Immunity

@article{crossref1930the,
    title = "THE EVOLUTION OF IMMUNITY.",
    year = "1930",
    journal = "The Lancet",
    url = "https://doi.org/10.1016/s0140-6736(00)88058-7",
    doi = "10.1016/s0140-6736(00)88058-7",
    number = "5558",
    openalex = "W4247901883",
    pages = "520-521",
    volume = "215"
}

@misc{marchalonis1977immunity1,
    author = "Marchalonis, J. J",
    title = "Immunity in Evolution",
    year = "1977",
    howpublished = "London, Arnold",
    note = "talkorigins\_source = {true}; raw\_reference = {Marchalonis, J. J., 1977, Immunity in Evolution: London, Arnold.}"
}

1. Introducing Insect Infection and Immunity A. IMMUNE MECHANISMS AND INTEGRATION 2. Recognition and Response to Microbial Infection of Drosophila 3. Roles of Hemolymph Proteins in Antimicrobial Defences of Manduca sexta 4. Drosophila as a Model for Studying Antiviral Defenses 5. Specificity of the Innate Immune System: A Closer Look at the Mosquito Pattern Recognition Receptor Repertoire 6. Comparative Genomics of Insect Immunity 7. Physiological Integration of Innate Immunity B. IMMUNE INTERACTIONS AND EVOLUTION 8. The Inherited Microbiota of Arthropods, and their Importance in Understanding Resistance and Immunity 9. Insect Viruses, Parasitoids and their Interactions with the Insect Immune System: Polydnaviruses as Tools to Deliver Wasp Virulence Factors to Impair Lepidopteran Host Immunity 10. Immune Responses and the Evolution of Resistance 11. The Impact of Physiological State on Immune Function in Insects 12. Costs and Genomic Aspects of Drosophila Immunity to Parasites and Pathogens 13. Population Genetics of Insect Immune Responses 14. Ecological and Evolutionary Implications of Specific Immune Responses 15. Reproductive Immunity Index

@book{openalexw1581020725,
    author = "Rolff, Jens and Reynolds, Stuart E.",
    title = "Insect Infection and Immunity: Evolution Ecology and Mechanisms",
    year = "2009",
    abstract = "1. Introducing Insect Infection and Immunity A. IMMUNE MECHANISMS AND INTEGRATION 2. Recognition and Response to Microbial Infection of Drosophila 3. Roles of Hemolymph Proteins in Antimicrobial Defences of Manduca sexta 4. Drosophila as a Model for Studying Antiviral Defenses 5. Specificity of the Innate Immune System: A Closer Look at the Mosquito Pattern Recognition Receptor Repertoire 6. Comparative Genomics of Insect Immunity 7. Physiological Integration of Innate Immunity B. IMMUNE INTERACTIONS AND EVOLUTION 8. The Inherited Microbiota of Arthropods, and their Importance in Understanding Resistance and Immunity 9. Insect Viruses, Parasitoids and their Interactions with the Insect Immune System: Polydnaviruses as Tools to Deliver Wasp Virulence Factors to Impair Lepidopteran Host Immunity 10. Immune Responses and the Evolution of Resistance 11. The Impact of Physiological State on Immune Function in Insects 12. Costs and Genomic Aspects of Drosophila Immunity to Parasites and Pathogens 13. Population Genetics of Insect Immune Responses 14. Ecological and Evolutionary Implications of Specific Immune Responses 15. Reproductive Immunity Index",
    url = "https://openalex.org/W1581020725",
    openalex = "W1581020725"
}

@misc{crossref2010evolution,
    title = "Evolution versus Creationism",
    year = "2010",
    booktitle = "Time Matters",
    url = "https://doi.org/10.1002/9781444323252.ch7",
    doi = "10.1002/9781444323252.ch7",
    pages = "171-212"
}

@article{boehm2012evolution,
    author = "Boehm, Thomas",
    title = "Evolution of Vertebrate Immunity",
    year = "2012",
    journal = "Current Biology",
    url = "https://doi.org/10.1016/j.cub.2012.07.003",
    doi = "10.1016/j.cub.2012.07.003",
    number = "17",
    openalex = "W2073416809",
    pages = "R722-R732",
    volume = "22",
    references = "doi101038334395a0, doi10103883713, doi101038nature03556, doi101038nature06245, doi101038nature09944, doi101038nature10213, doi101038nature10759, doi101038nbt1755, doi101126science1198687, doi101146annurevimmunol25022106141615"
}

