Improved inferences about landscape connectivity from spatial capture-recapture by integration of a movement model.

Gates Dupont, Daniel W Linden, Chris Sutherland
Author Information
  1. Gates Dupont: Department of Environmental Conservation, University of Massachusetts, 160 Holdsworth Way, Amherst, Massachusetts, 01003, USA. ORCID
  2. Daniel W Linden: Greater Atlantic Regional Fisheries Office, NOAA National Marine Fisheries Service, 55 Great Republic Drive, Gloucester, Massachusetts, 01930, USA. ORCID
  3. Chris Sutherland: Department of Environmental Conservation, University of Massachusetts, 160 Holdsworth Way, Amherst, Massachusetts, 01003, USA. ORCID

Abstract

Understanding how broad-scale patterns in animal populations emerge from individual-level processes is an enduring challenge in ecology that requires investigation at multiple scales and perspectives. Complementary to this need for diverse approaches is the recent focus on integrated modeling in statistical ecology. Population-level processes represent the core of spatial capture-recapture (SCR), with many methodological extensions that have been motivated by standing ecological theory and data-integration opportunities. The extent to which these recent advances offer inferential improvements can be limited by the data requirements for quantifying individual-level processes. This is especially true for SCR models that use non-Euclidean distance to relax the restrictive assumption that individual space use is stationary and symmetrical to make inferences about landscape connectivity. To meet the challenges of scale and data quality, we propose integrating an explicit movement model with non-Euclidean SCR for joint estimation of a shared cost parameter between individual and population processes. Here, we define a movement kernel for step selection that uses "ecological distance" instead of Euclidean distance to quantify availability for each movement step in terms of landscape cost. We compare performance of our integrated model to that of existing SCR models using realistic animal movement simulations and data collected on black bears. We demonstrate that an integrated approach offers improvements both in terms of bias and precision in estimating the shared cost parameter over models fit to spatial encounters alone. Simulations suggest these gains were only realized when step lengths were small relative to home range size, and estimates of density were insensitive to whether or not an integrated approach was used. By combining the fine spatiotemporal scale of individual movement processes with the estimation of population density in SCR, integrated approaches such as the one we develop here have the potential to unify the fields of movement, population, and landscape ecology and improve our understanding of landscape connectivity.

