https://phaidra.vetmeduni.ac.at/o:4836 From whole bodies to single cells: A guide to transcriptomic approaches for ecology and evolutionary biology Hoedjes, Katja M. Katja M. Hoedjes 0000-0001-6090-232X Amsterdam Institute for Life and Environment Vrije Universiteit Amsterdam Amsterdam The Netherlands Ritchie, Michael G. Michael G. Ritchie Centre for Biological Diversity University of St Andrews St Andrews UK Schlötterer, Christian Christian Schlötterer 0000-0003-4710-6526 University of Veterinary Medicine Vienna Abbott, Jessica K. Jessica K. Abbott Biology Department Lund University Lund Sweden Almudi, Isabel Isabel Almudi Departament de Genètica, Microbiologia i Estadística Universitat de Barcelona Barcelona Spain Coronado‐Zamora, Marta Marta Coronado‐Zamora Institute of Evolutionary Biology CSIC, UPF Barcelona Spain Durmaz Mitchell, Esra Esra Durmaz Mitchell Department of Biology University of Fribourg Fribourg Switzerland Flatt, Thomas Thomas Flatt 0000-0002-5990-1503 Department of Biology University of Fribourg Fribourg Switzerland Fricke, Claudia Claudia Fricke 0000-0002-0691-6779 Institute for Zoology/Animal Ecology Martin‐Luther‐University Halle‐Wittenberg Halle (Saale) Germany Glaser‐Schmitt, Amanda Amanda Glaser‐Schmitt Division of Evolutionary Biology LMU Munich Planegg‐Martinsried Germany González, Josefa Josefa González 0000-0001-9824-027X Institute of Evolutionary Biology CSIC, UPF Barcelona Spain Holman, Luke Luke Holman School of Applied Sciences Edinburgh Napier University Edinburgh UK Kankare, Maaria Maaria Kankare Department of Biological and Environmental Science University of Jyväskylä Jyväskylä Finland Lenhart, Benedict Benedict Lenhart Department of Biology University of Virginia Charlottesville Virginia USA Orengo, Dorcas J. Dorcas J. Orengo Departament de Genètica, Microbiologia i Estadística Universitat de Barcelona Barcelona Spain Snook, Rhonda R. Rhonda R. Snook 0000-0003-1852-1448 Department of Zoology Stockholm University Stockholm Sweden Yılmaz, Vera M. Vera M. Yılmaz Division of Evolutionary Biology LMU Munich Planegg‐Martinsried Germany Yusuf, Leeban Leeban Yusuf 0000-0001-6383-1176 Centre for Biological Diversity University of St Andrews St Andrews UK Grath, Sonja Sonja Grath Posnien, Nico Nico Posnien 0000-0003-0700-5595 Wiley journal article open access eng RNA sequencing (RNAseq) methodology has experienced a burst of technological developments in the last decade, which has opened up opportunities for studying the mechanisms of adaptation to environmental factors at both the organismal and cellular level. Selecting the most suitable experimental approach for specific research questions and model systems can, however, be a challenge and researchers in ecology and evolution are commonly faced with the choice of whether to study gene expression variation in whole bodies, specific tissues, and/or single cells. A wide range of sometimes polarised opinions exists over which approach is best. Here, we highlight the advantages and disadvantages of each of these approaches to provide a guide to help researchers make informed decisions and maximise the power of their study. Using illustrative examples of various ecological and evolutionary research questions, we guide the readers through the different RNAseq approaches and help them identify the most suitable design for their own projects. Bulk RNAseq Cellular Heterogeneity Deconvolution Gene Expression Single-cell RNAseq Transcriptomics http://creativecommons.org/licenses/by/4.0/ https://phaidra.vetmeduni.ac.at/api/object/o:4836/download 10.1111/mec.17382 https://phaidra.vetmeduni.ac.at/o:605 application/pdf Molecular Ecology issn:0962-1083 VoR Molecular Ecology 34 15 1.06 MB 2025