Parasites can dramatically reduce the fitness of their hosts, and natural selection should favor defense mechanisms that can protect hosts against disease. Much work has focused on understanding genetic and physiological immunity against parasites, but hosts can also use behaviors to avoid infection, reduce parasite growth or alleviate disease symptoms. It is increasingly recognized that such behaviors are common in insects, providing strong protection against parasites and parasitoids. We review the current evidence for behavioral immunity in insects, present a framework for investigating such behavior, and emphasize that behavioral immunity may act through indirect rather than direct fitness benefits. We also discuss the implications for host-parasite co-evolution, local adaptation, and the evolution of non-behavioral physiological immune systems. Finally, we argue that the study of behavioral immunity in insects has much to offer for investigations in vertebrates, in which this topic has traditionally been studied.

@article{doi103390insects3030789,
    author = "de Roode, Jacobus C. and Léfèvre, Thierry",
    title = "Behavioral Immunity in Insects",
    year = "2012",
    journal = "Insects",
    abstract = "Parasites can dramatically reduce the fitness of their hosts, and natural selection should favor defense mechanisms that can protect hosts against disease. Much work has focused on understanding genetic and physiological immunity against parasites, but hosts can also use behaviors to avoid infection, reduce parasite growth or alleviate disease symptoms. It is increasingly recognized that such behaviors are common in insects, providing strong protection against parasites and parasitoids. We review the current evidence for behavioral immunity in insects, present a framework for investigating such behavior, and emphasize that behavioral immunity may act through indirect rather than direct fitness benefits. We also discuss the implications for host-parasite co-evolution, local adaptation, and the evolution of non-behavioral physiological immune systems. Finally, we argue that the study of behavioral immunity in insects has much to offer for investigations in vertebrates, in which this topic has traditionally been studied.",
    url = "https://doi.org/10.3390/insects3030789",
    doi = "10.3390/insects3030789",
    openalex = "W2132875006",
    references = "openalexw1581020725"
}

@article{doi101038nrg3859,
    author = "Koonin, Eugene V. and Krupovìč, Mart",
    title = "Evolution of adaptive immunity from transposable elements combined with innate immune systems",
    year = "2014",
    journal = "Nature Reviews Genetics",
    url = "https://doi.org/10.1038/nrg3859",
    doi = "10.1038/nrg3859",
    openalex = "W2088981347",
    references = "boehm2012evolution"
}

Host responses against invading pathogens are basic physiological reactions of all living organisms. Since the appearance of the first eukaryotic cells, a series of defense mechanisms have evolved in order to secure cellular integrity, homeostasis, and survival of the host. Invertebrates, ranging from protozoans to metazoans, possess cellular receptors, which bind to foreign elements and differentiate self from non-self. This ability is in multicellular animals associated with presence of phagocytes, bearing different names (amebocytes, hemocytes, coelomocytes) in various groups including animal sponges, worms, cnidarians, mollusks, crustaceans, chelicerates, insects, and echinoderms (sea stars and urchins). Basically, these cells have a macrophage-like appearance and function and the repair and/or fight functions associated with these cells are prominent even at the earliest evolutionary stage. The cells possess pathogen recognition receptors recognizing pathogen-associated molecular patterns, which are well-conserved molecular structures expressed by various pathogens (virus, bacteria, fungi, protozoans, helminths). Scavenger receptors, Toll-like receptors, and Nod-like receptors (NLRs) are prominent representatives within this group of host receptors. Following receptor-ligand binding, signal transduction initiates a complex cascade of cellular reactions, which lead to production of one or more of a wide array of effector molecules. Cytokines take part in this orchestration of responses even in lower invertebrates, which eventually may result in elimination or inactivation of the intruder. Important innate effector molecules are oxygen and nitrogen species, antimicrobial peptides, lectins, fibrinogen-related peptides, leucine rich repeats (LRRs), pentraxins, and complement-related proteins. Echinoderms represent the most developed invertebrates and the bridge leading to the primitive chordates, cephalochordates, and urochordates, in which many autologous genes and functions from their ancestors can be found. They exhibit numerous variants of innate recognition and effector molecules, which allow fast and innate responses toward diverse pathogens despite lack of adaptive responses. The primitive vertebrates (agnathans also termed jawless fish) were the first to supplement innate responses with adaptive elements. Thus hagfish and lampreys use LRRs as variable lymphocyte receptors, whereas higher vertebrates [cartilaginous and bony fishes (jawed fish), amphibians, reptiles, birds, and mammals] developed the major histocompatibility complex, T-cell receptors, and B-cell receptors (immunoglobulins) as additional adaptive weaponry to assist innate responses. Extensive cytokine networks are recognized in fish, but related signal molecules can be traced among invertebrates. The high specificity, antibody maturation, immunological memory, and secondary responses of adaptive immunity were so successful that it allowed higher vertebrates to reduce the number of variants of the innate molecules originating from both invertebrates and lower vertebrates. Nonetheless, vertebrates combine the two arms in an intricate inter-dependent network. Organisms at all developmental stages have, in order to survive, applied available genes and functions of which some may have been lost or may have changed function through evolution. The molecular mechanisms involved in evolution of immune molecules, might apart from simple base substitutions be as diverse as gene duplication, deletions, alternative splicing, gene recombination, domain shuffling, retrotransposition, and gene conversion. Further, variable regulation of gene expression may have played a role.

