract - Two siphonous green algae were collected from the eastern coast of Korea. These species share the typical features of Derbesia sporophytes, such as erect and prostrate siphonous filaments and the presence of basal septum in lateral branches. One is characterized by the combined fea- tures of a relatively small tufted sporophytic thalli arising from a rhizoidal base, subdichotomous- ly branched filaments with a basal septum and one pyrenoid per subspherical to lenticular chloro- plast. The other shows a larger sporophytic thallus, sparsely subdichotomously branched filaments with a basal septum and one pyrenoid per spherical chloroplast. In a phylogenetic tree based on rbcL sequence, the two above-mentioned Korean algae nest in the same clades as Derbesia minima and D. indica, respectively. The genetic distance between the sequences within the clades was 0.5- 0.8%, which is considered to be included in the intra-specific range for the genus. These two sipho- nous Korean algae are identified as D. minima and D. indica, respectively, based on the morpho- logical and molecular analyses. These species are newly recorded in the Korean marine algal flora herein. Keywords : Derbesia minima, D. indica, green algae, first record, Korea INTRODUCTION Derbesia marina and Halicystis ovalis (Lyngbye) Areschoug are sporophytic and gametophytic phases of the one species. -
Evolutionary Dynamics of Chloroplast Genomes in Low Light: a Case Study of the Endolithic Green Alga Ostreobium Quekettii
bioRxiv preprint doi: https://doi.org/10.1101/049833; this version posted May 7, 2016. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Evolutionary dynamics of chloroplast genomes in low light: a case study of the endolithic green alga Ostreobium quekettii Vanessa R. Marcelino1*, Ma Chiela M. Cremen1, Chistopher J. Jackson1, Anthony W.D. Larkum2 and Heroen Verbruggen1 1 - School of Biosciences, University of Melbourne, Victoria, Australia. 2 - Plant Functional Biology and Climate Change Cluster, University of Technology Sydney, New South Wales, Australia *Author for correspondence: Vanessa Rossetto Marcelino School of Biosciences (bldg. 122, room 101), University of Melbourne, VIC 3010, Australia Telephone: (+61) 03 83448931. Email: [email protected] Running title: Genomic footprints of a low light lifestyle Data deposition: Chloroplast genome sequences will be deposited in GenBank Keywords: Genome streamlining, photosynthesis, rates of evolution, boring algae, stoichiogenomics 1 bioRxiv preprint doi: https://doi.org/10.1101/049833; this version posted May 7, 2016. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Abstract Some photosynthetic organisms live in extremely low light environments. Light limitation is associated with selective forces as well as reduced exposure to mutagens, and over evolutionary timescales it can leave a footprint on species’ genome. Here we present the chloroplast genomes of four green algae (Bryopsidales, Ulvophyceae), including the endolithic (limestone-boring) alga Ostreobium quekettii, which is a low light specialist. We use phylogenetic models and comparative genomic tools to investigate whether the chloroplast genome of Ostreobium corresponds to our expectations of how low light would affect genome evolution. -
176 New Discoveries Regarding the Benthic Marine Algal Flora of The
PSA ABSTRACTS 1 1 of K. micrum, but fail to complete the infection cycle. TAXON SAMPLING AND INFERENCES ABOUT Thus, in mixed-species dinoflagellate blooms, inter- ference from inappropriate hosts may influence the DIATOM PHYLOGENY success of spp. To explore that possibility, 1 2 Amoebophrya Alverson, A. J. & Theriot, E. C. we conducted laboratory studies to examine the effect 1 Section of Integrative Biology, University of Texas at of the toxic dinoflagellate K. micrum on success of Austin, TX 78713 USA; 2Texas Memorial Museum, Amoebophrya from A. sanguinea. Treatments consisted University of Texas at Austin, TX 78705 USA of A. sanguinea (1000/mL) plus corresponding dinos- pores (10,000/mL) in the presence of different K. Proper taxon sampling is one of the greatest micrum densities (0 to 100,000/mL). We also examined challenges to understanding phylogenetic relation- whether changes in parasite success were due to ships, perhaps as important as choice of optimality interaction with K. micrum cells, or from indirect criterion or data type. This has been demonstrated in effects of bacteria or dissolved substances present in diatoms where centric diatoms may either be strongly K. micrum cultures. Success of Amoebophrya was supported as monophyletic or paraphyletic when unaffected by low densities of K. micrum, but analyzing SSU rDNA sequences using the same decreased at high concentrations of K. micrum. optimality criterion. The effect of ingroup and out- Reduced parasite success appeared to result from group taxon sampling on relationships of diatoms is combined effects of non-host cells and dissolved explored for diatoms as a whole and for the order substances in K. -
