University of California, Irvine

Total Page:16

File Type:pdf, Size:1020Kb

University of California, Irvine UNIVERSITY OF CALIFORNIA, IRVINE Cephalopod-Inspired Reflectin-Based Photonic Devices DISSERTATION submitted in partial satisfaction of the requirements for the full degree of DOCTOR OF PHILOSOPHY in Materials Science and Engineering by Long Phan Dissertation Committee: Professor Alon A. Gorodetsky, Chair Professor Nancy Da Silva Professor Francesco Tombola 2016 Portions of Chapter 1 reprinted with permission from L. Phan, et al. Chem. Mater., 2016, 28, 6804–6816. © 2016 American Chemical Society Portions of Chapter 2 © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim Portions of Chapter 3 reproduced by permission of The Royal Society of Chemistry Portions of Chapter 4 © 2016 Gorodetsky Group for Biomolecular Electronics at the University of California, Irvine Portions of Chapter 5 reprinted with permission from L. Phan, et al. ACS Appl. Mater. Interfaces, 2016, 8, 278–284. © 2015 American Chemical Society Portions of Chapter 6 © 2016 The Royal Society of Chemistry All other materials © 2016 Long Phan DEDICATION To Mom and Dad, you risked your lives to provide me with this opportunity, and so, I will forever strive to honor your sacrifice. ii TABLE OF CONTENTS Page LIST OF FIGURES .........................................................................................................................v ACKNOWLEDGEMENTS ......................................................................................................... xvi CURRICULUM VITAE ............................................................................................................. xvii ABSTRACT OF THE DISSERTATION ......................................................................................xx CHAPTER 1: Dynamic Materials Inspired by Cephalopods ..........................................................1 1.1: Abstract ........................................................................................................................1 1.2: Introduction ..................................................................................................................1 1.3: Switchable Coloration ..................................................................................................5 1.4: Hierarchical Multiplexing and Pixelation ...................................................................11 1.5: Shape and Texture Modulation ...................................................................................18 1.6: Conclusion and Implications .....................................................................................23 1.7: References ...................................................................................................................26 CHAPTER 2: Reconfigurable Infrared Camouflage Coatings from a Cephalopod Protein ........33 2.1: Abstract ......................................................................................................................33 2.2: Introduction ................................................................................................................33 2.3: Results and Discussion ..............................................................................................34 2.4: Conclusion ..................................................................................................................41 2.5: Supplementary Information .......................................................................................41 2.6: Acknowledgements ....................................................................................................56 2.7: References ..................................................................................................................57 CHAPTER 3: Infrared Invisibility Stickers Inspired by Cephalopods .........................................60 3.1: Abstract ......................................................................................................................60 3.2: Introduction ................................................................................................................60 3.3: Results and Discussion ..............................................................................................62 3.4: Conclusion .................................................................................................................70 3.5: Supplementary Information ........................................................................................71 3.6: Acknowledgements .....................................................................................................78 3.7: References ..................................................................................................................78 CHAPTER 4: Protochromic Devices from Reflectin ...................................................................81 4.1: Abstract ......................................................................................................................81 4.2: Introduction ................................................................................................................81 4.3: Results and Discussion ..............................................................................................84 4.4: Conclusion .................................................................................................................92 4.5: Supplementary Information ........................................................................................93 4.6: Acknowledgements .....................................................................................................97 4.7: References ..................................................................................................................98 iii CHAPTER 5: Reflectin as a Material for Neural