Taxonomy of Neophocaena (Cetacea: Phocoenidae) and the Conservation Status of N
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Evolutionary History of the Porpoises
bioRxiv preprint doi: https://doi.org/10.1101/851469; this version posted November 22, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.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. 1 Evolutionary history of the porpoises (Phocoenidae) across the 2 speciation continuum: a mitogenome phylogeographic perspective 3 4 Yacine Ben Chehida1, Julie Thumloup1, Cassie Schumacher2, Timothy Harkins2, Alex 5 Aguilar3, Asunción Borrell3, Marisa Ferreira4, Lorenzo Rojas-Bracho5, Kelly M. Roberston6, 6 Barbara L. Taylor6, Gísli A. Víkingsson7, Arthur Weyna8, Jonathan Romiguier8, Phillip A. 7 Morin6, Michael C. Fontaine1,9* 8 9 1 Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, PO Box 11103 CC, 10 Groningen, The Netherlands 11 2 Swift Biosciences, 674 S. Wagner Rd., Suite 100, Ann Arbor, MI 48103, USA 12 3 IRBIO and Department of Evolutive Biology, Ecology and Environmental Sciences, Faculty of Biology, 13 University of Barcelona, Diagonal 643, 08071 Barcelona, Spain 14 4 MATB-Sociedade Portuguesa de Vida Selvagem, Estação de Campo de Quiaios, Apartado EC Quiaios, 3080- 15 530 Figueira da Foz, Portugal & CPRAM-Ecomare, Estrada do Porto de Pesca Costeira, 3830-565 Gafanha da 16 Nazaré, Portugal 17 5 Instituto Nacional de Ecología, Centro de Investigación Científica y de Educación Superior de Ensenada, 18 Carretera Ensenada-Tijuana 3918, Fraccionamiento Zona Playitas, Ensenada, BC 22860, Mexico 19 6 Southwest Fisheries Science Center, National Marine Fisheries Service, NOAA, 8901 La Jolla Shores Dr., La 20 Jolla, California 92037, USA 21 7 Marine and Freshwater Research Institute, PO Box 1390, 121 Reykjavik, Iceland 22 8 Institut des Sciences de l’Évolution (Université de Montpellier, CNRS UMR 5554), Montpellier, France 23 9 Laboratoire MIVEGEC (Université de Montpellier, UMR CNRS 5290, IRD 229), Centre IRD de Montpellier, 24 Montpellier, France 25 26 *Corresponding author: Michael C. -
Unsustainable Food Systems Threaten Wild Crop and Dolphin Species
INTERNATIONAL PRESS RELEASE Embargoed until: 07:00 GMT (16:00 JST) 5 December 2017 Elaine Paterson, IUCN Media Relations, t+44 1223 331128, email [email protected] Goska Bonnaveira, IUCN Media Relations, m +41 792760185, email [email protected] [In Japan] Cheryl-Samantha MacSharry, IUCN Media Relations, t+44 1223 331128, email [email protected] Download photographs here Download summary statistics here Unsustainable food systems threaten wild crop and dolphin species Tokyo, Japan, 5 December 2017 (IUCN) – Species of wild rice, wheat and yam are threatened by overly intensive agricultural production and urban expansion, whilst poor fishing practices have caused steep declines in the Irrawaddy Dolphin and Finless Porpoise, according to the latest update of The IUCN Red List of Threatened Species™. Today’s Red List update also reveals that a drying climate is pushing the Ringtail Possum to the brink of extinction. Three reptile species found only on an Australian island – the Christmas Island Whiptail-skink, the Blue- tailed Skink (Cryptoblepharus egeriae) and the Lister’s Gecko – have gone extinct, according to the update. But in New Zealand, conservation efforts have improved the situation for two species of Kiwi. “Healthy, species-rich ecosystems are fundamental to our ability to feed the world’s growing population and achieve the UN Sustainable Development Goal 2 – to end hunger by 2030,” says IUCN Director General Inger Andersen. “Wild crop species, for example, maintain genetic diversity of agricultural crops -
Beluga Whale Pvhl Enhances HIF-2A Activity Via Inducing
