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SPR-659: Genetic Variation of Pronghorn Across US Route 89 And

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SPR-659: Genetic Variation of Pronghorn Across US Route 89 And Genetic Variation of Pronghorn across US Route 89 and State Route 64 Final Report 659 March 2012 Arizona Department of Transportation Research Center Genetic Variation of Pronghorn across US Route 89 and State Route 64 Final Report 659 March 2012 Prepared by: Tad Theimer, Scott Sprague, Ellyce Eddy, and Russell Benford Department of Biological Sciences Northern Arizona University Box 5640 Flagstaff, AZ 86011 Prepared for: Arizona Department of Transportation In cooperation with U.S. Department of Transportation Federal Highway Administration The contents of this report reflect the views of the authors who are responsible for the facts and the accuracy of the data presented herein. The contents do not necessarily reflect the official views or policies of the Arizona Department of Transportation or the Federal Highway Administration. This report does not constitute a standard, specification, or regulation. Trade or manufacturers’ names that may appear herein are cited only because they are considered essential to the objectives of the report. The US government and the State of Arizona do not endorse products or manufacturers. Cover photos courtesy of Wikipedia Commons. Technical Report Documentation Page 1. Report No. 2. Government Accession No. 3. Recipient's Catalog No. FHWA-AZ-12-659 4. Title and Subtitle 5. Report Date GENETIC VARIATION OF PRONGHORN ACROSS US ROUTE 89 AND March 2012 STATE ROUTE 64 6. Performing Organization Code 7. Author 8. Performing Organization Report No. Tad Theimer, Scott Sprague, Ellyce Eddy, Russell Benford 9. Performing Organization Name and Address 10. Work Unit No. Northern Arizona University Box 5640, Beaver Street Flagstaff, AZ 86011 11. Contract or Grant No. SPR-PL-1(173) 659 12. Sponsoring Agency Name and Address 13.Type of Report & Period Covered Arizona Department of Transportation FINAL (05/2008 – 12/2011) 206 S. 17th Avenue Phoenix, AZ 85007 14. Sponsoring Agency Code ADOT Project Manager: Dr. Estomih M Kombe 15. Supplementary Notes Prepared in cooperation with the U.S. Department of Transportation, Federal Highway Administration 16. Abstract This study investigated whether highways acted as barriers to gene flow for pronghorn in northern Arizona. DNA samples from 132 pronghorn were analyzed using eight polymorphic microsatellite loci. Samples represented animals living on opposite sides of US Route 89 (US 89) and State Route 64 (SR 64). Two different modeling approaches indicated that both US 89 and SR 64, and to a lesser extent US Route 180 (US 180), acted as barriers to gene flow. The genetic structuring caused by highways, especially across US 89, is consistent with behavioral data that demonstrated pronghorn rarely cross this highway. This study found no evidence of inbreeding or reduced genetic variation in any of the populations examined, but those effects may take longer to appear. Based on these results, the researchers recommend future genetic monitoring of these populations or assessment of genetic variation across highways with larger traffic volumes or longer histories to determine whether the barrier effects documented here lead to loss of genetic diversity. 17. Key Words 18. Distribution Statement Pronghorn, Antilocapra americana, gene flow, genetics, Document is available to the U.S. public through the highways, microsatellites National Technical Information Service, Springfield, Virginia, 22161 19. Security Classification 20. Security Classification 21. No. of Pages 22. Price Unclassified Unclassified 38 SI* (MODERN METRIC) CONVERSION FACTORS APPROXIMATE CONVERSIONS TO SI UNITS Symbol When You Know Multiply By To Find Symbol LENGTH in inches 25.4 millimeters mm ft feet 0.305 meters m yd yards 0.914 meters m mi miles 1.61 kilometers km AREA in2 square inches 645.2 square millimeters mm2 ft2 square feet 0.093 square meters m2 yd2 square yard 0.836 square meters m2 ac acres 0.405 hectares ha mi2 square miles 2.59 square kilometers km2 VOLUME fl oz fluid ounces 29.57 milliliters mL gal gallons 3.785 liters L ft3 cubic feet 0.028 cubic meters m3 yd3 cubic yards 0.765 cubic meters m3 NOTE: volumes greater than 1000 L shall be shown in m3 MASS oz ounces 28.35 grams g lb pounds 0.454 kilograms kg T short tons (2000 lb) 0.907 megagrams (or "metric ton") Mg (or "t") TEMPERATURE (exact degrees) oF Fahrenheit 5 (F-32)/9 Celsius oC or (F-32)/1.8 ILLUMINATION fc foot-candles 10.76 lux lx fl foot-Lamberts 3.426 candela/m2 cd/m2 FORCE and PRESSURE or STRESS lbf poundforce 4.45 newtons N lbf/in2 poundforce per square inch 6.89 kilopascals kPa APPROXIMATE CONVERSIONS FROM SI UNITS Symbol When You Know Multiply By To Find Symbol LENGTH mm millimeters 0.039 inches in m meters 3.28 feet ft