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Table S1. Taxon sampling, habitat type, and Genbank numbers of specimens used in this study. Habitat is scored as 0=marine, 1=freshwater, 2=anadromous, and 3=catadromous. Taxa Habitat rag1 rag2 16s cytb Clupeidae Alosa aestivalis 2 NA DQ912146 DQ912076 EU552615 Alosa alabamae 2 NA KJ158109 KJ158129 KJ158091 Alosa alosa 0 NA NA NC_009575 NC_009575 Alosa chrysochloris 1 DQ912117 DQ912151 DQ912081 KJ158092 Alosa fallax 0 NA NA EU552737 EU552574 Alosa mediocris 2 KJ158146 KJ158110 KJ158130 KJ158093 Alosa pseudoharengus 2 DQ912115 DQ912149 DQ912079 AP009132 Alosa sapidissima 2 DQ912116 DQ912150 DQ912080 EU552616 Anodontostoma chacunda 0 NA NA AP011614 AP011614 Brevoortia aurea 0 NA NA NA EF564665 Brevoortia patronus 0 DQ912105 DQ912138 DQ912068 EU552618 Brevoortia smithi 0 KJ158148 KJ158112 KJ158131 KJ158094 Brevoortia tyrannus 0 DQ912106 DQ912139 DQ912069 EU552614 Clupea harengus 0 DQ912114 DQ912148 DQ912078 EU552606 Clupea pallasii 0 DQ912118 DQ912152 DQ912082 EU552599 Clupeichthys aesarnensis 1 NA NA AP011584 AP011584 Clupeichthys perakensis 1 NA NA AP011585 AP011585 Clupeoides borneensis 1 NA NA AP011586 AP011586 Clupeonella cultriventris 2 NA NA NC_015109 NC_015109 Corica laciniata 1 NA NA AP011589 AP011589 Dorosoma cepedianum 1 DQ912099 DQ912132 DQ912062 EU552586 Dorosoma petenense 1 KJ158147 KJ158111 NC_009580 EU552581 Ehirava fluviatilis 0 NA NA AP011588 AP011588 Escualosa thoracata 0 NA NA AP011601 AP011601 Ethmidium maculatum 0 NA NA AP011602 AP011602 Ethmalosa fimbriata 0 NA NA NC_009582 NC_009582 Etrumeus teres 0 DQ912110 DQ912143 DQ912073 EU552621 Etrumeus whiteheadi 0 NA NA EU552730 EU552567 Gilchristella aestuaria 1 NA NA EU552741 EU552578 Gudusia chapra 1 KJ158145 KJ158108 KJ158128 KJ158090 Harengula humeralis 0 KJ158135 KJ158098 KJ158116 NA Harengula jaguana 0 DQ912122 DQ912156 DQ912086 EU552617 Hilsa kelee 0 NA NA AP011613 AP011613 Hyperlophus vittatus 0 NA NA EU552750 EU552587 Jenkinsia lamprotaenia 0 DQ912107 DQ912140 DQ912070 EU552613 Konosirus punctatus 0 NA NA NA AB548682 Lile stolifera 0 KJ158137 KJ158100 KJ158119 KJ158080 Limnothrissa miodon 1 NA NA EU552720 EU552553 Microthrissa congica 1 NA NA EU552789 EU552625 Microthrissa royauxi 1 NA NA EU552790 EU552626 Nematalosa erebi 1 NA NA EU552755 EU552592 Nematalosa japonica 0 NA NA NC_009586 NC_009586 Odaxothrissa vittata 1 DQ912131 DQ912167 DQ912096 NC_009590 Opisthonema libertate 0 NA KJ158101 KJ158120 KJ158081 Opisthonema oglinum 0 DQ912111 DQ912144 DQ912074 EU552620 Pellonula vorax 1 NA NA EU552792 EU552628 Pellonula leonensis 1 DQ912130 DQ912166 DQ912095 EU552624 Potamalosa richmondia 1 NA NA AP011594 AP011594 Potamothrissa obtusirostris 1 NA NA EU552787 EU552623 Ramnogaster sp. 0 NA NA NA GQ890211 Rhinosardinia amazonica 1 NA NA EU552713 EU552550 Rhinosardinia bahiensis 1 KJ158149 KJ158113 KJ158132 KJ158095 Sardina pilchardus 0 NA DQ912158 NC_009592 AF472582 Sardinella aurita 0 DQ912104 DQ912137 DQ912067 EU552619 Sardinella lemuru 0 KJ158136 NA KJ158117 KJ158078 Sardinella maderensis 0 NA NA NC_009587 NC_009587 Sardinops sagax 0 NA NA NC_002616 EU552565 Sauvagella madagascariensis 1 NA NA EU552773 EU552610 Sauvagella robusta 1 NA NA EU552770 EU552608 Sierrathrissa leonensis 1 NA NA EU552756 EU552593 Spratelloides delicatulus 0 DQ912128 DQ912164 NC_009588 NC_009588 Spratelloides gracilis 