www.impactjournals.com/oncotarget/ Oncotarget, 2017, Vol. 8, (No. 26), pp: 42272-42287 Research Paper Beluga whale pVHL enhances HIF-2α activity via inducing HIF- 2α proteasomal degradation under hypoxia Jianling Bi1, Bo Hu1, Jing Wang1, Xing Liu1, Jinsong Zheng1, Ding Wang1 and Wuhan Xiao1,2 1The Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, P. R. China 2State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, P. R. China Correspondence to: Wuhan Xiao, email: [email protected] Ding Wang, email: [email protected] Keywords: beluga whale, cetaceans, hypoxia, HIF-2α, VHL Received: October 09, 2016 Accepted: January 09, 2017 Published: February 02, 2017 Copyright: Bi et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License 3.0 (CC BY 3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. ABSTRACT Aquatic mammals, such as cetaceans experience various depths, with accordingly diverse oxygenation, thus, cetaceans have developed adaptations for hypoxia, but mechanisms underlying this tolerance to low oxygen are unclear. Here we analyzed VHL and HIF-2α, in the hypoxia signaling pathway. Variations in VHL are greater than HIF-2α between cetaceans and terrestrial mammals, and beluga whale VHL (BW-VHL) promotes HIF-2α degradation under hypoxia. BW-VHL catalyzes BW-HIF-2α to form K48-linked poly- ubiquitin chains mainly at the lysine 429 of BW-HIF-2α (K429) and induces BW-HIF-2α for proteasomal degradation. -
Conservation Status and the Use of Irrawaddy Dolphins As a Flagship
Conservation status and the use of Irrawaddy dolphins as a flagship species for climate adaptation in the Peam Krasop Wildlife Sanctuary, Cambodia Building Resilience to Climate Change Impacts in Coastal Southeast Asia (BCR) Brian Smith, Sun Kong and Lieng Saroeun INTERNATIONAL UNION FOR CONSERVATION OF NATURE The designation of geographical entities in this Citation: Smith, B., Kong, S., and Saroeun, L. book, and the presentation of the material, do not (2014). Conservation status and the use of imply the expression of any opinion whatsoever on Irrawaddy dolphins as a flagship species for climate adaptation in the Peam Krasop Wildlife the part of IUCN or the European Union concerning Sanctuary, Cambodia. Thailand: IUCN. 80pp. the legal status of any country, territory, or area, or of its authorities, or concerning the delimitation of its Cover photo: Dolphins in Koh Kong Province, frontiers or boundaries. The views expressed in this Cambodia © IUCN Cambodia/Sun Kong publication do not necessarily reflect those of IUCN, the European Union or any other participating Layout by: Ria Sen organizations. Produced by: IUCN Southeast Asia Group This publication has been made possible by funding from the European Union. Available from: IUCN Asia Regional Office Published by: IUCN Asia in Bangkok, Thailand 63 Soi Prompong, Sukhumvit 39, Wattana 10110 Bangkok, Thailand Copyright: © 2014 IUCN, International Union for Tel: +66 2 662 4029 Conservation of Nature and Natural Resources IUCN Cambodia Reproduction of this publication for educational or #6B, St. 368, Boeng Keng Kang III, other non-commercial purposes is authorized Chamkarmon, PO Box 1504, Phnom Penh, without prior written permission from the copyright Cambodia holder provided the source is fully acknowledgeRia d. -
Review of Small Cetaceans. Distribution, Behaviour, Migration and Threats
Review of Small Cetaceans Distribution, Behaviour, Migration and Threats by Boris M. Culik Illustrations by Maurizio Wurtz, Artescienza Marine Mammal Action Plan / Regional Seas Reports and Studies no. 177 Published by United Nations Environment Programme (UNEP) and the Secretariat of the Convention on the Conservation of Migratory Species of Wild Animals (CMS). Review of Small Cetaceans. Distribution, Behaviour, Migration and Threats. 2004. Compiled for CMS by Boris M. Culik. Illustrations by Maurizio Wurtz, Artescienza. UNEP / CMS Secretariat, Bonn, Germany. 343 pages. Marine Mammal Action Plan / Regional Seas Reports and Studies no. 177 Produced by CMS Secretariat, Bonn, Germany in collaboration with UNEP Coordination team Marco Barbieri, Veronika Lenarz, Laura Meszaros, Hanneke Van Lavieren Editing Rüdiger Strempel Design Karina Waedt The author Boris M. Culik is associate Professor The drawings stem from Prof. Maurizio of Marine Zoology at the Leibnitz Institute of Wurtz, Dept. of Biology at Genova Univer- Marine Sciences at Kiel University (IFM-GEOMAR) sity and illustrator/artist at Artescienza. and works free-lance as a marine biologist. Contact address: Contact address: Prof. Dr. Boris Culik Prof. Maurizio Wurtz F3: Forschung / Fakten / Fantasie Dept. of Biology, Genova University Am Reff 1 Viale Benedetto XV, 5 24226 Heikendorf, Germany 16132 Genova, Italy Email: [email protected] Email: [email protected] www.fh3.de www.artescienza.org © 2004 United Nations Environment Programme (UNEP) / Convention on Migratory Species (CMS). This publication may be reproduced in whole or in part and in any form for educational or non-profit purposes without special permission from the copyright holder, provided acknowledgement of the source is made. -