Stem Cell Growth ..........................................102 5.1: Abstract ....................................................................................................................102 5.2: Introduction ..............................................................................................................102 5.3: Results and Discussion .............................................................................................104 5.4: Conclusion ................................................................................................................111 5.5: Supplementary Information .....................................................................................112 5.6: Acknowledgements ..................................................................................................117 5.7: References ................................................................................................................118 CHAPTER 6: Production and Electrical Characterization of the Reflectin A2 Isoform from Doryteuthis (Loligo) Pealeii ...............................................................................126 6.1: Abstract ....................................................................................................................126 6.2: Introduction ..............................................................................................................126 6.3: Results and Discussion .............................................................................................127 6.4: Conclusion ................................................................................................................135 6.5: Supplementary Information ......................................................................................135 6.6: Acknowledgements ...................................................................................................141 6.7: References ................................................................................................................142 CHAPTER 7: Conclusion ...........................................................................................................146 iv LIST OF FIGURES Figure 1.1: A) Painting by Giuseppe Arcimboldo depicting Vertumnus, the Roman mythological god of seasons, who is able to alter his form at will. B) Painting by Paulus Moreelse, in which Vertumnus has changed form into an old woman to woo Pomona. C) Medieval woodcut by Hans Weiditz of a human who has transformed into a wolf and is attacking two men. Part A [Public Domain] was reproduced via Wikimedia Commons. Part B [Public Domain] was reproduced via Wikimedia Commons. Part C [Public Domain] was reproduced via Wikimedia Commons. .........2 Figure 1.2: A) Camouflaged octopus positioned on a rock. The animal alters the coloration, texture, and morphology of its skin to match the surrounding environment, making it difficult to discern (left). When disturbed, the octopus changes its appearance and becomes visible (right). B) Squid with mottled and partially transparent skin, which is difficult to distinguish from the rock in the background (left). After the squid alters the coloration of its skin, the animal becomes clearly visible. Part A was reproduced with permission of Elsevier. Copyright 2007. ...............................3 Figure 1.3: A) Picture of cuttlefish skin that shows leucophores (white), iridophores (green), and chromatophores (yellow, red, and dark brown). B) Diagram of “typical” cephalopod skin that illustrates the optical functionality of leucophores, iridophores, and chromatophores. The leucophores serve as diffuse white reflectors, the iridophores serve as dynamic Bragg reflectors, and the chromatophores serve as size-variable spectral filters. The picture
Recommended publications
  • Seasonal and Size-Based Predation on Two Species of Squid by Four Fish
    605 Abstract-Longfin inshore (Loligo Seasonal and size-based predation on pealeii) and northern shortfin (lllex illecebrosus) squids are considered two species of squid by four fish predators important prey species in the North­ west Atlantic shelf ecosystem. The on the Northwest Atlantic continental shelf diets of four major squid predators, bluefish (Pomatomus saltatrix), goose­ Michelle D. Staudinger fish (Lophius americanus), silver hake (Merluccius bilinearis), and summer Department of Natural Resources Conservation flounder (Paralichthys dentatus), were 160 Holdsworth Way examined for seasonal and size-based University of Massachusetts, Amherst changes in feeding habits. Summer Amherst, Massachusetts 01003-9285 and winter, two time periods largely Email address: [email protected] absent from previous evaluations, were found to be the most impor­ tant seasons for predation on squid, and are also the periods when the majority of squid are landed by the regional fishery. Bluefish >450 mm, silver hake >300 mm, and summer Global depletion of marine predators significant predators of squid (Bow­ flounder >400 mm were all found has had dramatic effects on ecosys­ man et al., 2000). Squid represented to be significant predators of squid. tem structure and function (May et between 17% and 95% of the total These same size fish correspond to al., 1979; Jackson et al., 2001; Pauly mass consumed by these four finfish age classes currently targeted for et al., 2002). In many systems, the regionally. Dramatic changes in stock biomass expansion by management ramifications of such changes may not abundance and population structure committees. This study highlights be fully realized. Groundfish declines have occurred since specimens for the importance of understanding how have been linked to simultaneous Bowman et al.'s study were collect­ squid and predator interactions vary increases in cephalopod landings temporally and with changes in com­ ed 25-45 years ago.
