Regional breeding bird assessment of the Antarctic Peninsula


Conservation of seabirds in remote polar regions requires accurate information on the location of breeding sites, which is often limited by logistical constraints of surveying large areas. On the Antarctic Peninsula, many seabird colonies are visited briefly but regularly by commercial cruise vessels, a platform from which we were able to collect presence/absence data on the entire community of seabirds. We used a multistate occupancy model, accounting for limited detection during surveys, to estimate the probability of presence and breeding of all 16 species native to the area. Our results provide a much clearer view than that was previously available of how avian diversity is distributed across the region’s network of multi-species colonies and reveals species-specific differences in the effect of sea-ice concentration and site fidelity on breeding probability. Several breeding sites host an unusually large number of breeding species, but these known richness hotspots are scattered throughout the region and we were unable to identify any clear gradients in species richness that might explain why some sites are so species rich. While accounting for detection failure accelerates the pace of reliable inference on species occupancy, we find that as many as ten years of repeated visits are often required to fully catalog the seabird richness at bare rock sites along the Antarctic Peninsula. This work highlights the challenges of identifying high priority sites for special protection or management and the importance for continued surveys, even at nominally well-studied locations.

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  1. Bailey LL, MacKenzie DI, Nichols JD (2014) Advances and applications of occupancy models. Methods Ecol Evol 5:1269–1279.

    Article  Google Scholar 

  2. Bender NA, Crosbie K, Lynch HJ (2016) Patterns of tourism in the Antarctic Peninsula region: a 20-year analysis. Antarct Sci 28:194–203.

    Article  Google Scholar 

  3. BirdLife International and Handbook of the Birds of the World. 2013. Daption capense. The IUCN Red List of Threatened Species. Version 2019-1. Downloaded on 17 July 2019.

  4. BirdLife International and Handbook of the Birds of the World. 2016. Chionis albus. The IUCN Red List of Threatened Species. Version 2019-1. Downloaded on 17 July 2019.

  5. Cavalieri D, Parkinson C, Gloersen P, Zwally H (1996) Sea ice concentrations from Nimbus-7 SMMR and DMSP SSM/I-SSMIS passive microwave data, years 1990–2011. NASA DAAC at the National Snow and Ice Data Center, Boulder [Updated yearly]

  6. Cavalieri DJ, Germain KS, Swift CT (1995) Reduction of weather effects in the calculation of sea-ice concentration with the DMSP SSM/I. J Glaciol 41:455–464

    Article  Google Scholar 

  7. Chao A (1987) Estimating the population size for capture–recapture data with unequal catchability. Biometrics 43:783–791.

    CAS  Article  PubMed  Google Scholar 

  8. Coetzee BWT, Convey P, Chown SL (2017) Expanding the protected area network in Antarctica is urgent and readily achievable. Conserv Lett 10:670–680.

    Article  Google Scholar 

  9. Convey P, Morton A, Poncet J (1999) Survey of marine birds and mammals of the South Sandwich Islands. Polar Rec 35:107–124.

    Article  Google Scholar 

  10. Coria NR, Montalti D, Rombola E, Santos MM, Garcia Betoño MI, Juares MA (2011) Birds at Laurie Island, South Orkney Islands, Antarctica: breeding species and their distribution. Mar Ornithol 39:207–213

    Google Scholar 

  11. Croxall JP (1984) Seabirds. In: Laws RM (ed) Antarctic ecology, vol 2. Academic Press, London, pp 533–618

    Google Scholar 

  12. Dias MP et al (2018) Identification of marine Important Bird and Biodiversity Areas for penguins around the South Shetland Islands and South Orkney Islands. Ecol Evol 8:10520–10529.

    Article  PubMed  PubMed Central  Google Scholar 

  13. Donald PF et al (2019) Important Bird and Biodiversity Areas (IBAs): the development and characteristics of a global inventory of key sites for biodiversity. Bird Conserv Int 29:177–198.

