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Phylogeny and Phylogeography of a Shallow Water Fish

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Phylogeny and Phylogeography of a Shallow Water Fish UNIVERSITY OF CALIFORNIA, SAN DIEGO Evolution of the suborder Blennioidei: phylogeny and phylogeography of a shallow water fish clade. A dissertation submitted in partial satisfaction of the requirements for the degree Doctor of Philosophy in Marine Biology by Hsiu-Chin Lin Committee in charge: Professor Philip A. Hastings, Chair Professor Ron S. Burton Professor Richard H. Rosenblatt Professor Greg W. Rouse Professor Christopher J. Wills 2009 Copyright Hsiu-Chin Lin, 2009 All rights reserved The dissertation of Hsiu-Chin Lin is approved, and it is acceptable in quality and form for publication on microfilm and electronically: _____________________________________________ _____________________________________________ _____________________________________________ _____________________________________________ _____________________________________________ Chair University of California, San Diego 2009 iii DEDICATION This work is dedicated to my family who are not sure why I have to be far away from home but always have faith in me nonetheless. iv TABLE OF CONTENTS Signature Page……………………………………………………………………………iii Dedication Page…………………………………………………………………………..iv Table of Contents………………………………………………………………………….v List of Figures…………………………………………………………………………...viii List of Tables……………………………………………………………………………...x Acknowledgement………………………………………………………………………..xi Vita……………………………………………………………………………………....xiv Abstract………………………………………………………………………………….xvi Introduction………………………………………………………………………………..1 Chapter 1: Phylogeny of the Suborder Blennioidei (Teleostei: Perciformes)…………...10 Abstract………………………………………………………………………..…11 Introduction………………………………………………………………………12 Materials and methods…………………………...………………………………15 Results……………………………………………………………………………20 Discussion………………………………………………………………………..22 Future Work…..………………………………………….………………………37 Acknowledgements………………………………………………………………38 Tables…………………………………………………………………………….40 Figures……………………………………………………………………………47 References………………………………………………………………………..52 v Chapter 2: Phylogenetic relationships of a New World marine fish lineage (Family Chaenopsidae, Suborder Blennioidei) based on combined molecular and morphological data…………………………………………………………………………….…………59 Abstract…………………………………………………………………..………60 Introduction………………………………………………………………..……..61 Materials and methods…………………………………………………….……..64 Results……………………………………………………………...…….………69 Discussion………………………………………………………………………..72 Conclusions………………………………………………………………………86 Acknowledgements………………………………………………………………87 Tables…………………………………………………………………………….88 Figures……………………………………………………………………………92 Appendices……………………………………………………………………….98 References………………………………………………………………………104 Chapter 3: Colour variation is incongruent with mitochondrial lineages: cryptic speciation and subsequent diversification in a Gulf of California reef fish (Teleostei: Blennioidei)… ……………………………………………………………………………………….….111 Abstract……………………………………………………………………....…112 Introduction………………………………………………………………..……112 Materials and methods……………………………………………………….…114 Results………………………………………………………………………..…116 Discussion………………………………………………………………………120 Conclusions…………………………………………………………….…….…122 vi Acknowledgements…………………………………………………….………122 References……………………………………………………………….……..122 Chapter 4: A new endemic species of Barnacle Blenny (Teleostei: Chaenopsidae: Acanthemblemaria) from the Gulf of California, Mexico………………..……….……125 Abstract…………………………………………………………………………126 Introduction……………………………………………………..………………127 Materials and methods………………………………………….………………128 Results………………………………………………………………..…………132 Materials examined………………………………………………..……………139 Acknowledgements…………………………………………………..…………140 Tables…………………………………………………………………...………141 Figures……………………………………………………………………..……146 References………………………………………………………………………148 vii LIST OF FIGURES Chapter 1 Fig. 1.1 Phylogenetic relationships among major blennioid clades based on Bayesian analysis.………………………………………………………….………………………47 Fig. 1.2 Phylogenetic relationships of the Tripterygiidae with gobiesocids as the outgroup.…………………………………………………………………………………48 Fig. 1.3 Phylogenetic relationships of the Blenniidae with triplefins as the outgroup…..49 Fig. 1.4 Phylogenetic relationships of the Clinidae, Labrisomidae, Chaenopsidae and Dactyloscopidae.