Copepoda, Harpacticoida
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Evolutionary History of Inversions in the Direction of Architecture-Driven
bioRxiv preprint doi: https://doi.org/10.1101/2020.05.09.085712; this version posted May 10, 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 The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.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 4.0 International license. Evolutionary history of inversions in the direction of architecture- driven mutational pressures in crustacean mitochondrial genomes Dong Zhang1,2, Hong Zou1, Jin Zhang3, Gui-Tang Wang1,2*, Ivan Jakovlić3* 1 Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, and State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China. 2 University of Chinese Academy of Sciences, Beijing 100049, China 3 Bio-Transduction Lab, Wuhan 430075, China * Corresponding authors Short title: Evolutionary history of ORI events in crustaceans Abbreviations: CR: control region, RO: replication of origin, ROI: inversion of the replication of origin, D-I skew: double-inverted skew, LBA: long-branch attraction bioRxiv preprint doi: https://doi.org/10.1101/2020.05.09.085712; this version posted May 10, 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 The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.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 4.0 International license. Abstract Inversions of the origin of replication (ORI) of mitochondrial genomes produce asymmetrical mutational pressures that can cause artefactual clustering in phylogenetic analyses. It is therefore an absolute prerequisite for all molecular evolution studies that use mitochondrial data to account for ORI events in the evolutionary history of their dataset. -
ECOLOGY of TIGRIOPUS CALIFORNICUS (COPEPODA, IIARPACTICOIDA) in BARKLEY SOUND, BRITISH COLUMBIA James John Powlik B.Sc. (Hons.)
ECOLOGY OF TIGRIOPUS CALIFORNICUS (COPEPODA, IIARPACTICOIDA) IN BARKLEY SOUND, BRITISH COLUMBIA BY James John Powlik B.Sc. (hons.), The University of British Columbia (1988) M.Sc., The University of British Columbia (1990) A THESIS SUBMJTfED IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF DOCTOR OF PHILOSOPHY IN THE FACULTY OF GRADUATE STUDIES (Department of Oceanography) WE ACCEPT THIS THESIS AS CONFORMING HyiT)D THE UNIVERSITY OF BRITISH COLUMBIA APRIL, 1996 © James John Powilk, 1996 In presenting this thesis in partial fhffillment of the requirements for an advanced degree at the University ofBritish Columbia, I agree that the Library shall make it freely available for reference and study. I further agree that permission for extensive copying of this thesis for scholarly purposes may be granted by the head of my Department or by his or her representatives. It is understood that copying or publication of this thesis for financial gain shall not be allowed without my written permission. 2 Department of Oceanography The University ofBritish Columbia 1461 - 6270 University Blvd. Vancouver, B.C. CANADA V6T 1Z4 Date: ‘ ABSTRACT The thesis addresses several aspects of the habitat characters and population attributes of the splashpool copepod, Tigriopus californicus (Baker) in Barkley Sound, British Columbia. Overall, 90.1% of pools containing T. californicus were found at 3.0 to 5.0 m above lowest normal tide, with an average surface area-to-volume ratio of 7.06. Copepod habitation was found at water temperatures of 6 to 33°C; salinities of less than 1 to 139%; hydrogen ion concentrations (pH) of 6.1 to 9.5; and oxygen levels of 1.1 to 13.7 mg L1. -
A Gene-Based SNP Resource and Linkage Map for the Copepod
Foley et al. BMC Genomics 2011, 12:568 http://www.biomedcentral.com/1471-2164/12/568 RESEARCHARTICLE Open Access A gene-based SNP resource and linkage map for the copepod Tigriopus californicus Brad R Foley1, Colin G Rose1,2, Daniel E Rundle1,3, Wai Leong1, Gary W Moy4, Ronald S Burton4 and Suzanne Edmands1* Abstract Background: As yet, few genomic resources have been developed in crustaceans. This lack is particularly evident in Copepoda, given the extraordinary numerical abundance, and taxonomic and ecological diversity of this group. Tigriopus californicus is ideally suited to serve as a genetic model copepod and has been the subject of extensive work in environmental stress and reproductive isolation. Accordingly, we set out to develop a broadly-useful panel of genetic markers and to construct a linkage map dense enough for quantitative trait locus detection in an interval mapping