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1. Quantifying and addressing the prevalence and bias of study designs in the environmental and social sciences

Author

Alec P. Christie, David Abecasis, Mehdi Adjeroud, Juan C. Alonso, Tatsuya Amano, Alvaro Anton, Barry P. Baldigo, Rafael Barrientos, Jake E. Bicknell, Deborah A. Buhl, Just Cebrian, Ricardo S. Ceia, Luciana Cibils-Martina, Sarah Clarke, Joachim Claudet, Michael D. Craig, Dominique Davoult, Annelies De Backer, Mary K. Donovan, Tyler D. Eddy, Filipe M. França, Jonathan P. A. Gardner, Bradley P. Harris, Ari Huusko, Ian L. Jones, Brendan P. Kelaher, Janne S. Kotiaho, Adrià López-Baucells, Heather L. Major, Aki Mäki-Petäys, Beatriz Martín, Carlos A. Martín, Philip A. Martin, Daniel Mateos-Molina, Robert A. McConnaughey, Michele Meroni, Christoph F. J. Meyer, Kade Mills, Monica Montefalcone, Norbertas Noreika, Carlos Palacín, Anjali Pande, C. Roland Pitcher, Carlos Ponce, Matt Rinella, Ricardo Rocha, María C. Ruiz-Delgado, Juan J. Schmitter-Soto, Jill A. Shaffer, Shailesh Sharma, Anna A. Sher, Doriane Stagnol, Thomas R. Stanley, Kevin D. E. Stokesbury, Aurora Torres, Oliver Tully, Teppo Vehanen, Corinne Watts, Qingyuan Zhao, and William J. Sutherland

Subjects
Science
Abstract

Randomised controlled experiments are the gold standard for scientific inference, but environmental and social scientists often rely on different study designs. Here the authors analyse the use of six common study designs in the fields of biodiversity conservation and social intervention, and quantify the biases in their estimates.

Published
2020
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2. Genomic and morphological evidence of distinct populations in the endemic common (weedy) seadragon Phyllopteryx taeniolatus (Syngnathidae) along the east coast of Australia.

Author

O Selma Klanten, Michelle R Gaither, Samuel Greaves, Kade Mills, Kristine O'Keeffe, John Turnbull, Rob McKinnon, and David J Booth

Subjects
Medicine, Science
Abstract

The common or weedy seadragon, Phyllopteryx taeniolatus, is an iconic and endemic fish found across temperate reefs of southern Australia. Despite its charismatic nature, few studies have been published, and the extent of population sub-structuring remains poorly resolved. Here we used 7462 single nucleotide polymorphisms (SNPs) to identify the extent of population structure in the weedy seadragon along the temperate southeast coast of Australia. We identified four populations, with strong genetic structure (FST = 0.562) between them. Both Discriminant Analysis of Principle Components (DAPC) and Bayesian clustering analyses support four distinct genetic clusters (north to south: central New South Wales, southern NSW, Victoria and Tasmania). In addition to these genetic differences, geographical variation in external morphology was recorded, with individuals from New South Wales shaped differently for a few measurements to those from the Mornington Peninsula (Victoria). We posit that these genetic and morphological differences suggest that the Victorian population of P. taeniolatus was historically isolated by the Bassian Isthmus during the last glacial maximum and should now be considered at least a distinct population. We also recorded high levels of genetic structure among the other locations. Based on the genomic and to a degree morphological evidence presented in this study, we recommend that the Victorian population be managed separately from the eastern populations (New South Wales and Tasmania).

