Marine mammals: methodology for combining data

This report introduces a method for integrating digital aerial survey data and passive acoustic baseline data to record the abundance and distribution of marine mammals. The report applies the method in a test case study and provides recommendations on data collection.


References

Anderson, D. R. (2001) The need to get the basics right in wildlife field studies. Wildlife Society Bulletin, 29: 1294-1297

Booth, C.G., Oedekoven, C.S., Gillespie, D., Macaulay, J., Plunkett, R, Joy, R., Harris, D., Wood, J., Marques, T.A., Marshall, L., Verfuss, U.K., Tyack, P. Johnson, M., & Thomas, L. (2017). Assessing the Viability of Density Estimation for Cetaceans from Passive Acoustic Fixed Sensors throughout the Life Cycle of an Offshore E&P Field Development. Report number: SMRUC-OGP-2017-001. Submitted to IOGP Sound and Marine Life Joint Industry Programme (Unpublished).

Borchers, D. (2012). A non-technical overview of spatially explicit capture-recapture models. Journal of Ornithology, 152(2), S435-S444.

Borchers, D.L., Zucchini, W., Heide-Jørgensen, M.P., Cañadas, A. and Langrock, R. (2013). Using hidden Markov Models to deal with availability bias on line transect surveys. Biometrics, 69: 703-713.

Buckland, S. T., D. R. Anderson, K. P. Burnham, J. L. Laake, D. L. Borchers, and L. Thomas (2001). Introduction to Distance Sampling: Estimating Abundance of Biological Populations. Oxford: Oxford University Press.

Buckland, S., Rexstad, E., Marques, T.A. and Oedekoven, C., (2015). Distance Sampling: Methods and Applications. Springer.

Chelonia Ltd (2023).

Denwood, M.J. (2016). runjags: An R Package Providing Interface Utilities, Model Templates, Parallel Computing Methods and Additional Distributions for MCMC Models in JAGS. Journal of Statistical Software. 71.

Doser, J. W., Finley, A. O., Weed, A. S., & Zipkin, E. F. (2021). Integrating automated acoustic vocalization data and point count surveys for estimation of bird abundance. Methods in Ecology and Evolution, 12(6), 1040-1049.

Fleming, A. H., Yack, T., Redfern, J. V., Becker, E. A., Moore, T. J., & Barlow, J. (2018). Combining acoustic and visual detections in habitat models of Dall's porpoise. Ecological Modelling, 384, 198– 208.

Frasier, K.E., Garrison, L.P., Soldevilla, M.S., Wiggins S.M & Hildebrand, J A. (2021). Cetacean distribution models based on visual and passive acoustic data. Scientific Reports 11, 8240.

Gerrodette, T., Taylor, B.L., Swift, R., Rankin, S., Jaramillo-Legorreta, A.M. and Rojas-Bracho, L. (2011). A combined visual and acoustic estimate of 2008 abundance, and change in abundance since 1997, for the vaquita, Phocoena sinus. Marine Mammal Science, 27: E79-E100.

Gilles, A., Authier, M., Ramirez-Martinez, N.C., Araújo, H., Blanchard, A., Carlström, J., Eira, C., Dorémus, G., Fernández Maldonado, C, Geelhoed, S.C.V., Kyhn, L., Laran, S., Nachtsheim, D., Panigada, S., Pigeault, R., Sequeira, M., Sveegaard, S, Taylor, N.L., Owen, K., Saavedra, C., Vázquez-Bonales, J.A., Unger, B., Hammond, P.S. (2023). Estimates of cetacean abundance in European Atlantic waters in summer 2022 from the SCANS-IV aerial and shipboard surveys. Final report published 29 September 2023. 64 pp.

Hague E. L., Sinclair R. R. and Sparling C. E. (2020). Regional baselines for marine mammal knowledge across the North Sea and Atlantic areas of Scottish waters. Scottish Marine and Freshwater Science Vol 11 No 12.

Hammond, P.S., Berggren, P., Benke, H., Borchers, D.L., Collet, A., Heide-Jørgensen, M.P., Heimlich, S., Hiby, A.R., Leopold, M.F., Øien, N. (2002). Abundance of harbour porpoises and other cetaceans in the North Sea and adjacent waters. Journal of Applied Ecology. 39, 361–376.

Hammond, P.S., Macleod, K., Berggren, P., Borchers, D.L., Burt, M.L., Cañadas, A., Desportes, G., Donovan, G.P., Gilles, A., Gillespie, D., Gordon, J., Hedley, S., Hiby, L., Kuklik, I., Leaper, R., Lehnert, K., Leopold, M., Lovell, P., Øien, N., Paxton, C., Ridoux, V., Rogan, E., Samarra, F., Scheidat, M., Sequeira, M., Siebert, U., Skov, H., Swift, R., Tasker, M.L., Teilmann, J., Van Canneyt, O., Vázquez, J.A. (2013). Cetacean abundance and distribution in European Atlantic shelf waters to inform conservation and management. Biological Conservation 164: 107-122.

Hammond, PS, Lacey, C, Gilles, A, Viquerat, S, Börjesson, P, Herr, H, Macleod, K, Ridoux, V, Santos, MB, Scheidat, M, Teilmann, J, Vingada, J & Øien, N (2021). Estimates of cetacean abundance in European Atlantic waters in summer 2016 from the SCANS-III aerial and shipboard surveys. SCANS-III project report 1, 39 pp.

