Family Plethodontidae) in the Gulf Coastal Plain
Total Page：16
File Type：pdf, Size：1020Kb
The University of Southern Mississippi The Aquila Digital Community Dissertations Spring 5-1-2016 Ecology and Genetics of Lungless Salamanders (Family Plethodontidae) in the Gulf Coastal Plain Jennifer Yasmin Lamb University of Southern Mississippi Follow this and additional works at: https://aquila.usm.edu/dissertations Part of the Genetics Commons, and the Other Ecology and Evolutionary Biology Commons Recommended Citation Lamb, Jennifer Yasmin, "Ecology and Genetics of Lungless Salamanders (Family Plethodontidae) in the Gulf Coastal Plain" (2016). Dissertations. 336. https://aquila.usm.edu/dissertations/336 This Dissertation is brought to you for free and open access by The Aquila Digital Community. It has been accepted for inclusion in Dissertations by an authorized administrator of The Aquila Digital Community. For more information, please contact [email protected]. ECOLOGY AND GENETICS OF LUNGLESS SALAMANDERS (FAMILY PLETHODONTIDAE) IN THE GULF COASTAL PLAIN by Jennifer Yasmin Lamb A Dissertation Submitted to the Graduate School and the Department of Biological Sciences at The University of Southern Mississippi in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy Approved: ________________________________________________ Dr. Carl P. Qualls, Committee Chair Professor, Biological Sciences ________________________________________________ Dr. Brian R. Kreiser, Committee Member Professor, Biological Sciences ________________________________________________ Dr. Micheal A. Davis, Committee Member Associate Professor, Biological Sciences ________________________________________________ Dr. Jacob F. Schaefer, Committee Member Professor, Biological Sciences ________________________________________________ Dr. J. Hardin Waddle, Committee Member Research Ecologist, U. S. Geological Survey National Wetlands Research Center ________________________________________________ Dr. Karen S. Coats Dean of the Graduate School May 2016 COPYRIGHT BY Jennifer Yasmin Lamb 2016 Published by the Graduate School ABSTRACT ECOLOGY AND GENETICS OF LUNGLESS SALAMANDERS (FAMILY PLETHODONTIDAE) IN THE GULF COASTAL PLAIN by Jennifer Yasmin Lamb May 2016 During the last half century, lungless salamanders (Family Plethodontidae) have been the subject of numerous studies in the fields of ecology and genetics. While most works have focused on the species-rich Eastern Highlands region, there has been a recent shift towards plethodontid assemblages within the Coastal Plain. The research presented herein applies hierarchical occupancy models and both mitochondrial and nuclear genes to address questions pertinent to the biology and conservation of plethodontids within the Gulf Coastal Plain. The results of a multi-species Bayesian single-season occupancy model indicated that two environmental gradients, upstream drainage area and stream drying, influenced the probability of occurrence for multiple species of stream-breeding plethodontids. Further, species varied in their responses to these gradients. A second model was used to ask whether asymmetric interactions also influenced occurrence for three species of brook salamanders (Genus Eurycea). More specifically, the model tested whether the southern two-lined salamander (E. cirrigera) might act as the dominant predator and or competitor to either the three-lined (E. guttolineata) or dwarf (E. quadridigitata) salamanders. The results of this second model suggested that environmental gradients likely work in tandem with negative interactions to shape the distribution of E. guttolienata within the Gulf Coastal Plain. Like hierarchical occupancy models, genetic tools are also shedding light on complex relationships among and within ii species of lungless salamanders. This research investigated phylogeographic patterns within a wide-ranging species of plethodontid, the spotted dusky salamander (Desmognathus conanti). Sequence data revealed that there were geographically discrete, deeply divergent mitochondrial lineages within D. conanti which may be the result of isolation brought about by fluctuating sea levels during the late Miocene through the Pleistocene. Data from six rapidly mutating microsatellite markers indicated that there had been recent gene flow across some of these lineages in the southern Gulf Coastal Plain. However, these data also suggest that a northern lineage may have remained distinct. The relationships described and occurrence probabilities estimated by the aforementioned models, in combination with conclusions from analyses of genetic data, improve our ability to conserve regional plethodontid biodiversity within this unique physiographic province. iii ACKNOWLEDGMENTS I am incredibly fortunate to have worked with a committee consisting of individuals