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Phylogeography of the Natal Puddle Frog Phrynobatrachus Natalensis

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Phylogeography of the Natal Puddle Frog Phrynobatrachus Natalensis University of Texas at El Paso DigitalCommons@UTEP Open Access Theses & Dissertations 2016-01-01 Phylogeography Of The aN tal Puddle Frog Phrynobatrachus Natalensis (anura: Phrynobatrachidae) In Sub-Saharan Africa Joshua Adan Lara University of Texas at El Paso, [email protected] Follow this and additional works at: https://digitalcommons.utep.edu/open_etd Part of the Biology Commons Recommended Citation Lara, Joshua Adan, "Phylogeography Of The aN tal Puddle Frog Phrynobatrachus Natalensis (anura: Phrynobatrachidae) In Sub- Saharan Africa" (2016). Open Access Theses & Dissertations. 876. https://digitalcommons.utep.edu/open_etd/876 This is brought to you for free and open access by DigitalCommons@UTEP. It has been accepted for inclusion in Open Access Theses & Dissertations by an authorized administrator of DigitalCommons@UTEP. For more information, please contact [email protected]. PHYLOGEOGRAPHY OF THE NATAL PUDDLE FROG PHRYNOBATRACHUS NATALENSIS (ANURA: PHRYNOBATRACHIDAE) IN SUB-SAHARAN AFRICA JOSHUA ADAN LARA Master’s Program in Biology APPROVED: Eli Greenbaum, Ph.D Michael Moody, Ph.D Edward Castañeda, Ph.D Charles Ambler, Ph.D. Dean of the Graduate School Copyright © by Joshua Adan Lara 2016 PHYLOGEOGRAPHY OF THE NATAL PUDDLE FROG PHRYNOBATRACHUS NATALENSIS (ANURA: PHRYNOBATRACHIDAE) IN SUB-SAHARAN AFRICA by JOSHUA ADAN LARA, B.S. THESIS Presented to the Faculty of the Graduate School of The University of Texas at El Paso in Partial Fulfillment of the Requirements for the Degree of MASTER OF SCIENCE Department of Biological Sciences THE UNIVERSITY OF TEXAS AT EL PASO May 2016 ACKNOWLEDGMENTS First, I would like to thank my graduate committee, Dr. Eli Greenbaum, Dr. Michael Moody, and Dr. Edward Castañeda. I would like to give special thanks to my thesis advisor Dr. Eli Greenbaum, who took me on as a graduate student on short notice. I would like to thank the entire faculty at UTEP for providing support. I thank Breda Zimkus, Ph.D. (Harvard University’s Museum of Comparative Zoology), Werner Conradie (Port Elizabeth Museum, South Africa), Stephane Boissinot, Ph.D. (New York University, Abu Dhabi), and Mark-Oliver Rödel, Ph.D. (Museum für Naturkunde, Berlin, Germany) for access to specimens. Moreover, I would like to thank the UTEP Border Biomedical Research Center (BBRC) Genomics Analysis Core Facility, especially Ana Betancourt. I am also thankful to all my lab members Frank Portillo, Danny Hughes, Maria “Fernie” Medina, and Thornton Larson for all of their assistance. iv ABSTRACT The Family Phrynobatrachidae (Laurent, 1941) has one genus (Phrynobatrachus Günther, 1862) containing 89 species. Commonly known as puddle frogs, they comprise one of the most species rich sub-Saharan amphibian groups. The objective of this study was to investigate Phrynobatrachus natalensis from the Albertine Rift (AR) with systematic and phylogeographic methods. One mitochondrial DNA gene (16S = 555 base pairs [bp]) and one nuclear gene (RAG1 = 774 bp) were analyzed for 61 representatives of P. natalensis. Nine cryptic lineages were identified from Angola, Burundi, Côte d’Ivoire, Democratic Republic of the Congo, Ethiopia, Ghana, Mozambique, Namibia, Tanzania, Rwanda, and Uganda. Several of these lineages are likely new species. Genetic diversity among populations of P. natalensis for 16S was moderate to high (4–13%). Low genetic divergence was recovered in RAG1 (0–1%). Morphological characters were used to examine species boundaries in distinct lineages identified from the molecular phylogeny. No clear pattern was evident in these data. The results of this study suggest the diversity of P. natalensis has been severely underestimated. Additional research efforts should focus on the biogeographic patterns, reproductive isolation, acoustic calls, reproductive behavior, and ecology to determine species boundaries. Furthermore, it is imperative to sample more African sites, especially in the AR, to get a better understanding of African biodiversity. v TABLE OF CONTENTS ACKNOWLEDGMENTS ............................................................................................................ iv ABSTRACT .....................................................................................................................................v TABLE OF CONTENTS ............................................................................................................... vi LIST OF TABLES ....................................................................................................................... viii LIST OF FIGURES ....................................................................................................................... ix CHAPTER 1: INTRODUCTION ....................................................................................................1 1.1 Background .......................................................................................................................1 1.2 Natural history .................................................................................................................5 1.3 Reproduction ............................................................ ….....................................................6 1.4 Voice ...........................................................................................................................…. 7 1.5 Taxonomy and systematics ..........................................................................................….7 1.6 Study site ...........................................................................................................................9 1.7 Research objectives and questions ..................................................................................14 Chapter 2: MATERIALS AND METHODS .................................................................................15 2.1 Specimen acquisiton .......................................................................................................15 2.2 DNA extraction ...............................................................................................................15 2.3 DNA amplification, sequencing and alignment .............................................................16 2.4 Phylogenetic analyses .....................................................................................................19 2.5 Analyses of genetic distance ..........................................................................................19 2.6 Morphological analyses of adult frogs ............................................................................20 Chapter 3: RESULTS ....................................................................................................................22 3.1 Phylogenetic analyses .....................................................................................................22 3.2 Analyses of genetic distance ..........................................................................................23 3.3 Albertine Rift P. natalensis morphology ........................................................................23 Chapter 4: DISCUSSION ..............................................................................................................31 4.1 Taxonomic status and phylogeography of the Albertine Rift .........................................31 4.2 Conservation ...................................................................................................................35 4.3 Conclusion and future directions ....................................................................................38 vi RERFERNCES ........................................................................................................................…..39 APPENDIX I .................................................................................................................................49 APPENDIX II ................................................................................................................................52 VITA … .........................................................................................................................................53 vii LIST OF TABLES Table 2.3.1 Primers used for sequencing genes…………………………………………………18 Table 3.1.1 Model parameters specified by PartitionFinder and alternate models implemented in MrBayes ........................................................................................................................................ 22 Table 3.2.1 Uncorrected p-distances (16S) among selected individuals from the P. natalensis phylogeny…………..…………………………………………………………………………….27 Table 3.2.2 Uncorrected p-distances (RAG1) among selected individuals from the P. natalensis phylogeny……………...…………………………………………………………………………28 Table 3.3.1 Morphometric data of adult male voucher specimens of P. cf. natalensis from selected clades from Fig. 3.1.1 (in mm). Data are presented as mean + one standard deviation, followed by range……………………………………………………………………....…………29 Table 3.3.2 Principal components analysis comparing adult male specimens from clades of Albertine Rift P. cf. natalensis with raw mensural data regressed against snout–vent length. Eigenvalues, percent variance, cumulative variance, and loadings are shown for the first three principal components……………………………………………………………………………30 viii LIST OF FIGURES Figure 1.4 Map of sub-Saharan Africa showing the disjunct distribution of Phrynobatrachus natalensis. Sampled localities for the genetic analyses are shown with circles. Circle colors
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