Same data, different analysts: variation in effect sizes due to analytical decisions in ecology and evolutionary biology

Authors: Elliot Gould, Hannah S. Fraser, Timothy H. Parker, Shinichi Nakagawa, Simon C. Griffith, Peter A. Vesk, Fiona Fidler, Daniel G. Hamilton, Robin N. Abbey-Lee, Jessica K. Abbott, Luis A. Aguirre, Carles Alcaraz, Irith Aloni, Drew Altschul, Kunal Arekar, Jeff W. Atkins, Joe Atkinson, Christopher M. Baker, Meghan Barrett, Kristian Bell, Suleiman Kehinde Bello, Iván Beltrán, Bernd J. Berauer, Michael Grant Bertram, Peter D. Billman, Charlie K. Blake, Shannon Blake, Louis Bliard, Andrea Bonisoli-Alquati, Timothée Bonnet, Camille Nina Marion Bordes, Aneesh P. H. Bose, Thomas Botterill-James, Melissa Anna Boyd, Sarah A. Boyle, Tom Bradfer-Lawrence, Jennifer Bradham, Jack A. Brand, Martin I. Brengdahl, Martin Bulla, Luc Bussière, Ettore Camerlenghi, Sara E. Campbell, Leonardo L. F. Campos, Anthony Caravaggi, Pedro Cardoso, Charles J. W. Carroll, Therese A. Catanach, Xuan Chen, Heung Ying Janet Chik, Emily Sarah Choy, Alec Philip Christie, Angela Chuang, Amanda J. Chunco, Bethany L. Clark, Andrea Contina, Garth A. Covernton, Murray P. Cox, Kimberly A. Cressman, Marco Crotti, Connor Davidson Crouch, Pietro B. D’Amelio, Alexandra Allison de Sousa, Timm Fabian Döbert, Ralph Dobler, Adam J. Dobson, Tim S. Doherty, Szymon Marian Drobniak, Alexandra Grace Duffy, Alison B. Duncan, Robert P. Dunn, Jamie Dunning, Trishna Dutta, Luke Eberhart-Hertel, Jared Alan Elmore, Mahmoud Medhat Elsherif, Holly M. English, David C. Ensminger, Ulrich Rainer Ernst, Stephen M. Ferguson, Esteban Fernandez-Juricic, Thalita Ferreira-Arruda, John Fieberg, Elizabeth A. Finch, Evan A. Fiorenza, David N. Fisher, Amélie Fontaine, Wolfgang Forstmeier, Yoan Fourcade, Graham S. Frank, Cathryn A. Freund, Eduardo Fuentes-Lillo, Sara L. Gandy, Dustin G. Gannon, Ana I. García-Cervigón, Alexis C. Garretson, Xuezhen Ge, William L. Geary, Charly Géron, Marc Gilles, Antje Girndt, Daniel Gliksman, Harrison B. Goldspiel, Dylan G. E. Gomes, Megan Kate Good, Sarah C. Goslee, J. Stephen Gosnell, Eliza M. Grames, Paolo Gratton, Nicholas M. Grebe, Skye M. Greenler, Maaike Griffioen, Daniel M. Griffith, Frances J. Griffith, Jake J. Grossman, Ali Güncan, Stef Haesen, James G. Hagan, Heather A. Hager, Jonathan Philo Harris, Natasha Dean Harrison, Sarah Syedia Hasnain, Justin Chase Havird, Andrew J. Heaton, María Laura Herrera-Chaustre, Tanner J. Howard, Bin-Yan Hsu, Fabiola Iannarilli, Esperanza C. Iranzo, Erik N. K. Iverson, Saheed Olaide Jimoh, Douglas H. Johnson, Martin Johnsson, Jesse Jorna, Tommaso Jucker, Martin Jung, Ineta Kačergytė, Oliver Kaltz, Alison Ke, Clint D. Kelly, Katharine Keogan, Friedrich Wolfgang Keppeler, Alexander K. Killion, Dongmin Kim, David P. Kochan, Peter Korsten, Shan Kothari, Jonas Kuppler, Jillian M. Kusch, Malgorzata Lagisz, Kristen Marianne Lalla, Daniel J. Larkin, Courtney L. Larson, Katherine