framework for T. californicus–a first for copepods. Results: One hundred and ninety Single Nucleotide Polymorphisms (SNPs) were used to genotype our mapping population of 250 F2 larvae. We were able to construct a linkage map with an average intermarker distance of 1.8 cM, and a maximum intermarker distance of 10.3 cM. All markers were assembled into linkage groups, and the 12 linkage groups corresponded to the 12 known chromosomes of T. californicus. We estimate a total genome size of 401.0 cM, and a total coverage of 73.7%. Seventy five percent of the mapped markers were detected in 9 additional populations of T. californicus. Of available model arthropod genomes, we were able to show more colocalized pairs of homologues between T. -
Fractal Distribution of an Oceanic Copepod Neocalanus Cristatus in the Subarctic Pacific
Journal of Oceanography Vol. 51, pp. 261 to 266. 1995 Fractal Distribution of an Oceanic Copepod Neocalanus cristatus in the Subarctic Pacific ATSUSHI TSUDA Ocean Research Institute, University of Tokyo 1-15-1, Minamidai, Nakano, Tokyo 164, Japan (Received 13 April 1994; in revised form 28 June 1994; accepted 30 August 1994) Horizontal distribution of the copepod Neocalanus cristatus was shown to be fractal on the scale between tens of meters and over 100 km. The fractal dimensions ranged between 1.68–1.89, significantly higher than those of oceanic turbulence and phytoplankton distribution. 1. Introduction Heterogeneity in the horizontal distribution of zooplankton has been recognized for many years (e.g. Hardy, 1936). The phenomenon, however, has seldom been described precisely, although zooplankton patchiness is relevant to many aspects of biological oceanography. Recent studies reveal that copepod patches do not exhibit characteristic lengths (Mackas and Boyd, 1979; Tsuda et al., 1993) and that the patterns of copepod distribution are self-similar and independent of the scale of observation (Tsuda et al., 1993). These findings suggest that copepod distributions may be fractal. Mandelbrot (1967) introduced the concept of fractals for temporally or spatially irregular phenomena which show self-similarities over a wide range of scales. Many fractal objects have been found in nature (Mandelbrot, 1982), and the theory has been applied to some ecological studies (Morse et al., 1985; Pennycuick and Kline, 1986; Dicke and Burrough, 1988; Sugihara and May, 1990; McKinney and Frederick, 1992). In the oceans, environmental turbulence itself has fractal facets in many aspects (Mandelbrot, 1982; Sreenivasan and Meneveau, 1986). -
Molecular Species Delimitation and Biogeography of Canadian Marine Planktonic Crustaceans
Molecular Species Delimitation and Biogeography of Canadian Marine Planktonic Crustaceans by Robert George Young A Thesis presented to The University of Guelph In partial fulfilment of requirements for the degree of Doctor of Philosophy in Integrative Biology Guelph, Ontario, Canada © Robert George Young, March, 2016 ABSTRACT MOLECULAR SPECIES DELIMITATION AND BIOGEOGRAPHY OF CANADIAN MARINE PLANKTONIC CRUSTACEANS Robert George Young Advisors: University of Guelph, 2016 Dr. Sarah Adamowicz Dr. Cathryn Abbott Zooplankton are a major component of the marine environment in both diversity and biomass and are a crucial source of nutrients for organisms at higher trophic levels. Unfortunately, marine zooplankton biodiversity is not well known because of difficult morphological identifications and lack of taxonomic experts for many groups. In addition, the large taxonomic diversity present in plankton and low sampling coverage pose challenges in obtaining a better understanding of true zooplankton diversity. Molecular identification tools, like DNA barcoding, have been successfully used to identify marine planktonic specimens to a species. However, the behaviour of methods for specimen identification and species delimitation remain untested for taxonomically diverse and widely-distributed marine zooplanktonic groups. Using Canadian marine planktonic crustacean collections, I generated a multi-gene data set including COI-5P and 18S-V4 molecular markers of morphologically-identified Copepoda and Thecostraca (Multicrustacea: Hexanauplia) species. I used this data set to assess generalities in the genetic divergence patterns and to determine if a barcode gap exists separating interspecific and intraspecific molecular divergences, which can reliably delimit specimens into species. I then used this information to evaluate the North Pacific, Arctic, and North Atlantic biogeography of marine Calanoida (Hexanauplia: Copepoda) plankton. -
