Reading materials

This page hosts a list of reading materials on the topics related to the goals of SORTEE.

Light reading - popular articles / blogs:

• Bahlai, C. et al. (2019) HOpen Science Isn’t Always Open to All Scientists. American Scientist

• Finkel, A. (2019) ‘There is a problem’: Australia’s top scientist Alan Finkel pushes to eradicate bad science. The Conversation

• Loken, E. (2019) The replication crisis is good for science. The Conversation

• Dean, T. (2017) How we edit science part 2: significance testing, p-hacking and peer review. The Conversation

Books:

• Ritchie, S. (2020). Science fictions.

• Leng G., Leng R.I. (2020). The Matter of Facts: Skepticism, Persuasion, and Evidence in Science.

• Spiegelhalter D. (2019). The Art of Statistics: Learning from Data.

• Harris, R. (2017). Rigor Mortis: How Sloppy Science Creates Worthless Cures, Crushes Hope, And Wastes Billions.

Academic reading (journal articles - ecology and evolution focus):

2023

• Ivimey-Cook, E. R., Pick, J. L., Bairos-Novak, K., Culina, A., Gould, E., Grainger, M., … & Windecker, S. (2023). Implementing Code Review in the Scientific Workflow: Insights from Ecology and Evolutionary Biology. EcoEvoRxiv. SORTEE conference product!

• Braga, P. H. P., Hébert, K., Hudgins, E. J., Scott, E. R., Edwards, B. P., Sánchez Reyes, L. L., … & Crystal‐Ornelas, R. (2023). Not just for programmers: How GitHub can accelerate collaborative and reproducible research in ecology and evolution. Methods in Ecology and Evolution. SORTEE conference product!

• Nakagawa, S., Ivimey-Cook, E. R., Grainger, M. J., O’Dea, R. E., Burke, S., Drobniak, S. M., … & Lagisz, M. (2023). Method Reporting with Initials for Transparency (MeRIT) promotes more granularity and accountability for author contributions. Nature Communications, 14(1), 1788. SORTEE conference product!

2022

• Gomes, D. G., Pottier, P., Crystal-Ornelas, R., Hudgins, E. J., Foroughirad, V., Sánchez-Reyes, L. L., … & Gaynor, K. M. (2022). Why don’t we share data and code? Perceived barriers and benefits to public archiving practices. Proceedings of the Royal Society B, 289(1987), 20221113. SORTEE conference product!

• Roche DG, O’Dea RE, Kerr KA, Rytwinski T, Schuster R, Nguyen VM, Young N, Bennett JR, Cooke SJ. 2022. Closing the knowledge-action gap in conservation with open science. Conserv Biol. 36(3):e13835. doi: 10.1111/cobi.13835.

2021

• Brlík V., Pipek P., Brandis K., Chernetsov N., Costa F.J.V., Herrera M. L.G., Kiat Y., Lanctot R.B., Marra P.P., Norris D.R., Nwaogu C.J., Quillfeldt P., Saalfeld S.T., Stricker C.A., Thomson R.L., Zhao T., Procházka P. (2021) The reuse of avian samples: opportunities, pitfalls, and a solution. Ibis. doi: 10.1111/ibi.12997

• Bruna E.M., Chazdon R., Errington T.M., Nosek B.A. (2021) A proposal to advance theory and promote collaboration in tropical biology by supporting replications. Biotropica 53: 6-10, doi:10.1111/btp.12912

• Chacón-Labella J., Boakye M., Enquist B.J., Farfan-Rios W., Gya R., Halbritter A.H., Middleton S.L., von Oppen J., Pastor-Ploskonka S., Strydom T., Vandvik V., Geange S.R. (2021) From a crisis to an opportunity: Eight insights for doing science in the COVID-19 era and beyond. Ecology and Evolution 11: 3588-3596, doi:10.1002/ece3.7026

• Graham E.B., Averill C., Bond-Lamberty B., Knelman J.E., Krause S., Peralta A.L., Shade A., Smith A.P., Cheng S.J., Fanin N., Freund C., Garcia P.E., Gibbons S.M., Van Goethem M.W., Guebila M.B., Kemppinen J., Nowicki R.J., Pausas J.G., Reed S.P., Rocca J., Sengupta A., Sihi D., Simonin M., Słowiński M., Spawn S.A., Sutherland I., Tonkin J.D., Wisnoski N.I., Zipper S.C., Contributor Consortium (2021) Toward a Generalizable Framework of Disturbance Ecology Through Crowdsourced Science. Frontiers in Ecology and Evolution. 9: 588940, doi:10.3389/fevo.2021.588940