    [Show full text]
  • Reconstruction of Original Body Size and Estimation of Allometric
    101 Reconstruction of original body size tie length in squid) in population and other types of surveys, information and estimation of allometric relationships on total length may not always be for the Iongtin inshore squid <Loligo pealeit1 readily available. Therefore, knowl­ edge of allometric relationships may and northern shortfin squid (///ex il/ecebrosus> be useful to. accurately assess trophic interactions and predator-prey rela­ Michelle D. Staudinger' tionships. For the majority of ceph­ alopod species, there are currently 1 Francis Juanes no predictive equations to estimate Suzanne Carlson2 total length from mantle length and Email address for contact author: [email protected] to account for variability in growth. 1 Department of Natural Resources Conservation To improve descriptions of the feed­ University of Massachusetts Amherst ing habits of teuthophagous preda­ Amherst, Massachusetts, 01003-9285 tors and to increase the number of 2 School of Natural Science evaluations of size-based predation Hampshire CoRege on cephalopod prey we present 1) pre­ Amherst, Massachusetts, 01002 dictive equations for reconstructing original prey size and 2) allometric relationships of mantle length to total body length for the two most common species of cephalopods in the Northwest Atlantic Ocean, L. pealeii Quantification of predator-prey body mammals (Gannon et al., 1997; Wil­ and I. illecebrosus. size relationships is essential to under­ liams, 1999). standing trophic dynamics in marine As with the bones and otoliths of ecosystems. Prey lengths recovered prey fish, cephalopod beaks are often Materials and methods from predator stomachs help deter­ recovered from predator stomachs mine the sizes of prey most influential and may be used for identification of Loligo pealeii were collected by otter in supporting predator growth and prey species and the reconstruction trawl from coastal waters off Mas­ to ascertain size-specific effects of of original prey body size (Clarke, sachusetts during the months of May natural mortality on prey populations 1986).
    [Show full text]
  • Pharaoh Cuttlefish, Sepia Pharaonis, Genome Reveals Unique Reflectin
    fmars-08-639670 February 9, 2021 Time: 18:18 # 1 ORIGINAL RESEARCH published: 15 February 2021 doi: 10.3389/fmars.2021.639670 Pharaoh Cuttlefish, Sepia pharaonis, Genome Reveals Unique Reflectin Camouflage Gene Set Weiwei Song1,2, Ronghua Li1,2,3, Yun Zhao1,2, Herve Migaud1,2,3, Chunlin Wang1,2* and Michaël Bekaert3* 1 Key Laboratory of Applied Marine Biotechnology, Ministry of Education, Ningbo University, Ningbo, China, 2 Collaborative Innovation Centre for Zhejiang Marine High-Efficiency and Healthy Aquaculture, Ningbo University, Ningbo, China, 3 Institute of Aquaculture, Faculty of Natural Sciences, University of Stirling, Stirling, United Kingdom Sepia pharaonis, the pharaoh cuttlefish, is a commercially valuable cuttlefish species across the southeast coast of China and an important marine resource for the world fisheries. Research efforts to develop linkage mapping, or marker-assisted selection have been hampered by the absence of a high-quality reference genome. To address this need, we produced a hybrid reference genome of S. pharaonis using a long-read Edited by: platform (Oxford Nanopore Technologies PromethION) to assemble the genome and Andrew Stanley Mount, short-read, high quality technology (Illumina HiSeq X Ten) to correct for sequencing Clemson University, United States errors. The genome was assembled into 5,642 scaffolds with a total length of 4.79 Gb Reviewed by: and a scaffold N of 1.93 Mb. Annotation of the S. pharaonis genome assembly Simo Njabulo Maduna, 50 Norwegian Institute of Bioeconomy identified a total of 51,541 genes, including 12 copies of the reflectin gene, that enable Research (NIBIO), Norway cuttlefish to control their body coloration.