Conference Booklet.Pdf
International Scientific Conference Book of Abstracts Use of molecular-genetic and morphological methods to study the taxonomy, phylogeny, biogeography, and ecology ofEurytemora species International Scientific Conference May 13–17, 2019. Saint Petersburg, Russia Мероприятие проводится при финансовой поддержке The eventРоссийского is sponsored фонда by фундаментальныхRussian Foundation исследований for Basic Research projectпроект № 19-04-2004819-04-20048 Programme Monday, May 13. Arrival and Welcome Party Tuesday, May 14 10.00 Registration 11.00 Opening ceremony Speech by the Director of ZIN RAS Sergei Sinev Session 1: Phylogeny (Chairs: Carol Eunmi Lee, Victor Alekseev) 11.20 Carol Eunmi Lee. “Species” concepts in the Eurytemora affinis species complex 12.00 Coffee break 12.20 Vjacheslav Ivanenko, Korzhavina O.A., Nikinin M.A. Integrative taxonomy and phylogeny of copepods 13.00 Natalia I. Abramson. Genome — wide association studies: new challenge in ecological and evolutionary studies 13.40 Lunch 14.40 Tour of the Zoological Museum 15.30 Natalia Sukhikh, Carol Eunmi Lee, Ekaterina Abramova, Vincent Castric, Elena Fefilova, Sami Souissi, Victor Alekseev. A comparative analysis of genetic differentiation of Eurytemora species using CO1, ITS and 18SrRNA genes with an emphasis on E.affinis species complex 15.50 Imran Parvez, Md. Ashraful Alam. Phylogenetic relationships of cyprinid fishes (Cyprinidae) inferred from morphological traits and mitochondrial gene cytochrome b in Bangladesh 16.10 Coffee break Session 2: Biogeography (Chairs: Jiang-Shiou Hwang, Elena Kochanova) 16.30 Victor Alekseev. Cosmopolite species versus cryptic species two paradigms in copepod biogeography in molecular-genetic epoch and the future of morphological taxonomy 2 17.10 Elena Kochanova, Natalia Sukhikh, Victor Alekseev. -
Volume 2, Chapter 10-1: Arthropods: Crustacea
Glime, J. M. 2017. Arthropods: Crustacea – Copepoda and Cladocera. Chapt. 10-1. In: Glime, J. M. Bryophyte Ecology. Volume 2. 10-1-1 Bryological Interaction. Ebook sponsored by Michigan Technological University and the International Association of Bryologists. Last updated 19 July 2020 and available at <http://digitalcommons.mtu.edu/bryophyte-ecology2/>. CHAPTER 10-1 ARTHROPODS: CRUSTACEA – COPEPODA AND CLADOCERA TABLE OF CONTENTS SUBPHYLUM CRUSTACEA ......................................................................................................................... 10-1-2 Reproduction .............................................................................................................................................. 10-1-3 Dispersal .................................................................................................................................................... 10-1-3 Habitat Fragmentation ................................................................................................................................ 10-1-3 Habitat Importance ..................................................................................................................................... 10-1-3 Terrestrial ............................................................................................................................................ 10-1-3 Peatlands ............................................................................................................................................. 10-1-4 Springs ............................................................................................................................................... -
Latitudinal Variation on the Cold Tolerance of the Intertidal Copepod
Latitudinal variation in the cold tolerance of the intertidal copepod Tigriopus californicus Gemma Wallace1,2, Chris Neufeld1,3 Blinks – NSF REU – BEACON Research Fellowship Research Experience for Undergraduates Summer 2012 1 Friday Harbor Laboratories, University of Washington, Friday Harbor, WA 98250 2 Department of Biology, Whitman College, Walla Walla, WA 99362 3 Department of Biology, Quest University Canada, Squamish, BC, Canada V8B 0N8 Keywords: Tigriopus californicus, local adaptation, cold tolerance, freeze tolerance, chill coma, climate change Contact Information: Gemma Wallace 280 Boyer Avenue Walla Walla, WA 99362 [email protected] Wallace 1 Abstract Broadly distributed species may adapt to local temperature conditions such that isolated populations have different