RCL Master's Thesis

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FINE SCALE GENETIC STRUCTURE DRIVEN BY HABITAT-DEPENDENT SELECTION IN A MESOCARNIVORE. - A thesis submitted to the Graduate School in partial fulfillment of the requirementsfor the degree of Master of Science (Major Subject: Wildlife Science; Minor Subject: Experimental Statistics) by Rob Lonsinger

Text of RCL Master's Thesis

FINE SCALE GENETIC STRUCTURE DRIVEN BY HABITAT-DEPENDENT SELECTION IN A MESOCARNIVORE

BY ROBERT C. LONSINGER, B.S.

A thesis submitted to the Graduate School in partial fulfillment of the requirements for the degree of Master of Science

Major Subject: Wildlife Science Minor Subject: Experimental Statistics

New Mexico State University Las Cruces, New Mexico May 2010

Fine scale genetic structure driven by habitat-dependent selection in a mesocarnivore, a thesis prepared by Robert Lonsinger in partial fulfillment of the requirements for the degree, Master of Science, has been approved and accepted by the following:

Linda Lacey Dean of the Graduate School

Gary W. Roemer Chair of the Examining Committee

Date

Committee in Charge: Dr. Gary W. Roemer Dr. William Gould Dr. Caitriana Steele

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ACKNOWLEDGMENTS

I owe many thanks to my graduate advisor and friend, Dr. Gary W. Roemer, whose impact on me has been unsurpassed. His passion for ecology and teaching is contagious. He has provided me with support and guidance, from which I have grown into a better person both personally and professionally. His guidance and friendship has been irreplaceable. I thank the many friends and colleagues who provided invaluable assistance and guidance. Aaron Bueno Cabrera, James Doyle, Aaron Facka, Martin Moses, Missy Powell, James Ward and Bradford Westrich each assisted in the field. Fred Armstrong, Hildy Rieser and Renee West assisted with securing funding and logistical planning. Jack Kincaid and his mules were imperative to our backcountry stints. Funding was provided by the National Park Service and T&E, Inc. Assistantship support was provided by the Department of Fish, Wildlife and Conservation Ecology. Dr. Caiti Steele provided guidance with GIS modeling. Drs. David Daniel and William Gould provided guidance in the statistical analyses. Drs. Roemer, Gould and Steele reviewed and consequently greatly improved this thesis. I would like to thank my wife, Desiree Lonsinger, who endured many nights alone as I chased my ringtail quarry, for her unconditional support, both emotionally and financially and her continued encouragement throughout. My parents instilled in me a love for wild places, for which I am truly grateful.iii

VITA

1979 2002 2003-2004

Born in West Chester, Pennsylvania B.S. Biology (Magna cum Laude) Gannon University, Erie, Pennsylvania Employed seasonally: Telemetry Assistant, USFWS Red Wolf Recovery Field Assistant, Nez Perce Tribe Gray Wolf Recovery Wildlife Technician, Turner Endangered Species Fund Wildlife Assistant, Arizona Game and Fish Department Black-footed Ferret Reintroduction Project Graduate Assistant, Department of Fish, Wildlife and Conservation Ecology, New Mexico State University Sigma Xi The Wildlife Society American Society of Mammalogists

2004-2006

2006-2010

Professional Societies

Technical Publications

Facka AN, Lonsinger RC, Roemer GW (2008) Estimates of population size of Gunnisons prairie dogs in the Aubrey Valley, Arizona based on a new monitoring approach. Final report to the Arizona Game and Fish Department. 26pp. King C, Broecher J, Siniawski A, Lonsinger RC, Pebworth J, Van Pelt WE (2005) Results of the 2004 Black-footed Ferret Release Effort in Aubrey Valley, Arizona. Arizona Game and Fish Department, Nongame and Endangered Wildlife Program Technical Report. 20pp.

