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DNA Barcoding of Fish Eggs in the Gulf of Mexico

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DNA Barcoding of Fish Eggs in the Gulf of Mexico University of South Florida Scholar Commons Graduate Theses and Dissertations Graduate School March 2019 DNA Barcoding of Fish Eggs in the Gulf of Mexico Makenzie Burrows University of South Florida, [email protected] Follow this and additional works at: https://scholarcommons.usf.edu/etd Part of the Other Oceanography and Atmospheric Sciences and Meteorology Commons Scholar Commons Citation Burrows, Makenzie, "DNA Barcoding of Fish Eggs in the Gulf of Mexico" (2019). Graduate Theses and Dissertations. https://scholarcommons.usf.edu/etd/8342 This Thesis is brought to you for free and open access by the Graduate School at Scholar Commons. It has been accepted for inclusion in Graduate Theses and Dissertations by an authorized administrator of Scholar Commons. For more information, please contact [email protected]. DNA Barcoding of Fish Eggs in the Gulf of Mexico by Makenzie Burrows A thesis submitted in partial fulfillment of the requirements for the degree of Master of Science College of Marine Science University of South Florida Major Professor: Mya Breitbart, Ph.D. Ernst Peebles, Ph.D. Steven A. Murawski, Ph.D. Date of Approval: March 7, 2019 Keywords: Genetics, molecular biology, PCR, spawning, Cuba, Florida Copyright © 2019, Makenzie Burrows ACKNOWLEDGEMENTS First, I would like to thank my advisor Dr. Mya Breitbart for giving me the opportunity to grow and succeed in her lab, and for her constant support, passion and guidance. I would also like to thank my committee members Dr. Ernst Peebles and Dr. Steve Murawski for their expertise in fish and their help with statistical analyses. Special thanks are due to Jeremy Browning, for picking out all the eggs for these projects, Eva-Maria Bonnelycke for helping me process all the Cuba samples, and Mason Kerr for helping me get through all of the processing complications. I am eternally grateful to my amazing lab and the College of Marine Science community for always being supportive, fostering a creative environment, and giving me the best memories. I also want to thank my family for their endless love and encouragement. Thank you to my donors George & Jane Morgan, for awarding me the WLP Dorothy L. Morgan Endowed Scholarship in Marine Science. Thank you to my donors Dr. William Hogarth and Mr. & Mrs. William Foster, for awarding me the William T. Hogarth Fellowship in Marine Mammals. I thank all the students, staff, captain and crew of the R/V Weatherbird II for their help in collection of eggs from Chapter Two. A. Gracia and E. Escobar‐Briones for provided logistic assistance at Mexican ports of call. I sincerely thank E. Fetherston‐Resch, Dr. W. Hogarth, Dr. P. Kramer, and the FLRACEP Program Management Team for offering insights and guidance during the development and execution of this project. The research cruises were conducted under the Gulf of Mexico Research Initiative (GoMRI) through its Center for Integrated Modeling and Analysis of Gulf Ecosystems (C‐IMAGE, GoMRI Grant NA11NMF4720151). Sample processing, travel, and DNA barcoding were supported by grants 4710‐1126‐02 and 4710‐1126‐ 03 from the Florida RESTORE Act Centers of Excellence Program, with oversight by the US Treasury. I thank all the students, staff, captain and crew of the R/V Weatherbird II for their help in collection of eggs from Chapter Three. Special thanks to Dr. Chuanmin Hu and Yingjun Zhang for their help with satellite imagery figures and writing in Chapter Three TABLE OF CONTENTS List of Tables ................................................................................................................................. iii List of Figures ................................................................................................................................ iv Abstract ............................................................................................................................................v Chapter One: Introduction ...............................................................................................................1 The Gulf of Mexico .............................................................................................................1 Finding Spawning Locations - Larvae Versus Eggs ............................................................2 DNA Barcoding ...................................................................................................................3 Thesis Goals .........................................................................................................................4 Chapter Two: DNA Barcoding Reveals Clear Delineation Between Spawning Sites for Neritic Versus Oceanic Fishes in the Gulf of Mexico ...............................................................5 Abstract ................................................................................................................................5 Introduction ..........................................................................................................................6 Methods................................................................................................................................9 Study Site and Sample Collection............................................................................9 Genetic Identification of Fish Eggs .......................................................................10 Statistical Analysis .................................................................................................13 Results ................................................................................................................................15 Discussion ..........................................................................................................................22 Factors That Affect Egg Distribution ....................................................................22 Geographic Delineation of the Neritic and Oceanic Egg Communities ................25 DEPM and Egg Mortality ......................................................................................29 Conclusion .........................................................................................................................29 Chapter Three: DNA Barcoding of Fish Eggs Collected off Northwest Cuba and Across the Florida Straits During May 2017 .......................................................................................31 Abstract ..............................................................................................................................31 Introduction ........................................................................................................................32 Methods..............................................................................................................................34 Study Site and Sample Collection..........................................................................34 Genetic Identification.............................................................................................35 Data Analysis .........................................................................................................37 Satellite Imagery ....................................................................................................38 i Results ................................................................................................................................38 Discussion ..........................................................................................................................43 Conclusion .........................................................................................................................51 Chapter Four: Additional Discussion.............................................................................................52 Comparison of Two Studies...............................................................................................52 A Note on Preservation and Processing .............................................................................52 Future Work .......................................................................................................................53 References ......................................................................................................................................56 Appendix A: Chapter Two Copyright Clearance ...........................................................................65 ii LIST OF TABLES Table 1: Habitat, economic importance, catch statistics, and Bez's (2000) index of aggregation (Ia) for all fish‐egg taxa encountered during the survey ..........................17 Table 2: Cruise station locations ................................................................................................36 Table 2: Fish egg species identification .....................................................................................40 iii LIST OF FIGURES Figure 1: Map of plankton stations, identified by SIMPROF group ...........................................11 Figure 2: Stochastic species accumulation results for fish‐egg sampling in the Gulf of Mexico during 2015 and 2016 based on 1,000 jackknifed iterations that sampled the station data without replacement .............................................................16 Figure 3: Comparison of fish‐egg encounter frequency (number of stations) with Bez's (2000) index of aggregation, Ia ....................................................................................20 Figure 4: Heatmap of
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