m meters 1.09 yards yd km kilometers 0.621 miles mi AREA mm2 square millimeters 0.0016 square inches in2 m2 square meters 10.764 square feet ft2 m2 square meters 1.195 square yards yd2 ha hectares 2.47 acres ac km2 square kilometers 0.386 square miles mi2 VOLUME mL milliliters 0.034 fluid ounces fl oz L liters 0.264 gallons gal m3 cubic meters 35.314 cubic feet ft3 m3 cubic meters 1.307 cubic yards yd3 MASS g grams 0.035 ounces oz kg kilograms 2.202 pounds lb Mg (or "t") megagrams (or "metric ton") 1.103 short tons (2000 lb) T TEMPERATURE (exact degrees) oC Celsius 1.8C+32 Fahrenheit oF ILLUMINATION lx lux 0.0929 foot-candles fc cd/m2 candela/m2 0.2919 foot-Lamberts fl FORCE and PRESSURE or STRESS N newtons 0.225 poundforce lbf kPa kilopascals 0.145 poundforce per square inch lbf/in2 *SI is the symbol for the International System of Units. Appropriate rounding should be made to comply with Section 4 of ASTM E380. (Revised March 2003) TABLE OF CONTENTS I. EXECUTIVE SUMMARY.................................................................................................1 II. INTRODUCTION ...............................................................................................................3 Background........................................................................................................................3 Research Justification ........................................................................................................5 Research Objectives...........................................................................................................5 III. METHODS .........................................................................................................................7 Study Area .........................................................................................................................7 Sample Collection..............................................................................................................8 Genetic Analyses ..............................................................................................................8 IV. RESULTS .........................................................................................................................11 V. DISCUSSION....................................................................................................................15 VI. CONCLUSIONS................................................................................................................17 VII. RECOMMENDATIONS.................................................................................................19 APPENDIX A - DETAILED GENETIC METHODS ...................................................21 APPENDIX B - DETAILED GENETIC RESULTS.......................................................23 REFERENCES ................................................................................................................29 LIST OF TABLES TABLE 1 Summary of Genetic Results .................................................................................23 TABLE 2 Δk Values Produced by Program Structure for K Values from 1-8.......................25 TABLE 3 Allelic Richness Across All Loci for Each Population Based on Minimum Sample Size of Nine Individuals............................................................................26 TABLE 4 Results of Tests of Heterozygote Deficiency.........................................................27 LIST OF FIGURES FIGURE 1 A female (left) and male (right) American pronghorn (Antilocapra americana) photographed in northern Arizona........................................................3 FIGURE 2 US 89 north of Flagstaff, Arizona, bisects continuous grassland habitat appropriate for pronghorn (route of highway is shown by the dark line)................7 FIGURE 3 Capture/kill locations of 132 pronghorn in northern Arizona……………………………………………………………….....................8 FIGURE 4 Probability of population membership of 132 pronghorn based on the modeling program STRUCTURE…......................................................................11 FIGURE 5 Population assignment of individual pronghorn based on results using the program STRUCTURE.…….................................................................................12 FIGURE 6 A. Collection locations of 132 pronghorn. B. Pronghorn populations for an iteration when modeling program GENELAND yielded four populations as most likely. C. Pronghorn populations for an iteration that yielded three populations as the most likely.…………………………….....................................................13 ACKNOWLEDGEMENTS This project would not have been possible without the assistance and support of numerous individuals and agencies. We thank Estomih Kombe, Project Manager - Arizona Department of Transportation (ADOT) Research Center, John
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