0 DQ912129 DQ912165 NC_009589 NC_009589 Spratelloides robustus 0 NA NA EU552786 NA Sprattus antipodum 0 NA NA AP011608 AP011608 Sprattus muelleri 0 NA NA AP011607 AP011607 Sprattus sprattus 0 NA NA AP009234 AP009234 Stolothrissa tanganicae 1 NA NA EU552719 EU552552 Tenualosa ilisha 2 NA NA DQ400344 EU552622 Tenualosa thibaudeaui 1 NA NA AP011604 AP011604 Chirocentridae Chirocentrus dorab 0 DQ912127 DQ912163 AP006229 NC_006913 Denticipitidae Denticeps clupeoides 1 DQ912100 DQ912133 DQ912063 EU552629 Engraulidae Amazonsprattus scintilla 1 JQ012538 JQ012667 JQ012456 JQ012351 Anchoa cubana 0 JQ012550 JQ012705 JQ012447 JQ012342 Anchoa lyolepis 0 JQ012573 JQ012688 JQ012449 JQ012344 Anchoa cayorum 0 JQ012555 JQ012700 JQ012451 JQ012347 Anchoa mitchilli 0 JQ012552 JQ012698 JQ012462 JQ012357 Anchoa walkeri 0 JQ012568 JQ012713 JQ012474 JQ012369 Anchoa nasus 0 JQ012575 JQ012690 JQ012478 JQ012373 Anchoa chamensis 0 JQ012563 JQ012718 JQ012480 JQ012375 Anchoa parva 0 JQ012558 JQ012702 JQ012482 JQ012377 Anchoa lamprotaenia 0 JQ012630 JQ012696 JQ012484 JQ012379 Anchoa colonensis 0 JQ012559 JQ012716 JQ012488 JQ012383 Anchoa panamensis 0 JQ012570 JQ012712 JQ012497 JQ012392 Anchoa mundeoloides 0 JQ012565 JQ012715 JQ012524 JQ012419 Anchoa delicatissima 0 JQ012557 JQ012704 JQ012453 JQ012348 Anchoa schofieldi 0 JQ012571 JQ012711 JQ012454 JQ012349 Anchoa filfera 0 JQ012542 JQ012722 JQ012492 JQ012387 Anchoa spinifer 0 KJ158140 KJ158104 KJ158123 KJ158085 Anchoa sp. 0 KJ158141 KJ158105 KJ158124 KJ158086 Anchovia macrolepidota 0 JQ012561 JQ012709 JQ012499 JQ012394 Anchovia surinamensis 1 JQ012613 JQ012665 JQ012507 JQ012402 Anchovia clupeoides 0 KJ158142 KJ158106 KJ158125 KJ158087 Anchoviella guianensis 1 JQ012606 JQ012657 JQ012429 JQ012324 Anchoviella alleni 1 JQ012598 JQ012655 JQ012438 JQ012333 Anchoviella alleni 1 JQ012628 JQ012669 JQ012440 JQ012335 Anchoviella sp. 2 1 JQ012581 JQ012648 JQ012442 JQ012337 Anchoviella carrikeri 1 JQ012605 JQ012659 JQ012444 JQ012339 Anchoviella sp. 1 1 JQ012589 JQ012677 JQ012458 JQ012353 Anchoviella balboae 0 JQ012566 JQ012720 JQ012476 JQ012371 Anchoviella elongata 0 JQ012548 JQ012707 JQ012486 JQ012381 Anchoviella cf. guianensis 1 JQ012585 JQ012673 JQ012505 JQ012400 Anchoviella sp. 3 1 JQ012593 JQ012632 JQ012509 JQ012404 Anchoviella guianensis 1 JQ012591 JQ012652 JQ012511 JQ012406 Anchoviella brevirostris 0 JQ012608 JQ012686 JQ012517 JQ012412 Anchoviella lepidentistole 0 JQ012596 JQ012634 JQ012519 JQ012414 Anchoviella carrikeri 1 JQ012583 JQ012650 JQ012528 JQ012422 Anchoviella carrikeri 1 JQ012599 JQ012663 JQ012530 JQ012424 Anchoviella cf. guianensis 1 JQ012544 JQ012646 JQ012432 JQ012327 Anchoviella jamesi 1 KJ158138 KJ158102 NA KJ158083 Anchoviella manamensis 1 KJ158139 KJ158103 NA KJ158084 Cetengraulis edentulus 0 JQ012577 JQ012692 JQ012490 JQ012385 Cetengraulis mysticetus 0 JQ012579 JQ012694 JQ012495 JQ012390 Coilia brachygnathus 1 DQ912124 DQ912159 DQ912089 EU694410 Coilia lyndmani 1 NA NA NC_014271 NC_014271 Coilia mystus 0 DQ912126 DQ912162 DQ912092 EU694407 Coilia nasus 0 DQ912123 DQ912157 AP009135 AP009135 Coilia reynaldi 0 NA NA NC_014276 NC_014276 Encrasicholina devisi 0 JQ012626 JQ012684 JQ012469 JQ012364 Encrasicholina punctifer 0 NA NA AP011561 AP011561 Engraulis anchoita 0 NA NA JQ012521 JQ012416 Engraulis ringens 0 JQ012533 JQ012731 JQ012532 JQ012426 Engraulis eurystole 0 DQ912121 