Keywords

References

  1. Bocinsky, R. K. 2016. FedData: functions to automate downloading geospatial data available from several federated data sources. R package version 2.0.4. https://doi.org/10.5281/zenodo.1306302
  2. Borchers, D. L., and M. G. Efford. 2008. Spatially explicit maximum likelihood methods for capture-recapture studies. Biometrics 64:377-385.
  3. Christ, A., J. Ver Hoef, and D. L. Zimmerman. 2008. An animal movement model incorporating home range and habitat selection. Environmental and Ecological Statistics 15:27-38.
  4. Creel, S., J. Merkle, T. Mweetwa, M. S. Becker, H. Mwape, T. Simpamba, and C. Simukonda. 2020. Hidden Markov models reveal a clear human footprint on the movements of highly mobile African wild dogs. Scientific Reports 10:17908.
  5. Crooks, K. R., C. L. Burdett, D. M. Theobald, S. R. King, M. Di Marco, C. Rondinini, and L. Boitani. 2017. Quantification of habitat fragmentation reveals extinction risk in terrestrial mammals. Proceedings of the National Academy of Sciences of the United States of America 114:7635-7640.
  6. Crooks, K. R., C. L. Burdett, D. M. Theobald, C. Rondinini, and L. Boitani. 2011. Global patterns of fragmentation and connectivity of mammalian carnivore habitat. Philosophical Transactions of the Royal Society B: Biological Sciences 366:2642-2651.
  7. Dijkstra, E. W., et al. 1959. A note on two problems in connexion with graphs. Numerische Mathematik 1:269-271.
  8. Dupont, G., D. W. Linden, and C. Sutherland. 2021a. Supplement: Improved inferences about landscape connectivity from spatial capture-recapture by integration of a movement model. Open Science Framework. https://osf.io/684p9/
  9. Dupont, G., J. A. Royle, M. A. Nawaz, and C. Sutherland. 2021b. Optimal sampling design for spatial capture-recapture. Ecology 102. https://doi.org/10.1002/ecy.3262.
  10. Efford, M. 2004. Density estimation in live-trapping studies. Oikos 106:598-610.
  11. Etten, J. V. 2017. R package gdistance: distances and routes on geographical grids. Journal of Statistical Software 76:1-21.
  12. Gupta, A., B. Dilkina, D. J. Morin, A. K. Fuller, J. A. Royle, C. Sutherland, and C. P. Gomes. 2019. Reserve design to optimize functional connectivity and animal density. Conservation Biology 33:1023-1034.
  13. Haddad, N. M., et al. 2015. Habitat fragmentation and its lasting impact on earth’s ecosystems. Science Advances 1:e1500052.
  14. Hanks, E. M., and M. B. Hooten. 2013. Circuit theory and model-based inference for landscape connectivity. Journal of the American Statistical Association 108:22-33.
  15. Hooten, M. B., D. S. Johnson, B. T. McClintock, and J. M. Morales. 2017. Animal movement: statistical models for telemetry data. CRC Press, Boca Raton, Florida, USA.
  16. Howell, P. E., E. Muths, B. R. Hossack, B. H. Sigafus, and R. B. Chandler. 2018. Increasing connectivity between metapopulation ecology and landscape ecology. Ecology 99:1119-1128.
  17. Johnson, D. S., D. L. Thomas, J. M. Ver Hoef, and A. Christ. 2008. A general framework for the analysis of animal resource selection from telemetry data. Biometrics 64:968-976.
  18. Levin, S. A. 1992. The problem of pattern and scale in ecology: the Robert H. MacArthur award lecture. Ecology 73:1943-1967.
  19. Linden, D. W., A. P. Sirén, and P. J. Pekins. 2018. Integrating telemetry data into spatial capture-recapture modifies inferences on multi-scale resource selection. Ecosphere 9:e02203.
  20. McClintock, B. T., B. Abrahms, R. Chandler, P. B. Conn, S. J. Converse, R. Emmet, B. Gardner, N. J. Hostetter, and D. S. Johnson. 2021. An integrated path for spatial capture-recapture and animal movement modeling. Ecology:e3473.
  21. McRae, B. H., B. G. Dickson, T. H. Keitt, and V. B. Shah. 2008. Using circuit theory to model connectivity in ecology, evolution, and conservation. Ecology 89:2712-2724.
  22. Moorcroft, P. R., and A. Barnett. 2008. Mechanistic home range models and resource selection analysis: a reconciliation and unification. Ecology 89:1112-1119.
  23. Morales, J. M., P. R. Moorcroft, J. Matthiopoulos, J. L. Frair, J. G. Kie, R. A. Powell, E. H. Merrill, and D. T. Haydon. 2010. Building the bridge between animal movement and population dynamics. Philosophical Transactions of the Royal Society B: Biological Sciences 365:2289-2301.
  24. Morin, D. J., A. K. Fuller, J. A. Royle, and C. Sutherland. 2017. Model-based estimators of density and connectivity to inform conservation of spatially structured populations. Ecosphere 8:e01623.
  25. Murphy, S. M., D. T. Wilckens, B. C. Augustine, M. A. Peyton, and G. C. Harper. 2019. Improving estimation of puma (puma concolor) population density: clustered camera-trapping, telemetry data, and generalized spatial mark-resight models. Scientific Reports 9:1-13.
  26. Plard, F., R. Fay, M. Kéry, A. Cohas, and M. Schaub. 2019. Integrated population models: powerful methods to embed individual processes in population dynamics models. Ecology 100:e02715.
  27. R Core Team. 2020. R: a language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. https://www.r-project.org/
  28. Rayfield, B., M.-J. Fortin, and A. Fall. 2011. Connectivity for conservation: a framework to classify network measures. Ecology 92:847-858.
  29. Revilla, E., and T. Wiegand. 2008. Individual movement behavior, matrix heterogeneity, and the dynamics of spatially structured populations. Proceedings of the National Academy of Sciences of the United States of America 105:19120-19125.
  30. Royle, J. A., R. B. Chandler, K. D. Gazenski, and T. A. Graves. 2013a. Spatial capture-recapture models for jointly estimating population density and landscape connectivity. Ecology 94:287-294.
  31. Royle, J. A., R. B. Chandler, R. Sollmann, and B. Gardner. 2013b. Spatial capture-recapture. Academic Press, Cambridge, Massachusetts, USA.
  32. Royle, J. A., R. B. Chandler, C. C. Sun, and A. K. Fuller. 2013c. Integrating resource selection information with spatial capture-recapture. Methods in Ecology and Evolution 4:520-530.
  33. Royle, J. A., A. K. Fuller, and C. Sutherland. 2018. Unifying population and landscape ecology with spatial capture-recapture. Ecography 41:444-456.
  34. Royle, J. A., and K. V. Young. 2008. A hierarchical model for spatial capture-recapture data. Ecology 89:2281-2289.
  35. Sciaini, M., M. Fritsch, C. Scherer, and C. E. Simpkins. 2018. Nlmr and landscapetools: An integrated environment for simulating and modifying neutral landscape models in r. Methods in Ecology and Evolution 9:2240-2248.
  36. Shaw, A. K. 2020. Causes and consequences of individual variation in animal movement. Movement Ecology 8:1-12.
  37. Sollmann, R., B. Gardner, J. L. Belant, C. M. Wilton, and J. Beringer. 2016. Habitat associations in a recolonizing, low-density black bear population. Ecosphere 7:e01406.
  38. Sollmann, R., B. Gardner, A. W. Parsons, J. J. Stocking, B. T. McClintock, T. R. Simons, K. H. Pollock, and A. F. O’Connell. 2013. A spatial mark-resight model augmented with telemetry data. Ecology 94:553-559.
  39. Spiegel, O., S. T. Leu, C. M. Bull, and A. Sih. 2017. What’s your move? Movement as a link between personality and spatial dynamics in animal populations. Ecology Letters 20:3-18.
  40. Sun, C. 2014. Estimating black bear population density in the southern black bear range of New York with a non-invasive, genetic, spatial capture-recapture study. Thesis. Cornell University.
  41. Sutherland, C., A. K. Fuller, and J. A. Royle. 2015. Modelling non-Euclidean movement and landscape connectivity in highly structured ecological networks. Methods in Ecology and Evolution 6:169-177.
  42. Sutherland, C., J. A. Royle, and D. W. Linden. 2019. oscr: A spatial capture-recapture r package for inference about spatial ecological processes. Ecography 42:1459-1469.
  43. Tenan, S., P. Pedrini, N. Bragalanti, C. Groff, and C. Sutherland. 2017. Data integration for inference about spatial processes: A model-based approach to test and account for data inconsistency. PLOS ONE 12:e0185588.
  44. Tischendorf, L., and L. Fahrig. 2000. How should we measure landscape connectivity? Landscape Ecology 15:633-641.
  45. Tischendorf, L., A. Grez, T. Zaviezo, and L. Fahrig. 2005. Mechanisms affecting population density in fragmented habitat. Ecology and Society 10:1-13.
  46. Yang, L., et al. 2018. A new generation of the United States national land cover database: Requirements, research priorities, design, and implementation strategies. ISPRS Journal of Photogrammetry and Remote Sensing 146:108-123.
  47. Zeller, K. A., K. McGarigal, and A. R. Whiteley. 2012. Estimating landscape resistance to movement: a review. Landscape Ecology 27:777-797.

