Estimating occupancy of focal bee species
DOI:
https://doi.org/10.17161/jom.vi123.22555Abstract
Current bee monitoring efforts have a limited capacity for understanding factors affecting wild bee population changes, including the effects of management. To improve the effectiveness of wild bee monitoring, we first discuss principles of biological monitoring and provide a framework to design monitoring projects to estimate species occupancy, where occupancy is defined as the probability that a Sampling Unit or site is occupied by the focal species. Monitoring practitioners should first define the desired goal or question of monitoring and secondly select the appropriate state variable for monitoring (e.g., species richness, occupancy, abundance). These represent two critical, yet often overlooked, steps in the development of wild bee monitoring projects. As with all forms of demographic monitoring, practitioners who are interested in estimating species occupancy will need to develop a sampling scheme tailored to meet their monitoring objectives. Defining key sampling terms will provide the architecture of their scheme, including the Area of Interest, Sampling Unit, Season, and Replicate Survey. We also highlight data standards, including core data fields that must be collected during Surveys for bee occupancy data and additional, recommended data fields. We illustrate how these monitoring concepts are being applied to the design of a real-world monitoring project for the federally endangered rusty patched bumble bee (Bombus affinis Cresson). This framework was developed in association with the U.S. National Native Bee Monitoring Network.
Metrics
References
Adams, M. J., D.A.W. Miller, E. Muths, P.S. Corn, E.H.C. Grant, L.L. Bailey, G.M. Fellers, R.N. Fisher, W.J. Sadinski, & H. Waddle. 2013. Trends in amphibian occupancy in the United States. PloS ONE 8:e64347. https://doi.org/10.1371/journal.pone.0064347
Bailey, L.L., J.E. Hines, J.D. Nichols, & D.I. MacKenzie. 2007. Sampling design trade-offs in occupancy studies with imperfect detection: Examples and software. Ecological Applications 17:281–290. https://www.jstor.org/stable/40061993
Boone, M.L., Z.M. Portman, I. Lane, & S. Rao. 2023a. Occupancy of Bombus affinis (Hymenoptera: Apidae) in Minnesota is highest in developed areas when standardized surveys are employed. Environmental Entomology 52(5): 918–938. https://doi.org/10.1093/ee/nvad088
Boone, M.L., E. Evans, T. Arnold, & D.P. Cariveau. 2023b. Increasing sampling efficiency of Bombus communities with rare and endangered species by optimizing detection probabilities: A multi-species occupancy modelling approach using roadsides as a case study. Biological Conservation 283: 110122. https://doi.org/10.1016/j.biocon.2023.110122
Cameron, S.A., J.D. Lozier, J.P. Strange, J.B. Koch, N. Cordes, L.F. Solter, & T.L. Griswold. 2011. Patterns of widespread decline in North American bumble bees. Proceedings of the National Academy of Sciences 108: 662–667. https://doi.org/10.1073/pnas.1014743108
Chanprame, S., T.L. Griswold, & J.S. Wilson. 2024. Pollination biology and life history traits of the rare Las Vegas bear poppy (Arctomecon californica). Plants 13:1762. https://doi.org/10.3390/plants13131762
Colgan, A.M., R.G. Hatfield, A. Dolan, W. Velman, R.E. Newton, & T.A. Graves. 2024. Quantifying effectiveness and best practices for bumblebee identification from photographs. Scientific Reports 14: 830. https://doi.org/10.1038/s41598-023-41548-w
Corn, P.S., M. Adams, W. Battaglin, A. Gallant, D. James, M. Knutson, C. Langtimm, & J. Sauer. 2005. Amphibian Research and Monitoring Initiative: concepts and implementation. US Department of the Interior, US Geological Survey. https://armi.usgs.gov/content/?contentid=61.
Droege, S., J.D. Engler, E.A. Sellers, & L.O’Brien. 2016. National protocol framework for the inventory and monitoring of bees. US Department of the Interior, US Fish and Wildlife Service. http://ecos.fws.gov/ServCatFiles/reference/holding/47682
Du Clos, B., K.C. Seltmann, N.E. Turley, C. Maffei, E.M. Tucker, I.G. Lane, H.K. Levenson, &
S.H. Woodard. 2024a. Improving the standardization of wild bee occurrence data: Towards a formal wild bee data standard. Journal of Melittology 123(2): 1–x.