DQ912155 DQ912085 JQ012427 Engraulis japonicus 0 AY430205 NA NC003097 NC_003097 Engraulis mordax 0 JQ012546 JQ012728 JQ012455 JQ012350 Engraulis encrasicolus 0 JQ012540 JQ012726 JQ012464 JQ012359 Jurengraulis juruensis 1 JQ012610 JQ012732 JQ012434 JQ012329 Lycengraulis poeyi 0 JQ012621 JQ012642 JQ012475 JQ012370 Lycengraulis grossidens 0 JQ012622 JQ012639 JQ012501 JQ012396 Lycengraulis batesii 1 JQ012619 JQ012643 JQ012515 JQ012411 Lycothrissa crocodilus 0 JQ012534 JQ012683 JQ012526 JQ012420 Pterengraulis atherinoides 1 JQ012616 JQ012636 JQ012428 JQ012323 Setipinna melanochir 0 NA NA AP011565 AP011565 Setipinna taty 0 NA JQ012681 JQ012470 JQ012365 Setipinna cf. tenuifilis 0 NA JQ012682 JQ012503 JQ012398 Stolephorus cf. chinensis 0 NA NA AP011566 AP011566 Stolephorus cf. waitei 0 NA NA AP011567 AP011567 Stolephorus sp. 0 JQ012536 JQ012671 JQ012466 JQ012361 Thryssa baelama 0 NA NA NC_014264 NC_014264 Thryssa c.f. dussumieri 0 JQ012535 JQ012678 JQ012468 JQ012363 Thryssa mystax 0 JQ012537 JQ012680 JQ012471 JQ012366 Pristigasteridae Chirocentrodon bleekerianus NA NA KJ158121 NA Ilisha africana 0 NA NA NC_009584 NC_009584 Ilisha amazonica 1 KJ158151 KJ158115 KJ158134 KJ158097 Ilisha elongata 0 NA DQ912160 DQ912090 AP009141 Ilisha megaloptera 0 NA KJ158099 KJ158118 KJ158079 Odontognathus mucronatus 0 NA NA KJ158122 KJ158082 Pellona castelnaeana 1 DQ912102 DQ912135 DQ912065 EU552554 Pellona flavipinnis 1 DQ912101 DQ912134 DQ912064 EU552551 Pellona harroweri 0 KJ158143 KJ158107 KJ158126 KJ158088 Pristigaster cayana 1 KJ158150 KJ158114 KJ158133 KJ158096 Pristigaster whiteheadi 1 KJ158144 NA KJ158127 KJ158089 Sundasalangidae Sundasalanx mekongensis 1 NA NA AP006232 AP006232 Outgroups Salmonidae Oncorhynchus mykiss 2 U15663 U31670 NC_001717 NC_001717 Cyprinidae Danio rerio 1 U71093 DRU71094 NC_002333 NC_002333 Cyprinidae Cyprinus carpio 1 AY787040 DQ366994 NC_001606 NC_001606 Ictuluridae Ictalurus punctatus 1 AY423859 AY184245 NC003489 NC_003489 Hepsetidae Hepsetus odoe 1 DQ912097 AY804086 NC_015819 NC_015819 Chanidae Chanos chanos 0 AY430207 NA NC_004693 NC_004693 Table S2. Models of evolution and partitioning strategy selected by PartitionFinder and implemented in RAxML. Partition Model selected Model used rag1, 1st position SYM+G GTR+G rag1, 2nd position, rag2 2nd position SYM+I+G GTR+G rag1, 3rd position SYM+I+G GTR+G rag2, 1st position GTR+I+G GTR+G rag2, 3rd position K80+I+G HKY+G cytb, 1st position SYM+I+G GTR+G cytb 2nd position GTR+I+G GTR+G cytb, 3rd position GTR+G GTR+G 16s GTR+G GTR+G Fossil Calibrations To determine absolute divergence times, we used seven fossil and biogeographic age calibrations with exponential priors to set a hard minimum and soft maximum bound [1]. Several of the fossil calibrations have been used in recent studies [2-4], however we include additional clupeiform fossils that have not yet been included in diversification time analysis of this group.