• Lennox R.J., Harcourt R., Bennett J.R., Davies A., Ford A.T., Frey R.M., Hayward M.W., Hussey N.E., Iverson S.J., Kays R., Kessel S.T., McMahon C., Muelbert M., Murray T.S., Nguyen V.M., Pye J.D., Roche D.G., Whoriskey F.G., Young N., Cooke S.J. (2021) A novel framework to protect animal data in a world of ecosurveillance. BioScience 70: 468-476, doi: 10.1093/BIOSCI/BIAA035

• Manzano S., Julier A.C.M.(2021) How FAIR are plant sciences in the twenty-first century? the pressing need for reproducibility in plant ecology and evolution. Proceedings of the Royal Society B: Biological Sciences 288: 20202597, doi: 10.1098/rspb.2020.2597

• O’Dea R.E., Parker T.H., Chee Y.E., Culina A., Drobniak S.M., Duncan D.H., Fidler F., Gould E., Ihle M., Kelly C.D., Lagisz M., Roche D.G., Sánchez-Tójar A., Wilkinson D.P., Wintle B.C., Nakagawa S. (2021) Towards open, reliable, and transparent ecology and evolutionary biology. BMC Biology 19: 68, doi:10.1186/s12915-021-01006-3

• O’Dea R.E., Lagisz M., Jennions M.D., Koricheva J., Noble D.W.A., Parker T.H., Gurevitch J., Page M.J., Stewart G., Moher D., Nakagawa S. (2021) Preferred reporting items for systematic reviews and meta-analyses in ecology and evolutionary biology: a PRISMA extension. Biological Reviews 96: 1695-1722, doi:10.1111/brv.12721

• Romanelli J.P., Meli P., Naves R.P., Alves M.C., Rodrigues R.R. (2021) Reliability of evidence-review methods in restoration ecology. Conservation Biology 35: 142-154, doi:10.1111/cobi.13661

• Romanelli J.P., Silva L.G.M., Gonçalves M.C.P., Naves R.P., de Almeida D.R.A., de Resende A.F., Rodrigues R.R. (2021) Repeatability of the searching process in reviews of restoration outcomes. Restoration Ecology. doi: 10.1111/rec.13496

• Sequeira A.M.M., O’Toole M., Keates T.R., McDonnell L.H., Braun C.D., Hoenner X., Jaine F.R.A., Jonsen I.D., Newman P., Pye J., Bograd S.J., Hays G.C., Hazen E.L., Holland M., Tsontos V.M., Blight C., Cagnacci F., Davidson S.C., Dettki H., Duarte C.M., Dunn D.C., Eguíluz V.M., Fedak M., Gleiss A.C., Hammerschlag N., Hindell M.A., Holland K., Janekovic I., McKinzie M.K., Muelbert M.M.C., Pattiaratchi C., Rutz C., Sims D.W., Simmons S.E., Townsend B., Whoriskey F., Woodward B., Costa D.P., Heupel M.R., McMahon C.R., Harcourt R., Weise M. (2021) A standardisation framework for bio-logging data to advance ecological research and conservation. Methods in Ecology and Evolution 12: 996-1007, doi:10.1111/2041-210X.13593

• Yanai R.D., Mann T.A., Hong S.D., Pu G., Zukswert J.M. (2021) The current state of uncertainty reporting in ecosystem studies: a systematic evaluation of peer-reviewed literature. Ecosphere 12: e03535, doi: 10.1002/ecs2.3535

• Filazzola, A., & Cahill, J. F. (2021). Replication in field ecology: Identifying challenges and proposing solutions. Methods in Ecology and Evolution, 12, 1780– 1792.

• Marshall, BM & Strine, CT. 2021. Make like a glass frog: In support of increased transparency in herpetology. Herpetological Journal. 31: 35-45.

2020

• Nilsen, EB, Bowler, DE, Linnell, JDC. 2020. Exploratory and confirmatory research in the open science era. J Appl Ecol 57: 842– 847.

