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Assessment of the Population Structure of the South African Sardine Sardinops Sagx Using a Multi-Method Approach and the Morphol

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ASSESSMENT OF THE POPULATION STRUCTURE OF THE SOUTH AFRICAN SARDINE Sardinops sagax USING A MULTI-METHOD APPROACH AND THE MORPHOLOGICAL AND MOLECULAR CHARACTERIZATION OF A STOCK- DISCRIMINATING DIGENEAN PARASITE BIOTAG OF THE GENUS Cardiocephaloides By NWAMAKA MARY-IMMACULATA UKOMADU University of Cape Town Thesis presented for the degree of DOCTOR OF PHILOSOSPHY Department of Biological Sciences UNIVERSITY OF CAPE TOWN MARCH 2017 Supervisor: Dr. Cecile C. Reed (University of Cape Town, Biological Sciences) Co-supervisor: Dr. Carl van der Lingen (Department of Agriculture, Forestry and Fisheries and Marine Research Institute, University of Cape Town) The copyright of this thesis vests in the author. No quotation from it or information derived from it is to be published without full acknowledgement of the source. The thesis is to be used for private study or non- commercial research purposes only. Published by the University of Cape Town (UCT) in terms of the non-exclusive license granted to UCT by the author. University of Cape Town PLAGIARISM DECLARATION I know the meaning of plagiarism and declare that all the work in the document is my own, except that which has been properly acknowledged, including the maps which were produced by supervisor Dr. C. D. van der Lingen. 13-03-2017 Signature Removed Date Nwamaka Mary-Immaculata Ukomadu ii ASSESSMENT OF THE POPULATION STRUCTURE OF THE SOUTH AFRICAN SARDINE Sardinops sagax USING A MULTI-METHOD APPROACH AND MORPHOLOGICAL AND MOLECULAR CHARACTERIZATION OF A STOCK- DISCRIMINATING DIGENEAN PARASITE BIOTAG OF THE GENUS Cardiocephaloides NWAMAKA MARY-IMMACULATA UKOMADU MARCH 2017 ABSTRACT An understanding of the population structure of commercially exploited species is essential for effective fisheries management. Fish stocks are typically identified based on the observation of differences in genetic and/or phenotypic characteristics between fish from discrete units. Recent deliberations on the management of the South African purse-seine sardine fishery recognises the likely existence of two stocks, one on the west and another on the south coasts, following studies that have documented spatial variability in several phenotypic characteristics of this species around South Africa. Those studies typically examined spatial variability in a single characteristic (e.g. gill raker morphology and meristics, body shape, otolith shape, vertebral count, parasite loads), but the application of multiple stock identification methods to the same individual fish has been recommended in order to maximize the likelihood of correctly inferring and identifying fish stocks. This study seeks to assess the population structure of South African sardine Sardinops sagax using a combination of stock identification methods including meristic, morphometric and parasite markers. Most of the sardine samples used in this study were obtained off the west and south coasts of South Africa during pelagic surveys conducted in 2013 and 2014 by Fisheries Branch of the Department of Agriculture, Forestry and Fisheries, with some additional samples obtained from commercial fisheries. Fish caught from the west and south coasts are presumed to be part of the putative western and southern stocks respectively. The variables examined included body shape, gill arch length, gill raker spacing, number of gill rakers, otolith shape indices (otolith circularity and form factor), the number of vertebrae, and the abundance of a ‘tetracotyle’ type metacercarian parasite found in the eyes of sardine; these were first analysed individually and then collectively (excluding body shape data) in a multivariate analysis to test their effectiveness in discriminating between sardine iii from the putative western and southern sardine stocks. Analysis using geometric morphometrics revealed significant differences in body shape between sardine from the putative western and southern stocks. Results of GLM analyses indicated that gill arch length, the number of gill rakers, otolith form factor and circularity, and parasite abundance were effective univariate discriminators of sardine stocks. No significant difference in gill raker spacing and the number of vertebrae was found between individuals from the two stocks. A Stock Identification Index (SDI) of 0.75 derived from the univariate analyses, as well as results of the multivariate analysis of data provided strong evidence for the existence of two mixing stocks, therefore, supporting the two-stock hypothesis. The five multivariate classification models used in the study showed varying degree of allocation success. Overall classification accuracy ranged from a low 47% in the Linear Discriminant Analysis model to highs of 82% and 91% in the Classification Tree Analysis and Random Forest models, respectively. Both CTA and RF revealed the combination of variables with the strongest spatial discriminatory power to be the number of vertebrae and abundance of the ‘tetracotyle’ type metacercarian parasite. These results agree with those of previous studies and further support the inclusion of sardine population structure into management strategies for the purse-seine fishery for South African sardine. Given the importance of the ‘tetracotyle’ type metacercaria in the discrimination of South African western and southern sardine stocks, further studies were undertaken to identify and describe this parasite using light and scanning microscopy, as well as molecular tools. Such information will assist in the definitive identification of the first intermediate host of the parasite, presently hypothesized to be a sub-tidal gastropod occurring off the west coast only. Definitive