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    View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by CMFRI Digital Repository DBTR-H D Indian Council of Agricultural Research Ministry of Science and Technology Central Marine Fisheries Research Institute Department of Biotechnology CMFRI Training Manual Series No.15/2018 Training Manual In the frame work of the project: DBT sponsored Three Months National Training in Molecular Biology and Biotechnology for Fisheries Professionals 2015-18 Training Manual In the frame work of the project: DBT sponsored Three Months National Training in Molecular Biology and Biotechnology for Fisheries Professionals 2015-18 Training Manual This is a limited edition of the CMFRI Training Manual provided to participants of the “DBT sponsored Three Months National Training in Molecular Biology and Biotechnology for Fisheries Professionals” organized by the Marine Biotechnology Division of Central Marine Fisheries Research Institute (CMFRI), from 2nd February 2015 - 31st March 2018. Principal Investigator Dr. P. Vijayagopal Compiled & Edited by Dr. P. Vijayagopal Dr. Reynold Peter Assisted by Aditya Prabhakar Swetha Dhamodharan P V ISBN 978-93-82263-24-1 CMFRI Training Manual Series No.15/2018 Published by Dr A Gopalakrishnan Director, Central Marine Fisheries Research Institute (ICAR-CMFRI) Central Marine Fisheries Research Institute PB.No:1603, Ernakulam North P.O, Kochi-682018, India. 2 Foreword Central Marine Fisheries Research Institute (CMFRI), Kochi along with CIFE, Mumbai and CIFA, Bhubaneswar within the Indian Council of Agricultural Research (ICAR) and Department of Biotechnology of Government of India organized a series of training programs entitled “DBT sponsored Three Months National Training in Molecular Biology and Biotechnology for Fisheries Professionals”.
  • Age and Growth of Cetengraulis Edentulus (Clupeiformes: Engraulidae) in a Subtropical Bight of Southern Coast Brazil

    Age and Growth of Cetengraulis Edentulus (Clupeiformes: Engraulidae) in a Subtropical Bight of Southern Coast Brazil

    ZOOLOGIA 28 (3): 297–304, June, 2011 doi: 10.1590/S1984-46702011000300003 Age and growth of Cetengraulis edentulus (Clupeiformes: Engraulidae) in a subtropical bight of Southern Coast Brazil José Maria Souza-Conceição1 & Paulo Ricardo Schwingel2 1 Universidade da Região de Joinville. Rua Paulo Malschitzki 10, Campus Universitário, Zona Industrial, 89219-710 Joinville, SC, Brazil. E-mail: [email protected] 2 Centro de Ciências Tecnológicas da Terra e do Mar, Universidade do Vale do Itajaí. Rua Uruguai 458, Caixa Postal 360, 88302-202 Itajaí, SC, Brazil. E-mail: [email protected] ABSTRACT. Age and growth of Cetengraulis edentulus (Cuvier, 1828) in the Saco dos Limões bight (Southern Brazil) were studied. Sampling was carried out from August 2001 to July 2003. The study of age and growth was based on the interpretation of the periodicity of ring formation in the otoliths sagittae of 491 individuals, temporal variation of otolith edge, relative marginal increments (RMI), age-length key, and von Bertalanffy curve. Cetengraulis edentulus otoliths were adequate for the interpretation of age with 86% of legibility, in which a translucent zone and its adjacent opaque zone were deposited each year. The translucent zone is formed during the cold period and the opaque zone in the warm period. Fish aged 0 (<12 months) – 4.0 year old were found and the population structure reveals the predominance of – 1.05 (t – 0.002) individuals 1.0 and 2.0 year old. The species has a fast growth, and the growth equation is Lt = 156.70 (1 – e ). Cetengraulis edentulus attains the sexual maturity with 1.19 year for the females and 1.12 year for the males, which occur in all life stages throughout the year in the study area.