• Fraser, H., A. Barnett, T. H. Parker, F. Fidler. 2020. The role of replication studies in ecology. Ecology and Evolution. doi: 10.1002/ece3.6330

2019

• Powers, S. M., and Hampton, S. E.. 2019. Open science, reproducibility, and transparency in ecology. Ecological Applications 29( 1):e01822. 10.1002/eap.1822

• Nichols, JD, Kendall, WL, Boomer, GS. 2019. Accumulating evidence in ecology: Once is not enough. Ecol Evol. 9: 13991– 14004. https://doi.org/10.1002/ece3.5836

• Parker. T.H., H. Fraser, S. Nakagawa. 2019. Making conservation science more reliable with preregistration and registered reports. Conservation Biology. 33: 747-750. doi: 10.1111/cobi.13342

2018

• Fraser, H., T. H. Parker, S. Nakagawa, A. Barnett, F. Fidler (2018) Questionable research practices in ecology and evolution. PLOS ONE, 13(7): e0200303. doi:10.1371/journal.pone.0200303

• Parker, T.H.,S. Griffith, J. Bronstein, F. Fidler, S. Foster, H. Fraser, W. Forstmeier, J. Gurevitch, J. Koricheva, R. Seppelt, M. Tingley, S. Nakagawa. 2018. Empowering peer reviewers with a checklist to improve transparency. Nature Ecology & Evolution. 2: 929-935. doi: 10.1038/s41559-018-0545-z, pre-print doi: 10.17605/OSF.IO/U4MXD

2017

• Fidler, Fiona, Yung En Chee, Bonnie C. Wintle, Mark A. Burgman, Michael A. McCarthy, Ascelin Gordon (2017) Metaresearch for evaluating reproducibility in ecology and evolution BioScience. 67: 282-289. doi:10.1093/biosci/biw159

• Forstmeier, Wolfgang, Eric-Jan Wagonmakers,Timothy H. Parker (2017) Detecting and avoiding likely false-positive findings - a practical guide. Biological Reviews 92: 1941-1968. doi:10.1111/brv.12315

• Gerstner, K., Moreno-Mateos, D., Gurevitch, J., Beckmann, M., Kambach, S., Jones, H.P. and Seppelt, R. (2017), Will your paper be used in a meta-analysis? Make the reach of your research broader and longer lasting. Methods Ecol Evol, 8: 777-784.

• Malika Ihle, Isabel S. Winney, Anna Krystalli, Michael Croucher. 2017. Striving for transparent and credible research: practical guidelines for behavioral ecologists. Behavioral Ecology, 28: 348–354.

2016 and earlier

• Parker, Timothy H., Wolfgang Forstmeier, Julia Koricheva, Fiona Fidler, Jarrod D. Hadfield, Yung En Chee, Clint D. Kelly, Jessica Gurevitch, and Shinichi Nakagawa (2016) Transparency in ecology and evolution: real problems, real solutions. Trends in Ecology & Evolution 31: 711-19. doi:10.1016/j.tree.2016.07.002

• Kardish, Melissa R., Ulrich G. Mueller, Sabrina Amador-Vargas, Emma I. Dietrich, Rong Ma, Brian Barrett, and Chi-Chun Fang (2015) Blind trust in unblinded observation in ecology, evolution, and behavior. Frontiers in Ecology and Evolution 3: 51. doi:10.3389/fevo.2015.00051

• Mislan, K. A. S., Jeffrey M. Heer, and Ethan P. White (2015) Elevating the status of code in ecology. Trends in Ecology & Evolution 31: 4-7. doi:10.1016/j.tree.2015.11.006

• Nosek, Brian A., and others (2015) Promoting an open research culture. Science 348: 1422. doi:10.1126/science.aab2374

• Barto, E. Kathryn and Matthias C. Rillig (2012) Dissemination biases in ecology: effect sizes matter more than quality. Oikos, 121: 228-235. doi:10.1111/j.1600-0706.2011.19401.x

• Whitlock, Michael C. (2011) Data archiving in ecology and evolution: best practices. Trends in Ecology & Evolution 26: 61-65. doi:10.1016/j.tree.2010.11.006

• Borries, C., Sandel, A.A., Koenig, A., Fernandez-Duque, E., Kamilar, J.M., Amoroso, C.R., Barton, R.A., Bray, J., Di Fiore, A., Gilby, I.C., Gordon, A.D., Mundry, R., Port, M., Powell, L.E., Pusey, A.E., Spriggs, A. and Nunn, C.L. 2016. Transparency, usability, and reproducibility: Guiding principles for improving comparative databases using primates as examples. Evolutionary Anthropology, 25: 232-238 doi:10.1002/evan.21502

• Hampton, S. E., S. S. Anderson, S. C. Bagby, C. Gries, X. Han, E. M. Hart, M. B. Jones, W. C. Lenhardt, A. MacDonald, W. K. Michener, J. Mudge, A. Pourmokhtarian, M. P. Schildhauer, K. H. Woo, and N. Zimmerman. 2015. The Tao of open science for ecology. Ecosphere 6(7):120.

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