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64 results for “Immunity: evolution”
Induced immune reaction in the acorn worm, Saccoglossus kowalevskii, informs the evolution of antiviral immunity
<p>The data present in this repository reflect intermediate and processed data presented in the manuscript, <em>Induced immune reaction in the acorn worm, Saccoglossus kowalevskii, informs the evolution of antiviral immunity. </em>This manuscript is still under review; as such, this page will be updated upon publication.</p> <p> </p> <p><strong>Manuscript Abstract:</strong></p> <p>Evolutionary perspectives on the deployment of immune factors following infection have been shaped by studies on a limited number of biomedical model systems with a heavy emphasis on vertebrate species. Though their contributions to contemporary immunology cannot be understated, a broader phylogenetic perspective is needed to understand the evolution of immune systems across Metazoa. In our study, we leverage differential gene expression analyses to identify genes implicated in the antiviral immune response of the acorn worm hemichordate, <em>Saccoglossus kowalevskii</em>, and place them in the context of immunity evolution within deuterostomes – the animal clade composed of chordates, hemichordates, and echinoderms. Following acute exposure to the synthetic viral dsRNA analog, poly(I:C), we show that <em>S. kowalevskii </em>responds by regulating the transcription of genes associated with canonical innate immunity signaling pathways (e.g., NF-κB and IRF signaling) and metabolic processes (e.g., lipid metabolism), as well as many genes without clear evidence of orthology with those of model species. Aggregated across all experimental time point contrasts, we identify 423 genes that are differentially expressed in response to poly(I:C). We also identify 147 genes with altered temporal patterns of expression in response to immune challenge. By characterizing the molecular toolkit involved in hemichordate antiviral immunity, our findings provide vital evolutionary context for understanding the origins of immune systems within Deuterostomia.</p> <p> </p> <p><strong>Repository contents:</strong></p> <p>### Processed Data ###</p> <ul> <li><em>Full_DESeq2_matrix.csv </em>--> DESeq2 results for each contrast (e.g., 2hpi treatment vs. control)</li> <li><em>MaSigPro.Clusters.csv</em> --> Mean expression for each gene placed within a pDEG cluster</li> <li><em>MaSigPro.SigGenes.TreatmentvsControl.Robj</em> --> T.fit() R-object output from MaSigPro pipeline. This can be opened in R using the load() function.</li> </ul> <p>### Homology Assessment ###</p> <ul> <li><em>Orthofinder.tar.gz</em> --> OrthoFinder results</li> <li><em>Skowalevskii_Genome_Annotation.SPHuman_and_HOG.csv</em> --> Assignment of IDs to Skow1.1 genes conforming to "PANTHER-Human" and "HOG" output described in the main text of the paper</li> <li><em>Skowalevskii_Genome_Annotation.SPPANTHER.csv </em>--> Assignment of IDs to Skow1.1 genes conforming to "PANTHER-SwissProt" output described in the main text of the paper</li> </ul> <p>### Functional Annotation ###</p> <ul> <li><em>Skow.HMMER_Pfam.domtblout.tsv</em> --> Pfam annotation of the Skow1.1 genome assembly in HMMER's domblout format</li> <li><em>Skow.KofamKOALA.detail.tsv</em> --> KO annotation of the Skow1.1 genome assembly using KofamKOALA (detailed output)</li> <li><em>Skow.KofamKOALA.detail.tsv </em>--> KO annotation of the Skow1.1 genome assembly using KofamKOALA (mapper output)</li> <li><em>SkowAnnotations.GO.tsv</em> --> GO annotation of the Skow1.1 genome assembly</li> <li><em>SkowAnnotations.PF.tsv</em> --> PF annotation of the Skow1.1 genome assembly</li> <li><em>SkowAnnotations.PP.tsv</em> --> PP annotation of the Skow1.1 genome assembly</li> </ul> <p>### Enrichment Data ###</p> <ul> <li><em>DESeqEnrichments.tsv</em> --> Pearson's chi-squared enrichment calculations for every annotation present in the Skow1.1 genome assembly for genes resolved as significantly differentially expressed by DESeq2.</li> <li><em>MaSigProEnrichments.tsv</em> --> Pearson's chi-squared enrichment calculations for every annotation present in the Skow1.1 genome assembly for genes resolved as significantly differentially expressed by MaSigPro.</li> </ul>
Data from: Experimental evolution of insect immune memory versus pathogen resistance