@article{doi103389fimmu201400459,
    author = "Buchmann, Kurt",
    title = "Evolution of Innate Immunity: Clues from Invertebrates via Fish to Mammals",
    year = "2014",
    journal = "Frontiers in Immunology",
    abstract = "Host responses against invading pathogens are basic physiological reactions of all living organisms. Since the appearance of the first eukaryotic cells, a series of defense mechanisms have evolved in order to secure cellular integrity, homeostasis, and survival of the host. Invertebrates, ranging from protozoans to metazoans, possess cellular receptors, which bind to foreign elements and differentiate self from non-self. This ability is in multicellular animals associated with presence of phagocytes, bearing different names (amebocytes, hemocytes, coelomocytes) in various groups including animal sponges, worms, cnidarians, mollusks, crustaceans, chelicerates, insects, and echinoderms (sea stars and urchins). Basically, these cells have a macrophage-like appearance and function and the repair and/or fight functions associated with these cells are prominent even at the earliest evolutionary stage. The cells possess pathogen recognition receptors recognizing pathogen-associated molecular patterns, which are well-conserved molecular structures expressed by various pathogens (virus, bacteria, fungi, protozoans, helminths). Scavenger receptors, Toll-like receptors, and Nod-like receptors (NLRs) are prominent representatives within this group of host receptors. Following receptor-ligand binding, signal transduction initiates a complex cascade of cellular reactions, which lead to production of one or more of a wide array of effector molecules. Cytokines take part in this orchestration of responses even in lower invertebrates, which eventually may result in elimination or inactivation of the intruder. Important innate effector molecules are oxygen and nitrogen species, antimicrobial peptides, lectins, fibrinogen-related peptides, leucine rich repeats (LRRs), pentraxins, and complement-related proteins. Echinoderms represent the most developed invertebrates and the bridge leading to the primitive chordates, cephalochordates, and urochordates, in which many autologous genes and functions from their ancestors can be found. They exhibit numerous variants of innate recognition and effector molecules, which allow fast and innate responses toward diverse pathogens despite lack of adaptive responses. The primitive vertebrates (agnathans also termed jawless fish) were the first to supplement innate responses with adaptive elements. Thus hagfish and lampreys use LRRs as variable lymphocyte receptors, whereas higher vertebrates [cartilaginous and bony fishes (jawed fish), amphibians, reptiles, birds, and mammals] developed the major histocompatibility complex, T-cell receptors, and B-cell receptors (immunoglobulins) as additional adaptive weaponry to assist innate responses. Extensive cytokine networks are recognized in fish, but related signal molecules can be traced among invertebrates. The high specificity, antibody maturation, immunological memory, and secondary responses of adaptive immunity were so successful that it allowed higher vertebrates to reduce the number of variants of the innate molecules originating from both invertebrates and lower vertebrates. Nonetheless, vertebrates combine the two arms in an intricate inter-dependent network. Organisms at all developmental stages have, in order to survive, applied available genes and functions of which some may have been lost or may have changed function through evolution. The molecular mechanisms involved in evolution of immune molecules, might apart from simple base substitutions be as diverse as gene duplication, deletions, alternative splicing, gene recombination, domain shuffling, retrotransposition, and gene conversion. Further, variable regulation of gene expression may have played a role.",
    url = "https://doi.org/10.3389/fimmu.2014.00459",
    doi = "10.3389/fimmu.2014.00459",
    openalex = "W2146122014",
    references = "doi101002jezb22559, doi101038nature12826, doi104049jimmunol171116006"
}

Endogenous retroviruses (ERVs) are abundant in mammalian genomes and contain sequences modulating transcription. The impact of ERV propagation on the evolution of gene regulation remains poorly understood. We found that ERVs have shaped the evolution of a transcriptional network underlying the interferon (IFN) response, a major branch of innate immunity, and that lineage-specific ERVs have dispersed numerous IFN-inducible enhancers independently in diverse mammalian genomes. CRISPR-Cas9 deletion of a subset of these ERV elements in the human genome impaired expression of adjacent IFN-induced genes and revealed their involvement in the regulation of essential immune functions, including activation of the AIM2 inflammasome. Although these regulatory sequences likely arose in ancient viruses, they now constitute a dynamic reservoir of IFN-inducible enhancers fueling genetic innovation in mammalian immune defenses.

