Loma Linda University TheScholarsRepository@LLU: Digital Archive of Research, Scholarship & Creative Works Loma Linda University Electronic Theses, Dissertations & Projects 6-1999 The Molecular Systematics of the Side-blotched Lizards (IGUANIA: PHRYNOSOMATIDAE: UTA) Bradford Damion Hollingsworth Follow this and additional works at: https://scholarsrepository.llu.edu/etd Part of the Biology Commons Recommended Citation Hollingsworth, Bradford Damion, "The Molecular Systematics of the Side-blotched Lizards (IGUANIA: PHRYNOSOMATIDAE: UTA)" (1999). Loma Linda University Electronic Theses, Dissertations & Projects. 602. https://scholarsrepository.llu.edu/etd/602 This Dissertation is brought to you for free and open access by TheScholarsRepository@LLU: Digital Archive of Research, Scholarship & Creative Works. It has been accepted for inclusion in Loma Linda University Electronic Theses, Dissertations & Projects by an authorized administrator of TheScholarsRepository@LLU: Digital Archive of Research, Scholarship & Creative Works. For more information, please contact [email protected]. LOMA LINDAUNIVERSITY Graduate School E TH MOLECULAR SYSTEMATICS OF THESIDE-BLOTCHED LIZARDS (IGUANIA: PHRYNOSOMATIDAE: UTA) by BradfordDamion Hollingsworth A Dissertation in Partial Fulfillment of the Requirements forthe Degree Doctor of Philosophy in Biology June 1999 0 1999 Bradford Hollingsworth All Rights Reserved II Each person whose signature appears below certifies that this dissertation in their opinion is adequate, in scope and quality, as a dissertation for the degree of Doctor of Philosophy. Ronald L. Carter, Professor of Biology Co-Chairperson L. Lee Grismer, Professor of Biology H. Pau uchheim, Professor of Geology William K. Hayes, Associate Profs r of Biology e. Garry P. Lars 1, Assistant Research Scientist, Beckman Research Institute of the City of Hope lii ACKNOWLEDGMENTS I would like to thank the numerous individuals who assisted me during the course of this analysis. Most notable are those who contributed to my growth as a biologist and a person. My committee chairs Ron Carter and Lee Grismer patiently supported me and provided valuable advice both in the lab and field. In addition, I would like to thank Garry Larson, Bill Hayes, and Paul Buchheim for their assistance as committee members and the remaining members of the faculty and student body in the Department of Natural Sciences at Loma Linda University for offering an educational atmosphere full of inspiration. I am grateful to the Center of Molecular Biology and Gene Therapy for the use of their automated sequencer and the DNA Sequencing Facility at California State University, Northridge and their technician Janine Wengert for generating numerous sequences. Many thanks to John J. Wiens at the Carnegie Museum of Natural History for his assistance on conducting the computer analyses and his insights into phylogenetic methods and evolutionary processes. • I would like to thank the many individuals who helped me during the extensive field work done for this project, including Lee Grismer, Ron Carter, Mike Cryder, Erik Gergus, Jesse Grismer, Eric Link, Gene Kim, Chris Mattison, Erik Mellink, Roland Sosa, Humberto Wong, Nelson Wong, and the many Mexican ranchers and fisherman who served as guides and naturalists, in addition to providing me with food and shelter. iv TABLE OF CONTENTS LIST OF FIGURES vi LIST OF TABLES viii ABSTRACT 1 INTRODUCTION 3 MATERIAL AND METHODS 9 Sampling 9 Operational Taxonomic Units 9 Ingroup Monophyly 14 DNA Sequence Data 14 Tree Reconstruction 17 Selection of Outgroups 22 Confidence, Support, and Signal 26 Comparison With Previous Analyses 27 RESULTS 31 Confidence, Support, and Signal 31 Combined DNA Sequences 31 Maximum Parsimony Analyses 31 Maximum Likelihood Analyses 42 Comparison With Upton and Murphy (1997) S 45 DISCUSSION 61 Phylogenetic Analyses 61 Comparison with the Analysis of Upton and Murphy (1997) 64 Ancestral Nature of Insular Populations 65 Geographical Concordance 73 Cryptic Species Boundaries 79 Exclusivity and Non-exclusivity 83 Taxonomy 85 LITERATURE CITED 91 APPENDIX 101 Appendix 1: Results of the computer program PAUP 101 LIST OF FIGURES FIGURES PAGE 1. Locality map showing the location of the eight insular endemic species of Uta. All continental landmasses and unmarked islands are inhabited by Uta stansburiana 2. Locality map showing the region of study and the 98 samples used in this analysis 10 3. Outgroup topologies of phrynosomatid genera: a) traditional topology of Etheridge and de Queiroz (1988) and Wiens (1993); b) combined tree of Reeder and Wiens (1996) and Wiens and Reeder (1997); and c) combined data tree of Schulte et al. (1998) 24 4. Strict consensus tree of the unweighted parsimony analysis