Differences in the Trophic Ecology of Micronekton Driven by Diel Vertical Migration
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Whole-Genome Sequencing of 84 Japanese Eels Reveals Evidence Against Panmixia and Support for Sympatric Speciation
G C A T T A C G G C A T genes Article Whole-Genome Sequencing of 84 Japanese Eels Reveals Evidence against Panmixia and Support for Sympatric Speciation Yoji Igarashi 1 , Hong Zhang 1, Engkong Tan 1, Masashi Sekino 2, Kazutoshi Yoshitake 1, Shigeharu Kinoshita 1 , Susumu Mitsuyama 1, Tatsuki Yoshinaga 3, Seinen Chow 2, Hiroaki Kurogi 4, Akira Shinoda 5, Yu-San Han 6, Ryoshiro Wakiya 7, Noritaka Mochioka 7, Toshihiro Yamamoto 4, Hiroshi Kuwada 8,†, Yoshitsugu Kaji 9, Yutaka Suzuki 10, Takashi Gojobori 11, Takanori Kobayashi 2, Kenji Saitoh 2,‡ , Shugo Watabe 3 and Shuichi Asakawa 1,* 1 Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo, Tokyo 113-8657, Japan; [email protected] (Y.I.); [email protected] (H.Z.); [email protected] (E.T.); [email protected] (K.Y.); [email protected] (S.K.); [email protected] (S.M.) 2 National Research Institute of Fisheries Science, Japan Fisheries Research and Education Agency, Yokohama, Kanagawa 236-8648, Japan; [email protected] (M.S.); [email protected] (S.C.); [email protected] (T.K.); [email protected] (K.S.) 3 School of Marine Biosciences, Kitasato University, Sagamihara, Kanagawa 252-0373, Japan; [email protected] (T.Y.); [email protected] (S.W.) 4 Yokosuka Laboratory, National Research Institute of Aquaculture, Japan Fisheries Research and Education Agency, Yokosuka, Kanagawa 238-0316, Japan; [email protected] (H.K.); [email protected] (T.Y.) 5 Department -
Trophic Interactions of Bathyraja Trachura and Sympatric Fishes
California State University, Monterey Bay Digital Commons @ CSUMB Capstone Projects and Master's Theses 2010 Trophic interactions of Bathyraja trachura and sympatric fishes Mariah Dawson Boyle California State University, Monterey Bay Follow this and additional works at: https://digitalcommons.csumb.edu/caps_thes Recommended Citation Boyle, Mariah Dawson, "Trophic interactions of Bathyraja trachura and sympatric fishes" (2010). Capstone Projects and Master's Theses. 65. https://digitalcommons.csumb.edu/caps_thes/65 This Master's Thesis is brought to you for free and open access by Digital Commons @ CSUMB. It has been accepted for inclusion in Capstone Projects and Master's Theses by an authorized administrator of Digital Commons @ CSUMB. Unless otherwise indicated, this project was conducted as practicum not subject to IRB review but conducted in keeping with applicable regulatory guidance for training purposes. For more information, please contact [email protected]. TROPHIC INTERACTIONS OF BATHYRAJA TRACHURA AND SYMPATRIC FISHES A Thesis Presented to The Faculty of Moss Landing Marine Laboratories California State University Monterey Bay In Partial Fulfillment of the Requirements for the Degree Master of Science by Mariah Dawson Boyle November 2010 © 2010 Mariah Dawson Boyle ALL RIGHTS RESERVED ABSTRACT Quantifying deep-sea food webs can be resource intensive due to the difficulties of sampling fishes from the deep sea. The diet of fishes is often quantified through stomach content analysis, through this method has many sampling constraints, and it can be difficult to obtain sufficient samples for an in-depth study. This study attempts to fill a critical data gap by determining the diet and trophic level of the deep-sea Roughtail Skate, Bathyraja trachura, using traditional stomach content analysis. -
RACE Species Codes and Survey Codes 2018