@article{doi101126scienceaad5497,
    author = "Chuong, Edward B. and Elde, Nels C. and Feschotte, Cédric",
    title = "Regulatory evolution of innate immunity through co-option of endogenous retroviruses",
    year = "2016",
    journal = "Science",
    abstract = "Endogenous retroviruses (ERVs) are abundant in mammalian genomes and contain sequences modulating transcription. The impact of ERV propagation on the evolution of gene regulation remains poorly understood. We found that ERVs have shaped the evolution of a transcriptional network underlying the interferon (IFN) response, a major branch of innate immunity, and that lineage-specific ERVs have dispersed numerous IFN-inducible enhancers independently in diverse mammalian genomes. CRISPR-Cas9 deletion of a subset of these ERV elements in the human genome impaired expression of adjacent IFN-induced genes and revealed their involvement in the regulation of essential immune functions, including activation of the AIM2 inflammasome. Although these regulatory sequences likely arose in ancient viruses, they now constitute a dynamic reservoir of IFN-inducible enhancers fueling genetic innovation in mammalian immune defenses.",
    url = "https://doi.org/10.1126/science.aad5497",
    doi = "10.1126/science.aad5497",
    openalex = "W2290849670",
    references = "doi10103835057062, doi101038nbt1630, doi101038nbt2450, doi101038nbt3122, doi101038nmeth3317, doi101038nprot2013143, doi101093bioinformaticsbtp324, doi101093bioinformaticsbtr064, doi101093nargkh340, doi101093nargku365, doi101126science1211028"
}

@incollection{buchmann2018evolution,
    author = "Buchmann, Kurt",
    title = "Evolution of Immunity",
    year = "2018",
    booktitle = "Advances in Comparative Immunology",
    url = "https://doi.org/10.1007/978-3-319-76768-0\_1",
    doi = "10.1007/978-3-319-76768-0\_1",
    openalex = "W2887495960",
    pages = "3-22",
    references = "doi101016s0952791501003077, doi101038nature12826, doi101038ni1913, doi101111j01052896200400116x, doi101126science1190689, doi101186s1286501601873, doi101615critrevimmunolv32i610, doi103389fimmu201400001, doi103389fimmu201400459, doi103389fimmu201700001"
}

@article{doi101038s4158602103207w,
    author = "Gaebler, Christian and Wang, Zijun and Lorenzi, Julio C. C. and Muecksch, Frauke and Finkin, Shlomo and Tokuyama, Minami and Cho, Alice and Janković, Mila and Schaefer-Babajew, Dennis and Oliveira, Thiago Y. and Cipolla, Melissa and Viant, Charlotte and Barnes, Christopher O. and Bram, Yaron and Breton, Gaëlle and Hägglöf, Thomas and Mendoza, Pilar and Hurley, Arlene and Turroja, Martina and Gordon, Kristie and Millard, Katrina G. and Ramos, Víctor and Schmidt, Fabian and Weisblum, Yiska and Jha, Divya and Tankelevich, Michael and Martínez-Delgado, Gustavo and Yee, Jim and Patel, Roshni and Dizon, Juan and Unson-O’Brien, Cecille and Shimeliovich, Irina and Robbiani, Davide F. and Zhao, Zhen and Gazumyan, Anna and Schwartz, Robert E. and Hatziioannou, Théodora and Björkman, Pamela J. and Mehandru, Saurabh and Bieniasz, Paul D. and Caskey, Marina and Nussenzweig, Michel C.",
    title = "Evolution of antibody immunity to SARS-CoV-2",
    year = "2021",
    journal = "Nature",
    url = "https://doi.org/10.1038/s41586-021-03207-w",
    doi = "10.1038/s41586-021-03207-w",
    openalex = "W3121906900",
    references = "doi101001jama202012603, doi101002cytoa22625, doi101006abio19879999, doi1010160003269787900212, doi1010160022283682905150, doi101016jcell202005015, doi101038s415860202196x, doi101038s4158602024569, doi101038s4159102009135, doi101126scienceabf4063"
}