Driven by co-evolution with pathogens, host immunity continuously adapts to optimize defence against pathogens within a given environment. Recent advances in genetics, genomics and transcriptomics have enabled a more detailed investigation into how immunogenetic variation shapes the diversity of immune responses seen across domestic and wild animal species. However, a deeper understanding of the diverse molecular mechanisms that shape immunity within and among species is still needed to gain insight into-and generate evolutionary hypotheses on-the ultimate drivers of immunological differences. Here, we discuss current advances in our understanding of molecular evolution underpinning jawed vertebrate immunity. First, we introduce the immunome concept, a framework for characterizing genes involved in immune defence from a comparative perspective, then we outline how immune genes of interest can be identified. Second, we focus on how different selection modes are observed acting across groups of immune genes and propose hypotheses to explain these differences. We then provide an overview of the approaches used so far to study the evolutionary heterogeneity of immune genes on macro and microevolutionary scales. Finally, we discuss some of the current evidence as to how specific pathogens affect the evolution of different groups of immune genes. This review results from the collective discussion on the current key challenges in evolutionary immunology conducted at the ESEB 2021 Online Satellite Symposium: Molecular evolution of the vertebrate immune system, from the lab to natural populations.

Department of Biological Sciences University of Memphis Memphis Tennessee USA

Department of Biology California State University Fresno California USA

Department of Biology Lund University Lund Sweden

Department of Biology University of Central Florida Florida Orlando USA

Department of Biology University of Oxford Oxford UK

Department of Botany and Zoology Masaryk University Brno Czech Republic

Department of Ecology and Evolutionary Biology University of Connecticut Storrs Connecticut USA

Department of Ecology and Genetics Uppsala Universitet Uppsala Sweden

Department of Genetics and Breeding Institute of Animal Science Prague Uhříněves Czech Republic

Department of Genetics and Microbiology Faculty of Science Charles University Prague Czech Republic

Department of Parasitology University of Granada Granada Spain

Department of Science Engineering and Build Environment Deakin University Victoria Waurn Ponds Australia

Department of Veterinary Medicine University of Cambridge Cambridge UK

Department of Zoology Faculty of Science Charles University Prague Czech Republic

Faculty of Biology Institute of Environmental Sciences Jagiellonian University Kraków Poland

Institute for Immunology and Infection Research University of Edinburgh Edinburgh UK

Menzies Institute for Medical Research University of Tasmania Hobart Tasmania Australia

Research Unit for Evolutionary Immunogenomics Department of Biology University of Hamburg Hamburg Germany

School of Biological Sciences University of East Anglia Norwich UK

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