using 98 ingroup samples and 11 outgroup taxa 33 5. Strict consensus tree of the weighted parsimony analysis (Tv:Ti = 5) using 98 ingroup samples and 11 outgroup taxa 40 6. Maximum likelihood tree using the same data set as in the parsimony analysis pruned to a total of 56 samples (see Table 6) 43 7. Reanalysis of Upton and Murphy (1997): a) unweighted parsimony analysis; and b) weighted parsimony analysis (Tv:Ti =5) 47 8. Reanalysis of data set from this analysis pruned to 22 taxa to match those of Upton and Murphy (1997; see Table 9): a) unweighted analysis using two outgroup species; b) tree from unweighted analysis (see Fig. 4) pruned to 22 taxa; c) unweighted analysis using 11 outgroup species unconstrained; and d) unweighted analysis using 11 outgroup species constrained to Reeder and Wiens (1996) topology 51 9. Analysis of the combined data set from DNA sequence generated in this analysis and Upton and Murphy (1997): a) unweighted parsimony analysis; and b) weighted parsimony analysis (Tv:Ti = 5) 55 10. Maximum likelihood tree using the combined data set from DNA sequence generated in this analysis and Upton and Murphy (1997): a) unweighted parsimony analysis; and b) weighted parsimony analysis (Tv:Ti = 5) 58 11. Phylogenetic tree from weighted analysis depicting the placement of ancestral insular populations (indicated with heavy bars) 66 vi FIGURES PAGE 12. Model of evolution for insular taxa derived from mainland ancestors from Grismer (1999c). A, B, C, and a4 are contemporary species depicting the chronological order of island colonization; A being first to colonize and C being the third to colonize. al = first continental ancestor; a, = second continental ancestor; a3 = third continental ancestor; and a4 = the last continental ancestor to evolve. The solid bars indicate the acquisition of derived character states in the continental ancestors 69 13. Map depicting the geographic position of the strongly supported groups within haploclade A (see Fig. 5 for designations) 75 14. Map depicting the geographic position of the strongly supported groups within haploclade B (see Fig. 5 for designations) 76 15. Map depicting the geographic position of haploclades A and B. Contact zone occurs between Santa Agueda (M-22) and San Bruno (M-21.) 80 16. Phylogenetic tee depicting the placement of currently named species and likely evolutionary species 87 vii LIST OF TABLES TABLE PAGE 1. Taxonomy of Uta based on Ballinger and Tinkle (1972) and Grismer (1994a)... 4 2. Scalar levels of the hierarchy of replicators, their mode of inheritance and replication, and their expected historical pattern 7 3. Specimen localities with their corresponding codes and species designation 11 4. Sequences of primers used in the PCR and sequencing reactions 15 5. PCR conditions used to amplify cytochrome b and cytochrome oxidase III gene fragments 16 6. Specimens selected for phylogenetic analysis using maximum likelihood 19 7. Summary of parameters in nucleotide substitution models 20 8. List of outgroup taxa used in the maximum parsimony and likelihood analyses 23 9. Samples selected from this analysis to combine with samples in the data set of Upton and Murphy (1997) 28 10. Comparison of likelihood scores from a single tree chosen from the parsimony analysis using the 56 taxa and the DNA sequence from cytochrome b and cytochrome oxidase 46 11. Likelihood ratio tests comparing statistical differences between increasingly complex models of DNA sequence evolution using 56 taxa and the DNA sequence from cytochrome b and cytochrome oxidase 46 12. Sequential Bonferroni correction for statistical tables for the comparison of models using the likelihood ratio test (see Table 9) 46 13. Results of the Wilcoxon Sign-Ranks Tests for the comparison between reduced taxa data sets and their most-parsimonious trees for the unweighted analyses 50 14. Results of the Wilcoxon Sign-Ranks Tests for the comparison between reduced taxa data sets and their most-parsimonious trees for the weighted analyses 53 15. Comparison of likelihood scores from a single tree chosen from the parsimony analysis using the 22 taxa data sets combined from this analysis and Upton and Murphy (1997) 60 viii TABLE PAGE 16. Likelihood ratio tests comparing statistical differences between increasingly complex models of DNA sequence evolution using the 22 taxa data sets combined from this analysis and Upton and Murphy (1997) 60 17. Sequential Bonferroni correction for statistical tables for the comparison of models using the likelihood ratio test (see Table 16) 60 18. Categories of strongly supported and geographically concordant groups of two or more populations 74 ix ABSTRACT THE MOLECULAR SYSTEMATICS OF THE SIDE-BLOTCHED LIZARDS (IGUANIA: PHRYNOSOMATIDAE: UTA) by