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ORIGIN and BIOGEOGRAPHY of the CUBAN TREEFROG Osteopilus Septentrionalis in the BAHAMAS

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ORIGIN and BIOGEOGRAPHY of the CUBAN TREEFROG Osteopilus Septentrionalis in the BAHAMAS ORIGIN AND BIOGEOGRAPHY OF THE CUBAN TREEFROG Osteopilus septentrionalis IN THE BAHAMAS By JOSHUA ALAN RINGER A THESIS PRESENTED TO THE GRADUATE SCHOOL OF THE UNIVERSITY OF FLORIDA IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF MASTER OF SCIENCE UNIVERSITY OF FLORIDA 2019 © 2019 Joshua Alan Ringer To my beautiful parents, you have been nothing but supportive my entire life. Thank you for always letting me be me. Most importantly, thank you to my sister Virginia. You truly are my inspiration. Love you, always and forever ACKNOWLEDGMENTS I would like to thank my advisors Dr. Steve A. Johnson and Dr. David W. Steadman, as well as Dr. David C. Blackburn for all the support throughout my graduate career. I appreciate all the valuable suggestions and recommendations which helped tremendously in shaping this thesis. I could not thank Dr. Steadman enough for the constant motivation, and truly inspiring me to become a better scientist and researcher. Learning should be an adventure, and Dr. Steadman has always reminded me of that. I am also very grateful to Dr. David Reed, Dr. Verity Mathis, Dr. Aida Miro, Lauren Rowan, Aditi Jayarajan and the rest of the Reed Lab, for all the support and assistance in and out of the field. I’d like to thank Dr. Angelo Soto-Centeno for his immense help and patience with the morphometric chapter. I thank the Blackburn Lab, especially Danielle Hayes for always helping me with molecular techniques and analysis. Last but certainly not least, I thank my family and friends. Without the constant motivation, love and encouragement, none of this would have been possible. 4 TABLE OF CONTENTS Page ACKNOWLEDGMENTS ...................................................................................................... 4 LIST OF TABLES ................................................................................................................ 6 LIST OF FIGURES .............................................................................................................. 7 ABSTRACT .......................................................................................................................... 9 CHAPTER 1 THE BAHAMIAN ARCHIPELAGO AND LIFE HISTORY OF Osteopilus septentrionalis ............................................................................................................. 11 Background ................................................................................................................. 11 Species of Interest ...................................................................................................... 13 Objectives.................................................................................................................... 15 2 USING POPULATION GENETICS TO EVALUATE THE NATIVE STATUS OF THE CUBAN TREEFROG IN THE BAHAMAS .......................................................... 16 Introduction ................................................................................................................. 16 Methods ....................................................................................................................... 17 Collection of Specimens and Tissue Extraction .................................................. 17 Mitochondrial DNA Extraction and PCR .............................................................. 18 Results ........................................................................................................................ 19 Phylogenetic Analysis .......................................................................................... 19 Population Genetic Analysis ................................................................................ 19 Haplotype Network Reconstruction and Analysis ............................................... 20 Discussion ................................................................................................................... 21 3 ANCIENT AND MODERN MORPHOMETRICS OF CUBAN TREEFROGS IN THE BAHAMAS AND FLORIDA ................................................................................ 36 Introduction ................................................................................................................. 36 Methods ....................................................................................................................... 37 Results ........................................................................................................................ 38 Discussion ................................................................................................................... 40 4 DISCUSSION AND FUTURE DIRECTIONS ............................................................. 50 LIST OF REFERENCES ................................................................................................... 53 BIOGRAPHICAL SKETCH ................................................................................................ 58 5 LIST OF TABLES Table page 2-1 Locality of modern specimens of Osteopilus septentrionalis collected for this study. ...................................................................................................................... 24 2-2 Matrix of pairwise FST values comparing genetic differences between populations. ............................................................................................................ 26 2-3 Average number of pairwise differences between population (above diagonal) and corrected average pairwise difference (below diagonal) ............... 27 2-4 Molecular Diversity Indexes. .................................................................................. 27 2-5 Mean number of pairwise differences and nucleotide diversity at the intra- population level for each locality. ........................................................................... 27 2-6 Distribution and number of individuals of the 21 haplotypes in seven populations of O. septentrionalis............................................................................ 28 6 LIST OF FIGURES Figure page 2-1 Map showing the separation between Bahamian banks, ...................................... 29 2-2 Map of Abaco (LBB) showing the caves where anuran fossils were found. ....... 30 2-3 Map of Andros (GBB) indicating where Osteopilus septentrionalis specimens were collected. ........................................................................................................ 31 2-4 Map of Eleuthera (GBB) indicating where Osteopilus septentrionalis specimens were collected. ..................................................................................... 32 2-5 Map of Eleuthera (GBB) indicating where Osteopilus septentrionalis specimens were collected. ..................................................................................... 33 2-6 Haplotype tree inferred from all Osteopilus septentrionalis samples (n=146) in IQ-Tree 1.6.12; Osteopilus vastus (Genbank: AY843713.1), Osteopilus dominicensis (Genbank: AY843711.1), Osteopilus crucialis (Genbank: AY8437.10.1) were used as an outgroups. Numbers in parenthesis are the number of individuals from a given population that have that haplotype. Values above and to the left of the nodes represent maximum likelihood bootstrap scores (from IQ-Tree) using 1000 iterations. ..................................................................... 34 2-7 Haplotype network of O. septentrionalis 16s sequences from Florida, Cuba, and the Bahamas. Each circle represents a haplotype; size of the circle is proportional to number of individuals (larger size, more individuals). Mutations are indicated by hatch marks, and black dots represent inferred intermediate haplotypes. ........................................................................................ 35 3-1 Eleutherodactylus fossil ilium from the Great Bahama Bank, Cuba and Florida. .................................................................................................................... 42 3-2 Intraspecific variation between fossil ilium from the Bahamas (left) and modern Osteopilus (right). ...................................................................................... 43 3-3 Selected ilial characters measured in this study ................................................... 44 3-4 Selected humeral characters measured in this study ........................................... 45 3-5 PCA of modern Osteopilus with complimentary ilium and humerus; all 6 measurements are included reflecting PC1 and PC2 representing the highest proportion of variance............................................................................................. 46 3-6 Box plot of PCA plotting male vs female modern Osteopilus septentrionalis. Females on the left indicate a higher variation, where males appear to be much more restricted in size. Individual samples are indicated by black dots. .... 47 7 3-7 PCA of both modern and fossil ilia of Osteopilus from the Great Bahama Bank. PC1 and PC2 representing the highest proportion of variance. ................. 48 3-8 LDA histogram of modern and fossil GBB ilia showing the distribution of each measurement per locality. ...................................................................................... 49 8 Abstract of Thesis Presented to the Graduate School of the University of Florida in Partial Fulfillment of the Requirements for the Degree of Master of Science ORIGIN AND BIOGEOGRAPHY OF THE CUBAN TREEFROG Osteopilus septentrionalis IN THE BAHAMAS By Joshua Alan Ringer December 2019 Chair:
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