Under strong pathogen pressure, insects often evolve resistance to infection. Many insects are also protected via immune memory ('immune priming'), whereby sub-lethal exposure to a pathogen enhances survival after secondary infection. Theory predicts that immune memory should evolve when the pathogen is highly virulent, or when pathogen exposure is relatively rare. However, there are no empirical tests of these hypotheses, and the adaptive benefits of immune memory relative to direct resistance against a pathogen are poorly understood. To determine the selective pressures and ecological conditions that shape immune evolution, we imposed strong pathogen selection on flour beetle (Tribolium castaneum) populations, infecting them with Bacillus thuringiensis (Bt) for 11 generations. Populations injected first with heat-killed and then live Bt each generation evolved high basal resistance against multiple Bt strains. In contrast, populations injected only with a high dose of live Bt evolved a less effective but strain-specific priming response. Control populations injected with heat-killed Bt did not evolve priming; and in the ancestor, priming was effective only against a low Bt dose. Intriguingly, one replicate population first evolved priming and subsequently evolved basal resistance, suggesting the potential for dynamic evolution of different immune strategies. Our work is the first report showing that pathogens can select for rapid modulation of insect priming ability, allowing hosts to evolve divergent immune strategies (generalized resistance vs. specific immune memory) with potentially distinct mechanisms.
Data from: Incomplete host immunity favors the evolution of virulence in an emergent pathogen
Immune memory evolved to protect hosts from reinfection, but incomplete responses that allow future reinfection might inadvertently select for more harmful pathogens. We present empirical and modeling evidence that incomplete immunity promotes the evolution of higher virulence in a natural host-pathogen system. We performed sequential infections of house finches with Mycoplasma gallisepticum strains of varying virulence. Virulent bacterial strains generated stronger host protection against reinfection than less virulent strains, and thus excluded less virulent strains from infecting previously-exposed hosts. In a two-strain model, the resulting fitness advantage selected for an almost two-fold increase in pathogen virulence. Thus, the same immune systems that protect hosts from infection can concomitantly drive the evolution of more harmful pathogens in nature.
The evolution of immune function in decorated crickets
<p>While dietary macronutrients are known to regulate insect immunity, few studies have examined their evolutionary effects. Here, we evaluate this relationship in the cricket<em> Gryllodes sigillatus</em> by maintaining replicate populations on four diets differing in protein (P) to carbohydrate (C) ratio (P- or C-biased) and nutritional content (low- or high-nutrition) for >37 generations. We split each population into two; one maintained on their evolution diet and the other switched to their ancestral diet. We also maintained populations exclusively on the ancestral diet (baseline). After three generations, we measured three immune parameters in males and females from each population. Immunity was higher on P-biased than C-biased diets and on low- versus high-nutrition diets, although the latter was most likely driven by compensatory feeding. These patterns persisted in populations switched to their ancestral diet, indicating genetic divergence. Crickets evolving on C-biased diets had lower immunity than the baseline, whereas their P-biased counterparts had similar or higher immunity than the baseline, indicating that populations evolved with dietary manipulation. While females exhibited superior immunity for all assays, the sexes showed similar immune changes across diets. Our work highlights the important role that macronutrient intake plays in the evolution of immunity in the sexes.</p>
Diversity in CRISPR-based immunity protects susceptible genotypes by restricting phage spread and evolution
Diversity in host resistance often associates with reduced pathogen spread. This may result from ecological and evolutionary processes, likely with feedback between them. Theory and experiments on bacteria-phage interactions have shown that genetic diversity of the bacterial adaptive immune system can limit phage evolution to overcome resistance. Using the CRISPR-Cas bacterial immune system and lytic phage, we engineered a host-pathogen system where each bacterial host genotype could be infected by only one phage genotype. With this model system, we explored how CRISPR diversity impacts the spread of phage when they can overcome a resistance allele, how immune diversity affects the evolution of the phage to increase its host range, and if there was feedback between these processes. We show that increasing CRISPR diversity benefits susceptible bacteria via a dilution effect, which limits the spread of the phage. We suggest that this ecological effect impacts the evolution of novel phage genotypes, which then feeds back into phage population dynamics.
