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A standard protocol to report discrete stage‐structured demographic information

A standard protocol to report discrete stage‐structured demographic information
A standard protocol to report discrete stage‐structured demographic information
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.
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.
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.compadre-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.
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.
comparative demography, matrix population models, open access, reproducibility
2041-210X
2065-2083
Gascoigne, Samuel J. L.
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Rolph, Simon
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Sankey, Daisy
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Nidadavolu, Nagalakshmi
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Stell pičman, Adrian S.
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Hernández, Christina M.
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Philpott, Matthew E. R.
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Salam, Aiyla
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Bernard, Connor
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Fenollosa, Erola
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Lee, Young Jun
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Mclean, Jessica
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Hetti achchige perera, Shathuki
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Spacey, Oliver G.
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Kajin, Maja
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Vinton, Anna C.
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Archer, C. Ruth
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Burns, Jean H.
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Buss, Danielle L.
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Caswell, Hal
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Childs, Dylan Z.
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Capdevila, Pol
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Compagnoni, Aldo
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Crone, Elizabeth
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Ezard, Thomas H. G.
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Hodgson, Dave
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Knight, Tiffany M.
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Jones, Owen R.
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Jongejans, Eelke
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Mcdonald, Jenni
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Tenhumberg, Brigitte
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Thomas, Chelsea C.
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Tyre, Andrew J.
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Ramula, Satu
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Stott, Iain
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Tremblay, Raymond L.
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Wilson, Phil
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Vaupel, James W.
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et al.
Gascoigne, Samuel J. L.
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Rolph, Simon
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Sankey, Daisy
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Nidadavolu, Nagalakshmi
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Stell pičman, Adrian S.
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Hernández, Christina M.
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Philpott, Matthew E. R.
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Salam, Aiyla
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Bernard, Connor
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Fenollosa, Erola
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Lee, Young Jun
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Mclean, Jessica
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Hetti achchige perera, Shathuki
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Spacey, Oliver G.
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Kajin, Maja
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Vinton, Anna C.
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Caswell, Hal
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Childs, Dylan Z.
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Capdevila, Pol
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Compagnoni, Aldo
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Crone, Elizabeth
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Ezard, Thomas H. G.
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Hodgson, Dave
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Knight, Tiffany M.
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Jones, Owen R.
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Mcdonald, Jenni
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Tenhumberg, Brigitte
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Thomas, Chelsea C.
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Tyre, Andrew J.
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Ramula, Satu
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Stott, Iain
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Tremblay, Raymond L.
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Wilson, Phil
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Vaupel, James W.
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Salguero‐gómez, Roberto
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Gascoigne, Samuel J. L., Rolph, Simon and Sankey, Daisy , et al. (2023) A standard protocol to report discrete stage‐structured demographic information. Methods in Ecology and Evolution, 14 (8), 2065-2083. (doi:10.1111/2041-210X.14164).

Record type: Article

Abstract

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.
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.
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.compadre-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.
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.