Du Clos, B., K.C. Seltmann, N.E. Turley, C. Maffei, E.M. Tucker, I.G. Lane, H.K. Levenson, &
S.H. Woodard. 2024b. Templates for The Wild Bee Data Standard (1.0.0). Zenodo. https://doi.org/10.5281/zenodo.14187861.
Ellis, K., C.R. V. Otto, L.L. Bailey, T. Smith, S. Choy, & L. Hatch. 2025. Integrating data to assess occupancy patterns of an endangered bumble bee. Conservation Biology: e14458. https://doi.org/10.1111/cobi.14458.
Fournier, A.M.V., E.R. White, & S.B. Heard. 2019. Site‐selection bias and apparent population declines in long‐term studies. Conservation Biology 33: 1370–1379. https://doi.org/10.1111/cobi.13371
Grant, E.H.C., D.A.W. Miller, B.R. Schmidt, M.J. Adams, S.M. Amburgey, T. Chambert, S.S. Cruickshank, R.N. Fisher, D.M. Green, B.R. Hossack, P.T.J. Johnson, M.B. Joseph, T.A.G. Rittenhouse, M.E. Ryan, J.H. Waddle, S.C. Walls, L.L. Bailey, G.M. Fellers, T.A. Gorman, A.M. Ray, D.S. Pilliod, S.J. Price, D. Saenz, W. Sadinski, & E. Muths. 2016. Quantitative evidence for the effects of multiple drivers on continental-scale amphibian declines. Scientific Reports 6:25625. http://dx.doi.org/10.1038/srep25625.
Graves, T.A., W.M. Janousek, S.M. Gaulke, A.C. Nicholas, D.A. Keinath, C.M. Bell, S. Cannings, R.G. Hatfield, J.M. Heron, & J.B. Koch. 2020. Western bumble bee: Declines in the continental United States and range‐wide information gaps. Ecosphere 11:e03141. https://doi.org/10.1002/ecs2.3141
Grixti, J.C., L.T. Wong, S.A. Cameron, & C. Favret. 2009. Decline of bumble bees (Bombus) in the North American Midwest. Biological Conservation 142: 75–84. https://doi.org/10.1016/j.biocon.2008.09.027
Hamer, A.J., D. Schmera, & M.J. Mahony. 2021. Multi‐species occupancy modeling provides novel insights into amphibian metacommunity structure and wetland restoration. Ecological Applications 31: e2293. https://doi.org/10.1002/eap.2293
Hepner, M.J., E. Orcutt, K. Price, K. Goodell, T. Roulston, R.P. Jean, & R.T. Richardson. 2024. Montane Central Appalachian forests provide refuge for the critically endangered rusty patched bumble bee (Bombus affinis). Forest Ecology and Management 556: 121751. https://doi.org/10.1016/j.foreco.2024.121751
Janousek, W.M., M.R. Douglas, S. Cannings, M.A. Clément, C.M. Delphia, J.G. Everett, R.G. Hatfield, D.A. Keinath, J.B.U. Koch, & L.M. McCabe. 2023. Recent and future declines of a historically widespread pollinator linked to climate, land cover, and pesticides. Proceedings of the National Academy of Sciences 120: e2211223120. https://doi.org/10.1073/pnas.2211223120
Kays, R., B.S. Arbogast, M. Baker‐Whatton, C. Beirne, H.M. Boone, M. Bowler, S.F. Burneo, M.V. Cove, P. Ding, & S. Espinosa. 2020. An empirical evaluation of camera trap study design: How many, how long and when? Methods in Ecology and Evolution 11: 700–713. https://doi.org/10.1111/2041-210X.13370
Levenson, H.K., B. Du Clos, T.A. Smith, S. Jepsen, J.G. Everett, N.M. Williams, & S.H. Woodard. 2024. A call for standardization in wild bee data collection and curation. Journal of Melittology 123: 4–17. https://doi.org/10.17161/jom.vi123.22533
Levenson H.K., O. Messinger Carril, N.E. Turley, C. Maffei, G. LeBuhn, T. Griswold, NM. Williams, K.L.J. Hung, R.E. Irwin, B. Du Clos, & S.H. Woodard. 2025. Standardized protocol for collecting community-level bee data. Journal of Melittology. https://doi.org/10.17161/jom.vi123.22649
MacKenzie, D.I., & J.D. Nichols. 2004. Occupancy as a surrogate for abundance estimation. Animal Biodiversity and Conservation 27: 461–467. https://doi.org/10.1111/mec.15042