Mitochondrial Genomics Reveals the Evolutionary History of The
www.nature.com/scientificreports OPEN Mitochondrial genomics reveals the evolutionary history of the porpoises (Phocoenidae) across the speciation continuum Yacine Ben Chehida 1, Julie Thumloup1, Cassie Schumacher2, Timothy Harkins2, Alex Aguilar 3, Asunción Borrell 3, Marisa Ferreira 4,5, Lorenzo Rojas‑Bracho6, Kelly M. Robertson7, Barbara L. Taylor7, Gísli A. Víkingsson 8, Arthur Weyna9, Jonathan Romiguier9, Phillip A. Morin 7 & Michael C. Fontaine 1,10* Historical variation in food resources is expected to be a major driver of cetacean evolution, especially for the smallest species like porpoises. Despite major conservation issues among porpoise species (e.g., vaquita and fnless), their evolutionary history remains understudied. Here, we reconstructed their evolutionary history across the speciation continuum. Phylogenetic analyses of 63 mitochondrial genomes suggest that porpoises radiated during the deep environmental changes of the Pliocene. However, all intra-specifc subdivisions were shaped during the Quaternary glaciations. We observed analogous evolutionary patterns in both hemispheres associated with convergent evolution to coastal versus oceanic environments. This suggests that similar mechanisms are driving species diversifcation in northern (harbor and Dall’s) and southern species (spectacled and Burmeister’s). In contrast to previous studies, spectacled and Burmeister’s porpoises shared a more recent common ancestor than with the vaquita that diverged from southern species during the Pliocene. The low genetic diversity observed in the vaquita carried signatures of a very low population size since the last 5,000 years. Cryptic lineages within Dall’s, spectacled and Pacifc harbor porpoises suggest a richer evolutionary history than previously suspected. These results provide a new perspective on the mechanisms driving diversifcation in porpoises and an evolutionary framework for their conservation. -
Disentangling Porpoise Bycatch
Disentangling porpoise bycatch Interaction between areas of finless porpoise occurrence and spatial distribution of fishing gear Catarina Fonseca September 2013 A thesis submitted in partial fulfilment of the requirements for the degree of Master of Science and the Diploma of Imperial College London Declaration of own work I declare that this thesis: Disentangling porpoise bycatch: Interaction between areas of finless porpoise occurrence and spatial distribution of fishing gear is entirely my own work and that where material could be construed as the work of others, it is fully cited and referenced, and/or with appropriate acknowledgement given. Signature …………………………………………………….. Name of student: Catarina Fonseca Name of Supervisor: Samuel Turvey Marcus Rowcliffe i Contents list List of Figures .......................................................................................................... iv List of Tables ............................................................................................................ v List of Acronyms ...................................................................................................... vi Abstract ................................................................................................................. vii Acknowledgments ................................................................................................. viii 1. Introduction ......................................................................................................... 1 1.1 Problem statement ............................................................................................................ -