Impaired immune function accompanies social evolution in spiders
<p><span>An efficient immune system is essential to the survival of many animals. Sociality increases risk of pathogen transmission, which should select for enhanced immune function. However, two hypotheses instead predict a weakened immune function: relaxed selection caused by social immunity/protection, and reduced efficacy of selection due to inbreeding, reproductive skew, and female bias in social species that reduces effective population size and accelerate genetic drift. We assessed the effect of social evolution on immune function in a comparative study of two social spider species and their closely related subsocial sister species (genus <em>Stegodyphus</em>). The haemolymph of social species was less efficient in inhibiting the growth of potentially pathogenic bacteria than that of subsocial species. Reduced efficacy of selection in social species was supported by comparative genomic analysis of immune genes showing substantially elevated non-synonymous substitutions in one of the social species. We propose that this impaired immune function is likely to be a result of reduced efficacy of selection because the evolution of sociality in spiders is accompanied by demographic processes that elevate genetic drift. There may also be positive feedback between pathogen-induced local extinctions and the resulting elevation of genetic drift which further weakens responses to selection by pathogens.</span></p>
Data from: Evolution of personal and social immunity in the context of parental care
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Impaired immune function accompanies social evolution in spiders
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Data from: Incomplete host immunity favors the evolution of virulence in an emergent pathogen
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The evolution of immune function in decorated crickets
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Diversity in CRISPR-based immunity protects susceptible genotypes by restricting phage spread and evolution
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Data from: Contemporary evolution of the innate immune receptor gene TLR3 in an isolated vertebrate population
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Data from: Rapid seasonal evolution in innate immunity of wild Drosophila melanogaster
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Data from: Experimental evolution of insect immune memory versus pathogen resistance
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Data from: Rapid evolution of larval life history, adult immune function and flight muscles in a poleward moving damselfly
Although a growing number of studies have documented the evolution of adult dispersal-related traits at the range edge of poleward-expanding species, we know little about evolutionary changes in immune function or traits expressed by nondispersing larvae. We investigated differentiation in larval (growth and development) and adult traits (immune function and flight-related traits) between replicated core and edge populations of the poleward-moving damselfly Coenagrion scitulum. These traits were measured on individuals reared in a common garden experiment at two different food levels, as allocation trade-offs may be easier to detect under energy shortage. Edge individuals had a faster larval life history (growth and development rates), a higher adult immune function and a nearly significant higher relative flight muscle mass. Most of the differentiation between core and edge populations remained and edge populations had a higher relative flight muscle mass when corrected for latitude-specific thermal regimes, and hence could likely be attributed to the range expansion process per se. We here for the first time document a higher immune function in individuals at the expansion front of a poleward-expanding species and documented the rarely investigated evolution of faster life histories during range expansion. The rapid multivariate evolution in these ecological relevant traits between edge and core populations is expected to translate into changed ecological interactions and therefore has the potential to generate novel eco-evolutionary dynamics at the expansion front.