MacKenzie, D.I., J.D. Nichols, J.A. Royle, K.H. Pollock, L. Bailey, & J.E. Hines, eds. 2017. Occupancy Estimation and Modeling: Inferring Patterns and Dynamics of Species Occurrence [2nd Edition]. Elsevier. Burlington, MA; 641 pp. https://doi.org/10.1016/C2012-0-01164-7
MacKenzie, D.I., & J.A. Royle. 2005. Designing occupancy studies: General advice and allocating survey effort. Journal of Applied Ecology 42: 1105–1114. https://doi.org/10.1111/j.1365-2664.2005.01098.x
MacIvor, J.S., & L. Packer. 2016. The bees among us: Modelling occupancy of solitary bees. PLoS ONE 11: e0164764. https://doi.org/10.1371/journal.pone.0164764
Marsh, D.M., & P.C. Trenham. 2008. Current trends in plant and animal population monitoring. Conservation Biology 22: 647–655. https://doi.org/10.1111/j.1523-1739.2008.00927.x
Montero‐Castaño, A., J.B.U. Koch, T.T. Lindsay, B. Love, J.M. Mola, K. Newman, & J.K. Sharkey. 2022. Pursuing best practices for minimizing wild bee captures to support biological research. Conservation Science and Practice 4: e12734. https://doi.org/10.1111/csp2.12734
Muths, E., R.E. Jung, L.L. Bailey, M.J. Adams, P.S. Corn, C.K. Dodd, G.M. Fellers, W.J. Sadinski, C.R. Schwalbe, & S.C. Walls. 2005. Amphibian Research and Monitoring Initiative (ARMI): A successful start to a national program in the United States. Applied Herpetology 2(4): 355–371. https://doi.org/10.1163/157075405774483139
Newton, J.P., P.W. Bateman, M.J. Heydenrych, J.H. Kestel, K.W. Dixon, K.S. Prendergast, N.E. White, & P. Nevill. 2023. Monitoring the birds and the bees: Environmental DNA metabarcoding of flowers detects plant-animal interactions. Environmental DNA 5: 488–502. https://doi.org/10.1002/edn3.399
Nichols, J.D., & B.K. Williams. 2006. Monitoring for conservation. Trends in Ecology & Evolution 21: 668–673. https://doi.org/10.1016/j.tree.2006.08.007
Noon, B.R., L.L. Bailey, T.D. Sisk, & K.S. McKelvey. 2012. Efficient species‐level monitoring at the landscape scale. Conservation Biology 26: 432–441. https://www.jstor.org/stable/23256395
Olson, G.S., R.G. Anthony, E.D. Forsman, S.H. Ackers, P.J. Loschl, J.A. Reid, K.M. Dugger, E.M. Glenn, & W.J. Ripple. 2005. Modeling of site occupancy dynamics for northern spotted owls, with emphasis on the effects of barred owls. The Journal of Wildlife Management 69: 918–932. https://doi.org/10.2193/0022-541X(2005)069[0918:MOSODF]2.0.CO;2
Otto, C.R.V., A.C. Schrage, L.L. Bailey, J.M. Mola, T.A. Smith, I. Pearse, S. Simanonok, & R. Grundel. 2023. Addressing detection uncertainty in Bombus affinis (Hymenoptera: Apidae) surveys can improve inferences made from monitoring. Environmental Entomology 52: 108–118. https://doi.org/10.1093/ee/nvac090
Otto, C.R.V., S.H. Woodard, & L.L. Bailey. 2025. A case for occupancy as a state variable for wild bee monitoring. Biological Conservation 302: 110932. https://doi.org/10.1016/j.biocon.2024.110932.
Packer, L., & G. Darla-West. 2021. Bees: How and why to sample them. In: Santos, J.C., & G. W. Fernandes (Eds.), Measuring Arthropod Biodiversity: A Handbook of Samling Methods: 55–83. Springer, Cham, CH; xvii+599 pp. https://doi.org/10.1007/978-3-030-53226-0_3
Portman, Z.M., B. Bruninga-Socolar, & D.P. Cariveau. 2020. The state of bee monitoring in the United States: A call to refocus away from bowl traps and towards more effective methods. Annals of the Entomological Society of America 113: 337–342. https://doi.org/10.1093/aesa/saaa010
Rousseau, J.S., S.H. Woodard, S. Jepsen, B. Du Clos, A. Johnston, B.N. Danforth, & A.D. Rodewald. 2024. Advancing bee conservation in the US: Gaps and opportunities in data collection and reporting. Frontiers in Ecology and Evolution 12. https://doi.org/10.3389.fevo.2024.1346795.