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ABSTRACT

FINE SCALE GENETIC STRUCTURE DRIVEN BY HABITAT-DEPENDENT SELECTION IN A MESOCARNIVORE By Robert C. Lonsinger

Master of Science New Mexico State University Las Cruces, New Mexico, 2010 Dr. Gary W. Roemer, Chair

Habitat preferences and prey specializations influence interspecific partitioning and the distribution of species. Heterogeneity among conspecifics and the affinity of individuals to settle in habitats similar to where they were born may, in the absence of physical barriers to dispersal, influence the genetic structure of populations. We aimed to evaluate levels of population genetic structuring in a mesocarnivore, the ringtail (Bassariscus astutus), and hypothesized that fine-scale genetic structure could occur in this species and may be related to habitat-dependent selection that would result in genetically identifiable clusters. We used 15v

microsatellite loci and two programs, STRUCTURE and GENELAND, to assess levels of population genetic structure. Our findings reveal complex hierarchical population genetic structure in absence of physical barriers to dispersal; STRUCTURE and GENELAND identified two and six subpopulations, respectively. Discriminant function analyses were then used to test for differences in habitat among clusters identified a priori by GENELAND. All the DAs proved to be robust, assigning a significantly high proportion (>80%) of individuals to their observed genetic cluster, indicating discriminant power that cannot be explained by random chance alone. Finally, using the ringtail as a short-range dispersal generalist we evaluated the degree of connectivity between two protected areas, Guadalupe Mountains National Park and Carlsbad Caverns National Park. Observed levels of population genetic structure could be differentiated with confidence based exclusively on habitat and landscape characteristics suggesting that this structure is driven by habitat-dependent selection during dispersal and settlement, despite a high degree of connectivity across the study region.

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TABLE OF CONTENTS

LIST OF TABLES ................................................................................ LIST OF FIGURES .............................................................................. ABBREVIATIONS .............................................................................. INTRODUCTION ................................................................................ METHODS ........................................................................................... Study Area ................................................................................ Genetic Sampling ...................................................................... Landscape and Habitat Sampling.............................................. Genetic Analysis ....................................................................... Standard Genetic Measures....................................................... STRUCTURE Analysis ............................................................ GENELAND Analysis .............................................................. Assessment of Habitat-Dependent Genetic Structure ............... RESULTS ............................................................................................. Trapping and Habitat Sampling ................................................ Genetic Sampling and Standard Genetic Measures .................. Bayesian Clustering Analyses................................................... Discriminant Analysis of Habitat-Dependent Genetic Structure ....................................................................................

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DISCUSSION ....................................................................................... Ringtails as a Model for Assessing Fine Scale Genetic Structure .................................................................................... Discriminant Analysis of Habitat-Specific Clustering ............. REFERENCES ..................................................................................... APPENDIX A: R Programming Language Code for Discriminant Analyses, Testing for Violations of Model Assumptions and Randomization Tests .............................................................................

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LIST OF TABLES Table 1. Range, Median, Mean and Standard Deviation of Habitat and Landscape Variables .................................................... 2. Standard Genetic Measures and Tests for HardyWeinberg Equilibrium Across 15 loci ................................ 3. Mean Number of Alleles Per Locus, Observed and Expected Heterozygosity, Fixation Indices and Tests of Heterozygote Deficiency for Clusters Identified by GENELAND ....................................................................... 4. Pairwise FST Matrix for Clusters Identified by GENELAND ....................................................................... 5. Eigenvalues, Proportion of Variation Explained, Wilks and APER for Two Linear Discriminant Analyses............. 6. Scaling Coefficients of Habitat and Landscape Variables for Two Linear Discriminant Analyses............................... Page

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LIST OF FIGURES Figure 1. Study Region and Ringtails Trapping Locations ................ 2. Representation of STRUCTURE Results ........................... 3. Proportion of Individual Ancestry in Each Cluster Identified by STRUCTURE ................................................ 4. Maps of Probability of Population Membership for Each of Six Clusters Identified by GENELAND ........................ 5. Maps of Probability of Population Membership for Each of Three Subdivisions of Cluster 3 ..................................... 6. Distribution of APERs From Randomization Tests of Two Linear and One Quadratic Discriminant Analyses ............. 7. Scatter Plots of Individuals Against the Two Linear Discriminants with the Greatest Discrimination for Two Linear Discriminant Analyses............................................. 8. Three-dimensional Scatter Plot of Individuals Against All Three Linear Discriminants for LDA2 ............................................... 9. Photographs of Habitat Ty