    Article  Google Scholar 

  14. Dorazio RM, Royle JA (2005) Estimating size and composition of biological communities by modeling the occurrence of species. J Am Stat Assoc 100:389–398

    CAS  Article  Google Scholar 

  15. Gelman A, Carlin JB, Stern HS, Dunson DB, Vehtari A, Rubin DB (2013) Bayesian data analysis, 3rd edn. Chapman and Hall-CRC, Boca Raton, FL

    Google Scholar 

  16. Gotelli NJ, Colwell RK (2011) Estimating species richness. In: Magurran AE, McGill BJ (eds) Biological diversity: frontiers in measurement and assessment. Oxford University Press, New York, pp 39–54

    Google Scholar 

  17. Harris C, Carr R, Lorenz K, Jones S (2011) Important Bird Areas in Antarctica: Antarctic Peninsula, South Shetland Islands, South Orkney Islands–final report. Prepared for BirdLife International and the Polar Regions Unit of the UK Foreign & Commonwealth Office. Environmental Research & Assessment Ltd., Cambridge

    Google Scholar 

  18. Harris CM (2005) Aircraft operations near concentrations of birds in Antarctica: the development of practical guidelines. Biol Conserv 125:309–322

    Article  Google Scholar 

  19. Humphries GRW, Naveen R, Schwaller M, Che-Castaldo C, McDowall P, Schrimpf M, Lynch HJ (2017) Mapping Application for Penguin Populations and Projected Dynamics (MAPPPD): data and tools for dynamic management and decision support. Polar Rec 53:160–166.

    Article  Google Scholar 

  20. Kennicutt MC et al (2015) A roadmap for Antarctic and Southern Ocean science for the next two decades and beyond. Antarct Sci 27:3–18.

    Article  Google Scholar 

  21. Kéry M, Schaub M (2012) Bayesian population analysis using WinBUGS: a hierarchical perspective. Academic Press, Waltham, MA

    Google Scholar 

  22. Knox GA (2006) Biology of the Southern Ocean. CRC Press, Boca Raton, FL

    Google Scholar 

  23. Lee JR, Raymond B, Bracegirdle TJ, Chadès I, Fuller RA, Shaw JD, Terauds A (2017) Climate change drives expansion of Antarctic ice-free habitat. Nature 547:49–54.

    CAS  Article  PubMed  Google Scholar 

  24. Lunn D, Jackson C, Best N, Thomas A, Spiegelhalter D (2012) The BUGS book: a practical introduction to bayesian analysis. Chapman & Hall/CRC Press, New York

    Google Scholar 

  25. Lynch HJ, Naveen R, Casanovas P (2013) Antarctic Site Inventory breeding bird survey data, 1994–2013. Ecology 94:2653–2653.

    Article  Google Scholar 

  26. Lynch HJ, Naveen R, Trathan PN, Fagan WF (2012a) Spatially integrated assessment reveals widespread changes in penguin populations on the Antarctic Peninsula. Ecology 93:1367–1377

    Article  Google Scholar 

  27. Lynch HJ, White R, Black AD, Naveen R (2012b) Detection, differentiation, and abundance estimation of penguin species by high-resolution satellite imagery. Polar Biol 35:963–968.

    Article  Google Scholar 

  28. MacKenzie DI, Nichols JD, Seamans ME, Gutiérrez RJ (2009) Modeling species occurrence dynamics with multiple states and imperfect detection. Ecology 90:823–835.

    Article  PubMed  Google Scholar 

  29. Mittelbach GG (2012) Community ecology. Sinauer Associates Inc, Sunderland, MA

    Google Scholar 

  30. Naveen R (2003) Compendium of Antarctic Peninsula visitor sites, 2nd edn. A report to the United States Environmental Protection Agency. Oceanites Inc, Washington

    Google Scholar 

  31. Naveen R, Lynch HJ (2011) Antarctic Peninsula compendium, 3rd edn. Environmental Protection Agency, Washington

    Google Scholar 

  32. Oksanen J, Blanchet FG, Friendly M, Kindt R, Legendre P, McGlinn D, Minchin PR, O'Hara RB, Simpson GL, Solymos P, Stevens MHH, Szoecs E, Wagner H (2019) vegan: Community Ecology Package. R package version 2.5-6.