with a wide breadth of research interests and experiences. Their consistent enthusiasm for and dedication to my development as an ecologist have been invaluable. I thank J. Hardin Waddle and Brian R. Kreiser for their willingness to take on a student with plenty of interest but no prior experience in their respective fields and Carl P. Qualls whose early patience and guidance fostered my sense of independence and confidence. I am also grateful to Micheal A. Davis for always reminding me that I will never regret reaching for a goal, and Jacob F. Schaefer for challenging me to think multiple steps ahead and in multiple potential directions. These projects could not have been accomplished without assistance from many other individuals. James R. Lee, Lynn McCoy Kathy Shelton and Will Selman’s prior experiences in Mississippi wetlands were useful in locating important collection localities for Desmognathus. I am grateful for pertinent insights into the ecology and evolution of Desmognathus provided by D. Bruce Means, Joseph Bernardo, and David A. Beamer. I would also like to thank the following individuals for their willingness to tackle the challenge of wrangling salamanders in the field, their assistance and advice in the laboratory, and other support: Mac H. Alford, Ronald Altig, Jeff Boundy, Grover J. Brown III, Matthew W. H. Chatfield, Scott R. Clark, Angela Getz, Andrew Heaton, Aaron Holbrook, Cybil Huntzinger, Robert L. Jones, James R. Lee, Arianna LeVine, Tom Mann, Daniel McNair, Marks McWhorter, Brandon C. Morris, Kevin Narum, Skye Necaise, Charlotte Petre, Scott Peyton, Ariana Rupp, Bjorn Schmidt, Abby Sinclair, Laura Stewart, and Avery Sward as well as Herpetology classes at USM in 2013 and iv 2015 and the Gulf Coast Research Lab in 2014 and 2015. Over the course of this experience, I have learned that a successful PhD is the culmination of a personal passion surrounded and bolstered by a supportive, engaged community. The former cannot persist without the latter. I would also like to acknowledge and thank the funding and granting agencies that made this work possible. This research was funded by a U.S. Geological Survey Cooperative Agreement (#G10AC00689), a National Science Foundation (NSF) Graduate Research Fellowship under Grant No. 0940712 and an NSF “Molecules to Muscles” GK-12 Fellowship Award No. 0947944 through the University of Southern Mississippi. Laboratory and field work were also partially funded by a 2014 grant from the Chicago Herpetological Society and the USM Department of Biological Sciences. Scientific collection permits were provided by the Mississippi Department of Wildlife, Fisheries, and Parks and the Louisiana Department of Wildlife and Fisheries. The Louisiana State University Museum of Natural Science’s Collection of Genetic Resources provided a tissue loan permit for multiple samples from Louisiana. All work was conducted in accordance with the appropriate institutional Animal Care guidelines. Any use of trade, firm, or product names is for descriptive purposes only and does not imply endorsement by the U.S. Government. v DEDICATION To Brandon C. Morris, my husband and closest friend, who has marveled, endured, and celebrated by my side throughout this process, and with whom I am excited to share my next adventure. I could not have hoped for a better teammate. To my parents, Brian K. and Laura J. Lamb, and my sister, Jessica K. L. Jones, each of which has cheered for me loudly and without fail. I could not have asked for better role models. To my grandmother, Ellen G. Lamb, and grandfather, William S. Lamb, whose tenacity and compassion I hope to live up to. vi TABLE OF CONTENTS ABSTRACT ........................................................................................................................ ii ACKNOWLEDGMENTS ................................................................................................. iv DEDICATION ................................................................................................................... vi LIST OF TABLES .............................................................................................................. x LIST OF ILLUSTRATIONS ............................................................................................ xii CHAPTER I – ESTIMATING OCCUPANCY AND DETECTION PROBABILITIES FOR STREAM-BREEDING SALAMANDERS ............................................................... 1 Abstract ........................................................................................................................... 1 Introduction ..................................................................................................................... 2 Methods..........................................................................................................................