Published
2020
Full Text
View/download PDF

3. Scaling of Activity Space in Marine Organisms across Latitudinal Gradients

Author

Vinay Udyawer, Charlie Huveneers, Fabrice Jaine, Russell C. Babcock, Stephanie Brodie, Marie-Jeanne Buscot, Hamish A. Campbell, Robert G. Harcourt, Xavier Hoenner, Elodie J. I. Lédée, Colin A. Simpfendorfer, Matthew D. Taylor, Asia Armstrong, Adam Barnett, Culum Brown, Barry Bruce, Paul A. Butcher, Gwenael Cadiou, Lydie I. E. Couturier, Leanne Currey-Randall, Michael Drew, Christine L. Dudgeon, Ross G. Dwyer, Mario Espinoza, Luciana C. Ferreira, Anthony Fowler, David Harasti, Alastair R. Harborne, Nathan A. Knott, Kate Lee, Matt Lloyd, Michael Lowry, Teagan Marzullo, Jordan Matley, Jaime D. McAllister, Rory McAuley, Frazer McGregor, Mark Meekan, Kade Mills, Bradley M. Norman, Beverly Oh, Nicholas L. Payne, Vic Peddemors, Toby Piddocke, Richard D. Pillans, Richard D. Reina, Paul Rogers, Jayson M. Semmens, Amy Smoothey, Conrad W. Speed, Dylan van der Meulen, Michelle R. Heupel, Australian Institute of Marine Science (AIMS), Flinders Univ S Australia, Coll Sci & Engn, Natl Ctr Groundwater Res & Training, GPO Box 2100, Adelaide, SA, Australia, Partenaires INRAE, Sydney Institute of Marine Science, Macquarie University [Sydney], Queensland Bioscience Precinct, Environmental Research Division [USA], Southwest Fisheries Science Center (SWFSC), NOAA National Marine Fisheries Service (NMFS), National Oceanic and Atmospheric Administration (NOAA)-National Oceanic and Atmospheric Administration (NOAA)-NOAA National Marine Fisheries Service (NMFS), National Oceanic and Atmospheric Administration (NOAA)-National Oceanic and Atmospheric Administration (NOAA), University of California [Santa Cruz] (UC Santa Cruz), University of California (UC), University of Tasmania [Launceston] (UTAS), Charles Darwin University [Australia], Department of Biological Sciences, Macquarie University, Macquarie University, Department of Biological Sciences, CISRO Oceans and Atmosphere, Carleton University, James Cook University (JCU), Industry and Investment NSW, Port Stephens Fisheries Institute, University of Queensland [Brisbane], National Oceanic and Atmospheric Administration (NOAA), Department of Biological Sciences [North Ryde], Macquarie University, The University of Tennessee [Knoxville], NSW DPI NEW SOUTH WALES GOVERNMENT DEPARTMENT OF PRIMARY INDUSTRIES FISHERIES NSW WOLLONGONG AUS, Partenaires IRSTEA, Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA)-Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA), University of Technology Sidney (UTS), Laboratoire des Sciences de l'Environnement Marin (LEMAR) (LEMAR), Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Institut Universitaire Européen de la Mer (IUEM), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Université de Brest (UBO), University of the Sunshine Coast (USC), Universidad de Costa Rica (UCR), Indian Ocean Marine Res Ctr, Florida International University [Miami] (FIU), New South Wales Dept Primary Ind, University of New South Wales [Sydney] (UNSW), University of Windsor [Ca], University of Tasmania [Hobart, Australia] (UTAS), The University of Western Australia (UWA), Murdoch University, Victorian Natl Pk Assoc, Southern Cross University (SCU), Monash university, and South Australian Research and Development Institute [Australia]

Subjects
Brownian bridge kernel utilization distribution (KUD), continental network, Integrated Marine Observing System (IMOS), spatial ecology, Integrated Marine Ob-serving System (IMOS), Brownian bridge kernel utilizationdistribution (KUD), [SDE.BE]Environmental Sciences/Biodiversity and Ecology, metabolic theory, acoustic telemetry, Ecology, Evolution, Behavior and Systematics
Abstract