Alaska Fisheries Science Center Resource Assessment and Conservation Engineering MAY 2019 GROUNDFISH SURVEY & SPECIES CODES U.S. Department of Commerce | National Oceanic and Atmospheric Administration | National Marine Fisheries Service SPECIES CODES Resource Assessment and Conservation Engineering Division LIST SPECIES CODE PAGE The Species Code listings given in this manual are the most complete and correct 1 NUMERICAL LISTING 1 copies of the RACE Division’s central Species Code database, as of: May 2019. This OF ALL SPECIES manual replaces all previous Species Code book versions. 2 ALPHABETICAL LISTING 35 OF FISHES The source of these listings is a single Species Code table maintained at the AFSC, Seattle. This source table, started during the 1950’s, now includes approximately 2651 3 ALPHABETICAL LISTING 47 OF INVERTEBRATES marine taxa from Pacific Northwest and Alaskan waters. SPECIES CODE LIMITS OF 4 70 in RACE division surveys. It is not a comprehensive list of all taxa potentially available MAJOR TAXONOMIC The Species Code book is a listing of codes used for fishes and invertebrates identified GROUPS to the surveys nor a hierarchical taxonomic key. It is a linear listing of codes applied GROUNDFISH SURVEY 76 levelsto individual listed under catch otherrecords. codes. Specifically, An individual a code specimen assigned is to only a genus represented or higher once refers by CODES (Appendix) anyto animals one code. identified only to that level. It does not include animals identified to lower The Code listing is periodically reviewed -
An Unusual Amino Acid Substitution Within Hummingbird Cytochrome C Oxidase Alters a Key Proton-Conducting Channel
bioRxiv preprint doi: https://doi.org/10.1101/610915; this version posted August 8, 2019. 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. An unusual amino acid substitution within hummingbird cytochrome c oxidase alters a key proton-conducting channel Cory D. Dunn a * and Vivek Sharma a,b * a Institute of Biotechnology Helsinki Institute of Life Science University of Helsinki 00014 Helsinki Finland b Department of Physics University of Helsinki 00014 Helsinki Finland * Co-Corresponding Authorship Cory Dunn, Ph.D. Vivek Sharma, Ph.D. P.O. Box 56 P.O. Box 64 University of Helsinki University of Helsinki 00014 Finland 00014 Finland Email: [email protected] Email: [email protected] Phone: +358 50 311 9307 Phone: +358 50 5759 509 bioRxiv preprint doi: https://doi.org/10.1101/610915; this version posted August 8, 2019. 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 are specifically encoded by the mitochondrial genome, suggesting that adaptations required Hummingbirds in flight exhibit the highest for exceptional metabolic performance might be metabolic rate of all vertebrates. The found at this location. Here, we find that all bioenergetic requirements associated with hummingbirds harbor a remarkable change hovering flight raise the possibility of positive within their mitochondrial DNA that appears to selection upon proteins encoded by be required for outstanding metabolic properties hummingbird mitochondrial DNA. Here, we of this organism. -
Anguilliformes, Saccopharyngiformes, and Notacanthiformes (Teleostei: Elopomorpha)
* Catalog of Type Specimens of Recent Fishes in the National Museum of Natural History, Smithsonian Institution, 6: Anguilliformes, Saccopharyngiformes, and Notacanthiformes (Teleostei: Elopomorpha) DAVID G. SMITH I SMITHSONIAN CONTRIBUTIONS TO ZOOLOGY • NUMBER 566 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 Astrophysics Smithsonian Contributions to Botany Smithsonian Contributions to the Earth Sciences Smithsonian Contributions to the Marine Sciences Smithsonian Contributions to Paleobiology Smithsonian Contributions to Zoology Smithsonian Folklife Studies Smithsonian Studies in Air and Space Smithsonian Studies in History and Technology In these series, the Institution publishes small papers and full-scale monographs that report the research and collections of its various museums and bureaux or of professional colleagues in the world of science and scholarship. The publications are distributed by mailing lists to libraries, universities, and similar institutions throughout the world. Papers or monographs'submitted for series publication are received by the Smithsonian Institution Press, subject to its own review for format and style, only through departments of the various Smithsonian museums or bureaux, where the manuscripts are given substantive review. -
Annotated Checklist of Deep-Sea Fishes from the Pacific Coast Off