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Accepted/In Press date: 18 May 2023
e-pub ahead of print date: 20 June 2023
Published date: August 2023
Additional Information: Funding Information: We thank the hundreds of population ecologists who have contributed open-access matrix population models ready for fully reproducible research, and those who have, throughout the last 15 years, answered our emails asking for additional data and metadata. We also thank Chloé R. Nater and one anonymous reviewer for their helpful comments. Conversations leading to this manuscript were initiated during a workshop held at the University of Exeter Cornwall campus with support of NERC grant (NE/N006798/1) to Jenni McDonald and Dave Hodgson. We acknowledge the support of the Evolutionary Demography Laboratory at the Max Planck Institute for Demographic Research (MPIDR) in the development of the COMPADRE Plant Matrix Database and COMADRE Animal Matrix Database, and the maintenance of COMPADRE & COMADRE through the distributed network of digitising nodes including MPIDR, University of Oxford, University of Exeter, Southampton University, Trinity College Dublin, Lincoln Park Zoo, University of Southern Denmark and iDiv. Roberto Salguero-Gómez was supported by a NERC Independent Research Fellowship (NE/M018458/1). Christina M. Hernández was supported by a US-NSF grant (DEB-1933497). Pol Capdevila was supported by a Maria Zambrano Next Generation EU Fellowship. Judy P. Che-Castaldo, Owen R. Jones, Roberto Salguero-Gómez and Chelsea C. Thomas were supported by an NSF Advances in Bioinformatics Development Award (#DBI-1661342). Danielle L. Buss was funded by NERC Discovery Science grant NE/L007770/1. Tiffany M. Knight was supported by the Helmholtz Association and the Alexander von Humboldt foundation. Hal Caswell was supported by the European Research Council, Advanced Grant 788195. Lastly, this paper is in memoriam of our dear friend and colleague James W. Vaupel, who sadly passed before the submission of this manuscript. His multiple contributions to demography will no doubt outlive multiple Bristlecone pine generation times. Funding Information: We thank the hundreds of population ecologists who have contributed open‐access matrix population models ready for fully reproducible research, and those who have, throughout the last 15 years, answered our emails asking for additional data and metadata. We also thank Chloé R. Nater and one anonymous reviewer for their helpful comments. Conversations leading to this manuscript were initiated during a workshop held at the University of Exeter Cornwall campus with support of NERC grant (NE/N006798/1) to Jenni McDonald and Dave Hodgson. We acknowledge the support of the Evolutionary Demography Laboratory at the Max Planck Institute for Demographic Research (MPIDR) in the development of the COMPADRE Plant Matrix Database and COMADRE Animal Matrix Database, and the maintenance of COMPADRE & COMADRE through the distributed network of digitising nodes including MPIDR, University of Oxford, University of Exeter, Southampton University, Trinity College Dublin, Lincoln Park Zoo, University of Southern Denmark and iDiv. Roberto Salguero‐Gómez was supported by a NERC Independent Research Fellowship (NE/M018458/1). Christina M. Hernández was supported by a US‐NSF grant (DEB‐1933497). Pol Capdevila was supported by a Maria Zambrano Next Generation EU Fellowship. Judy P. Che‐Castaldo, Owen R. Jones, Roberto Salguero‐Gómez and Chelsea C. Thomas were supported by an NSF Advances in Bioinformatics Development Award (#DBI‐1661342). Danielle L. Buss was funded by NERC Discovery Science grant NE/L007770/1. Tiffany M. Knight was supported by the Helmholtz Association and the Alexander von Humboldt foundation. Hal Caswell was supported by the European Research Council, Advanced Grant 788195. Lastly, this paper is in memoriam of our dear friend and colleague James W. Vaupel, who sadly passed before the submission of this manuscript. His multiple contributions to demography will no doubt outlive multiple Bristlecone pine generation times. Publisher Copyright: © 2023 The Authors. Methods in Ecology and Evolution published by John Wiley & Sons Ltd on behalf of British Ecological Society.
Keywords: comparative demography, matrix population models, open access, reproducibility

Identifiers

Local EPrints ID: 479841
URI: http://eprints.soton.ac.uk/id/eprint/479841
ISSN: 2041-210X
PURE UUID: 9022eeb6-b7d6-4a50-94d4-76d504a16784
ORCID for Thomas H. G. Ezard: ORCID iD orcid.org/0000-0001-8305-6605

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Date deposited: 27 Jul 2023 15:46
Last modified: 22 Jun 2024 01:46

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Contributors

Author: Samuel J. L. Gascoigne
Author: Simon Rolph
Author: Daisy Sankey
Author: Nagalakshmi Nidadavolu
Author: Adrian S. Stell pičman
Author: Christina M. Hernández
Author: Matthew E. R. Philpott
Author: Aiyla Salam
Author: Connor Bernard
Author: Erola Fenollosa
Author: Young Jun Lee
Author: Jessica Mclean
Author: Shathuki Hetti achchige perera
Author: Oliver G. Spacey
Author: Maja Kajin
Author: Anna C. Vinton
Author: C. Ruth Archer
Author: Jean H. Burns
Author: Danielle L. Buss
Author: Hal Caswell
Author: Judy P. Che‐castaldo
Author: Dylan Z. Childs
Author: Pol Capdevila
Author: Aldo Compagnoni
Author: Elizabeth Crone
Author: Thomas H. G. Ezard ORCID iD
Author: Dave Hodgson
Author: Tiffany M. Knight
Author: Owen R. Jones
Author: Eelke Jongejans
Author: Jenni Mcdonald
Author: Brigitte Tenhumberg
Author: Chelsea C. Thomas
Author: Andrew J. Tyre
Author: Satu Ramula
Author: Iain Stott
Author: Raymond L. Tremblay
Author: Phil Wilson
Author: James W. Vaupel
Author: Roberto Salguero‐gómez
Corporate Author: et al.

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