Unifying models have shown that the amount of space used by animals (e.g., activity space, home range) scales allometrically with body mass for terrestrial taxa; however, such relationships are far less clear for marine species. We compiled movement data from 1,596 individuals across 79 taxa collected using a continental passive acoustic telemetry network of acoustic receivers to assess allometric scaling of activity space. We found that ectothermic marine taxa do exhibit allometric scaling for activity space, with an overall scaling exponent of 0.64. However, body mass alone explained only 35% of the variation, with the remaining variation best explained by trophic position for teleosts and latitude for sharks, rays, and marine reptiles. Taxon-specific allometric relationships highlighted weaker scaling exponents among teleost fish species (0.07) than sharks (0.96), rays (0.55), and marine reptiles (0.57). The allometric scaling relationship and scaling exponents for the marine taxonomic groups examined were lower than those reported from studies that had collated both marine and terrestrial species data derived using various tracking methods. We propose that these disparities arise because previous work integrated summarized data across many studies that used differing methods for collecting and quantifying activity space, introducing considerable uncertainty into slope estimates. Our findings highlight the benefit of using large-scale, coordinated animal biotelemetry networks to address cross-taxa evolutionary and ecological questions.

Published
2023

4. Continental‐scale acoustic telemetry and network analysis reveal new insights into stock structure

Author

Mario Espinoza, Victor M. Peddemors, Anthony J. Fowler, Robert Harcourt, Ross G. Dwyer, Rory McAuley, Dylan E. van der Meulen, Lachlan Fetterplace, Colin A. Simpfendorfer, Matthew D. Taylor, Paul A. Butcher, Gwenaël Cadiou, Elodie J. I. Lédée, Michelle R. Heupel, Nathan A. Knott, Jaime D. McAllister, Richard D. Pillans, Adam Barnett, Kilian M. Stehfest, Jayson M. Semmens, Matias Braccini, Hamish A. Campbell, Russell C. Babcock, Luciana C. Ferreira, Stephanie Brodie, Kade Mills, Charlie Huveneers, Amy F. Smoothey, Michael B. Lowry, Alastair R. Harborne, Fabrice R. A. Jaine, Vinay Udyawer, Xavier Hoenner, Mark G. Meekan, and Conrad W. Speed

Subjects
Structure (mathematical logic), Scale (ratio), Meteorology, Telemetry, Environmental science, Fisheries management, Management, Monitoring, Policy and Law, Aquatic Science, Oceanography, Ecology, Evolution, Behavior and Systematics, Stock (geology), Network analysis
Published
2021