  33. Plummer M (2015) JAGS: A program for analysis of Bayesian graphical models using Gibbs sampling, 4.0.0 edn.

  34. R Development Core Team (2017) R: a language and environment for statistical computing. R Foundation for Statistical Computing.

  35. Schrimpf M, Naveen R, Lynch HJ (2018) Population status of the Antarctic shag Phalacrocorax (atriceps) bransfieldensis. Antarct Sci 30:151–159.

    Article  Google Scholar 

  36. Shirihai H, Jarrett B, Cox J (2007) Complete guide to Antarctic wildlife, 2nd edn. A&C Black Publishers Ltd, London

    Google Scholar 

  37. Su Y-S, Yajima M (2015) R2jags: Using R to Run 'JAGS'.

  38. Trathan PN, Warwick-Evans V, Hinke JT, Young EF, Murphy EJ, Carneiro APB, Dias MP, Kovacs KM, Lowther AD, Godø OR, Kokubun N, Kim JH, Takahashi A, Santos M (2018) Managing fishery development in sensitive ecosystems: identifying penguin habitat use to direct management in Antarctica. Ecosphere 9:e02392.

    Article  Google Scholar 

  39. Wauchope HS, Shaw JD, Terauds A (2019) A snapshot of biodiversity protection in Antarctica. Nat Commun 10:6.

    CAS  Article  Google Scholar 

  40. Willig MR, Kaufman DM, Stevens RD (2003) Latitudinal gradients of biodiversity: pattern, process, scale, and synthesis. Annu Rev Ecol Evol Syst 34:273–309.

    Article  Google Scholar 

  41. Woehler E (1993) The distribution and abundance of Antarctic and Subantarctic penguins. Cambridge, United Kingdom, Scientific Committee on Antarctic Research (SCAR)

    Google Scholar 

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We thank R. Naveen and all of the Antarctic Site Inventory field staff for data collection. B. Şen, L. Prowant, C. Foley, M. Lynch, and C. Youngflesh were helpful in interpretation of the results, and C. Graham, D. Futuyma, and R. Veit provided feedback on early versions of the manuscript. We also appreciate the very helpful comments by the anonymous reviewers.


Financial support was provided by the National Science Foundation/Office of Polar Programs, award no. 1255058, and the National Aeronautics and Space Administration, award no. NNX14AC32G. Additional logistical support was provided by a number of member organizations of the International Association of Antarctica Tour Operators, chiefly One Ocean Expeditions.

Author information




MBS and HJL conceived the project; MBS analyzed most of the model results with guidance from CCC and HJL; all authors contributed to the design of the occupancy model and to the written manuscript.

Corresponding author

Correspondence to Michael B. Schrimpf.

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The authors declare that they have no conflict of interest.

Ethical approval

Fieldwork was permitted through the National Science Foundation as per the Antarctic Conservation Act (most recent permit: ACA 2019-001). Observation of birds was approved by the Stony Brook University Institutional Animal Care and Use Committee (2011-1881-R2-6.19.20-BI).

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Supplementary file 1 Additional details about the posterior predictive check procedure and results (PDF 2857 kb)

Supplementary file 2 Additional parameter posterior distributions (PDF 108 kb)

Supplementary file 3 Additional details regarding the effect of removing the site-fidelity term from the model (PDF 112 kb)

Supplementary file 4 Maps of breeding probability of all species at all investigated sites (PDF 1494 kb)

Supplementary file 5 Site metadata and breeding probabilities of all species in table form. Note that both the results of the combined “any skua” model (AnySkua) and the summed state of total skuas (TotSkua) are also included (CSV 34 kb)

Supplementary file 6 Additional details about the downsampling procedure to further investigate the results of the Chao2 estimated species richness. In addition, source code and full model results are available at GitHub, via the following URL: (PDF 149 kb)

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Schrimpf, M.B., Che-Castaldo, C. & Lynch, H.J. Regional breeding bird assessment of the Antarctic Peninsula. Polar Biol 43, 111–122 (2020).

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  • Occupancy
  • Species distributions
  • Important bird areas
  • Antarctic specially protected areas