    [Show full text]
  • Diet Analysis of Stranded Bottlenose Dolphins (<I>Tursiops Truncatus</I
    Old Dominion University ODU Digital Commons Biological Sciences Theses & Dissertations Biological Sciences Spring 2020 Diet Analysis of Stranded Bottlenose Dolphins (Tursiops truncatus) in Virginia Kristen Marie Volker Old Dominion University, [email protected] Follow this and additional works at: https://digitalcommons.odu.edu/biology_etds Part of the Biology Commons, Ecology and Evolutionary Biology Commons, and the Marine Biology Commons Recommended Citation Volker, Kristen M.. "Diet Analysis of Stranded Bottlenose Dolphins (Tursiops truncatus) in Virginia" (2020). Master of Science (MS), Thesis, Biological Sciences, Old Dominion University, DOI: 10.25777/6bas-rj82 https://digitalcommons.odu.edu/biology_etds/113 This Thesis is brought to you for free and open access by the Biological Sciences at ODU Digital Commons. It has been accepted for inclusion in Biological Sciences Theses & Dissertations by an authorized administrator of ODU Digital Commons. For more information, please contact [email protected]. DIET ANALYSIS OF STRANDED BOTTLENOSE DOLPHINS (TURSIOPS TRUNCATUS) IN VIRGINIA by Kristen Marie Volker B.S. December 2008, University of New England A Thesis Submitted to the Faculty of Old Dominion University in Partial Fulfillment of the Requirements for the Degree of MASTER OF SCIENCE BIOLOGY OLD DOMINION UNIVERSITY MAY 2020 Approved by: Ian Bartol (Director) Holly Gaff (Member) Kent Carpenter (Member) Damon Gannon (Member) ABSTRACT DIET ANALYSIS OF STRANDED BOTTLENOSE DOLPHINS (TURSIOPS TRUNCATUS) IN VIRGINIA Kristen Marie Volker Old Dominion University, 2020 Director: Dr. Ian Bartol This study describes the diet of bottlenose dolphins (Tursiops truncatus) stranded in Virginia via stomach content analysis and considers factors such as proportion of numerical abundance and reconstructed mass, frequency of occurrence, average reconstructed prey size, prey diversity and quantity, and otolith degradation code.
    [Show full text]
  • Loudness-Dependent Behavioral Responses and Habituation to Sound by the Longfin Squid (Doryteuthis Pealeii)
    1 2 Loudness-dependent behavioral responses and habituation to sound by the 3 longfin squid (Doryteuthis pealeii) 4 5 6 T. Aran Mooney1*, Julia E. Samson1, 2, Andrea D. Schlunk1 and Samantha Zacarias1 7 8 9 1Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA, 02543, USA 10 2Biology Department, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA 11 12 13 *Corresponding author: [email protected], (508) 289-2714 14 15 16 Keywords: noise, bioacoustics, soundscape, auditory scene, invertebrate 17 18 19 20 1 21 Abstract 22 Sound is an abundant cue in the marine environment, yet we know little regarding the 23 frequency range and levels which induce behavioral responses in ecologically key marine 24 invertebrates. Here we address the range of sounds that elicit unconditioned behavioral responses 25 in squid Doryteuthis pealeii, the types of responses generated, and how responses change over 26 multiple sound exposures. A variety of response types were evoked, from inking and jetting to 27 body pattern changes and fin movements. Squid responded to sounds from 80-1000 Hz, with 28 response rates diminishing at the higher and lower ends of this frequency range. Animals 29 responded to the lowest sound levels in the 200-400 Hz range. Inking, an escape response, was 30 confined to the lower frequencies and highest sound levels; jetting was more widespread. 31 Response latencies were variable but typically occurred after 0.36 s (mean) for jetting and 0.14 s 32 for body pattern changes; pattern changes occurred significantly faster. These results 33 demonstrate that squid can exhibit a range of behavioral responses to sound include fleeing, 34 deimatic and protean behaviors, all of which are associated with predator evasion.