S. Lauck, M. Elise Lauterbur, Alan Law, Don-Jean Léandri-Breton, Jonas J. Lembrechts, Kiara L’Herpiniere, Eva J. P. Lievens, Daniela Oliveira de Lima, Shane Lindsay, Martin Luquet, Ross MacLeod, Kirsty H. Macphie, Kit Magellan, Magdalena M. Mair, Lisa E. Malm, Stefano Mammola, Caitlin P. Mandeville, Michael Manhart, Laura Milena Manrique-Garzon, Elina Mäntylä, Philippe Marchand, Benjamin Michael Marshall, Charles A. Martin, Dominic Andreas Martin, Jake Mitchell Martin, April Robin Martinig, Erin S. McCallum, Mark McCauley, Sabrina M. McNew, Scott J. Meiners, Thomas Merkling, Marcus Michelangeli, Maria Moiron, Bruno Moreira, Jennifer Mortensen, Benjamin Mos, Taofeek Olatunbosun Muraina, Penelope Wrenn Murphy, Luca Nelli, Petri Niemelä, Josh Nightingale, Gustav Nilsonne, Sergio Nolazco, Sabine S. Nooten, Jessie Lanterman Novotny, Agnes Birgitta Olin, Chris L. Organ, Kate L. Ostevik, Facundo Xavier Palacio, Matthieu Paquet, Darren James Parker, David J. Pascall, Valerie J. Pasquarella, John Harold Paterson, Ana Payo-Payo, Karen Marie Pedersen, Grégoire Perez, Kayla I. Perry, Patrice Pottier, Michael J. Proulx, Raphaël Proulx, Jessica L Pruett, Veronarindra Ramananjato, Finaritra Tolotra Randimbiarison, Onja H. Razafindratsima, Diana J. Rennison, Federico Riva, Sepand Riyahi, Michael James Roast, Felipe Pereira Rocha, Dominique G. Roche, Cristian Román-Palacios, Michael S. Rosenberg, Jessica Ross, Freya E. Rowland, Deusdedith Rugemalila, Avery L. Russell, Suvi Ruuskanen, Patrick Saccone, Asaf Sadeh, Stephen M. Salazar, Kris Sales, Pablo Salmón, Alfredo Sánchez-Tójar, Leticia Pereira Santos, Francesca Santostefano, Hayden T. Schilling, Marcus Schmidt, Tim Schmoll, Adam C. Schneider, Allie E. Schrock, Julia Schroeder, Nicolas Schtickzelle, Nick L. Schultz, Drew A. Scott, Michael Peter Scroggie, Julie Teresa Shapiro, Nitika Sharma, Caroline L. Shearer, Diego Simón, Michael I. Sitvarin, Fabrício Luiz Skupien, Heather Lea Slinn, Grania Polly Smith, Jeremy A. Smith, Rahel Sollmann, Kaitlin Stack Whitney, Shannon Michael Still, Erica F. Stuber, Guy F. Sutton, Ben Swallow, Conor Claverie Taff, Elina Takola, Andrew J. Tanentzap, Rocío Tarjuelo, Richard J. Telford, Christopher J. Thawley, Hugo Thierry, Jacqueline Thomson, Svenja Tidau, Emily M. Tompkins, Claire Marie Tortorelli, Andrew Trlica, Biz R. Turnell, Lara Urban, Stijn Van de Vondel, Jessica Eva Megan van der Wal, Jens Van Eeckhoven, Francis van Oordt, K. Michelle Vanderwel, Mark C. Vanderwel, Karen J. Vanderwolf, Juliana Vélez, Diana Carolina Vergara-Florez, Brian C. Verrelli, Marcus Vinícius Vieira, Nora Villamil, Valerio Vitali, Julien Vollering, Jeffrey Walker, Xanthe J. Walker, Jonathan A. Walter, Pawel Waryszak, Ryan J. Weaver, Ronja E. M. Wedegärtner, Daniel L. Weller, Shannon Whelan, Rachel Louise White, David William Wolfson, Andrew Wood, Scott W. Yanco, Jian D. L. Yen, Casey Youngflesh, Giacomo Zilio, Cédric Zimmer, Gregory Mark Zimmerman, Rachel A. Zitomer

