Florida International University FIU Digital Commons FIU Electronic Theses and Dissertations University Graduate School 6-7-2018 Evolutionary and Population Dynamics of Crustaceans in the Gulf of Mexico Laura Timm Florida International University, [email protected] DOI: 10.25148/etd.FIDC006826 Follow this and additional works at: https://digitalcommons.fiu.edu/etd Part of the Biology Commons, Evolution Commons, Genomics Commons, Marine Biology Commons, Molecular Genetics Commons, and the Population Biology Commons Recommended Citation Timm, Laura, "Evolutionary and Population Dynamics of Crustaceans in the Gulf of Mexico" (2018). FIU Electronic Theses and Dissertations. 3807. https://digitalcommons.fiu.edu/etd/3807 This work is brought to you for free and open access by the University Graduate School at FIU Digital Commons. It has been accepted for inclusion in FIU Electronic Theses and Dissertations by an authorized administrator of FIU Digital Commons. For more information, please contact [email protected]. FLORIDA INTERNATIONAL UNIVERSITY Miami, Florida EVOLUTIONARY AND POPULATION DYNAMICS OF CRUSTACEANS IN THE GULF OF MEXICO A dissertation submitted in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY in BIOLOGY by Laura E. Timm 2018 To: Dean Michael R. Heithaus choose the name of dean of your college/school College of Arts, Sciences and Education choose the name of your college/school This dissertation, written by Laura E. Timm, and entitled Evolutionary and Population Dynamics of Crustaceans in the Gulf of Mexico, having been approved in respect to style and intellectual content, is referred to you for judgment. We have read this dissertation and recommend that it be approved. _______________________________________ Jose Eirin-Lopez _______________________________________ Mauricio Rodriguez-Lanetty _______________________________________ Eric von Wettberg _______________________________________ Wensong Wu _______________________________________ Heather Bracken-Grissom, Major Professor Date of Defense: June 7, 2018 The dissertation of Laura E. Timm is approved. _______________________________________ Dean Michael R. Heithaus College of Arts, Sciences and Education _______________________________________ Andrés G. Gil Vice President for Research and Economic Development and Dean of the University Graduate School Florida International University, 2018 ii © Copyright 2018 by Laura E. Timm All rights reserved. iii DEDICATION This dissertation is dedicated to all my teachers, most especially my mother (who began teaching me at birth and has not stopped yet). My teachers are many and most are neither teachers nor mentors by profession. A few of them are blood relatives; a few others will always be my family, regardless of the genetic distance. They range in age and background and most do not play nice. Six of them did not live to see this come to fruition. This is for all of them. And it is paltry repayment for what they gave me. iv ACKNOWLEDGMENTS This dissertation would not have been possible without the input and assistance of many people. My advisor, Dr. Heather Bracken-Grissom provided tireless support as a mentor, role model, and scientist. Moreover, she taught me how to do these things for myself, as well as countless other skills spanning the realms of research, writing, and thinking; for which she has my sincerest gratitude. I also thank the member of my committee: Dr. Eirin-Lopez, who taught me the basics of epigenetics and the importance of considering its effects when interpreting results; Dr. Mauricio Rodriguez-Lanetty, who provided valuable insight into transcriptomics and the other directions my research could take; Dr. Eric von Wettberg, whose guidance in the realm of population genetics was always timely and helpful; and Dr. Wensong Wu, who provided some of the best statistical instruction I have ever encountered. I am grateful to Dr. Joan Browder, Mr. Tom Jackson, Ms. Shaina Simon, and Dr. Ian Zink for their contributions to Chapter III. Chapter IV was made possible by specimen donation from Dr. Michael Heithaus and Dr. Dean Grubbs, and assistance from Dr. Diana Churchill and Ms. Barbara Moahamad. I also extend thanks to the Deep Pelagic Nekton Dynamics of the Gulf of Mexico (DEEPEND) consortium. I count the opportunity to work with this collection of world-class researchers, who contributed advice and earnest feedback, as one of the best parts of my graduate school experience. I learned to be a scientist in DEEPEND. Specifically, the research presented in Chapter V would not have been possible without the mentorship of Dr. Tammy Frank, who taught me to identify midwater Gulf crustaceans at sea. Dr. Tracey Sutton, Ms. April Cook, Dr. Matt Johnston, and Dr. Rosanna Milligan were instrumental in