Royle, J.A., & R.M. Dorazio. 2006. Hierarchical models of animal abundance and occurrence. Journal of Agricultural, Biological, and Environmental Statistics 11: 249–263.
Strange, J.P., M.M. López-Uribe, L. Whiteman, B.N. Danforth, S. Jha, H.K. Levenson, B. Du Clos, J.B.U. Koch, & S.H. Woodard. 2024. Standardized protocols for collecting bee samples for pathogen data. Journal of Melittology 123(7): 1–x.
Strickland, G.J., & J.H. Roberts. 2019. Utility of eDNA and occupancy models for monitoring an endangered fish across diverse riverine habitats. Hydrobiologia 826: 129–144. https://doi.org/10.1007/s10750-018-3723-8
Sutherland, W.J., W.M. Adams, R.B. Aronson, R. Aveling, T.M. Blackburn, S. Broad, G. Ceballos, I.M. Côtét, R.M. Cowling, G.A.B. Da Fonseca, E. Dinerstein, P.J. Ferraro, E. Fleishman, C. Gascon, M. Hunter Jr., J. Hutton, P. Kareiva, A. Kuria, D.W. Macdonald, K. Mackinnon, F.J. Madgwick, M.B. Mascia, J. Mcneely, E.J. Milner-Gulland, S. Moon, C.G. Morley, S. Nelson, D. Osborn, M. Pai, E.C.M. Parsons, L.S. Peck, H. Possingham, S.V. Prior, A.S. Pullin, M.R.W. Rands, J. Ranganathan, K.H. Redford, J.P. Rodriguez, F. Seymour, J. Sobel, N.S. Sodhi, A. Stott, K. Vance-Borland, & A.R. Watkinson. 2009. One hundred questions of importance to the conservation of global biological diversity. Conservation Biology 23: 557–567. https://doi.org/10.1111/j.1523-1739.2009.01212.x
US Fish and Wildlife Service. 2021. Recovery Plan for Rusty Patched Bumble Bee (Bombus affinis). https://www.fws.gov/media/recovery-plan-rusty-patched-bumble-bee.
Weller, T.J. 2008. Using occupancy estimation to assess the effectiveness of a regional multiple-species conservation plan: Bats in the Pacific Northwest. Biological Conservation 141: 2279–2289. https://doi.org/10.1016/j.biocon.2008.06.018
Wieczorek, J., D. Bloom, R. Guralnick, S. Blum, M. Döring, R. Giovanni, T. Robertson, & D. Vieglais. 2012. Darwin Core: An evolving community-developed biodiversity data standard. PLoS ONE 7(1): e29715. https://doi.org/10.1371/journal.pone.0029715.
Williams, B.K., J.D. Nichols, & M.J. Conroy. 2002. Analysis and Management of Animal Populations. Academic Press, San Diego, CA; xvii+817 pp.
US Fish and Wildlife Service. 2016. Rusty Patched Bumble Bee (Bombus affinis) Species Status Assessment: Final Report, Version 1. https://www.fws.gov/midwest/endangered/insects/rpbb/pdf/SSAReportRPBBwAdd.pdf.
Yoccoz, N.G., J.D. Nichols, & T. Boulinier. 2001. Monitoring of biological diversity in space and time. Trends in Ecology & Evolution 16: 446–453. https://doi.org/10.1016/S0169-5347(01)02205-4
Downloads
Published
Issue
Section
License
Copyright (c) 2025 Clint Otto, Larissa Bailey, Brianne Du Clos, Tamara A. Smith, Elaine C. Evans, Ian Pearse, Saff Killingsworth, Sarina Jepsen, S. Hollis Woodard
This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License.
Copyright for articles published in Journal of Melittology is retained by the authors, with first publication rights granted to the journal. By virtue of their appearance in this open access journal, articles are free to use, with proper attribution and permission of the authors, in educational and other non-commercial settings.