    [Show full text]
  • Geographic and Temporal Patterns in Size and Maturity of the Longfin Inshore Squid (Loligo Pealeii) Off the Northeastern United States
    Geographic and temporal patterns in size and maturity of the longfin inshore squid (Loligo pealeii) off the northeastern United States Item Type article Authors Hatfield, Emma M.C.; Cadrin, Steven X. Download date 04/10/2021 18:55:59 Link to Item http://hdl.handle.net/1834/31057 200 Abstract–Analysis of 32 years of stan­ Geographic and temporal patterns dardized survey catches (1967–98) indi­ cated differential distribution patterns in size and maturity of the longfin inshore squid for the longfin inshore squid (Loligo pealeii) over the northwest Atlantic (Loligo pealeii) off the northeastern United States U.S. continental shelf, by geographic region, depth, season, and time of day. Emma M.C. Hatfield Catches were greatest in the Mid- Atlantic Bight, where there were sig­ Steven X. Cadrin nificantly greater catches in deep water Northeast Fisheries Science Center during winter and spring, and in National Marine Fisheries Service, NOAA shallow water during autumn. Body 166 Water Street size generally increased with depth Woods Hole, Massachusetts 02543 in all seasons. Large catches of juve­ Present address (for E.M.C. Hatfield): FRS Marine Laboratory niles in shallow waters off southern Victoria Road New England during autumn resulted Aberdeen AB11 9DB from inshore spawning observed during Scotland, United Kingdom late spring and summer; large propor­ E-mail address (for E. M. C. Hatfield): e.hatfi[email protected] tions of juveniles in the Mid-Atlantic Bight during spring suggest that sub­ stantial winter spawning also occurs. Few mature squid were caught in sur­ vey samples in any season; the major­ ity of these mature squid were cap­ tured south of Cape Hatteras during The longfin inshore squid, Loligo pea- mers, 1967; 1969; Serchuk and Rathjen, spring.
    [Show full text]
  • UNIVERSITY of CALIFORNIA, IRVINE Protonic Conduction and Photochemical Modification of Protein Reflectin THESIS Submitted In
    UNIVERSITY OF CALIFORNIA, IRVINE Protonic Conduction and Photochemical Modification of Protein Reflectin THESIS submitted in partial satisfaction of the requirements for the degree of MASTER OF SCIENCE in Chemical and Biochemical Engineering by Yegor Van Dyke Thesis Committee: Professor Alon A. Gorodetsky, Chair Professor Hung D. Nguyen Professor Frank G. Shi 2016 Chapter 1 © 2016 American Chemical Society Chapter 2 © 2016 Gorodetsky Group Chapter 3 © 2016 Yegor Van Dyke TABLE OF CONTENTS LIST OF FIGURES ....................................................................................................................... iii ACKNOWLEDGMENTS ............................................................................................................. vi ABSTRACT OF THE THESIS .................................................................................................... vii CHAPTER 1: Photochemical Doping of Protonic Transistors from a Cephalopod Protein ..................................................................................................................... 1 1.1 Abstract ..................................................................................................................................... 1 1.2 Introduction ………….............................................................................................................. 4 1.3 Experimental Section ................................................................................................................ 5 1.3.1 Preparation of Wild-Type and Mutant Reflectins
    [Show full text]
  • Ink from Longfin Inshore Squid, Doryteuthis Pealeii, As a Chemical and Visual Defense Against Two Predatory Fishes, Summer Floun
    CORE Metadata, citation and similar papers at core.ac.uk Provided by Woods Hole Open Access Server Reference: Biol. Bull. 225: 152–160. (December 2013) © 2013 Marine Biological Laboratory Ink From Longfin Inshore Squid, Doryteuthis pealeii, as a Chemical and Visual Defense Against Two Predatory Fishes, Summer Flounder, Paralichthys dentatus, and Sea Catfish, Ariopsis felis CHARLES D. DERBY*, MIHIKA TOTTEMPUDI, TIFFANY LOVE-CHEZEM, AND LANNA S. WOLFE Neuroscience Institute and Department of Biology, Georgia State University, Atlanta, Georgia 30303; and The Marine Biological Laboratory, Woods Hole, Massachusetts 02543 Abstract. Chemical and visual defenses are used by many Introduction organisms to avoid being approached or eaten by predators. Anti-predatory defenses can be found in many forms An example is inking molluscs—including gastropods such throughout the animal kingdom, operating through a variety as sea hares and cephalopods such as squid, cuttlefish, and of sensory systems of predators, including olfactory, visual, octopus—which release a colored ink upon approach or and auditory (Ruxton et al., 2004; Caro, 2005; Eisner et al., attack. Previous work showed that ink can protect molluscs 2007). Some molluscs use ink as a chemical defense against through a combination of chemical, visual, and other ef- predators. Previous work on slow-moving inking mol- fects. In this study, we examined the effects of ink from luscs—sea hares, Aplysia spp.—revealed a variety of mol- longfin inshore squid, Doryteuthis pealeii, on the behavior ecules acting as chemical defenses through a variety of of two species of predatory fishes, summer flounder, mechanisms (Derby, 2007; Derby and Aggio, 2011). One Paralichthys dentatus, and sea catfish, Ariopsis felis.
