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KING-THESIS-2017.Pdf (2.949Mb) MOLECULAR PHYLOGENETIC INVESTIGATION OF THE CLINGFISHES (TELEOSTEI: GOBIESOCIDAE) A Thesis by CRAGEN DANIELLE KING Submitted to the Office of Graduate and Professional Studies of Texas A&M University in partial fulfillment of the requirements for the degree of MASTER OF SCIENCE Chair of Committee, Kevin W. Conway Committee Members, Gary Voelker David Portnoy Interdisciplinary Faculty Chair, Duncan MacKenzie December 2017 Major Subject: Marine Biology Copyright 2017 Cragen Danielle King ABSTRACT Currently, there are roughly 170 species of clingfishes (family Gobiesocidae) divided between ten subfamilies in a “phenetic” classification scheme proposed over 60 years ago. Recently, an alternative classification scheme was proposed which included only two subfamilies. For this study, a large scale multi-locus investigation on the phylogenetic relationships of the Gobiesocidae was conducted using both mitochondrial and nuclear DNA sequence data to assess whether the two available classification schemes reflect the evolutionary relationships of the group. Phylogenetic hypotheses are obtained from Bayesian and Maximum Likelihood analyses of two mitochondrial (12S and COI; 1062 bp) and five nuclear genes (ENC1, GLYT, MYH6, SH3PX3, and ZIC1; 3785 bp) for 81 species of clingfishes. Four of the ten subfamilies (Aspasminae, Diademichthyinae, Diplocrepinae, and Gobiesocinae) and four genera (Aspasmichthys, Cochleoceps, Lepadichthys, and Lepadogaster) are obtained as not monophyletic. The resulting topologies also do not recover the two-subfamily classification scheme as useful for classifying clingfishes because subfamily Cheilobranchinae is obtained as a monophyletic group that is deeply embedded inside the second subfamily Gobiesocinae. The two available classification schemes and their included subfamilies are discussed in detail. ii DEDICATION I dedicate this thesis to my grandparents, parents, siblings, and to the Smiths for all of their love and support. And to the clingfishes. Keep holding on. iii ACKNOWLEDGMENTS I thank Kevin W. Conway, Gary Voelker, Johanna Harvey, Jerry Huntley, Kole Kubicek, and Katrina Keith (Texas A&M University) for providing advice and assistance in analyses and laboratory procedures. I also thank my committee members, including Kevin W. Conway, Gary Voelker, and David Portnoy (Texas A&M University) for helpful comments and discussions. Furthermore, I thank M. McGrouther (AMS), M. Sabaj-Perez (ANSP), R. Britz (BMNH), A. Bentley (KU), S. Kullander, B. Krajrup (NRM), A. Stewart (NMNZ), E. Katayama, G. Shinohara (NSMT-P), P. Hastings, H.J. Walker (SIO), E. Bermingham, H. Prestridge (TCWC), C. Baldwin, J. Williams (USNM), E. Hilton (VIMS), M. Erdmann, C. Griffiths, R. Chabaria, D. Bloom, N. Nakayama, H. H. Tan, J. Van Tassell, B. Victor, Lukas Rüber, and Hector Espinosa Pérez for providing the tissues used in this study. iv CONTRIBUTORS AND FUNDINGS SOURCES Contributors This work was supported by a thesis committee consisting of Professor Dr. Kevin W. Conway and Dr. Gary Voelker of the Department of Wildlife and Fisheries and Professor Dr. David Portnoy of the Department of Life Sciences. All work for the thesis was completed by the student, under the advisement of Dr. Kevin W. Conway of the Department of Wildlife and Fisheries. Funding Sources This work was made possible by Texas AgriLife Research and the National Science Foundation under Grant Number 1256793. v TABLE OF CONTENTS Page ABSTRACT ....................................................................................................................... ii DEDICATION .................................................................................................................. iii ACKNOWLEDGMENTS ................................................................................................ iv CONTRIBUTORS AND FUNDING SOURCES .............................................................. v TABLE OF CONTENTS .................................................................................................. vi LIST OF FIGURES ......................................................................................................... viii LIST OF TABLES ............................................................................................................ ix 1. INTRODUCTION .......................................................................................................... 1 2. MATERIALS AND METHODS ................................................................................... 5 2.1 Taxon sampling ................................................................................................ 5 2.2 DNA extraction and PCR amplification ........................................................... 9 2.3 Sequence alignment and phylogenetic analyses ............................................. 10 2.4 Species tree estimation ................................................................................... 13 2.5 Tests of alternative hypotheses....................................................................... 13 3. RESULTS ..................................................................................................................... 15 3.1 Phylogenetic relationships .............................................................................. 15 3.2 Tests of alternative hypotheses....................................................................... 21 4. DISCUSSION .............................................................................................................. 22 4.1 Monophyly of the Gobiesocidae and its subfamilies ..................................... 22 4.1a Subfamily Aspasminae ..................................................................... 24 4.1b Subfamily Cheilobranchinae ............................................................ 27 4.1c Subfamily Chorisochisminae ............................................................ 28 4.1d Subfamily Diademichthyinae ........................................................... 29 4.1e Subfamily Diplocrepinae .................................................................. 31 4.1f Subfamily Gobiesocinae ................................................................... 32 vi 4.1g Subfamily Haplocylicinae ................................................................ 34 4.1h Subfamily Lepadogastrinae .............................................................. 35 4.1i Subfamily Protogobiesocinae ............................................................ 37 4.1j Subfamily Trachelochisminae ........................................................... 38 4.2 Remarks on the two alternative classifications .............................................. 40 5. CONCLUSION ............................................................................................................ 42 REFERENCES ................................................................................................................. 43 APPENDIX A .................................................................................................................. 50 APPENDIX B .................................................................................................................. 51 APPENDIX C .................................................................................................................. 53 APPENDIX D .................................................................................................................. 55 APPENDIX E ................................................................................................................... 62 APPENDIX F ................................................................................................................... 69 vii LIST OF FIGURES FIGURE Page 1 Phylogram obtained from the Maximum Likelihood analysis of the combined dataset labeled according to the subfamilies in the classification scheme established by Briggs (1955) with the addition of the Cheilobranchinae. ...................................................................................... 16 2 Phylogram obtained from the Maximum Likelihood analysis of the combined dataset labeled according to the two subfamilies in the classification scheme utilized by Van der Laan et al., (2014) and Nelson et al. (2016). ......................................................................................................... 41 3 Phylogram obtained from the Bayesian analysis of the combined dataset. ......... 50 4 Topologies resulting from the analysis of the mtDNA dataset.. .......................... 51 5 Topologies resulting from the analysis of the nDNA dataset. ............................. 53 6 Phylograms obtained from the Bayesian analyses of the 12S (1), COI (2), ENC1 (3), GLYT (4), MYH6 (5), SH3PX3 (6), and ZIC1 (7) datasets............... 55 7 Phylograms obtained from the Maximum Likelihood analyses of the 12S (1), COI (2), ENC1 (3), GLYT (4), MYH6 (5), SH3PX3 (6), and ZIC1 (7) datasets. ................................................................................................. 62 8 Species tree estimated using StarBEAST. Numbers above branches represent the posterior probabilities. .................................................................... 69 viii LIST OF TABLES TABLE Page 1 Subfamilies and included genera of the Gobiesocidae ........................................... 3 2 Family and subfamily designations, museum voucher numbers, and Genbank accession numbers of taxa included in this study. .................................. 6 3 Summary
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