Deep-sea Fauna and Pollutants off Pacifi c Coast of Northern Japan, edited by T. Fujita, National Museum of Nature and Science Monographs, No. 39, pp. 683-735, 2009 Annotated Checklist of Deep-sea Fishes from the Pacifi c Coast off Tohoku District, Japan Gento Shinohara1, Yoji Narimatsu2, Tsutomu Hattori2, Masaki Ito2, Yohko Takata3 and Keiichi Matsuura4 1 Department of Zoology, National Museum of Nature and Science, 3̶23̶1 Hyakunin-cho, Shinjuku-ku, Tokyo, 169̶0073 Japan E-mail: [email protected] 2 Hachinohe Station, Tohoku National Fisheries Research Institute, Fisheries Research Agency, 25̶259 Shimomekurakubo, Same-machi, Hachinohe, Aomori, 031̶0841 Japan 3 Center for Molecular Biodiversity Research, National Museum of Nature and Science, 3̶23̶1 Hyakunin-cho, Shinjuku-ku, Tokyo, 169̶0073 Japan 4 Collection Center, National Museum of Nature and Science, 3̶23̶1 Hyakunin-cho, Shinjuku-ku, Tokyo, 169̶0073 Japan Abstract: An inventory of deep-sea fi shes from the Pacifi c side of the Tohoku District is presented on the basis of specimens collected in the years 2005̶2007 and a literature survey. A total of 496 species in 118 families are listed with collection records and/or taxonomic remarks. A new Japanese name was established for Diceratias trilobus. Key words: deep-water fi shes, fi sh fauna, distribution, Tohoku District Introduction The Tohoku (meaning northeast in Japanese) District is a northern part of Honshu Island, Japan. The Pacifi c side is washed by the cold Oyashio Current from the north and warm Kuro shio Current from the south, resulting in good fi shing grounds for a scomberesocid Cololabis saira, a gadid Gadus macrocephalus and several scorpaenids (e.g., Sebastolobus macrochir). -
Downloaded from the NCBI Refseq Database (O’Leary Et Al
bioRxiv preprint doi: https://doi.org/10.1101/610915; this version posted May 14, 2020. 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. An unusual amino acid substitution within hummingbird cytochrome c oxidase alters a key proton-conducting channel Cory D. Dunn a *, Bala Anı Akpınar a, and Vivek Sharma a,b * a Institute of Biotechnology Helsinki Institute of Life Science University of Helsinki 00014 Helsinki Finland b Department of Physics University of Helsinki 00014 Helsinki Finland * Co-Corresponding Authorship Cory Dunn, Ph.D. Vivek Sharma, Ph.D. P.O. Box 56 P.O. Box 64 University of Helsinki University of Helsinki 00014 Finland 00014 Finland Email: [email protected] Email: [email protected] Phone: +358 50 311 9307 Phone: +358 50 5759 509 bioRxiv preprint doi: https://doi.org/10.1101/610915; this version posted May 14, 2020. 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 Hummingbirds in flight exhibit the highest metabolic rate of all vertebrates. The bioenergetic requirements associated with sustained hovering flight raise the possibility of unique amino acid substitutions that would enhance aerobic metabolism. Here, we have identified a non- conservative substitution within the mitochondria-encoded cytochrome c oxidase subunit I (COI) that is fixed within hummingbirds, but not among other vertebrates. This unusual change is also rare among metazoans, but can be identified in several clades with diverse life histories. -
Trophic Structure and Food Resources of Epipelagic and Mesopelagic Fishes in the North Pacific Subtropical Gyre Ecosystem Inferred from Nitrogen Isotopic Compositions
LIMNOLOGY and Limnol. Oceanogr. 60, 2015, 1156–1171 OCEANOGRAPHY VC 2015 Association for the Sciences of Limnology and Oceanography doi: 10.1002/lno.10085 Trophic structure and food resources of epipelagic and mesopelagic fishes in the North Pacific Subtropical Gyre ecosystem inferred from nitrogen isotopic compositions C. Anela Choy,*1,2 Brian N. Popp,3 Cecelia C. S. Hannides,1,3 Jeffrey C. Drazen1 1Department of Oceanography, University of Hawaii at Manoa, Honolulu, Hawaii 2Present address: Monterey Bay Aquarium Research Institute, Moss Landing, California 3Department of Geology & Geophysics, University of Hawaii at Manoa, Honolulu, Hawaii Abstract We used bulk tissue d13C and d15N values