Protocols

Protocols sit at the practical center of transparent research. They turn research ideas into clear, reviewable plans and create stable public records of how a project is designed before results shape the story.

At COSSEE, protocols are part of a broader commitment to open, rigorous, and reusable research. They are especially important for synthesis projects, evidence maps, systematic reviews, and studies where analytical decisions should be visible early.

Registrations

Registrations are structured records of a project’s questions, hypotheses, design choices, and planned analyses. They help distinguish planned work from later interpretation and make studies easier to evaluate on their design merits.

Within ecology and evolution, registrations can support both empirical studies and synthesis projects, including meta-analyses, systematic reviews, and evidence maps.

Recent public pre-registrations from Shinichi Nakagawa and Malgorzata (Losia) Lagisz on the Open Science Framework, newest first (full lists: Nakagawa, Lagisz).

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

Registered Reports

Registered Reports are publications that are peer-reviewed at the protocol stage. In Stage 1, the introduction and methods are reviewed before the full study is completed. If the design is judged to be strong, the paper receives provisional acceptance. In Stage 2, the completed report is reviewed for compliance with the pre-registered questions and methods, and publication does not depend on whether the results are novel or statistically significant.

Registered Reports in BMC Biology

  1. Yang, Y., Sánchez-Tójar, A., O’Dea, R. E., Noble, D. W. A., Koricheva, J., Jennions, M. D., Parker, T. H., Lagisz, M., & Nakagawa, S. (2023). Publication bias impacts on effect size, statistical power, and magnitude (Type M) and sign (Type S) errors in ecology and evolutionary biology. BMC Biology, 21(1), 71. https://doi.org/10.1186/s12915-022-01485-y
  2. Foo, Y. Z., Lagisz, M., O’Dea, R. E., & Nakagawa, S. (2023). The influence of immune challenges on the mean and variance in reproductive investment: a meta-analysis of the terminal investment hypothesis. BMC Biology, 21(1), 107. https://doi.org/10.1186/s12915-023-01603-4
  3. Parker, T. H., Fraser, H., Nakagawa, S., Gould, E., Griffith, S. C., Vesk, P. A., & Fidler, F. et al. (in revision). Same data, different analysts: variation in effect sizes due to analytical decisions in ecology and evolutionary biology. BMC Biology.

Registered Reports in Ecological Solutions and Evidence

  1. Vendl, C., Taylor, M. D., Braeunig, J., Gibson, M. J., Hesselson, D., Neely, G. G., Lagisz, M.#, Nakagawa, S.# (2021). Profiling research on PFAS in wildlife: protocol of a systematic evidence map and bibliometric analysis. Ecological Solutions and Evidence, 2, e12106. https://doi.org/10.1002/2688-8319.12106
    Follow-up publication: Vendl, C., Taylor, M. D., Braeunig, J., Gibson, M. J., Hesselson, D., Neely, G. G., Lagisz, M.#, Nakagawa, S.# (2024). Profiling research on PFAS in wildlife: a systematic evidence map and bibliometric analysis. Ecological Solutions and Evidence, 5, e12292. https://doi.org/10.1002/2688-8319.12292
  2. Burke, S., Pottier, P., Macartney, E. L., Drobniak, S. M., Lagisz, M.#, Ainsworth, T. #, Nakagawa, S.# (2022). Mapping literature reviews on coral health: protocol for a review map, critical appraisal, and bibliometric analysis. Ecological Solutions and Evidence, 3, e12190. https://doi.org/10.1002/2688-8319.12190
    Follow-up publication: Burke, S., Pottier, P., Macartney, E. L., Drobniak, S. M., Lagisz, M.#, Ainsworth, T. #, Nakagawa, S.# (2023). Mapping literature reviews on coral health: a review map, critical appraisal and bibliometric analysis. Ecological Solutions and Evidence, 4, e12287. https://doi.org/10.1002/2688-8319.12287
  3. Young, S. #, Haddaway, N. R. #, Nakagawa, S.#, Lagisz, M.#, Callaghan, M. # (2021). Understanding collaboration and term usage dynamics in agricultural buffer strip research: a research weaving protocol. Ecological Solutions and Evidence, 2, e12084. https://doi.org/10.1002/2688-8319.12084
    Follow-up publication: Young, S., Lagisz, M., Callaghan, M., Nakagawa, S., Haddaway, N. R. (2024). Collaboration and term usage dynamics in agricultural buffer strip research: research weaving. Ecological Solutions and Evidence, 5(3), e12376. https://doi.org/10.1002/2688-8319.12376