5. Quantifying and addressing the prevalence and bias of study designs in the environmental and social sciences

Author

Ari Huusko, William J. Sutherland, Tyler D. Eddy, Doriane Stagnol, Deborah A. Buhl, Matt Rinella, Tatsuya Amano, Teppo Vehanen, Thomas R. Stanley, C. Roland Pitcher, David Abecasis, Ricardo S. Ceia, Anjali Pande, Brendan P. Kelaher, Shailesh Sharma, Juan C. Alonso, Adrià López-Baucells, Luciana Cibils-Martina, Heather L. Major, Jill A. Shaffer, Monica Montefalcone, Bradley P. Harris, Jake E. Bicknell, Annelies De Backer, Ian L. Jones, Aki Mäki-Petäys, Juan J. Schmitter-Soto, María C. Ruiz-Delgado, Corinne Watts, Oliver Tully, Norbertas Noreika, Kade Mills, Christoph F. J. Meyer, Just Cebrian, Michele Meroni, Qingyuan Zhao, Rafael Barrientos, Dominique Davoult, Michael D. Craig, Carlos Ponce, Mary K. Donovan, Alec P. Christie, Jonathan P. A. Gardner, Carlos Palacín, Alvaro Antón, Robert A. McConnaughey, Beatriz Martín, Aurora Torres, Daniel Mateos-Molina, Filipe França, Sarah Clarke, Kevin D. E. Stokesbury, Janne S. Kotiaho, Mehdi Adjeroud, Ricardo Rocha, Anna A. Sher, Barry P. Baldigo, Carlos A. Martín, Philip A. Martin, Joachim Claudet, Christie, Alec P [0000-0002-8465-8410], Abecasis, David [0000-0002-9802-8153], Alonso, Juan C [0000-0003-0450-7434], Amano, Tatsuya [0000-0001-6576-3410], Anton, Alvaro [0000-0003-4108-6122], Baldigo, Barry P [0000-0002-9862-9119], Barrientos, Rafael [0000-0002-1677-3214], Bicknell, Jake E [0000-0001-6831-627X], Cebrian, Just [0000-0002-9916-8430], Ceia, Ricardo S [0000-0001-7078-0178], Cibils-Martina, Luciana [0000-0002-2101-4095], Claudet, Joachim [0000-0001-6295-1061], De Backer, Annelies [0000-0001-9129-9009], Donovan, Mary K [0000-0001-6855-0197], França, Filipe M [0000-0003-3827-1917], Gardner, Jonathan PA [0000-0002-6943-2413], Kotiaho, Janne S [0000-0002-4732-784X], López-Baucells, Adrià [0000-0001-8446-0108], Major, Heather L [0000-0002-7265-1289], Mateos-Molina, Daniel [0000-0002-9383-0593], McConnaughey, Robert A [0000-0002-8537-3695], Meyer, Christoph FJ [0000-0001-9958-8913], Noreika, Norbertas [0000-0002-3853-7677], Pitcher, C Roland [0000-0003-2075-4347], Rocha, Ricardo [0000-0003-2757-7347], Schmitter-Soto, Juan J [0000-0003-4736-8382], Shaffer, Jill A [0000-0003-3172-0708], Sharma, Shailesh [0000-0002-7918-4070], Sher, Anna A [0000-0002-6433-9746], Vehanen, Teppo [0000-0003-3441-6787], Apollo - University of Cambridge Repository, Ecologie marine tropicale des océans Pacifique et Indien (ENTROPIE [Perpignan]), Institut de Recherche pour le Développement (IRD), Centre de recherches insulaires et observatoire de l'environnement (CRIOBE), Université de Perpignan Via Domitia (UPVD)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS), Université de Perpignan Via Domitia (UPVD)-École pratique des hautes études (EPHE), Christie, Alec P. [0000-0002-8465-8410], Alonso, Juan C. [0000-0003-0450-7434], Baldigo, Barry P. [0000-0002-9862-9119], Bicknell, Jake E. [0000-0001-6831-627X], Ceia, Ricardo S. [0000-0001-7078-0178], Donovan, Mary K. [0000-0001-6855-0197], França, Filipe M. [0000-0003-3827-1917], Gardner, Jonathan P. A. [0000-0002-6943-2413], Kotiaho, Janne S. [0000-0002-4732-784X], Major, Heather L. [0000-0002-7265-1289], McConnaughey, Robert A. [0000-0002-8537-3695], Meyer, Christoph F. J. [0000-0001-9958-8913], Pitcher, C. Roland [0000-0003-2075-4347], Schmitter-Soto, Juan J. [0000-0003-4736-8382], Shaffer, Jill A. [0000-0003-3172-0708], Sher, Anna A. [0000-0002-6433-9746], and Repositório da Universidade de Lisboa

Subjects
0106 biological sciences, Research design, Scientific community, SCIENTIFIC COMMUNITY, Medio ambiente natural, sosiaalitieteet, Psychological intervention, General Physics and Astronomy, Social Sciences, QH75, 01 natural sciences, Environmental impact, purl.org/becyt/ford/1 [https], 010104 statistics & probability, 706/648, Credibility, Prevalence, Social science, ComputingMilieux_MISCELLANEOUS, GE, Multidisciplinary, Ecology, article, Sampling (statistics), Biodiversity, näyttöön perustuvat käytännöt, satunnaistetut vertailukokeet, ENVIRONMENTAL IMPACT, Research Design, Scale (social sciences), [SDE]Environmental Sciences, H1, Science, Environment, 010603 evolutionary biology, General Biochemistry, Genetics and Molecular Biology, Social sciences, Bias, tutkimusmenetelmät, QH541, 704/172/4081, Humans, 0101 mathematics, purl.org/becyt/ford/1.6 [https], ympäristötieteet, poliittinen päätöksenteko, Clinical study design, metodologia, 706/689, General Chemistry, 15. Life on land, Ecología, Literature, Pairwise comparison, Observational study, 631/158, luotettavuus
Abstract

