A standard protocol to report discrete stage-structured demographic information

Authors

Samuel J. L. Gascoigne, University of Oxford
Simon Rolph, University of Sheffield
Daisy Sankey, University of Oxford
Nagalakshmi Nidadavolu, University of Oxford
Adrian S. Stell Pičman, University of Oxford, University of Ljubljana
Christina M. Hernández, Cornell University
Matthew E. R. Philpott, University of Oxford
Aiyla Salam, University of Oxford
Connor Bernard, University of Oxford
Erola Fenollosa, University of Oxford
Young Jun Lee, University of Oxford
Jessica McLean, University of Oxford
Shathuki Hetti Achchige Perera, University of Oxford
Oliver G. Spacey, University of Oxford
Maja Kajin, University of Oxford, University of Ljubljana
Anna C. Vinton, University of Oxford
C. Ruth Archer, University of Ulm
Jean H. Burns, Case Western Reserve University
Danielle L. Buss, University of Cambridge, University of Exeter
Hal Caswell, University of Amsterdam
Judy P. Che-Castaldo, U.S. Fish and Wildlife Service
Dylan Z. Childs, University of Sheffield
Pol Capdevila, University of Bristol
Aldo Compagnoni, University of Oxford, Martin Luther University Halle-Wittenburg, German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena- Leipzig
Elizabeth Crone, Tufts University
Thomas H. G. Ezard, University of Southampton
Dave Hodgson, University of Exeter
Tiffany M. Knight, Martin Luther University Halle-Wittenburg, German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena- Leipzig
Owen R. Jones, University of Southern Denmark
Eelke Jongejans, Radboud University, NIOO-KNAW
Jenni McDonald, National Cat Centre, University of Bristol
Brigitte Tenhumberg, University of Nebraska - LincolnFollow
Chelsea C. Thomas, Alexander Center for Applied Population Biology
Andrew J. Tyre, University of Nebraska-Lincoln, Bayer U.S. –Crop Science
Satu Ramula, University of Turku
Iain Stott, University of Lincoln
Raymond L. Tremblay, University of Puerto Rico, University of Puerto Rico-Humacao
Phil Wilson, University of Exeter
James James Vaupel, University of Southern Denmark
Roberto Salguero-Gómez, University of Oxford, University of Queensland, Max Planck Institute for Demographic Research

Document Type

Article

Date of this Version

5-18-2023

Citation

Methods Ecol Evol. 2023;00:1–19. DOI: 10.1111/2041-210X.14164

Comments

Open access.

Abstract

1. Stage-based demographic methods, such as matrix population models (MPMs), are powerful tools used to address a broad range of fundamental questions in ecology, evolutionary biology and conservation science. Accordingly, MPMs now exist for over 3000 species worldwide. These data are being digitised as an ongoing process and periodically released into two large open-access online repositories: the COMPADRE Plant Matrix Database and the COMADRE Animal Matrix Database. During the last decade, data archiving and curation of COMPADRE and COMADRE, and subsequent comparative research, have revealed pronounced variation in how MPMs are parameterized and reported.

2. Here, we summarise current issues related to the parameterisation and reporting of MPMs that arise most frequently and outline how they affect MPM construction, analysis, and interpretation. To quantify variation in how MPMs are reported, we present results from a survey identifying key aspects of MPMs that are frequently unreported in manuscripts. We then screen COMPADRE and COMADRE to quantify how often key pieces of information are omitted from manuscripts using MPMs.

3. Over 80% of surveyed researchers (n = 60) state a clear benefit to adopting more standardised methodologies for reporting MPMs. Furthermore, over 85% of the 300 MPMs assessed from COMPADRE and COMADRE omitted one or more elements that are key to their accurate interpretation. Based on these insights, we identify fundamental issues that can arise from MPM construction and communication and provide suggestions to improve clarity, reproducibility and future research utilising MPMs and their required metadata. To fortify reproducibility and empower researchers to take full advantage of their demographic data, we introduce a standardised protocol to present MPMs in publications. This standard is linked to www.compa dre-db.org, so that authors wishing to archive their MPMs can do so prior to submission of publications, following examples from other open-access repositories such as DRYAD, Figshare and Zenodo.

4. Combining and standardising MPMs parameterized from populations around the globe and across the tree of life opens up powerful research opportunities in evolutionary biology, ecology and conservation research. However, this potential can only be fully realised by adopting standardised methods to ensure reproducibility.