and d15N values of individual amino acids (AA) to characterize the trophic structure of a pelagic fish assemblage from the North Pacific Subtropical Gyre (NPSG) ecosystem. We focus on energy flow between fishes inhabiting distinct epipelagic, mesopelagic, and upper bathypelagic habitats and on predatory fish foraging across and within these depth habitats. Trophic positions (TPs) esti- 15 mated from a combination of trophic and source AA d N values (TPTr-Src) spanned a narrow range of 0.7 TP for 10 species of large fishes, including tunas, billfishes, and gempylids (TPTr-Src 4.3-5.0). Similarly, 13 species 15 of small micronekton fishes encompassed a range of 1.2 TP (TPTr-Src 2.6-3.8). The d N values of three source 15 AAs were found to increase with increasing depth of capture across the 13 micronekton fish species (d NPhe 15 15 range 5 6.6&; d NGly range 5 13.4&; d NSer range 5 13.6&), indicating that some species from epipelagic, mesopelagic, and upper bathypelagic communities access distinct food resources, such as suspended particles. -
Gulf of the Farallones N Ational Marine Sanctuary
GULF OF THE FARALLONES N ATIONAL MARINE SANCTUARY FINAL MANAGEMENT PLAN UPDATED IN RESPONSE TO THE SANCTUARY EXPANSION UPDATED DECEMBER 2014 U.S. DEPARTMENT OF COMMERCE NATIONAL OCEANIC AND ATMOSPHERIC ADMINISTRATION NATIONAL OCEAN SERVICE OFFICE OF NATIONAL MARINE SANCTUARIES GULF OF THE FARALLONES NATIONAL MARINE SANCTUARY FINAL MANAGEMENT PLAN Updated December 2014 The Gulf of the Farallones National Marine Sanctuary (GFNMS) Management Plan has been updated in response to the sanctuary expansion. A sanctuary management review is conducted at a sanctuary periodically, in accordance with the National Marine Sanctuaries Act (NMSA; 16 U.S.C. 1431 et seq.). The updated plan applies to the entire area encompassed by the sanctuary. The issue areas and programs addressed in this document were built with guidance from the general public, sanctuary staff, agency representatives, experts in the field and the sanctuary advisory council. For readers that would like to learn more about the management plan, GFNMS policies and community-based management processes, we encourage you to visit our website at www.farallones.noaa.gov. Readers who do not have Internet access may call the sanctuary office at (415) 561-6622 to request relevant documents or further information. The National Oceanic and Atmospheric Administration’s (NOAA) Office of National Marine Sanctuaries (ONMS) seeks to increase public awareness of America’s ocean and Great Lakes treasures by conducting scientific research, monitoring, exploration and educational programs. Today, the program manages thirteen national marine sanctuaries and one marine national monument that together encompass more than 170,000 square miles of America’s ocean and Great Lakes natural and cultural resources. -
Vessel Spill Response Technologies
VESSEL SPILL RESPONSE TECHNOLOGIES GULF OF THE FARALLONES AND CORDELL BANK NATIONAL MARINE SANCTUARIES Report of a Joint Working Group of the Gulf of the Farallones and Cordell Bank National Marine Sanctuaries Advisory Councils June 2012 We would like to thank: PRBO Conservation Science for supporting the working group's meetings and the institutions, agencies, and organizations that supported their staff and representatives in participating. iii Working Group Members Yvonne Addassi, Office of Spill Prevention and Response, CA Dept. of Fish and Game Sarah Allen, Ocean Stewardship Program, National Park Service Richard Charter, Ocean Foundation; GFNMS Advisory Council Barbara Emley, San Francisco Community Fishing Association; GFNMS Advisory Council Ellen Faurot-Daniels, Office of Spill Prevention and Response, CA Dept. of Fish and Game Jaime Jahncke (Chair), PRBO Conservation Science; GFNMS and CBNMS Adv. Councils Gerry McChesney, Farallon National Wildlife Refuge, US Fish and Wildlife Service Renee McKinnon, US Coast Guard - Sector San Francisco (June 2011- February 2012) James Nunez, US Coast Guard - Sector San Francisco (March 2012 - June 2012) Patrick Rutten (Chair), NOAA Restoration Center; GFNMS Advisory Council Deb Self, San Francisco Baykeeper (June 2011- February 2012) Jordan Stout, Office of Response and Restoration, NOAA Bob Wilson, Farallones Marine Sanctuary Association; Marine Mammal Center; GFNMS Advisory Council Ian Wren, San Francisco Baykeeper (March 2012 - June 2012) Invited Agency Observers Leslie Abramson, Gulf of -