    [Show full text]
  • Mackerel Closure Framework (Framework 12) ATLANTIC MACKEREL, SQUID, and BUTTERFISH FISHERY MANAGEMENT PLAN
    Mackerel Closure Framework (Framework 12) ATLANTIC MACKEREL, SQUID, AND BUTTERFISH FISHERY MANAGEMENT PLAN Measures to Modify Atlantic Mackerel In-Season Closure Provisions Includes Draft Supplemental Environmental Assessment and Initial Regulatory Flexibility Analysis Prepared by the Mid-Atlantic Fishery Management Council (Council) in collaboration with the National Marine Fisheries Service (NMFS) Council Address NMFS Address Mid-Atlantic Fishery Management Council NMFS Greater Atlantic Regional Fisheries Office 800 North State Street, Suite 201 55 Great Republic Drive Dover, DE 19901 Gloucester, MA 01930 Submitted to NOAA: 1.0 EXECUTIVE SUMMARY AND TABLE OF CONTENTS This supplemental environmental assessment (SEA) updates the attached previously approved Environmental Assessment (EA) for: “Specifications and Management Measures For: Atlantic Mackerel (2016-2018, Including River Herring and Shad Cap); Butterfish Mesh Rules; and Longfin Squid Pre- Trip Notification System (PTNS)” (also described in this document as the “2016-2018 Mackerel EA” or “original EA”) that analyzed the catch limits, commercial quotas, recreational harvest limits, and management measures (called specifications) for Atlantic Mackerel for the 2016-2018 fishing years. This document is not a stand-alone document, but rather a supplement and is intended to be utilized in conjunction with the previously approved EA (final rule 4/26/16: https://www.greateratlantic.fisheries.noaa.gov/regs/2016/April/16msb2016specsfr.pdf). Unless otherwise noted, the original EA prepared for this action and attached to this SEA remains applicable. Therefore, sections addressed in this supplement should be considered within the context of the original EA. In this Framework Adjustment to the Atlantic Mackerel, Squid, and Butterfish Fishery Management Plan (MSB FMP) the Council considers measures to modify the in-season closure provisions for the Atlantic mackerel (“mackerel” hereafter) fishery.
    [Show full text]
  • Squid Fishing: from Hook to Plate
    FROM HOOK TO PLATE ver the past few years, squid fishing has become less of an oddity and more of a summertime staple on New Hampshire’s coast. Their documented range extends up to Newfoundland, but until recently, the major concentrations of squid stayed south of Cape Cod. Anglers anticipate the arrival of squid in the Piscataqua River in early summer, and they are fished for as far north as mid-coast Maine. Squid jigs can be found in most seacoast New Hampshire tackle shops during the summer. These are as odd looking as the squid themselves, with upward-turned metal pins at the end of the jig in the place of hooks. Squid are fascinating creatures; let’s explore their unique traits and life history a bit before we go fishing. Camouflage, Communication and Courtship The longfin inshore squid (Doryteuthis pealeii) is a fast growing, short lived molluscan inverte- brate. It is a cephalopod (meaning “head foot”), closely related to the octopus and cuttlefish. These creatures all have their feeding and major sensory organs on the part of their bodies to which the tentacles attach. While this peculiar body structure may be the first thing you notice about a squid, the second is likely to be its dazzling ability to camouflage. Squid have “chromatophores,” which are cells dense in pigment. Nerves and muscles control the contraction or dilation of these pigmented sacs, resulting in a change in color or pattern on the creature. This can be done at a very high speed, resulting in what looks like flashing. This behavior serves several purposes, including camouflage, communica- tion and courtship.