keeping me oriented in the wealth of metadata resulting from each v DEEPEND cruise, as well as navigating the Gulf of Mexico Research Initiative’s Information & Data Cooperative, for which they deserve special recognition here. Likewise, the members of the Point Sur crew and Mr. Gray Lawson, the MOC10 net operator, provided the necessary support to collect the specimens used in Chapter V. Across all chapters of this dissertation, Dr. Emily Warschefsky and my CRUSTOMICS lab mates provided support, advice, and encouragement. Bioinformatics advice was provided by Mr. Joseph Ahrens and Mr. Jordon Rahaman in the Siltberg-Liberles’ lab, and computational support for FIU’s High Performance Computing Cluster was readily provided by Dr. Cassian D’Cunha. My lab assistants, Ms. Barbara Moahamad and Ms. Lys Isma, were invaluable assets in the lab. They contributed greatly to this work through their dedication and hard work. I thank the Gulf of Mexico Research Initiative, which funded the majority of my research through the DEEPEND consortium. Moreover, the annual Gulf of Mexico Oil Spill and Ecosystem Sciences Conference provided me an international audience with whom to share my research. Finally, I thank Florida International University. Through fellowships and travel grants, FIU has nurtured my career and provided me the space, time, and resources to pursue my passion for science without starving. Thank you. vi ABSTRACT OF THE DISSERTATION EVOLUTIONARY AND POPULATION DYNAMICS OF CRUSTACEANS IN THE GULF OF MEXICO by Laura E. Timm Florida International University, 2018 Miami, Florida Professor Heather Bracken-Grissom, Major Professor Evolution occurs and can be conceptualized along a spectrum, bounded on one extreme by the relationships between deep lineages – such as phyla, classes, and orders – and on the other by the molecular dynamics of operational taxonomic units within a species, defined as population genetics. The purpose of this dissertation was to better understand the evolutionary and population dynamics of crustaceans within the Gulf of Mexico. In the second chapter of my dissertation, I provide a guide to best phylogenetic practice while reviewing infraordinal relationships within Decapoda, including the promise held by next-generation sequencing (NGS) approaches such as Anchored Hybrid Enrichment. Chapter III is a phylogenetic study of species relationships within the economically important shrimp genus, Farfantepenaeus, targeting three mitochondrial genes and uncovering an intriguing pattern of latitudinal speciation. As the first inclusive molecular phylogeny of the genus, we find support for the newly described species F. isabelae, but a lack of support for the species status of F. notialis. Additionally, our results suggest the existence of two distinct subspecies of F. brasiliensis. Chapter IV investigates the relative impacts of habitat heterogeneity and the presence of a possible glacial refugium in vii determining population dynamics of the Giant Deep-Sea Isopod, Bathynomus giganteus in the northern Gulf of Mexico. Through hybrid population genetics/genomics analyses and Bayesian testing of population models, we find strong evidence for habitat heterogeneity determining population dynamics for this charismatic deep-sea invertebrate. Chapter V further investigates the role of environment in determining and maintaining genetic diversity and population connectivity, specifically focused on establishing biological baselines with which we can diagnose health and resilience of the Gulf of Mexico. This was accomplished through a comparative NGS population genomics study of three species of mesopelagic crustaceans: Acanthephyra purpurea, Systellaspis debilis, and Robustosergia robusta. While diversity and connectivity differs in each species, the comparative results bespeak the importance of access to the Gulf Loop Current in determining and maintaining population dynamics. Overall, my work significantly contributes to our knowledge of Crustacea at the phylogenetic- and population genetic-level. viii TABLE OF CONTENTS CHAPTER PAGE PREFACE ............................................................................................................................1 I. INTRODUCTION ................................................................................................3 LITERATURE CITED ................................................................................................10 II. THE FOREST FOR THE TREES: EVALUATING MOLECULAR PHYLOGENIES WITH AN EMPHASIS ON HIGHER-LEVEL DECAPODA .......................................................................................................17 ABSTRACT .................................................................................................................18