The Chloroplast Genomes of Bryopsis Plumosa And
Leliaert and Lopez-Bautista BMC Genomics (2015) 16:204 DOI 10.1186/s12864-015-1418-3 RESEARCH ARTICLE Open Access The chloroplast genomes of Bryopsis plumosa and Tydemania expeditiones (Bryopsidales, Chlorophyta): compact genomes and genes of bacterial origin Frederik Leliaert1,2* and Juan M Lopez-Bautista1 Abstract Background: Species of Bryopsidales form ecologically important components of seaweed communities worldwide. These siphonous macroalgae are composed of a single giant tubular cell containing millions of nuclei and chloroplasts, and harbor diverse bacterial communities. Little is known about the diversity of chloroplast genomes (cpDNAs) in this group, and about the possible consequences of intracellular bacteria on genome composition of the host. We present the complete cpDNAs of Bryopsis plumosa and Tydemania expeditiones, as well as a re-annotated cpDNA of B. hypnoides, which was shown to contain a higher number of genes than originally published. Chloroplast genomic data were also used to evaluate phylogenetic hypotheses in the Chlorophyta, such as monophyly of the Ulvophyceae (the class in which the order Bryopsidales is currently classified). Results: Both DNAs are circular and lack a large inverted repeat. The cpDNA of B. plumosa is 106,859 bp long and contains 115 unique genes. A 13 kb region was identified with several freestanding open reading frames (ORFs) of putative bacterial origin, including a large ORF (>8 kb) closely related to bacterial rhs-family genes. The cpDNA of T. expeditiones is 105,200 bp long and contains 125 unique genes. As in B. plumosa, several regions were identified with ORFs of possible bacterial origin, including genes involved in mobile functions (transposases, integrases, phage/plasmid DNA primases), and ORFs showing close similarity with bacterial DNA methyltransferases. -
Biological Activities of Tropical Green Algae from Australia
Biological Activities of Tropical Green Algae from Australia A thesis in fulfilment of the requirements for the degree of DOCTOR OF PHILOSOPHY By NA WANG School of Chemical Engineering Faculty of Engineering April 2016 THE UNIVERSITY OF NEW SOUTH WALES Thesis/Dissertation Sheet Surname or Family name: Wang First name: Na Other name/s: Abbreviation for degree as given in the University calendar: School: Chemical Engineering Faculty: Engineering Title: Biological Activities of Tropical Green Algae from Australia Abstract Macroalgae are rich in bioactive components such as carotenoids, phenolic compounds and proteins/peptides, which may play a significant role in the prevention of diseases like cancer, obesity and diabetes. The aim of this thesis was to examine the in vitro biological activities of phenolic compounds, carotenoids and protein hydrolysates from three edible green macroalgae (Ulva ohnoi, Derbesia tenuissima and Oedogonium intermedium) cultured in tropical Australia. The phenolic components were extracted with 60% aqueous ethanol and their antioxidant activities were determined by four different assays (ABTS, DPPH, FRAP and ORAC). The extracts exhibited moderate levels of antioxidant activities. However, analysis of the extracts by HPLC-PDA, GC-MS, LC-MS and 1H NMR failed to detect any phenolic components, while a number of free amino acids, fatty acids and sugars were found, which were likely responsible for the measured antioxidant activities. Carotenoids were extracted from the algae by dichloromethane, and the extracts exhibited significant antioxidant activities, as well as potent inhibitory effects against several metabolically important enzymes including α-amylase, α-glucosidase, pancreatic lipase and hyaluronidase. However, the carotenoid extracts were poor inhibitors of angiotensin-converting enzyme (ACE). -
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Cryptogamie, Algologie, 2014, 35 (3): 207-219 © 2014 Adac. Tous droits réservés The forgotten genus Pseudoderbesia (Bryopsidales, Chlorophyta) Frederik LELIAERT a,b*, Heroen VERBRUGGENc, Sofie D’HONDTa, Juan M. LÓPEZ-BAUTISTAb & Olivier DE CLERCKa aPhycology Research Group, Biology Department, Ghent University, Ghent, Belgium bDepartment of Biological Sciences, The University of Alabama, Tuscaloosa, AL, U.S.A. cSchool of Botany, University of Melbourne, Victoria, Australia Abstract – The poorly known siphonous green algal genus Pseudoderbesia was originally described from the Caribbean coast of Colombia, and the Canary Islands. Here we describe a collection of Pseudoderbesia from Rhodes, Greece, representing the first report of the genus since its original description in 1991. Cultured plants of Pseudoderbesia were characterized by upright, regularly dichotomously branched siphons, developing from long stolonoid siphons. Molecular