Source: BMC Biology, Vol 23, Iss 1, Pp 1-36 (2025)

Subject Terms: Analytical heterogeneity, Metascience, Many-analyst, Replication crisis, Reproducibility, Biology (General), QH301-705.5

File Description: electronic resource

Relation: https://doaj.org/toc/1741-7007

Access URL: https://doaj.org/article/de5863fbbfd4411f8ee09e352a483284

Positive selection in the genomes of two Papua New Guinean populations at distinct altitude levels

Authors: Mathilde André, Nicolas Brucato, Georgi Hudjasov, Vasili Pankratov, Danat Yermakovich, Francesco Montinaro, Rita Kreevan, Jason Kariwiga, John Muke, Anne Boland, Jean-François Deleuze, Vincent Meyer, Nicholas Evans, Murray P. Cox, Matthew Leavesley, Michael Dannemann, Tõnis Org, Mait Metspalu, Mayukh Mondal, François-Xavier Ricaut

Source: Nature Communications, Vol 15, Iss 1, Pp 1-15 (2024)

Subject Terms: Science

File Description: electronic resource

Relation: https://doaj.org/toc/2041-1723

Access URL: https://doaj.org/article/d5c9f645930e48fb9ecbef2fff72864e

Serratia‐based toxin cluster elements are associated with a type I fimbria

Authors: Lesley Sitter, Marion Schoof, Travis R. Glare, Murray P. Cox, Peter C. Fineran, Paul P. Gardner, Mark R. H. Hurst

Source: MicrobiologyOpen, Vol 13, Iss 1, Pp n/a-n/a (2024)

Subject Terms: fimbria, grass grub, plasmid, repA, Serratia, toxin complex, Microbiology, QR1-502

File Description: electronic resource

Relation: https://doaj.org/toc/2045-8827

Access URL: https://doaj.org/article/5a610a7efe55480faa75a0c810a6675f

Deep ancestry of Bornean hunter-gatherers supports long-term local ancestry dynamics

Authors: Pradiptajati Kusuma, Murray P. Cox, Graeme Barker, Herawati Sudoyo, J. Stephen Lansing, Guy S. Jacobs

Source: Cell Reports, Vol 42, Iss 11, Pp 113346- (2023)

Subject Terms: CP: Genomics, Biology (General), QH301-705.5

File Description: electronic resource

Relation: http://www.sciencedirect.com/science/article/pii/S221112472301358X; https://doaj.org/toc/2211-1247

Access URL: https://doaj.org/article/60fdaf27c4a44ab59a721a88cf8d351d

The Venturia inaequalis effector repertoire is dominated by expanded families with predicted structural similarity, but unrelated sequence, to avirulence proteins from other plant-pathogenic fungi

Authors: Mercedes Rocafort, Joanna K. Bowen, Berit Hassing, Murray P. Cox, Brogan McGreal, Silvia de la Rosa, Kim M. Plummer, Rosie E. Bradshaw, Carl H. Mesarich

Source: BMC Biology, Vol 20, Iss 1, Pp 1-24 (2022)

Subject Terms: Venturia inaequalis, Apple scab fungus, Biotrophic subcuticular pathogen, Effectors and effector families, Virulence and avirulence, RNA-seq transcriptome, Biology (General), QH301-705.5

File Description: electronic resource

Relation: https://doaj.org/toc/1741-7007

Access URL: https://doaj.org/article/2660844a6e2941cbaf57f65a35c37829

Reconstruction of gene innovation associated with major evolutionary transitions in the kingdom Fungi

Authors: Baojun Wu, Weilong Hao, Murray P. Cox

Source: BMC Biology, Vol 20, Iss 1, Pp 1-11 (2022)

Subject Terms: Fungi, Gene gain, Horizontal transfer, Mitochondria, Trait transitions, Biology (General), QH301-705.5

File Description: electronic resource

Relation: https://doaj.org/toc/1741-7007

Access URL: https://doaj.org/article/e3096d4d7dad4acfba89f84dfe3c0dc4

Epichloë scottii sp. nov., a new endophyte isolated from Melica uniflora is the missing ancestor of Epichloë disjuncta

Authors: Torsten Thünen, Yvonne Becker, Murray P. Cox, Samad Ashrafi

Source: IMA Fungus, Vol 13, Iss 1, Pp 1-18 (2022)

Subject Terms: Epichloë, Melica uniflora, New species, Alkaloid profile, BUSCO multigene-phylogeny, Oxford nanopore, Botany, QK1-989

File Description: electronic resource

Relation: https://doaj.org/toc/2210-6359

Access URL: https://doaj.org/article/89e3208739e6447e86509f55a5ef0be1

Denisovan introgression has shaped the immune system of present-day Papuans

Authors: Davide M. Vespasiani, Guy S. Jacobs, Laura E. Cook, Nicolas Brucato, Matthew Leavesley, Christopher Kinipi, François-Xavier Ricaut, Murray P. Cox, Irene Gallego Romero

Source: PLoS Genetics, Vol 18, Iss 12 (2022)

Subject Terms: Genetics, QH426-470

File Description: electronic resource

Relation: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9731433/?tool=EBI; https://doaj.org/toc/1553-7390; https://doaj.org/toc/1553-7404

