Evolutionary Genetics of the Family Placobranchidae (Mollusca: Gastropoda: Opisthobranchia: Sacoglossa) Anna Lee Bass University of South Florida
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University of South Florida Scholar Commons Graduate Theses and Dissertations Graduate School 2006 Evolutionary genetics of the family Placobranchidae (Mollusca: Gastropoda: Opisthobranchia: Sacoglossa) Anna Lee Bass University of South Florida Follow this and additional works at: http://scholarcommons.usf.edu/etd Part of the American Studies Commons Scholar Commons Citation Bass, Anna Lee, "Evolutionary genetics of the family Placobranchidae (Mollusca: Gastropoda: Opisthobranchia: Sacoglossa)" (2006). Graduate Theses and Dissertations. http://scholarcommons.usf.edu/etd/2453 This Dissertation is brought to you for free and open access by the Graduate School at Scholar Commons. It has been accepted for inclusion in Graduate Theses and Dissertations by an authorized administrator of Scholar Commons. For more information, please contact [email protected]. Evolutionary Genetics Of The Family Placobranchidae (Mollusca: Gastropoda: Opisthobranchia: Sacoglossa) by Anna Lee Bass A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy Department of Biology College of Arts and Sciences University of South Florida Co-Major Professor: Dr. Earl Mccoy, Ph.D. Co-Major Professor: Dr. Stephen Karl, Ph.D. Dr. Sidney Pierce, Ph.D. Dr. James Garey, Ph.D. Date of Approval: September 29, 2006 Keywords: phylogeny, population genetics, mitochondrial dna, nuclear dna, cladogenesis © Copyright 2006 , Anna Lee Bass DEDICATION I dedicate this dissertation to my parents, Roberta and Robert Bass. My mother instilled in me a great respect for diversity and appreciation for beauty. Although most of the time her view was oriented towards human beings, it was easy extending this appreciation and respect to other animals. I thank her for the ability to see this. My father has been a great source of strength that has supported me through good and bad times. He tried his best to teach me math and in doing so instilled in me a great appreciation for the power of it. Even though my parents do not really understand my fascination with biology, they have always supported my choice to pursue biological studies. They have been a consistent source of funding throughout my career and I thank them for that. For these reasons and many other others, I dedicate this dissertation to them. Thus they are to overcome the temptation to categorize things too quickly, so they may keep their perceptions neutral and view events - and people - as they actually are. From the Itty Bitty Buddha by Nicola Dixon (2002) ACKNOWLEDGEMENTS I wish to thank my committee, Stephen Karl, Earl McCoy, Sidney Pierce and James Garey. Florence Thomas was a former committee member who provided excellent guidance and support over the years. Thanks to everyone for their guidance and support. I particularly want to thank my lab mates, Andrey Castro, Caitlin Curtis, Kenneth Hayes, Tonia Schwartz, Emily Severance and Cecelia Puchuletegui, who made significant intellectual contributions during my tenure at USF. I also want to thank them for their patience, humor and general grooviness. They made my graduate career an enjoyable experience and I know that I could not have done it without them. Other Biology graduate students, Terry Campbell, Tatiana Cornelisen, Mark Driscoll, Jeff Hanten, Mary Harmon, Sean Kinane, Allison Meyers, Brent Nichols and Kristen Penney, also contributed to this dissertation either through field, statistical or maintenance of sanity assistance. None of this work could have been conducted without the people who responded to my requests for help with the collection of the sea slug specimens. In particular, Clay Carlson and Patty Jo Hoff quickly and unwaveringly supplied samples from Guam. I also thank the following for either sending me specimens or helping me collect specimens in Florida and the Bahamas: Victor Bonito, Chris & Jane Bowen, Andrey Castro, Lucas Cervera, Nick Curtis, Anne Dupont, Pauline Fiene, Daniel Geiger, Kenneth Hayes, Nishina Masayoshi, Sandra Millen, Mike Miller, Robert Oms, Cory Pittman, Victor Raphael, Luiz Rocha, Emily Severance and Cynthia Trowbridge. Other persons who have contributed to my growth as a biologist, teacher and person are Jodi & Alexandra Nettleton, Johnny El-Rady, Theresa & Jim Demastes, Marilyn Myerson, Susan Meiers, Rachel Crawford, Matt Garvey, and Mr. O'Malley. They always offered encouragement and support and thanks is simply insufficient. The Department of Biology has a wonderful staff and I gratefully thank Janet Gauthier, Pat Homer, Kathleen Hotchkiss, Betty Loraam, Ray Martinez, Dawn McGowan, Christine Smith, Robin Sylvester and Totka Tzaneva. Travel and research funding were provided by the Conchologists of America, PADI, Department of Biology Tharpe Fellowships and Roberta & Robert Bass. Finally, I wish to thank Dustin Binge and Daniel Majchrzak, members of the Research Computing Core Facility at the University of South Florida, for their patience and assistance while I was