phylogenetic analysis based on rbcL and tufA sequences confirmed the placement of Pseudoderbesia in the family Bryopsidaceae, and shows a sister relationship with Bryopsis. Although this is the first record of Pseudoderbesia from the Mediterranean Sea, it is possible that the genus is more widespread and has previously been confused with morphologically similar, but unrelated taxa, such as Pseudochlorodesmis furcellata, or that it has been erroneously attributed to juvenile stages of larger bryopsidalean algae. Bryopsidineae / marine green algae / molecular systematics / Pseudoderbesia arbuscula / Ulvophyceae INTRODUCTION The siphonous green algal genus Pseudoderbesia was described by Calderon and Schnetter (1991) based on isolates from the Caribbean coast of Colombia, and the Canary Islands. The Colombian samples were formally described as a new species, P. arbuscula E.Calderon & Schnetter, while the authors remained indecisive on whether or not the morphologically slightly different samples from the Canary Islands represented a separate species. -
Bryopsidalesclassificationcpge
REASSESSMENT OF THE CLASSIFICATION OF BRYOPSIDALES (CHLOROPHYTA) BASED ON CHLOROPLAST PHYLOGENOMIC ANALYSES Ma. Chiela M. Cremen1, Frederik Leliaert2,3, John West1, Daryl W. Lam4, Satoshi Shimada5, Juan M. Lopez-Bautista4, and Heroen Verbruggen1 1 School of BioSciences, University of Melbourne, Parkville, 3010 Victoria, Australia 2 Botanic Garden Meise, 1860 Meise, Belgium 3 Department of Biology, Phycology Research Group, Ghent University, 9000 Ghent, Belgium 4 Department of Biological Sciences, The University of Alabama, 35487 Alabama, U.S.A. 5 Faculty of Core Research, Natural Science Division, Ochanomizu University, 2-1-1 Otsuka, Bunkyo, Tokyo 112-8610, Japan ABSTRACT The Bryopsidales is a morphologically diverse group of mainly marine green macroalgae characterized by a siphonous structure. The order is comprisedcomposed of three suborders – Ostreobineae, Bryopsidineae, and Halimedineae. While previous studies improved the higher-level classification of the order, the taxonomic placement of some genera in Bryopsidineae (Pseudobryopsis and Lambia) as well as the relationships between the families of Halimedineae remains uncertain. In this study, we re-assess the phylogeny of the order with datasets derived from chloroplast genomes, drastically increasing the taxon sampling by sequencing 32 new chloroplast genomes. The phylogenies presented here provided good support for the major lineages (suborders and most families) in Bryopsidales. In Bryopsidineae, Pseudobryopsis hainanensis was inferred as a distinct lineage from the three established families allowing us to establish the family Pseudobryopsidaceae. The Antarctic species Lambia antarctica was shown to be an early-branching lineage in the family Bryopsidaceae. In Halimedineae, we revealed several inconsistent phylogenetic positions of macroscopic taxa, and several entirely new lineages of microscopic species. -
Bryopsidales, Chlorophyceae) from the Natal Coast
Life history and cytological studies in Bryopsis flanaganii (Bryopsidales, Chlorophyceae) from the Natal Coast I.S. Harper and R.N. Pienaar Department of Botany, University of Natal, Pietermaritzburg Bryopsis flanaganii Barton from the Natal coast appears to Introduction possess a monophasic life history in culture. Gametangia are Members of the siphonaceous green algae (Bryopsidales, formed from lateral branches and release anisogametes. according to Silva 1982) are characterized by a multinucleate Zygotes germinate immediately and develop into erect siphons similar to those of the parent thalli. These germlings coenocytic thallus. Development of the septa occurs only at do not, however, produce lateral branches under laboratory the base of gametangia or sporangia during the reproductive conditions. Nuclear divisions occurring during the formation phase, or in response to wounding. Septa may also occa of the gametes are mitotic and the chromosome number of sionally be laid down in older parts of the thallus. Early texts B. flanaganii is 11 . The chromosomes form an equatorial (Fritsch 1935; Smith 1955; Chapman 1964) reported that the plate at metaphase and separate at anaphase leaving behind life history of these algae was gametic with a single diploid a persistent interzonal spindle. The nucleus of the zygote is characteristically large and persistent. gametophyte phase. Cytological evidence in support of such S. A fr. J. Bot. 1985, 51: 401 - 407 gametic life histories has, however, only been provided for Codium (Williams 1925; Schussnig 1950) and Derbesia Bryopsis flanaganii Barton van die Natalse kus het (Neumann 1969a; Rietema 1972), while the evidence for waarskynlik 'n enkelfase-lewensiklus onder kultuurtoestande. Caulerpa (Schussnig 1939) has been questioned (Goldstein & Gametangia word op sytakke gevorm en stel anisogamete Morrall 1970).