thermal tolerance ranges than the species as a whole. Therefore, to accurately predict how species’ ranges will be affected by global climate change, bioclimate models would benefit from knowing the thermal tolerance of different populations within latitudinally distributed species. In this study, the intertidal copepod Tigriopus californicus was used as a model system to study how local adaptation influences the cold resistance of isolated populations. Among five populations spanning 18 degrees in latitude, two metrics were used to compare cold tolerance: post-freezing recovery and the temperature of chill coma onset (CTmin). Recovery rates following freezing were faster in copepods from colder northern latitudes. Likewise, northern populations exhibited lower chill coma onset temperatures. Importantly, both metrics showed a consistent latitudinal trend suggesting that any single metric could be used equivalently in future studies investigating latitudinal variation in cold tolerance. Our results provide evidence that populations within a single species can display strong local adaptation to spatially varying climatic conditions. -
Population Genetics of Tigriopus Californicus (Copepoda: Harpacticoida): I.Population Structure Along the Central California Coast*
MARINE ECOLOGY - PROGRESS SERIES Vol. 1, 29-39. 1979 Published July 30 Mar. Ecol. Prog. Ser. Population Genetics of Tigriopus californicus (Copepoda: Harpacticoida): I. Population Structure Along the Central California Coast* R. S. Burtonl, M. W. Feldmanl and J. W. CurtsingerZ ' Department of Biological Sciences, Stanford University, Stanford, California 94305, USA Department of Genetics, North Carolina State University, P.O.B. 5487, Raleigh, North Carolina 27650, USA ABSTRACT: Polyacrylam~degel electrophoresis revealed three genetic polymorphisms among central California populations of the supralittoral copepod Tigriopus californicus. Laboratory analysis of mated pairs and their progeny confirmed the allelic nature of esterase (EST), phosphoglucose isomerase (PGI), and leucine aminopeptidase (LAP) electromorphs. Polymorphism within each enzyme system was localized such that only a few of the nine or more sites sampled were polymorphic while the others were fixed on the same allele. While the Pescadero site (located near the middle of the 250 km transect studied) was polymorphic for PG1 with two alleles at 0.5 frequency, one of these forms never reached a frequency of 0.04 or higher in any of the other populations sampled, including a population located only 1.5 km to the south. Similar population differentiation was observed with respect to the EST locus, and to a lesser extent, the LAP locus. EST phenotype frequencies at Moss Beach exhibited both microgeographic and temporal variation. No obvious patterns, however, were observed among the phenotype frequencies, and estimated allele frequencies indicate that remarkable consistency existed among all the 'Moss Beach population samples. These data indicate that T. californicuspopulations located within habitat patches are genetically relatively homogeneous, while populations occupying habitats isolated by stretches of sandy beach can show strong genetic differentiation over short geographic distances. -
Diet-Dependent UVAR and UVBR Resistance in the High Shore Harpacticoid Copepod Tigriopus Brevicornis
MARINE ECOLOGY PROGRESS SERIES Vol. 276: 299–303, 2004 Published August 2 Mar Ecol Prog Ser NOTE Diet-dependent UVAR and UVBR resistance in the high shore harpacticoid copepod Tigriopus brevicornis John Davenport1,*, Aine Healy1, Noreen Casey2, James J. A. Heffron2 1Department of Zoology & Animal Ecology and Environmental Research Institute, and 2Department of Biochemistry, University College Cork, Lee Maltings, Prospect Row, Cork, Ireland ABSTRACT: This study tested the hypotheses (1) that the upper shore rock pool harpacticoid cope- pod Tigriopus brevicornis is protected against ultra-violet radiation (UVR) by the orange pigment astaxanthin, and (2) that astaxanthin levels would be greater in summer than winter. Wild orange copepods lost their pigment and became white if fed on yeast in the dark; their colour was restored when they were fed microalgae. White T. brevicornis were significantly more susceptible to UVR than wild or restored orange T. brevicornis. At similar intensities of radiation, copepods showed dura- tion of survival in the order UVAR > UVBR. Astaxanthin protected T. brevicornis against UVAR and UVBR, with the degree of effectiveness of protection being in the order UVAR > UVBR. There was no significant increase in astaxanthin levels during summer in T. brevicornis collected from 3 different shores. It is suggested that UVAR protection by astaxanthin largely follows from its effectiveness as an antioxidant, and that there are adequate plant resources available to maintain astaxanthin levels in T. brevicornis throughout the year. KEY WORDS: Astaxanthin · Ultra-violet radiation · Tigriopus · Antioxidant Resale or republication not permitted without written consent of the publisher INTRODUCTION true in Tigriopus spp., although their small size has inhibited confirmatory studies so far. -