MeSH Term

Animals
Movement
Population Density
Ursidae

Word Cloud

Created with Highcharts 10.0.0movementprocessesintegratedSCRlandscapespatialdataconnectivitycostanimalecologycapture-recapturemodelsindividualmodelpopulationstepindividual-levelapproachesrecentimprovementsusenon-EuclideandistanceinferencesscaleestimationsharedparametertermsapproachdensityintegrationUnderstandingbroad-scalepatternspopulationsemergeenduringchallengerequiresinvestigationmultiplescalesperspectivesComplementaryneeddiversefocusmodelingstatisticalPopulation-levelrepresentcoremanymethodologicalextensionsmotivatedstandingecologicaltheorydata-integrationopportunitiesextentadvancesofferinferentialcanlimitedrequirementsquantifyingespeciallytruerelaxrestrictiveassumptionspacestationarysymmetricalmakemeetchallengesqualityproposeintegratingexplicitjointdefinekernelselectionuses"ecologicaldistance"insteadEuclideanquantifyavailabilitycompareperformanceexistingusingrealisticsimulationscollectedblackbearsdemonstrateoffersbiasprecisionestimatingfitencountersaloneSimulationssuggestgainsrealizedlengthssmallrelativehomerangesizeestimatesinsensitivewhetherusedcombiningfinespatiotemporalonedeveloppotentialunifyfieldsimproveunderstandingImprovedSpecialFeature:LinkingCapture-RecaptureMovementfunction

Similar Articles

Cited By