Building trust in science and evidence-based decision-making depends heavily on the credibility of studies and their findings. Researchers employ many different study designs that vary in their risk of bias to evaluate the true effect of interventions or impacts. Here, we empirically quantify, on a large scale, the prevalence of different study designs and the magnitude of bias in their estimates. Randomised designs and controlled observational designs with pre-intervention sampling were used by just 23% of intervention studies in biodiversity conservation, and 36% of intervention studies in social science. We demonstrate, through pairwise within-study comparisons across 49 environmental datasets, that these types of designs usually give less biased estimates than simpler observational designs. We propose a model-based approach to combine study estimates that may suffer from different levels of study design bias, discuss the implications for evidence synthesis, and how to facilitate the use of more credible study designs., Randomised controlled experiments are the gold standard for scientific inference, but environmental and social scientists often rely on different study designs. Here the authors analyse the use of six common study designs in the fields of biodiversity conservation and social intervention, and quantify the biases in their estimates.

Published
2020

6. Genomic and morphological evidence of distinct populations in the endemic common (weedy) seadragon Phyllopteryx taeniolatus (Syngnathidae) along the east coast of Australia

Author

Kristine O’Keeffe, Michelle R. Gaither, David J. Booth, Rob McKinnon, Samuel Greaves, John W. Turnbull, Kade Mills, and O. Selma Klanten

Subjects
Heredity, Single Nucleotide Polymorphisms, Population genetics, Geographical Locations, Syngnathidae, Mathematical and Statistical Techniques, South Australia, education.field_of_study, Principal Component Analysis, Multidisciplinary, geography.geographical_feature_category, Heterozygosity, biology, Geography, Ecology, Statistics, Discriminant Analysis, Last Glacial Maximum, Smegmamorpha, Phylogeography, Biogeography, Genetic structure, Physical Sciences, Medicine, Phyllopteryx taeniolatus, Research Article, Ecological Metrics, Genotype, Science, Population, Oceania, Research and Analysis Methods, Polymorphism, Single Nucleotide, Temperate climate, Genetics, Animals, Statistical Methods, education, Reef, geography, Evolutionary Biology, Population Biology, Ecology and Environmental Sciences, Australia, Biology and Life Sciences, Genetic Variation, Species Diversity, Bayes Theorem, biology.organism_classification, Genetic Loci, People and Places, Multivariate Analysis, Earth Sciences, Population Genetics, Mathematics
Abstract

The common or weedy seadragon,Phyllopteryx taeniolatus, is an iconic and endemic fish found across temperate reefs of southern Australia. Despite its charismatic nature, few studies have been published, and the extent of population sub-structuring remains poorly resolved. Here we used 7462 single nucleotide polymorphisms (SNPs) to identify the extent of population structure in the weedy seadragon along the temperate southeast coast of Australia. We identified four populations, with strong genetic structure (FST= 0.562) between them. Both Discriminant Analysis of Principle Components (DAPC) and Bayesian clustering analyses support four distinct genetic clusters (north to south: central New South Wales, southern NSW, Victoria and Tasmania). In addition to these genetic differences, geographical variation in external morphology was recorded, with individuals from New South Wales shaped differently for a few measurements to those from the Mornington Peninsula (Victoria). We posit that these genetic and morphological differences suggest that the Victorian population ofP.taeniolatuswas historically isolated by the Bassian Isthmus during the last glacial maximum and should now be considered at least a distinct population. We also recorded high levels of genetic structure among the other locations. Based on the genomic and to a degree morphological evidence presented in this study, we recommend that the Victorian population be managed separately from the eastern populations (New South Wales and Tasmania).

Published
2020

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