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Photographic Mark-Recapture: Applications and Utility for the Study of an Endangered Salamander

This article explores the use of photographic mark-recapture for studying the endangered aquatic salamander, Eurycea tonkawae. It discusses different software programs and their pros and cons, as well as the advantages and disadvantages of using photo ID compared to other marking methods.

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Photographic Mark-Recapture: Applications and Utility for the Study of an Endangered Salamander

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  1. Photographic Mark-Recapture: Applications and Utility for the Study of an Endangered Aquatic Salamander, Eurycea tonkawae Nathan F. Bendik

  2. PhotoID • Using photographs to identify individual animals that have unique natural marks • Manually (by-eye) • Computer-assisted

  3. Example organisms

  4. Why photo ID?

  5. Why PhotoID (for E. tonkawae)? • Less invasive than Visible Implant Elastomer tags • Cheaper over the long run • Faster in the field • Easier to implement

  6. Automated Matching Programs

  7. Wild-ID

  8. Wild-ID • Pros: • Simple: provide photos folder and a database folder, and it scores the photos • No manual input of data for each photo- FAST • Can easily add more photos later to a saved project db • Allows user to “accept” or “reject” up to 20 potential matches • Saves sessions so you can quit matching and return any time • Cons: • No individual metadata • Workflow is not “smart” • Brute force: takes all photos in folder and scores them sequentially (by name) in one direction, i.e., B to A, but not A to B • Cannot parse out known non-matches • Requires file naming scheme and significant manipulation in R to process data and combine with metadata Bolger, D. T., T. A. Morrison, B. Vance, D. Lee, and H. Farid. 2012. A computer-assisted system for photographic mark–recapture analysis. Methods in Ecology and Evolution 3:813–822.

  9. StripeSpotter

  10. StripeSpotter • Pros: • Workflow is intuitively structured with capture-recapture in mind • Includes 2 matching algorithms • Extracts EXIF data (e.g. date, time, exposure) • Allows inclusion of individual metadata for each record such as sex, location, etc. • .csv output convenient and detailed- very useful for post-processing data • Cons: • Many steps; may be cumbersome for large photo databases • Select animal’s body using mouse via rectangle selection tool • Save new animal to database • To match, user must click “identify animal” for each individual and • Use the rectangle selection tool • Does not save session history (remember where you left off or don’t quit mid-session) M. Lahiri, C. Tantipathananandh, R. Warungu, D.I. Rubenstein, T.Y. Berger-Wolf. Biometric Animal Databases from Field Photographs: Identification of Individual Zebra in the Wild. Proceedings of the ACM International Conference on Multimedia Retrieval (ICMR 2011), Trento, Italy, 2011

  11. I3S: Interactive Individual Identification System

  12. I3S: Interactive Individual Identification System • Pros: • Works well where other programs may perform poorly (e.g. less complex patterns but easily distinguishable spots) • Matching seems fast • Easy to check images one at a time (e.g. against a large database) to ID an animal • Cons: • Must generate fingerprint file for each photo (lots of clicking) • Capture-recapture data processing must be done manually (either as you are matching or based on the resulting database). Van Tienhoven, A.M., Den Hartog, J.E., Reijns, R.A., & Peddemors, V.M. 2007. A computer-aided program for pattern-matching natural marks on the spotted raggedtooth shark Carcharias taurus (Rafinesque, 1810). Journal of Applied Ecology 44:273–280.

  13. Applications for E. tonkawae • Standard mark-recapture data analysis (pop. size, survival…) • Analysis of movement patterns • Change in body condition of individuals

  14. No rain, no spring flow…. emerges from underground after 10 months 3 months regrowth 17 months post-drought Bendik, N. F., and A. G. Gluesenkamp. 2013. Body length shrinkage in an endangered amphibian is associated with drought. Journal of Zoology 290:35–41.

  15. PhotoID: Validation • Compared visible implant elastomer tags (VIEs) to computer-assisted photoID (752 VIE-tagged individuals, 1367 photos) • Used scores from Wild-ID Bendik, N. F., T. A. Morrison, A. G. Gluesenkamp, M. S. Sanders, and L. J. O’Donnell. 2013. Computer-Assisted Photo Identification Outperforms Visible Implant Elastomers in an Endangered Salamander, Eurycea tonkawae. PLoS ONE 8:e59424.

  16. Error Rates • VIE • 1.9% False Rejections • 1.8% False Acceptances • Computer-assisted PhotoID • 0.76% False Rejections • 0 False Acceptances Change in similarity score over time

  17. Field setup

  18. Software

  19. Advantages • Photographs are easy to obtain and cheap • Less invasive than toe clipping, VIEs, PIT tagging • Can be a lot faster in the field (time to take one photo vs. inject three tiny elastomer blobs in a two-inch salamander) • Can be more accurate (but not necessarily)

  20. Disadvantages • Animals can be hard to photograph; need good quality photographs • Lighting • Sharpness • Consistent angle • Changing natural marks increase error rates • Growth • Injury • Requires more computer time (summore–alotmore) • Back problems • Eye strain • CTS

  21. Acknowledgements • Collaborators Tom Morrison, Andy Gluesenkamp, Mark Sanders, Lisa O’Donnell, Kira McEntire • Field Assistance Blake Sissel, Matt Westbrook, Liza Colucci, Mike Colucci, Laurie Dries, Heather Perry, Leah Gluesenkamp, Beth Bendik, Alisha Shah, Helen Snook, Todd Jackson, Melanie Pavlas-Snyder, COA Interns • Technical Assistance Bennett Vance, Josh O’Brien, Rob Clayton • Megan Chesser and Danny Martin

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