Molecular Species Identification of Whale Meat in South Korean Markets
Molecular species identification of whale meat in South Korean markets S-M. Lee1, Y-Y. Choi2, M-S. Min1, H. Lee1 and M-Y. Lee3 1 The Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Republic of Korea; and Conservation Genome Resource Bank for Korean Wildlife (CGRB), College of Veterinary Medicine, Seoul National University, Republic of Korea 2 Oceans Committee, Korean Federation for Environmental Movements, Seoul, South Korea 3 DNA Analysis Division, Seoul Institute, National Forensic Service, Seoul, Republic of Korea Corresponding author: H. Lee / M-Y Lee E-mail: [email protected] / [email protected] Genet. Mol. Res. 18 (2): gmr18171 Received October 04, 2018 Accepted May 13, 2019 Published May 28, 2019 DOI http://dx.doi.org/10.4238/gmr18171 ABSTRACT. Commercial whaling has been banned since the moratorium of the International Whaling Commission in 1986. However, domestic sale of cetaceans that are caught as bycatch is still allowed in South Korea. Although whale meat is not very popular in South Korea, it is consumed in certain areas. To identify the species composition of whale meat in South Korean markets, we collected 54 samples that were sold as minke whale meat at restaurants and markets of four cities: Seoul, Ulsan, Busan, and Pohang. Of the 54 whale meat samples, 51 were successfully identified using the partial mitochondrial cytochrome b gene (806–1,140 bp) amplified for species identification. Molecular species identification revealed three species among the samples: minke whale (52%), common dolphin (22%), and narrow-ridged finless porpoise (26%). We also gathered data for cetacean bycatch in South Korea. -
Biological Assessment of Ecologically Important Areas for the Mammal Taxonomic Group of the Yellow Sea Ecoregion
Biological Assessment Report of the Yellow Sea Ecoregion (2008) Biological Assessment of Ecologically Important Areas for the Mammal Taxonomic Group of the Yellow Sea Ecoregion Korea Part Author: WON Chang Man (Seal and otter) Affiliation: Wildlife Biologist / Division of Wildlife, National Institute of Environmental Research Mailing address: Gyeongseo-Dong, Seo-gu, Incheon, Republic of Korea (404-170) Email address: [email protected] Author: KIM Zang Geun (Cetaceans) Affiliation: Director General / Cetacean Research Institute, National Fisheries Research and Development Institute Mailing address: Cetacean Research Institute, 139-29, Maeam-dong, Nam-gu, Ulsan City, Republic of Korea Email address: [email protected] Ecological Sub-regions Definition of sub-regions Sub-regions were defined by unique bio-geographical features such as oceanography, topography and pack ice that characterize feeding and breeding areas and migratory routes Sub-region 1 Sub-region 1 is defined by the northern limit and semi-closed areas in the Bohai Sea that have pack ice in the winter. Sub-region 2 Sub-region is defined by the area that covers both the Yellow Sea and East China Sea, including Korea and Tsushima Strait. Common Criteria for Identification of Ecologically Important Areas of the Yellow Sea Ecoregion The Mammal Taxonomic Group adopted the following common criteria to identify Ecologically Important Areas for mammals in the Yellow Sea Ecoregion (YSE) (Table 1). Table 1 List of Adopted Common Criteria for the Mammal Taxonomic Group Selected Indicator -
Genome Sequence of the Freshwater Yangtze Finless Porpoise
G C A T T A C G G C A T genes Article Genome Sequence of the Freshwater Yangtze Finless Porpoise Yuan Yuan 1,2,†, Peijun Zhang 3,†, Kun Wang 1,2, Mingzhong Liu 3, Jing Li 1, Jinsong Zheng 4, Ding Wang 4, Wenjie Xu 1, Mingli Lin 3, Lijun Dong 3, Chenglong Zhu 1, Qiang Qiu 1,2,* and Songhai Li 3,* ID 1 Center for Ecological and Environmental Sciences, Northwestern Polytechnical University, Xi’an 710072, China; [email protected] (Y.Y.); [email protected] (K.W.); [email protected] (J.L.); [email protected] (W.X.); [email protected] (C.Z.) 2 Qingdao Research Institute, Northwestern Polytechnical University, Qingdao 266200, China 3 Marine Mammal and Marine Bioacoustics