GLD for Marine Renewable Energy
AGENDA ITEM 15 MAY 20-21, 2021-LCDC MEETING ATTACHMENT A STATE OF OREGON GEOGRAPHIC LOCATION DESCRIPTION Analysis of Reasonably Foreseeable Effects of Federal Actions Related to Marine Renewable Energy Projects on Resources and Uses Occurring within the Federal Waters of the Oregon Ocean Stewardship Area. Oregon Department of Land Conservation and Development Coastal Management Program (March 20, 2015) This document, pursuant to 15 C.F.R. § 930.53, describes a geographic area in federal waters where certain federal license or permit activities, under 15 C.F.R. Part 930, Subpart D, and Outer Continental Shelf (OCS) authorizations, under 15 C.F.R. Part 930, Subpart E, will be subject to review by the Oregon Coastal Management Program (OCMP) under the Coastal Zone Management Act (CZMA) Federal Consistency Provision. The OCMP is seeking federal consistency review over certain federal actions listed below, taking place in the federal waters within a part of the Oregon Ocean Stewardship Area (OSA), as described in Oregon’s Statewide Planning Goal 19 Ocean Resources. That area will be delineated as the Geographic Location Description and will hereafter be referred to as the GLD. The document consists of the following parts: (I) a description of the specific geographic location within federal waters to which it applies, including a brief description of the types of marine renewable energy uses that are anticipated; (II) a list of federal license or permit activities and OCS authorizations related to marine renewable energy development that will be subject to OCMP review when the federal action or activity that is being proposed is located within the geographic area; and (III) an analysis of the reasonably foreseeable effects the activity may have on specific marine resources and uses within Oregon’s coastal zone. -
Novel Gene Rearrangement in the Mitochondrial Genome Of
www.nature.com/scientificreports OPEN Novel gene rearrangement in the mitochondrial genome of Muraenesox cinereus and the phylogenetic relationship of Anguilliformes Kun Zhang1,3, Kehua Zhu1,3, Yifan Liu1,3*, Hua Zhang2, Li Gong1,3, Lihua Jiang1,3, Liqin Liu1,3, Zhenming Lü1,3 & Bingjian Liu1,2,3* The structure and gene sequence of the fsh mitochondrial genome are generally considered to be conservative. However, two types of gene arrangements are found in the mitochondrial genome of Anguilliformes. In this paper, we report a complete mitogenome of Muraenesox cinereus (Anguilliformes: Muraenesocidae) with rearrangement phenomenon. The total length of the M. cinereus mitogenome was 17,673 bp, and it contained 13 protein-coding genes, two ribosomal RNAs, 22 transfer RNA genes, and two identical control regions (CRs). The mitochondrial genome of M. cinereus was obviously rearranged compared with the mitochondria of typical vertebrates. The genes ND6 and the conjoint trnE were translocated to the location between trnT and trnP, and one of the duplicated CR was translocated to the upstream of the ND6. The tandem duplication and random loss is most suitable for explaining this mitochondrial gene rearrangement. The Anguilliformes phylogenetic tree constructed based on the whole mitochondrial genome well supports Congridae non-monophyly. These results provide a basis for the future Anguilliformes mitochondrial gene arrangement characteristics and further phylogenetic research. Anguilliformes is a kind of ecologically diverse fsh, mainly marine fsh. Its body is very slender, its cross- sectional area is reduced, and it generally lacks ventral fns1,2. Traditional morphological taxonomy divides the eel-shaped order (the largest one) into three sub-orders: Anguilloidei, Congroidei and Muraenoidei3.