Access URL: https://doaj.org/article/ac87af9cda4a4dfca324079e95b2edb5

A single fungal strain was the unexpected cause of a mass aspergillosis outbreak in the world’s largest and only flightless parrot

Authors: David J. Winter, Bevan S. Weir, Travis Glare, Johanna Rhodes, John Perrott, Matthew C. Fisher, Jason E. Stajich, Andrew Digby, Peter K. Dearden, Murray P. Cox

Source: iScience, Vol 25, Iss 12, Pp 105470- (2022)

Subject Terms: Animals, Microbiology, Microbiology parasite, Parasitology, Science

File Description: electronic resource

Relation: http://www.sciencedirect.com/science/article/pii/S2589004222017424; https://doaj.org/toc/2589-0042

Access URL: https://doaj.org/article/31ef4f10188845308f0b9b8f4c904938

An informatics consult approach for generating clinical evidence for treatment decisions

Authors: Alvina G. Lai, Wai Hoong Chang, Constantinos A. Parisinos, Michail Katsoulis, Ruth M. Blackburn, Anoop D. Shah, Vincent Nguyen, Spiros Denaxas, George Davey Smith, Tom R. Gaunt, Krishnarajah Nirantharakumar, Murray P. Cox, Donall Forde, Folkert W. Asselbergs, Steve Harris, Sylvia Richardson, Reecha Sofat, Richard J. B. Dobson, Aroon Hingorani, Riyaz Patel, Jonathan Sterne, Amitava Banerjee, Alastair K. Denniston, Simon Ball, Neil J. Sebire, Nigam H. Shah, Graham R. Foster, Bryan Williams, Harry Hemingway

Source: BMC Medical Informatics and Decision Making, Vol 21, Iss 1, Pp 1-14 (2021)

Subject Terms: Computer applications to medicine. Medical informatics, R858-859.7

File Description: electronic resource

Relation: https://doaj.org/toc/1472-6947

Access URL: https://doaj.org/article/78307b29f564469e8cd433172aa802e4

Chromosome-level assembly of the Phytophthora agathidicida genome reveals adaptation in effector gene families

Authors: Murray P. Cox, Yanan Guo, David J. Winter, Diya Sen, Nicholas C. Cauldron, Jason Shiller, Ellie L. Bradley, Austen R. Ganley, Monica L. Gerth, Randy F. Lacey, Rebecca L. McDougal, Preeti Panda, Nari M. Williams, Niklaus J. Grunwald, Carl H. Mesarich, Rosie E. Bradshaw

Source: Frontiers in Microbiology, Vol 13 (2022)

Subject Terms: Phytophthora, oomycete, kauri dieback, forest disease, chromosome-level genome assembly, chromatin conformation capture, Microbiology, QR1-502

File Description: electronic resource

Relation: https://www.frontiersin.org/articles/10.3389/fmicb.2022.1038444/full; https://doaj.org/toc/1664-302X

Access URL: https://doaj.org/article/01390332fb02429695084cf6f33e539f

Tradition and change: celebrating food systems resilience at two Indigenous Māori community events

Authors: Priscilla M. Wehi, Murray P. Cox, Hēmi Whaanga, Tom Roa

Source: Ecology and Society, Vol 28, Iss 1, p 19 (2023)

Subject Terms: biocultural diversity, food systems, kaitiakitanga, indigenous peoples, māori, resilience, socioecological systems, Biology (General), QH301-705.5, Ecology, QH540-549.5

File Description: electronic resource

Relation: https://www.ecologyandsociety.org/vol28/iss1/art19/; https://doaj.org/toc/1708-3087

Access URL: https://doaj.org/article/1ea7e9452ff941e69c99590da1d8da3f

Deep ancestry of collapsing networks of nomadic hunter–gatherers in Borneo

Authors: J. Stephen Lansing, Guy S. Jacobs, Sean S. Downey, Peter K. Norquest, Murray P. Cox, Steven L. Kuhn, John H. Miller, Safarina G. Malik, Herawati Sudoyo, Pradiptajati Kusuma

Source: Evolutionary Human Sciences, Vol 4 (2022)

Subject Terms: Hunter–gatherers, prosocial behaviour, Borneo, Austronesia, song language, Human evolution, GN281-289, Evolution, QH359-425

File Description: electronic resource

Relation: https://www.cambridge.org/core/product/identifier/S2513843X22000032/type/journal_article; https://doaj.org/toc/2513-843X

Access URL: https://doaj.org/article/5faff5c3b7a74759825f6b53cfbd746f

Chromosome-Level Reference Genome of Venturia effusa, Causative Agent of Pecan Scab