Laboratory, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China; [email protected] (P.Z.); [email protected] (M.L.); [email protected] (M.L.); [email protected] (L.D.) 4 Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; [email protected] (J.Z.); [email protected] (D.W.) * Correspondence: [email protected] (Q.Q.); [email protected] (S.L.) † These authors contributed equally to this work. Received: 26 February 2018; Accepted: 11 April 2018; Published: 16 April 2018 Abstract: The Yangtze finless porpoise (Neophocaena asiaeorientalis ssp. asiaeorientalis) is a subspecies of the narrow-ridged finless porpoise (N. asiaeorientalis). In total, 714.28 gigabases (Gb) of raw reads were generated by whole-genome sequencing of the Yangtze finless porpoise, using an Illumina HiSeq 2000 platform. -
YANGTZE FINLESS PORPOISE the Yangtze Finless Porpoise Is a Small Mammal That Can Be Found in the Yangtze River in China
© Michel Gunther / WWF YANGTZE FINLESS PORPOISE The Yangtze finless porpoise is a small mammal that can be found in the Yangtze River in China. Read on to discover more interesting facts about them. Finless porpoises live in the Yangtze Where River in China, where they can be found CHARACTERISTICS FAMILY they in the main river channel and two large • Unlike most porpoises they don’t have a fin on Yangtze finless porpoises live lakes connected to the river – Poyang their back or a beak. in small groups of up to ten live and Dongting and in two oxwbow lakes, individuals. Female finless • They have a rounded head and are a dark to pale Tien ezhou and He wangmiao, where porpoises give birth to a calf up to grey colour. they have been recently translocated to. 79cm long, usually in the spring or wwf.org.uk/where_we_work/asia/ • They have moderately large flippers. summer. The calves feed on their asian_rivers/ mother’s milk until they are old • They can’t breathe under water, so have to come enough to catch their own prey. to the surface regularly to breathe air like you. • Weigh up to 72kg. • They don’t leap out of the water like a dolphin, but they do like to ‘spy hop’ – this is when they look like they are standing up in the water and then use their Yangtze River, China fins to spin round so they can see what’s happening. DID YOU KNOW VIDEO Porpoises are part of a group of marine mammals Watch footage: called cetaceans, which includes all whales and dolphins too. -
Curriculum Vitae
1 Curriculum Vitae Thomas Allen Jefferson, Ph.D. 13037 Yerba Valley Way Lakeside, CA 92040 USA Email: [email protected] PERSONAL Birthdate- April 13, 1962 Marital status- married EDUCATION September 1991 to May 1995- Texas A&M University, College Station, TX. Ph.D. in Wildlife and Fisheries Sciences received May 12, 1995. August 1986 to May 1989- Moss Landing Marine Laboratories, Moss Landing, CA. M.Sc. in Marine Science received August 18, 1989. September 1981 to March 1986- University of California, Santa Cruz, CA. B.A. in Biology received March 24, 1986. WORK EXPERIENCE Independent Researcher May 1998 to present – Marine Mammal and Turtle Division, Southwest Fisheries Science Center, NMFS, NOAA Fisheries. Conducting research on the population biology and conservation of cetaceans, primarily in southeast Asia and off the west coast of North America. Honorary Assistant Professor July 2002 to present – University of Hong Kong. Co-advising a number of graduate students on marine mammal thesis projects. Foundation Co-Director July 1996 to March 2001 - Ocean Park Conservation Foundation. Responsible for administration of OPCF activities, including implementation of the 11 marine mammal projects in the OPCF Action Plan, and development of new projects. Research Associate September 1995 to November 2002 - Ocean Park Conservation Foundation. Principal Investigator responsible for overseeing and coordinating a long-term research and monitoring program on humpback dolphins (Sousa chinensis) and finless porpoises (Neophocaena phocaenoides) in Hong Kong waters. Researcher/Consultant May to June 1995- National Taiwan Ocean University, Marine Mammal Program. Responsible for training students and staff in marine mammal identification, survey methods, and line transect analysis.