    [Show full text]
  • Wgceph Report 2018
    ICES WGCEPH REPORT 2018 ECOSYSTEM PROCESSES AND DYNAMICS STEERING GROUP ICES CM 2018/EPDSG:12 REF. SCICOM Interim Report of the Working Group on Cephalopod Fisheries and Life History (WGCEPH) 5-8 June 2018 Pasaia, San Sebastian, Spain International Council for the Exploration of the Sea Conseil International pour l’Exploration de la Mer H. C. Andersens Boulevard 44–46 DK-1553 Copenhagen V Denmark Telephone (+45) 33 38 67 00 Telefax (+45) 33 93 42 15 www.ices.dk [email protected] Recommended format for purposes of citation: ICES. 2019. Interim Report of the Working Group on Cephalopod Fisheries and Life History (WGCEPH), 5–8 June 2018, Pasaia, San Sebastian, Spain. ICES CM 2018/EPDSG:12. 194 pp. https://doi.org/10.17895/ices.pub.8103 The material in this report may be reused for non-commercial purposes using the recommended citation. ICES may only grant usage rights of information, data, imag- es, graphs, etc. of which it has ownership. For other third-party material cited in this report, you must contact the original copyright holder for permission. For citation of datasets or use of data to be included in other databases, please refer to the latest ICES data policy on ICES website. All extracts must be acknowledged. For other re- production requests, please contact the General Secretary. The document is a report of an Expert Group under the auspices of the International Council for the Exploration of the Sea and does not necessarily represent the views of the Council. © 2019 International Council for the Exploration of the Sea ICES WGCEPH REPORT 2018 | i Contents Executive summary ...............................................................................................................
    [Show full text]
  • Accounting Explicitly for Predation Mortality in Surplus Production Models: an Application to Longfin Inshore Squid
    North American Journal of Fisheries Management 29:1555–1566, 2009 [Article] American Fisheries Society 2009 DOI: 10.1577/M08-221.1 Accounting Explicitly for Predation Mortality in Surplus Production Models: an Application to Longfin Inshore Squid HASSAN MOUSTAHFID,MEGAN C. TYRRELL, AND JASON S. LINK* National Oceanic and Atmospheric Administration Fisheries Service, Northeast Fisheries Science Center, 166 Water Street, Woods Hole, Massachusetts 02543, USA Abstract.—One approach to better account for ecosystem considerations in fisheries science is to incorporate ecological interactions into conventional stock assessment models. The longfin inshore squid Loligo pealeii is one of two squid species of ecological and commercial significance in the northwest Atlantic Ocean. A surplus production model with quarterly time steps was fitted to longfin inshore squid total removal (fishing and predation removal) and tuned with fishery-dependent, fishery-independent, and predation- dependent indices to examine the effect of incorporating predation into a single-species model. Total consumption of squid by all predatory fish exceeded the landings in most years of this analysis. The model output indicated that biological reference points for longfin inshore squid differ considerably when predation removals are included. It appears that by not including predation, the model underestimates stock biomass and overestimates fishery surplus production. Short-term stochastic projections of such estimates demonstrate that increasing predation mortality and fishing mortality will decrease the biomass of longfin inshore squid. Failing to account for predation when performing stock assessments for longfin inshore squid and other similar forage species may misrepresent reference point estimates and result in management advice that could lead to biomass declines.
    [Show full text]