Published Protocols

Published protocols are peer-reviewed, stand-alone publications that outline the hypotheses and methods of a planned project. They are followed by separate publications presenting the results of the work.

  1. Burke, S., Pottier, P., Macartney, E. L., Drobniak, S. M., Lagisz, M., Ainsworth, T., & Nakagawa, S. (2022). Mapping literature reviews on coral health: protocol for a review map, critical appraisal, and bibliometric analysis. Ecological Solutions and Evidence. https://doi.org/10.1002/2688-8319.12190
  2. Vendl, C., Taylor, M. D., Breunig, J., Gibson, M. J., Hesselson, D., Neely, G. G., Lagisz, M., Nakagawa, S. (2022). PFAS exposure of humans, animals and the environment: protocol of an evidence review map and bibliometric analysis. Environment International, 158, 106973. https://doi.org/10.1016/j.envint.2021.106973
  3. Macartney, E. L., Drobniak, S. M., Nakagawa, S., Lagisz, M.# (2021). Non-genetic inheritance of environmental exposures: a protocol for a map of systematic reviews with bibliometric analysis. Environmental Evidence, 10, 31. https://doi.org/10.1186/s13750-021-00245-9
  4. Vendl, C., Taylor, M. D., Breunig, J., Gibson, M. J., Hesselson, D., Neely, G. G., Lagisz, M.#, Nakagawa, S.# (2021). Profiling research on PFAS in wildlife: protocol of a systematic evidence map and bibliometric analysis. Ecological Solutions and Evidence, 2, e12106. https://doi.org/10.1002/2688-8319.12106
  5. Martin, J. M., Bertram, M. G., Blanchfield, P. J., Brand, J. A., Brodin, T., Brooks, B. W., Cerveny, D., Lagisz, M., Ligocki, I. Y., Michelangeli, M., Nakagawa, S., Orford, J. T., Sundin, J., Tan, H., Wong, B. B. M., & McCallum, E. (2021). Evidence of the impacts of pharmaceuticals on aquatic animal behaviour: a systematic map protocol. Environmental Evidence, 10, 26. https://doi.org/10.1186/s13750-021-00241-z
  6. Young, S., Haddaway, N. R., Nakagawa, S., Lagisz, M., Callaghan, M. (2021). Understanding collaboration and term usage dynamics in agricultural buffer strip research: a research weaving protocol. Ecological Solutions and Evidence, 2, e12084. https://doi.org/10.1002/2688-8319.12084
  7. Page, M. J., Moher, D., Fidler, F. M., Higgins, J. P. T., Brennan, S. E., Haddaway, N. R., Hamilton, D. G., Kanukula, R., Karunananthan, S., Maxwell, L. J., McDonald, S., Nakagawa, S., Nunan, D., Tugwell, P., Welch, V. A., & McKenzie, J. E. (2021). The REPRISE project: protocol for an evaluation of REProducibility and Replicability In Syntheses of Evidence. Systematic Reviews, 10, 112. https://doi.org/10.1186/s13643-021-01670-0
  8. Miyahara, M., Hillier, S. L., Pridham, L., & Nakagawa, S. (2014). Task-oriented interventions approaches for children with developmental co-ordination disorder (Protocol). Cochrane Database of Systematic Reviews, CD010914. https://doi.org/10.1002/14651858.CD010914

Registered protocols on OSF

Protocols registered by Shinichi Nakagawa and Malgorzata (Losia) Lagisz on the Open Science Framework, newest first.

Notes: Bold font indicates known COSSEE research group members listed in these publications. # indicates equal contribution.