1. Susannah Woodruff, Rob Lonsinger, Lisette Waits Fish and Wildlife Sciences, University of Idaho MONITORING SPECIES OF CONCERN ON MILITARY LANDS USING NONINVASIVE GENETIC SAMPLING

2. OUTLINE  Need for noninvasive genetic monitoring  Project goals and objectives  Methodological approach  Application to Sonoran pronghorn (Antilocapra americana sonoriensis)  Benefits of approach  Conclusions and future applications

3. PROBLEM STATEMENT  DoD needs reliable monitoring methods to:  Evaluate impacts of military training  Monitor at-risk species  Monitoring programs should:  Provide unbiased and reliable data  Apply to large spatial areas  Be conducted over multiple seasons or years  Be cost-effective

4. PROJECT GOAL AND OBJECTIVES  Demonstrate effectiveness noninvasive genetic sampling and capture-recapture methods (NGS-CR) to monitor species  Design and implement monitoring for kit fox (transect) and Sonoran pronghorn (targeted)

5. PROJECT GOAL AND OBJECTIVES  Demonstrate effectiveness noninvasive genetic sampling and capture-recapture methods (NGS-CR) to monitor species  Design and implement monitoring for kit fox (transect) and Sonoran pronghorn (targeted)  Compare cost-benefit of monitoring based on NGS-CR versus alternatives  Facilitate use of method on other DoD installations

6. TRADITIONAL METHODS

7. WHAT IS NONINVASIVE GENETIC SAMPLING?  Inventory and monitor -- collecting feces, hair, feathers  Primary advantages: > Lack of disturbance > Tag permanence > Reduce capture bias; increase probabilities Spencer Rettler 2013

8. SPECIES ID Developed mtDNA primer Mule deer vs. Pronghorn Woodruff et al. 2014 Rapid species identification of Sonoran pronghorn (Antilocapra americana sonoriensis) from fecal pellet DNA.

9. SPECIES ID Sonoran pronghorn ~124 bp

10. SPECIES ID Mule deer ~179 bp

11. INDIVIDUAL ID Kit Fox: 7-9 nuclear (n) DNA microsatellite loci Pronghorn: 8-10 nDNA microsatellite loci 11 Sample 133 / 3642 / 44 Sample 233 / 3644 / 44 Sample 333 / 3942 / 48 Locus 1 Locus 2 Locus 3

12. Pollock’s Robust Design: = field capture occasion Time (e.g., 1 year) Primary Period 1 Primary Period 2 CAPTURE RECAPTURE METHODS Primary Period K abundance survival, reproduction, movements Time (e.g., 1 year) survival, reproduction, movements abundance

13. Pollock’s Robust Design: = field capture occasion Primary Period 1 Primary Period 2 CAPTURE RECAPTURE METHODS Primary Period K abundance survival, reproduction, movements survival, reproduction, movements abundance  CAPWIRE (Capture With Replacement)  Allows for sampling individuals multiple times per session

14.  1800s: 1000’s of Sonoran pronghorn  Habitat loss, drought, human disturbance  2002: <50 remain after severe drought  2014: 202 (CI: 171-334) in United States SONORAN PRONGHORN

15. Source: USFWS Final EA for Reestablishment of Sonoran Pronghorn

16. SAMPLING LOCATIONS

17. TARGETED SAMPLING

18. 3-4 times 1 time

19. TARGETED SAMPLING

20.  Capture history for each individual INDIVIDUAL CAPTURE HISTORY 0 0 1 1 1 1

21. RESULTS

22. CAPTURE DISTRIBUTIONS - PRONGHORN 22

23. MINIMUM COUNTS 2014 SiteNumber of Samples/Session# Individuals S1S2S3DNAObs. ER242328128-10 CB15192594-8 KH33 271110 UK9089913830 NH20 2498 DH7578772325 PP32303410 3J38679NA

24. MINIMUM COUNTS 2014 SiteNumber of Samples/Session# Individuals S1S2S3DNAObs. ER242328128-10 CB15192594-8 KH33 271110 UK9089913830 NH20 2498 DH7578772325 PP32303410 3J38679NA

25. RESULTS Season# Samples# Individuals PCR Success nDNA Summer 2013 73094 (49M:30F:15FA)82% Summer 2014 922109 (56M:34F:19FA)82% New Sites Summer 2014 13715 (5M:8F:2FA)82% M-=male, F=female, FA=fawn

26. POPULATION ESTIMATE

27. SURVIVAL BY CLASS

28. BENEFITS OF APPROACH  Greater spatial extent covered (K)  Increased temporal frequency (P)  More individuals detected (KP)  More parameters estimated (KP)  Precise estimates (CV < 10%) and standardized approach (KP)  Easier to implement than current methods (KP)  Lower cost/detection (KP) K=kit fox P=pronghorn

29.  NGS is a valuable new monitoring approach  Detect species  Estimate population size  Detect movements  Survival, reproduction, genetic diversity  Lab costs of ~$20/sample species ID, $40-$50/sample for individual ID  Provides cost-effective, easy-to-implement monitoring alternative  Potential application to many DoD species  Many sampling alternatives CONCLUSIONS

30.  JOHN HERVERT  ROBERT KNIGHT  WAITS LAB  JIM ATKINSON  ERIC GESE  OTHERS I FORGOT… ACKNOWLEDGEMENTS

31. QUESTIONS?