An Evolutionary Perspective of Dopachrome Tautomerase Enzymes in Metazoans
Article An Evolutionary Perspective of Dopachrome Tautomerase Enzymes in Metazoans Umberto Rosani 1,2,*, Stefania Domeneghetti 1, Lorenzo Maso 1, K. Mathias Wegner 2 and Paola Venier 1,* 1 Department of Biology, University of Padova, Padova, 35121, Italy; [email protected] (S.D.); [email protected] (L.M.) 2 Alfred Wegener Institute (AWI)—Helmholtz Centre for Polar and Marine Research, Wadden Sea Station Sylt, List auf Sylt25992, Germany; [email protected] * Correspondence: [email protected] (U.R.); [email protected] (P.V.) Received: 16 May 2019; Accepted: 24 June 2019; Published: 28 June 2019 Abstract: Melanin plays a pivotal role in the cellular processes of several metazoans. The final step of the enzymically-regulated melanin biogenesis is the conversion of dopachrome into dihydroxyindoles, a reaction catalyzed by a class of enzymes called dopachrome tautomerases. We traced dopachrome tautomerase (DCT) and dopachrome converting enzyme (DCE) genes throughout metazoans and we could show that only one class is present in most of the phyla. While DCTs are typically found in deuterostomes, DCEs are present in several protostome phyla, including arthropods and mollusks. The respective DCEs belong to the yellow gene family, previously reported to be taxonomically restricted to insects, bacteria and fungi. Mining genomic and transcriptomic data of metazoans, we updated the distribution of DCE/yellow genes, demonstrating their presence and active expression in most of the lophotrochozoan phyla as well as in copepods (Crustacea). We have traced one intronless DCE/yellow gene through most of the analyzed lophotrochozoan genomes and we could show that it was subjected to genomic diversification in some species, while it is conserved in other species. -
Epibiotic Ciliates Scyphidia Sp. and Diatoms on Tigriopus Fulvus
Journal of Biological Research 2014; volume 87:4600 Epibiotic ciliates Scyphidia sp. and diatoms on Tigriopus fulvus (Copepoda: Harpacticoida) exoskeleton Luigi Pane, Guido Bonello, Gian Luigi Mariottini Department of Earth, Environment and Life Sciences, University of Genoa, Italy Abstract Introduction Several microorganisms – epibionts – can adhere to living sup- Epibiosis is an ecological relationship in which microorganisms, ports taking advantage for their survival, feeding and movement. such as bacteria, fungi, algae, and protozoans, live attached to a living Epibiosis occurs particularly in aquatic environments, on both benth- support, the basibiont, during all or single phases of their life cycle.1,2 ic and planktonic organisms, among which copepods and cladocerans Even though it is considered essentially as a commensal relationship, represent an important living support. The harpacticoid copepod epibiosis can cause negative effects on the host, such as decrease of Tigriopus fulvus, living in the splashpools of rocky coasts, was stud- survival, growth and reproduction, motio n difficulties, increase of pre- ied to recognize the occurrence of epibionts on the exoskeleton sur- dation pressure interfering with the escape capability and swimming face using scanning electon microscopy techniques. The first evi- of host, direct damage or induction of diseases, competition for food, dence of ciliate Scyphidia sp. on Tigriopus fulvus has been described increasing energy demands, susceptibility to predation and faster and the occurrence of algae Cocconeis sp. has been observed as well. sinking rate.3-6 In particular, in food-limited environments ciliate Epibionts were found to adhere to antennae, a site linked to the epibionts can affect the survival of zooplankters,4,7 and decrease their exploitation of water currents carrying food particles to mouthparts fitness due to raised ener getic demand for locomotion.8 Nevertheless, and to swimming legs.