Systematics of Callogobius (Teleostei: Gobiidae) by Naomi Rachel Delventhal A Thesis submitted to the Faculty of Graduate Studies of The University of Manitoba in partial fulfillment of the requirement of the degree of DOCTOR OF PHILOSOPHY Department of Biological Sciences University of Manitoba Winnipeg Copyright © 2018 by Naomi R Delventhal i Abstract Callogobius is a large genus of gobies characterized by fleshy ridges of papillae on the head in both horizontal and vertical rows. The taxonomy and phylogenetics of the genus are difficult and poorly understood. The purpose of my research is to better categorize the diversity within Callogobius by identifying and describing morphological characters and using them to aid species identification and discovery of monophyletic sub-groups within the genus. In this thesis, I construct separate phylogenetic hypothesizes for the intrarelationships of Callogobius using morphological and molecular data, respectively. Parsimony analysis using morphological characters (external anatomy and osteology) supports the presence of three monophyletic groups within Callogobius, the hasseltii, sclateri and maculipinnis groups. A fourth group, the tutuilae group, contains several species, at least some of which share some characters with members of the sclateri group. A molecular phylogenetic approach using four genes (zic1, a partial fragment containing 12S, tRNAVal and 16S, rag1 and sreb2) and analyzed using maximum parsimony, maximum likelihood and Bayesian inference supports the monophyly of Callogobius, the hasseltii, sclateri and maculipinnis groups; the tutuilae group is resolved as paraphyletic with respect to the sclateri group. Reductive traits, such as small size and loss of head pores appear to have evolved multiple times independently. In addition to phylogenetic analyses, I address some of the taxonomic issues within Callogobius through the descriptions of two new species, C. winterbottomi and C. pilosimentum, a redescription of C. clarki, removal of Gobiopsis liolepis from Callogobius, and a regional review of the Red Sea species (including a key). My taxonomic and phylogenetic study demonstrates that it is possible to find concordance between multiple methods even in taxa characterized by diversity and reductive characters. ii Acknowledgements As I finish this dissertation, I feel the desire to thank just about everyone with whom I've interacted in the last twelve years since I've started my degree. For the sake of brevity, however, I'll keep this section short and concise. I am grateful to the continuous support from my advisor R. Mooi and my committee members B. Ford, J. Hare and B. Sharanowski. Their suggestions, along with those of my external examiner L. Parenti, have greatly improved the final version of this dissertation. I received funding from the University of Manitoba Graduate Fellowship, an NSF Graduate Research Fellowship, a field work grant from the Leonard P. Schulz fund, and a grant from the Foundation for Science and Disability. A. Gill provided additional financial aid through an NSF grant and R. Mooi provided financial support through an NSERC Discovery Grant 327844-06. I am indebted to countless individuals for loan of specimens and/or hosting my visits (institutional names abbreviated following Fricke & Eschmeyer [2017]). These individuals include, but are not limited to: M. Sabaj Pérez (ANSP), K.-T. Shao (ASIZP), Y. Ikeda (BLIP), J. Maclaine (BMNH), A. Suzumoto (BPBM), H. Endo (BSKU), D. Catania (CAS), M. Rogers (FMNH), D. Golani (HUJ), H. Wellendorf (NMW), K. Matsuura (NSMT), G. Shinohara (NSMT), I-S. Chen (NTOUP), M. van Oijen (RMNH), R. Winterbottom (ROM), O. Gon (SAIAB), T.J. Alpermann (SRI), L. Parenti (USNM), J. Williams (USNM), S. Morrison (WAM), K. Hagiwara (YCM), N. Bogutskaya (ZIN), Z. Jaafar (ZRC) and R. Barman (ZSI). I thank J.Van Tassell, R. Robertson, I-S. Chen & students, U. Satapoomin & staff, M. Aizawa, and Y. Ikeda for putting up with me on field trips to collect gobies. H. Ho took me to collect specimens from the fish markets in Taiwan. I have enjoyed many interesting and helpful iii conversations about Callogobius taxonomy; in particular I thank A. Gill, H. Larson, R. Winterbottom, D. Hoese, J. Williams, Y. Ikeda, and Akihito. I am grateful to Department of Biological Sciences support staff M. Stopchyki (nee Foster) and J. Stringer, who tirelessly problem-solve for graduate students. I thank J. Anderson (former Department Head, Biological Sciences) for her understanding and support as I completed my Ph.D. amidst unforeseen challenges. I would not have been able to complete my degree without assistance from the University of Manitoba Accessibility Services; in particular I am grateful to L. Banash, J. Duong, A. Matheson and J. Cordovan. L. McDonald assisted in data collection from C. sp. 20, and K. Gardner helped with creating tables. J. Klapecki provided support at the Manitoba Museum. Finally, I thank my family for their support and patience with me over the years. iv TABLE OF CONTENTS Abstract .......................................................................................................................................... ii Acknowledgments.......................................................................................................................... iii Table of contents ..............................................................................................................................v List of tables ................................................................................................................................. viii List of figures ...................................................................................................................................x Chapter One. Introduction ..........................................................................................................1 Challenges in Callogobius alpha taxonomy .................................................................................3 History of Callogobius phylogeny ...............................................................................................4 Research objectives and approach ................................................................................................6 Chapter outline .............................................................................................................................7 Chapter Two. Intrarelationships of Callogobius (Teleostei: Gobiidae): a morphological perspective ........................................................................................................................9 SUMMARY ...............................................................................................................................10 INTRODUCTION ......................................................................................................................11 METHODS .................................................................................................................................13 Taxon selection .......................................................................................................................14 Character selection and coding ...............................................................................................15 Phylogenetic analysis .............................................................................................................16 RESULTS ...................................................................................................................................17 Character descriptions ............................................................................................................19 Phylogenetic hypotheses ........................................................................................................57 Description, membership and phylogenetic diagnoses of proposed maculipinnis, sclateri and hasseltii groups ........................................................................................................61 tutuilae group (unassigned species)........................................................................................67 DISCUSSION ............................................................................................................................69 MATERIAL EXAMINED .........................................................................................................72 Chapter Three. Molecular phylogenetics of Callogobius (Teleostei: Gobiidae) .....................74 SUMMARY ...............................................................................................................................75 INTRODUCTION ......................................................................................................................76 METHODS .................................................................................................................................82 Gene sampling and DNA sequencing.....................................................................................86 Sequence assembly, alignment and substation model selection .............................................87 Phylogenetic inference ...........................................................................................................87 RESULTS ...................................................................................................................................89 DISCUSSION ............................................................................................................................95