  • Food Resources of Lake Tanganyika Sardines Metabarcoding of the Stomach Content of Limnothrissa Miodon and Stolothrissa Tanganicae

    Food Resources of Lake Tanganyika Sardines Metabarcoding of the Stomach Content of Limnothrissa Miodon and Stolothrissa Tanganicae

    FACULTY OF SCIENCE Food resources of Lake Tanganyika sardines Metabarcoding of the stomach content of Limnothrissa miodon and Stolothrissa tanganicae Charlotte HUYGHE Supervisor: Prof. F. Volckaert Thesis presented in Laboratory of Biodiversity and Evolutionary Genomics fulfillment of the requirements Mentor: E. De Keyzer for the degree of Master of Science Laboratory of Biodiversity and Evolutionary in Biology Genomics Academic year 2018-2019 © Copyright by KU Leuven Without written permission of the promotors and the authors it is forbidden to reproduce or adapt in any form or by any means any part of this publication. Requests for obtaining the right to reproduce or utilize parts of this publication should be addressed to KU Leuven, Faculteit Wetenschappen, Geel Huis, Kasteelpark Arenberg 11 bus 2100, 3001 Leuven (Heverlee), Telephone +32 16 32 14 01. A written permission of the promotor is also required to use the methods, products, schematics and programs described in this work for industrial or commercial use, and for submitting this publication in scientific contests. i ii Acknowledgments First of all, I would like to thank my promotor Filip for giving me this opportunity and guiding me through the thesis. A very special thanks to my supervisor Els for helping and guiding me during every aspect of my thesis, from the sampling nights in the middle of Lake Tanganyika to the last review of my master thesis. Also a special thanks to Franz who helped me during the lab work and statistics but also guided me throughout the thesis. I am very grateful for all your help and advice during the past year.
  • 61661147.Pdf

    61661147.Pdf

    Resource Inventory of Marine and Estuarine Fishes of the West Coast and Alaska: A Checklist of North Pacific and Arctic Ocean Species from Baja California to the Alaska–Yukon Border OCS Study MMS 2005-030 and USGS/NBII 2005-001 Project Cooperation This research addressed an information need identified Milton S. Love by the USGS Western Fisheries Research Center and the Marine Science Institute University of California, Santa Barbara to the Department University of California of the Interior’s Minerals Management Service, Pacific Santa Barbara, CA 93106 OCS Region, Camarillo, California. The resource inventory [email protected] information was further supported by the USGS’s National www.id.ucsb.edu/lovelab Biological Information Infrastructure as part of its ongoing aquatic GAP project in Puget Sound, Washington. Catherine W. Mecklenburg T. Anthony Mecklenburg Report Availability Pt. Stephens Research Available for viewing and in PDF at: P. O. Box 210307 http://wfrc.usgs.gov Auke Bay, AK 99821 http://far.nbii.gov [email protected] http://www.id.ucsb.edu/lovelab Lyman K. Thorsteinson Printed copies available from: Western Fisheries Research Center Milton Love U. S. Geological Survey Marine Science Institute 6505 NE 65th St. University of California, Santa Barbara Seattle, WA 98115 Santa Barbara, CA 93106 [email protected] (805) 893-2935 June 2005 Lyman Thorsteinson Western Fisheries Research Center Much of the research was performed under a coopera- U. S. Geological Survey tive agreement between the USGS’s Western Fisheries