………………………………………………………………………....50 Fig. 1.5 Phylogenetic relationships of the tribes of Blenniidae………………………….51 Fig. 1.6 Generic relationships of the blenniid tribe Salariini…………………………….51 Chapter 2 Fig. 2.1 Substitutions versus divergence plots for each genetic marker…………………92 Fig. 2.2 50% majority consensus tree of the concatenated molecular dataset…………...93 Fig. 2.3 50% majority consensus trees of each gene and morphological data…………...94 Fig. 2.4 Reconstructed phylogeny of the Chaenopsidae using Bayesian inference approach based on total evidence………………………………………………………..95 Fig. 2.5 Hypothesized generic relationships of the Chaenopsinae………………………96 Fig. 2.6 Alternative species-level relationships of the genus Coralliozetus……………..97 Chapter 3 Fig. 3.1 Collecting sites of Acathemblemaria crockeri in the Gulf of California……...113 Fig. 3.2 Maximum parsimonious (MP) phylogeny based on 558bp mtDNA COI data of 68 A. crockeri with A. macrospilus as the outgroup……………………………………117 Fig. 3.3 Haplotype networks with estimated matriarchal phylogeny based on the tRNA- Pro/D-loop dataset of 115 Acanthemblemaria crockeri………………………………..118 Fig. 3.4 Occurrences and relative frequencies of the northern “Gulf” color morph, southern “Cape” color morph, and female intermediate morphs……………..…….…..119 Chapter 4 Fig. 4.1 Collecting sites of Acanthemblemaria macrospilus and A. hastingsi sp. nov. for molecular (1-15) and morphological data (A-E) in the Tropical Eastern Pacific………146 viii Fig. 4.2 Bayesian Inference phylogeny based on 560bp COI, 422bp D-loop and the combined data with A. hancocki as the outgroup………………………………………146 Fig. 4.3 (A) Acanthemblemaria hastingsi, sp. nov., holotype (SIO 65-272), 43.6 mm SL. (B) Acanthemblemaria hastingsi, sp. nov., life colors………………………………….147 Fig. 4.4 Scanning electron microscope image of Acanthemblemaria hastingsi head spination………………………………………………………………………………...147 ix LIST OF TABLES Chapter 1 Table 1.1 Localities and voucher IDs for terminal taxa used for phylogenetic analysis…………………………………………………………………………………...40 Table 1.2 Currently recognized subfamilies and tribes of five families of the Blennioidei……………………………………………………………………………….44 Table 1.3 Species allocated to three genera previously placed in the genus Labrisomus…. …………………………………………………………………........................................46 Chapter 2 Table 2.1 Localities, voucher IDs, and Genbank accession numbers for chaenopsids….88 Table 2.2 Primers used for PCR amplification and sequencing…………………………90 Table 2.3 Summary of parameters of each datasets……………………………………...90 Table 2.4 Estimates of evolutionary divergence between geminate species at either side of the Central America…………………………………………………………………...91 Chapter 3 Table 3.1 Study sites, biogeographic regions and sample sizes of Acanthemblemaria crockeri..………………………………………………………………..........................115 Table 3.2 Pairwise Tamura-Nei divergence of tRNA-Pro/D-loop between study sites of (a) the northern “Gulf” species and (b) the southern “Cape” species…………………..119 Chapter 4 Table 4.1 Study sites and sample sizes of Acanthemblemaria macrospilus for molecular analyses. …………………………………………………………..................................141 Table 4.2 Collecting sites and accession numbers for COI and D-loop haplotypes and S7- 1 genotypes.………………………………………………………….............................142 Table 4.3 (a) Nineteen S7-1 haplotypes predicted from PHASE and (b) the haplotype phase of each specimen collected from the Gulf of California and southwestern Mexico. ...………………………………………………………...................................................143 Table 4.4 Vertebral and fin elements of 40 cleared and stained paratypes of A. hastingsi. ...………………………………………………………...................................................144 Table 4.5 Size ratios sorted by sex………………….......................................................145 x ACKNOWLEDGEMENTS This dissertation would not have been possible without the help of many people. First, I would like to give deep thanks to my adviser Philip A. Hastings who gave me the opportunity to pursue my research interests in fish evolution, provided helpful advice on research, and respected me as though I were a colleague. As an international student, I especially appreciate his understanding of our cultural difference and his unlimited patience while correcting both my spoken and written English. Many thanks are also due to my other committee members: Ron Burton, Richard Rosenblatt, Greg Rouse, and Chris Wills. Ron Burton and his lab (Kristen Gruenthal, Chris Ellison, and others) provided insight whenever I struggled in molecular experiments or with the sequencing machine. Greg Rouse and his lab (Nerida Wilson, Danwei Huang, and others) helped me with the most up-to-date analytical software. Richard Rosenblatt taught me how to do good scientific writing. A special thanks goes to my qualifying committee member Nancy Knowlton and her lab (Flavia Nunes, Laetetia Plaisance, Melissa Roth, and others) who generously provided lab space and molecular equipment throughout my doctoral career. This dissertation would not be completed as smoothly without the friendly and helpful Hastings’ lab members: Brad Erisman, John Hyde, Grant Galland, HJ Walker, Octavio Aburto, and Cindy Klepadlo. A special thanks for the hospitality the Marine Biology family offered,
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