identification of the first intermediate host (or hosts) will enable the full life cycle of this parasite to be determined and the parasite endemic area to be identified; a critical knowledge gap in application of the parasite biotag approach to stock discrimination using this ‘tetracotyle’ type metacercarian parasite. Metacercariae collected from fresh sardine sampled from a commercial landing in Gans Bay, South Africa, were manually excysted, relaxed in warm water, fixed in 70% ethanol and stained with haematoxylin for light microscopy. The metacercarial body is oval-shaped, measuring 762 – 967 x 512 - 677µm. It is divided by transverse folds into a forebody, midbody and hindbody. Diagnostic iv features include the unique, large excretory bladder lobes situated on the lateral sides of the body; two large pseudosuckers in the anterior part of the midbody; an acetabulum which is larger than the oral sucker; and a large lobulated holdfast organ in the posterior half of the midbody. These features are those of the metacercariae of the genus Cardiocephaloides, confirming the previous hypothesis regarding the genus of this digenean biotag. Analysis of partial 28S rDNA region sequence data showed that the metacercariae and the adult Cardiocephaloides found in the African penguin Spheniscus demersus are of the same species, likely C. physalis. This study is the first documentation of the morphological and molecular characterization of the stock- discriminating Cardiocephaloides metacercaria found in eyes of Sardinops sagax in South Africa. v CONTENTS PLAGIARISM DECLARATION ................................................................................................... ii ABSTRACT .............................................................................................................................. iii CONTENTS .............................................................................................................................. vi LIST OF FIGURE LEGENDS ...................................................................................................... viii LIST OF TABLE HEADINGS ...................................................................................................... xiv ACKNOWLEDGEMENTS ........................................................................................................ xvii CHAPTER 1. OVERVIEW SMALL PELAGIC FISH…………………………………………………………………………………………………………..1 BIOLOGY OF SARDINE (Sardinops sagax)…………………………………………………………………………….2 SARDINOPS SAGAX IN SOUTHERN AFRICAN WATERS………………………………………………………….3 SARDINOPS SAGAX PURSE-SEINE FISHERY IN SOUTH AFRICA……………………………………………...7 STOCK IDENTIFICATION………………………………………………………………………………………………….....10 STOCK IDENTIFICATION METHODS…………………………………………………………………………………....11 STOCK IDENTIFICATION: A MULTI-DISCIPLINARY APPROACH……………………………………………..18 SOUTH AFRICAN SARDINE: MONO-STOCK OR MULTI-STOCK?...............................................19 AIMS OF THE STUDY……………………………………………………………………………………………………………24 THESIS CHAPTERS……………………………………………………………………………………………………………….25 REFERENCES……………………………………………………………………………………………………………………....26 CHAPTER 2. ASSESSMENT OF THE STOCK STRUCTURE OF THE SOUTH AFRICAN SARDINE Sardinops sagax USING A MULTIPLE METHOD APPROACH STOCK IDENTIFICATION………………………………………………………………………………………………………51 STOCK STRUCTURE OF SARDINE POPULATIONS………………………………………………………………….53 SOUTH AFRICAN SARDINE STOCK STRUCTURE……………………………………………………………………54 MATERIALS AND METHODS………………………………………………………………………………………………..59 DATA ANALYSES………………………………………………………………………………………………………………….65 RESULTS……………………………………………………………………………………………………………………………..76 DISCUSSION………………………………………………………………………………………………………………………126 REFERENCES………………………………………………………………………………………………………..……………142 CHAPTER 3. MORPHOLOGY OF A STRIGEID METACERCARIA FOUND IN THE EYES OF SARDINE, Sardinops sagax FROM GANSBAAI, SOUTHWESTERN COAST OF SOUTH AFRICA.
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    Clinostomum Album N. Sp. and Clinostomum Marginatum (Rudolphi, 1819), Parasites of the Great Egret Ardea Alba L

    University of Nebraska - Lincoln DigitalCommons@University of Nebraska - Lincoln USDA National Wildlife Research Center - Staff U.S. Department of Agriculture: Animal and Plant Publications Health Inspection Service 2017 Clinostomum album n. sp. and Clinostomum marginatum (Rudolphi, 1819), parasites of the great egret Ardea alba L. from Mississippi, USA Thomas G. Rosser Mississippi State University Neely R. Alberson Mississippi State University Ethan T. Woodyard Mississippi State University Fred L. Cunningham USDA/APHIS/WS National Wildlife Research Center, [email protected] Linda M. Pote Mississippi State University See next page for additional authors Follow this and additional works at: https://digitalcommons.unl.edu/icwdm_usdanwrc Part of the Life Sciences Commons Rosser, Thomas G.; Alberson, Neely R.; Woodyard, Ethan T.; Cunningham, Fred L.; Pote, Linda M.; and Griffin,a M tt .,J "Clinostomum album n. sp. and Clinostomum marginatum (Rudolphi, 1819), parasites of the great egret Ardea alba L. from Mississippi, USA" (2017). USDA National Wildlife Research Center - Staff Publications. 1930. https://digitalcommons.unl.edu/icwdm_usdanwrc/1930 This Article is brought to you for free and open access by the U.S. Department of Agriculture: Animal and Plant Health Inspection Service at DigitalCommons@University of Nebraska - Lincoln. It has been accepted for inclusion in USDA National Wildlife Research Center - Staff ubP lications by an authorized administrator of DigitalCommons@University of Nebraska - Lincoln. Authors Thomas G. Rosser, Neely R. Alberson, Ethan T. Woodyard, Fred L. Cunningham, Linda M. Pote, and Matt .J Griffin This article is available at DigitalCommons@University of Nebraska - Lincoln: https://digitalcommons.unl.edu/icwdm_usdanwrc/ 1930 Syst Parasitol (2017) 94:35–49 DOI 10.1007/s11230-016-9686-0 Clinostomum album n.