Florida International University FIU Digital Commons FIU Electronic Theses and Dissertations University Graduate School 11-10-2020 Connections in the Underworld: A Morphological and Molecular Study of Diversity and Connectivity among Anchialine Shrimp. Robert Eugene Ditter Florida International University, [email protected] Follow this and additional works at: https://digitalcommons.fiu.edu/etd Part of the Biodiversity Commons, Bioinformatics Commons, Biology Commons, Ecology and Evolutionary Biology Commons, Genetics and Genomics Commons, Marine Biology Commons, Natural Resources and Conservation Commons, Oceanography Commons, Other Environmental Sciences Commons, Speleology Commons, and the Zoology Commons Recommended Citation Ditter, Robert Eugene, "Connections in the Underworld: A Morphological and Molecular Study of Diversity and Connectivity among Anchialine Shrimp." (2020). FIU Electronic Theses and Dissertations. 4561. https://digitalcommons.fiu.edu/etd/4561 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 CONNECTIONS IN THE UNDERWORLD: A MORPHOLOGICAL AND MOLECULAR STUDY OF DIVERSITY AND CONNECTIVITY AMONG ANCHIALINE SHRIMP A dissertation submitted in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY in BIOLOGY by Robert E. Ditter 2020 To: Dean Michael R. Heithaus College of Arts, Sciences and Education This dissertation, written by Robert E. Ditter, and entitled Connections in the Underworld: A Morphological and Molecular Study of Diversity and Connectivity among Anchialine Shrimp, 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 M. Eirin-Lopez _______________________________________ Jessica U. Liberles _______________________________________ Demian Chapman _______________________________________ Dean Whitman _______________________________________ Eric S. Cole _______________________________________ Heather D. Bracken-Grissom, Major Professor Date of Defense: November 10, 2020 The dissertation of Robert E. Ditter 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, 2020 ii © Copyright 2020 by Robert E. Ditter All rights reserved. iii DEDICATION This dissertation is dedicated Peggy Sue Wayne who gave me courage and motivation to always follow my dreams, no matter how silly it may seem or what other people think. I would also like to dedicate this dissertation to Matt Inman and Jibbers Crabst who gave me the inspiration to tough it out and finish, even during times of crisis. Last, but not least I would like to dedicate this to all my teachers, my parents, everyone whose has shed blood that made this all possible and Ms. Aubree Zenone. Without their support, none of this would have been possible. iv ACKNOWLEDGMENTS My dissertation is the product of started as a simple undergraduate research project that blossomed into the what it is today. None of this would be possible without the immeasurable help that I received along the way. My major professor/advisor/life coach, Dr. Heather Bracken-Grissom, who taught me, all about the various facets of real science, provided me with just the right motivation and support to keep me moving forward with lots of fun along the way, how to communicate even if it is uncomfortable, and last but not least how to work around people no matter how terrible and disagreeable that person may be. She also taught be how to better manage personal and work relationships, and how to keep a better work/life balance… Thanks boss lady! I also want to thank Dr. Eirin-Lopez, who taught me epigenetics and the effects the environment can have on evolution, and for offering his encouragement along the way; Dr. Eric Cole, whom I meet as an undergrad. He taught me a lot about bushwhacking and San Sal, he was always a helpful sounding board for ideas and places to travel, and he is truly one of the most positive people I have ever met; Dr. Eric Bishop von Wettberg, who helped guide me through population genetics and gave me a lot of helpful feedback on useful software to tryout and experimental design; Dr. Jessica Siltberg-Liberles, for teaching sound bioinformatics practices and providing me feedback on all of my bioinformatics questions; Dr. Dean Whitman who helped me understand my results on a geographic timeline and to puzzle out important events in the geologic record; and Dr. Demian Chapman, who happily took over the spot of a committee member that had left the university. I am grateful to the members of the CRUSTOMICS lab