learning how to use Linux computing language. Note to Reader: The original of this document contains color that is necessary for understanding the data. The original dissertation is on file with the USF library in Tampa, Florida. TABLE OF CONTENTS List of Tables iii List of Figures iv Abstract vi Overview 1 Chapter 1: Phylogenetic Relationships Within The Family Placobranchidae 5 Introduction 5 Materials and Methods 9 Results 16 Variation at the individual level 16 Saturation tests for protein coding genes 17 Divergence levels 18 Phylogeny 20 Nucleotide substitution patterns and relative rates 21 Total evidence phylogeny 22 Discussion 27 Divergence levels among taxonomic categories and within species variation 27 Phylogeny of the Placobranchidae and associated families 29 Gene performance in phylogenetic reconstruction 31 References 33 Chapter 2: Evidence of Increased Cladogenesis in the Family Placobranchidae 65 Introduction 65 Materials and Methods 67 Results 72 Character tracing 73 Lineages through time 75 Discussion 75 References 82 i Chapter 3: Comparative Population Genetic Structure Among Three Species of Placobranchids 100 Introduction 100 Materials and Methods 103 Results 108 Elysia tuca 108 Elysia crispata 110 Elysia subornata 114 Discussion 117 Elysia subornata variation 117 Elysia crispata variation 120 Within and among population variation 121 References 128 About the Author End Page ii LIST OF TABLES Table 1.1 List of species used in the phylogenetic analysis. 44 Table 1.2 Models of evolution used in estimates of divergence at various taxonomic levels. 47 Table 1.3 Maximum likelihood estimates of divergence based on mtDNA. 48 Table 1.4 Maximum likelihood estimates of divergence based on Histone 3. 49 Table 1.5 Bayesian parameter estimates from the GTR+I+G. 50 Table 2.1 Sacoglossan families, genera and number of species currently recognized. 91 Table 2.2 Taxonomic list of species used in the phylogenetic analysis 92 Table 2.3 Character matrix for species used in the ancestral state reconstructions for three life history traits. 94 Table 3.1 Primers used in amplification of three species of sacoglossans. 134 Table 3.2 Cytochrome c oxidase subunit I haplotypes by location for species of sacoglossans. 135 Table 3.3 Haplotype and nucleotide diversity estimates + standard deviations for three species of sacoglossans. 136 Table 3.4 Summary of uncorrected p and maximum likelihood (ML) distances. 137 Table 3.5 Accession numbers for sequences of 16S and Histone 3 gene regions. 138 Table 3.6 Results of overall estimate of ΦST and select life history traits for three species of sacoglossans. 139 iii LIST OF FIGURES Figure 1.1 Saturation as indicated by non-linear relationship between uncorrected p-distances versus uncorrected p transversion distances for 3rd positions of A) cox 1 and B) Histone 3. 52 Figure 1.2 Maximum likelihood estimates of sequence divergence based on mtDNA. 53 Figure 1.3 Maximum likelihood estimates of sequence divergence based on Histone 3. 54 Figure 1.4 Bayesian phylogram for mtDNA. 55 Figure 1.5 Bayesian phylogram for Histone 3. 56 Figure 1.6 Proportion of nucleotides A) by gene for all three genes and B) by position for the protein coding genes. 57 Figure 1.7 Relative rates of evolution A) by gene and B) by gene for 16S and by position for the protein coding genes. 58 Figure 1.8 Relative rates derived from the instantaneous rate matrix for all genes generated from GTR+I+G by gene model settings. 59 Figure 1.9 Bayesian phylogram of GTR+I+G model for the combined mtDNA and nucDNA datasets. 60 Figure 1.10 Maximum parsimony cladogram of concatenated mtDNA and nucDNA datasets. 61 Figure 1.11 Maximum parsimony phylogram of concatenated mtDNA and nucDNA datasets with branch lengths proportional to unambiguous changes. 62 Figure 1.12 Bayesian phylogram of a subsample of taxa used to test long branch division by multiple short branches. 63 iv Figure 1.13 Portion of Bayesian phylogram based on total evidence (Figure 1.9). 64 Figure 2.1 Bayesian phylogram based on concatenated mtDNA and nucDNA datasets. 95 Figure 2.2 Most parsimonious reconstruction of larval development on the Bayesian phylogeny. 96 Figure 2.3 Most parsimonious reconstruction of level of kleptoplasty on the Bayesian phylogeny. 97 Figure 2.4 Most parsimonious reconstruction of food choice on the Bayesian phylogeny. 98 Figure 2.5 NPRS transformed ultrametric tree with a scale bar proportional to smoothed rate of substitution. 99 Figure 3.1 Results of Neighbor Joining (NJ) analysis of Elysia tuca cox 1 haplotypes from the Gulf of Mexico (GOM), Florida Keys (FLK) and the Bahamas (BA). 140 Figure 3.2 Results of Neighbor Joining (NJ) analysis of Elysia crispata cox 1 haplotypes from Florida Keys (FLK), Belize, Bahamas (BA1 & BA2) and the United States Virgin Islands (USVI). 141 Figure 3.3 Regression of 3rd position transitions (◊) and transversions (×) against uncorrected p-distances for Elysia crispata haplotypes and Elysia diomedea. 142 Figure 3.4 Results of Neighbor Joining (NJ) analysis of Elysia subornata cox 1 haplotypes from the Florida Keys (FLK) and Indian River Lagoon (IRL).