Evidence for reduced immune gene diversity and activity during the evolution of termites
<p class="Normal tm5 tm6">This dataset contains data from a termite immunity related study described in the paper: "He Shulin, Sieksmeyer Thorben, Che Yanli, Mora M. Alejandra Esparza, Stiblik Petr, Banasiak Ronald, Harrison Mark C., Šobotník Jan, Wang Zongqing, Johnston Paul R. and McMahon Dino P. 2021Evidence for reduced immune gene diversity and activity during the evolution of termitesProc. R. Soc. B.288:20203168.http://doi.org/10.1098/rspb.2020.3168". </p> <p class="Normal tm5 tm6">The study investigates the evolution of termite molecular immune system: evolution of immune gene family along a constructed phylogeny, different individual immune response between three termite castes, a subsocial cockroach and a non-social cockroach, the caste specific expression of immune genes, different social immune response between a social termite species and a non-social cockroach species.</p> <p class="Normal tm5 tm6">In the first experiment, we de novo sequenced 18 cockroach and termite species, spanning the full spectrum of solitary and social lifestyles, including two solitary cockroach species, two species of subsocial <em><span class="tm7">Cryptocercus</span></em> wood-feeding cockroaches and 14 termite species. We exploited a transcriptomic approach to compare the immune gene repertoire of these sequenced species.</p> <p class="Normal tm5 tm6">In the second experiment, we compared individual immune responses in a solitary cockroach, <em><span class="tm7">B. orientalis</span></em>, a subsocial wood-feeding roach, <em><span class="tm7">Cryptocercus meridianus</span></em>, and each caste of a social termite, <em><span class="tm7">Neotermes castaneus</span></em>, following direct injection with heat-killed microbes.</p> <p class="Normal tm5 tm6">In the third experiment, we explored total gene expression differences between castes without immune challenge.</p> <p class="Normal tm5 tm6">In the fourth experiment, we studied gene expression changes in each caste of <em><span class="tm7">N. castaneus</span></em> following colony exposure to immune-challenged nestmates, and compared these with gene expression changes in the solitary cockroach, <em><span class="tm7">B. orientalis</span></em>, following group exposure to immune-challenged conspecifics.</p> <p class="Normal tm5 tm6">Main results of the experiments are that (1) immune gene families show contractions and expansions during temite evolution; (2) compared with cockroaches, termites showed weak individual immune response; (3) termites have caste-specific constitutive immunity; (4) Compared with cockroach, termite showed a stronger gene expression changes in response to a social immune challenge.</p>
Data from: Evolution of the immune system influences speciation rates in teleost fishes
Teleost fishes constitute the most species-rich vertebrate clade and exhibit extensive genetic and phenotypic variation, including diverse immune defense strategies. The genomic basis of a particularly aberrant strategy is exemplified by Atlantic cod, in which a loss of major histocompatibility complex (MHC) II functionality coincides with a marked expansion of MHC I genes. Through low-coverage genome sequencing (9–39×), assembly and comparative analyses for 66 teleost species, we show here that MHC II is missing in the entire Gadiformes lineage and thus was lost once in their common ancestor. In contrast, we find that MHC I gene expansions have occurred multiple times, both inside and outside this clade. Moreover, we identify an association between high MHC I copy number and elevated speciation rates using trait-dependent diversification models. Our results extend current understanding of the plasticity of the adaptive immune system and suggest an important role for immune-related genes in animal diversification.
Pleiotropy promotes the evolution of inducible immune responses in a model of host-pathogen coevolution
<p>The archives uploaded here include the code used to perform the evolutionary simulations as described in <em>Pleiotropy promotes the evolution of inducible immune responses in a model of host-pathogen coevolution </em>authors: Martin,R. Tate, A. as well as the data that was used in the generation of the figures for that paper. Code requires the Julia programming language and necessary packages to run.</p>
Evaluating ImmuNe Changes in the Evolution of Pre Type 1 Diabetes With Adult ONset
ClinicalTrials.gov study NCT06006468. IPD Sharing: NO. Countries: 1. Publications: 28.
Data from: The evolution of highly variable immunity genes across a passerine bird radiation.
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