Jacobson, E., Forney, K. and Barlow, J. (2017). Using visual survey data to estimate passive acoustic detection parameters for harbor porpoise abundance estimates. The Journal of the Acoustical Society of America. 141. 219-230.

Jaramillo-Legorreta, A. M., L. Rojas-Bracho and T. Gerrodette. (1999). A new abundance estimate for vaquitas: First step for recovery. Marine Mammal Science 15:957–973.

Kellner, K. (2018). jagsUI: A wrapper around rjags to streamline JAGS analyses. R package 1.5.0.

Laake, J. L., Calambokidis, J., Osmek, S. D., and Rugh, D. J. (1997). Probability of detecting harbor porpoise from aerial surveys: Estimating g(0), Journal of Wildlife Management. 61, 63–75.

Mackenzie, M.L, Scott-Hayward, L.A.S., Oedekoven, C.S., Skov, H., Humphreys, E., and Rexstad E. (2013). Statistical Modelling of Seabird and Cetacean data: Guidance Document. University of St. Andrews contract for Marine Scotland; SB9 (CR/2012/05).

Marques, T. A., Thomas, L., Martin, S., Mellinger, D., Ward, J., Moretti, D., Harris, D. V., & Tyack, P. L. (2013). Estimating animal population density using passive acoustics. Biological Reviews of the Cambridge Philosophical Society, 88(2), 287–309.

Marshall, L. (2022a). dssd: Distance sampling survey design.

Marshall, L. (2022b). Dsims: Distance sampling simulations.

Miller, D.L., Burt, M.L., Rexstad, E.A. and Thomas, L. (2013), Spatial models for distance sampling data: recent developments and future directions. Methods in Ecology and Evolution, 4: 1001-1010.

Miller DL, Rexstad E, Thomas L, Marshall L, Laake JL (2019). “Distance Sampling in R.” Journal of Statistical Software, 89(1), 1–28.

Miller, D. L., Rexstad E., Burt L, Bravington M. V., Hedley S., Ferguson M., Kelly. N (2022). “dsm: Density Surface Modelling of Distance Sampling Data

NatureScot, 2023. Advice on marine renewables development - marine ornithology: Guidance Note 2: Guidance to support Offshore Wind Applications: Advice for Marine Ornithology Baseline Characterisation Surveys and Reporting.

NIMBLE Development Team. (2023). NIMBLE: MCMC, Particle Filtering, and Programmable Hierarchical Modeling.

Rankin, S., Oedekoven, C. S., & Archer, F. (2020). Mark recapture distance sampling: using acoustics to estimate the fraction of dolphins missed by observers during shipboard line-transect surveys. Environmental and Ecological Statistics, 27(2), 233–251. Advance online publication.

Schliep, E. M., Gelfand, A. E., Clark, C. W., Mayo, C. M., McKenna B, Parks, S.E., Yack, T. M. and Schick, R. S (2023) Assessing Marine Mammal Abundance: A Novel Data Fusion.

Scott Hayward, L. A. S., MacKenzie, M. L., Ashe, E., & Williams, R. (2015). Modelling killer whale feeding behaviour using a spatially adaptive complex region spatial smoother (CReSS) and generalised estimating equations (GEEs). Journal of Agricultural, Biological and Environmental Statistics, 20(3), 305-322. Advance online publication.

Scott-Hayward L.A.S., Walker C.G., Mackenzie M.L. (2021). “Vignette for the MRSea Package v1.3: Statistical Modelling of bird and cetacean distributions in offshore renewable development areas.” University of St. Andrews. Centre for Research into Ecological and Environmental Modelling.

Seber, G. A. F. (1982) The Estimation of Animal Abundance, 2nd Ed. Griffin, London.

Stevenson, B. C., Borchers, D. L., Altwegg, R., Swift, R. J., Gillespie, D. M., and Measey, G. J. (2015). A general framework for animal density estimation from acoustic detections across a fixed microphone array. Methods in Ecology and Evolution, 6: 38–48.

Su, Y & Yajima, M (2022) R2jags.

Teilmann, J., Christiansen, C.T., Kjellerup, S., Dietz, R. and Nachman, G. (2013). Geographic, seasonal, and diurnal surface behavior of harbor porpoises. Marine Mammal Science, 29: E60-E76.

Thompson P.M., Brookes K.L., Graham I.M., Barton T.R., Needham K., Bradbury G., Merchant N.D. (2013). Short-term disturbance by a commercial two-dimensional seismic survey does not lead to long-term displacement of harbour porpoises. Proceedings of the Royal Society B: Biological Sciences 280: 20132001.

Walker C.G., Mackenzie M.L., Donovan C., O’Sullivan M. (2010). SALSA - A Spatially Adaptive Local Smoothing Algorithm. Journal of Statistical Computation and Simulation, 81(2), 179-191

Williamson, L.D., Brookes, K.L., Scott, B.E., Graham, I.M., Bradbury, G., Hammond, P.S. and Thompson, P.M. (2016). Echolocation detections and digital video surveys provide reliable estimates of the relative density of harbour porpoises. Methods in Ecology and Evolution, 7: 762-769.

Williamson, L. D., Scott, B. E., Laxton, M. R., Bachl, F. E., Illian, J. B., Brookes, K. L., & Thompson, P. M. (2022). Spatiotemporal variation in harbor porpoise distribution and foraging across a landscape of fear. Marine Mammal Science, 38(1), 42–57.

Contact

Email: ScotMER@gov.scot

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