for all of their help over the years, especially Dr. Jorge Pérez-Moreno for putting up with my shenanigans; v Dr. Laura Timm, for letting me pick her brain; and Dr. Daniel Deleo for being the best postdoc anyone can ask for and whom helped turn my PhD experience into a positive one. I would like to say, thank you, to William “Bill” Chamberlain, whom I do not think the Marine Science program or the Marine Science Program, cheers. I am also very grateful to Drs. Rob Erdman (Big Rob), Anna Goebel, Randy Cross and the rest of the FGCU Marine Science faculty. They gave me amazing guidance early on during my undergrad and I cannot say how much I appreciate them. I offer my thanks to Ms. Claire Burgett and Ms. Aubree Zenone, who taught me to value all perspectives, whose friendship helped me through many difficulties along the way, and Claire taught me how to art ☺. And, of course, I would like to thank my parents. I would also like to thank Drs. Thomas Iliffe, T.-Y. Chan, Darryl Felder, Craig Layman and Jocelyn Curtis-Quick and the Cape Eleuthera Institute, The Bahamas for their assistance in the collection of specimens. I also thank the curators at USNM and MNHN for providing valuable additional material of Parhippolyte. I would like to thank Dr. John E. Mylroie for his valuable feedback and assistance. I also extend my gratitude to Drs. Raymond Bauer for his expert advice and feedback. I am grateful for the support and assistance of the Gerace Research Centre and Bahamian citizens during field work on San Salvador, Bahamas. These studies were supported in part by a student research award from the Gerace Research Centre, The Crustacean Society - Graduate Student Fellowship, The National Speleological Society - Ralph Stone Graduate Fellowship Grant, and Florida International University Tropics graduate research grant awarded to RED. Additional support was provided by Florida International University. vi ABSTRACT OF THE DISSERTATION CONNECTIONS IN THE UNDERWORLD: A MORPHOLOGICAL AND MOLECULAR STUDY OF DIVERSITY AND CONNECTIVITY AMONG ANCHIALINE SHRIMP by Robert E Ditter Florida International University, 2020 Miami, Florida Professor Heather D. Bracken-Grissom, Major Professor This research investigates the distribution and population structure of crustaceans endemic to anchialine systems in the tropical western Atlantic focusing on cave-dwelling shrimp from the family Barbouriidae. Taxonomic and molecular tools (genetic and genomic) are utilized to examine population dynamics and the presence of phenotypic hypervariation (PhyV) of the critically endangered species Barbouria cubensis (von Martens, 1872). The presence of PhyV and its geographic distribution is investigated among anchialine populations of B. cubensis from 34 sites on Abaco, Eleuthera, and San Salvador, Bahamas. Examination of 54 informative morphological characters revealed PhyV present in nearly 90% (n=463) of specimens with no identifiable geographic distribution. Updated range descriptions of Macrobrachium lucifugum Holthuis, 1974, Parhippolyte sterreri (Hart & Manning, 1981) and B. cubensis in the western Atlantic are provided with observations on the behavior of B. cubensis from over 10 years of work. Molecular phylogenetic analyses of a combination of two mitochondrial and five nuclear gene regions are used for molecular barcoding, to further investigate PhyV and to vii re-examine the current classification of the family Barbouriidae. The results find no evidence of cryptic speciation, or genetic differentiation among individuals of B. cubensis (n=72). Morphological and molecular evidence supports synonymizing Janicea within Parhippolyte and recognition of the sub-families Calliasmatinae Ditter et al., 2020 and Barbouriinae Christoffersen, 1987. Connectivity among anchialine systems and population structure of B. cubensis across the tropical western Atlantic is examined using a combination of next generation molecular tools. Genomic analyses suggest a single highly connected population of B. cubensis with low genetic diversity and a low effective population size, which conflicts with the generally accepted isolation paradigm of anchialine systems. Our findings support the value added to genomic studies by generating a partial draft genome constructed using de novo hybrid assembly of short read RADseq and Nanopore long read sequencing data through the investigation of the anchialine isolation paradigm.