Authors: David J. Winter, Nikki D. Charlton, Nick Krom, Jason Shiller, Clive H. Bock, Murray P. Cox, Carolyn A. Young

Source: Molecular Plant-Microbe Interactions, Vol 33, Iss 2, Pp 149-152 (2020)

Subject Terms: genomics, metabolomics, proteomics, Microbiology, QR1-502, Botany, QK1-989

File Description: electronic resource

Relation: https://doaj.org/toc/0894-0282; https://doaj.org/toc/1943-7706

Access URL: https://doaj.org/article/e5f6c03987874f9c8f5124c0c67aa143

Correlated Transcriptional Responses Provide Insights into the Synergy Mechanisms of the Furazolidone, Vancomycin, and Sodium Deoxycholate Triple Combination in Escherichia coli

Authors: Catrina Olivera, Murray P. Cox, Gareth J. Rowlands, Jasna Rakonjac

Source: mSphere, Vol 6, Iss 5 (2021)

Subject Terms: Microbiology, QR1-502

File Description: electronic resource

Relation: https://doaj.org/toc/2379-5042

Access URL: https://doaj.org/article/4e2a70120eee41738881fb64be0772e9

Characterization of Bicistronic Transcription in Budding Yeast

Authors: Baojun Wu, Murray P. Cox

Source: mSystems, Vol 6, Iss 1 (2021)

Subject Terms: yeast, bicistronic transcripts, modulation of translation, trans-splice mechanisms, Microbiology, QR1-502

File Description: electronic resource

Relation: https://doaj.org/toc/2379-5077

Access URL: https://doaj.org/article/cea67e62e0614367b34b4345d72790da

Correction to: Archaic mitochondrial DNA inserts in modern day nuclear genomes

Authors: Robert Bücking, Murray P. Cox, Georgi Hudjashov, Lauri Saag, Herawati Sudoyo, Mark Stoneking

Source: BMC Genomics, Vol 21, Iss 1, Pp 1-3 (2020)

Subject Terms: Biotechnology, TP248.13-248.65, Genetics, QH426-470

File Description: electronic resource

Relation: https://doaj.org/toc/1471-2164

Access URL: https://doaj.org/article/ba22055d9076488bb58814bf0c13df4b

Telomere-to-Telomere Genome Sequences across a Single Genus Reveal Highly Variable Chromosome Rearrangement Rates but Absolute Stasis of Chromosome Number

Authors: Mathieu Quenu, Artemis D. Treindl, Kate Lee, Daigo Takemoto, Torsten Thünen, Samad Ashrafi, David Winter, Austen R. D. Ganley, Adrian Leuchtmann, Carolyn A. Young, Murray P. Cox

Source: Journal of Fungi, Vol 8, Iss 7, p 670 (2022)

Subject Terms: Epichloë, genome structure, chromosome evolution, structural variation, Biology (General), QH301-705.5

File Description: electronic resource

Relation: https://www.mdpi.com/2309-608X/8/7/670; https://doaj.org/toc/2309-608X

Access URL: https://doaj.org/article/3f7f0c6dc4be456795e1e094703619d4

Investigating the origins of eastern Polynesians using genome-wide data from the Leeward Society Isles

Authors: Georgi Hudjashov, Phillip Endicott, Helen Post, Nano Nagle, Simon Y. W. Ho, Daniel J. Lawson, Maere Reidla, Monika Karmin, Siiri Rootsi, Ene Metspalu, Lauri Saag, Richard Villems, Murray P. Cox, R. John Mitchell, Ralph L. Garcia-Bertrand, Mait Metspalu, Rene J. Herrera

Source: Scientific Reports, Vol 8, Iss 1, Pp 1-12 (2018)

Subject Terms: Medicine, Science

File Description: electronic resource

Relation: https://doaj.org/toc/2045-2322

Access URL: https://doaj.org/article/48b25fe81f454f5c84f7efffa4a36855

Genomic admixture tracks pulses of economic activity over 2,000 years in the Indian Ocean trading network

Authors: Nicolas Brucato, Pradiptajati Kusuma, Philippe Beaujard, Herawati Sudoyo, Murray P. Cox, François-Xavier Ricaut

Source: Scientific Reports, Vol 7, Iss 1, Pp 1-6 (2017)

Subject Terms: Medicine, Science

File Description: electronic resource

Relation: https://doaj.org/toc/2045-2322

Access URL: https://doaj.org/article/9a568dcebdbc4e3f9d0e017a777bfb9b