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200 results for “Coevolution”
Data for: Feedback between coevolution and epidemiology can help or hinder the maintenance of genetic variation in host-parasite models
<p>Antagonistic coevolution has long been suggested to help maintain host genetic variation. While, ecological and epidemiological feedbacks are known to have important consequences on coevolutionary allele frequency dynamics, their effects on the maintenance of genetic variation remains poorly understood.Here, we extend our previous work on the maintenance of genetic variation in a classic matching-alleles coevolutionary model by exploring the effects of ecological and epidemiological feedbacks, where both allele frequencies and population sizes are allowed to vary over time. We find that coevolution rarely maintains more host genetic variation than expected under neutral genetic drift alone. When and if coevolution maintains or depletes genetic variation relative to neutral drift is determined, predominantly, by two factors: the deterministic stability of the Red Queen allele frequency cycles and the chance of allele fixation in the pathogen, as this results in directional selection and depletion of genetic variation in the host. Compared to purely coevolutionary models with constant host and pathogen population sizes, ecological and epidemiological feedbacks stabilize Red Queen cycles deterministically, but population fluctuations in the pathogen increase the rate of allele fixation in the pathogen, especially in epidemiological models. Our results illustrate the importance of considering the ecological and epidemiological context in which coevolution occurs when examining the impact of Red Queen cycles on genetic variation.</p>
Coevolution with hosts underpins speciation in brood parasitic cuckoos
<p>Coevolution is considered to be a likely driver of speciation, but evidence linking macroevolutionary patterns to microevolutionary processes is scarce. We report that coevolution with hosts drives divergence in bronze-cuckoos. Bronze-cuckoo hosts reject cuckoo nestlings, selecting for mimicry of host nestlings by cuckoos. This has generated a diversity of bronze-cuckoo nestling morphologies matching those of their respective hosts across their geographic range and promotes diversification in sympatry; little bronze-cuckoos that exploit multiple host species in sympatry show evidence of genetic differentiation and corresponding divergence in nestling morphology. This process is reflected in macroevolutionary patterns: rates of speciation are faster in virulent cuckoos than in more benign species and simulation models indicate greater support for a sympatric mode of speciation in bronze-cuckoos than in sister taxa.</p>
The coevolution of rostral keratin cover and toothrow distribution in Mesozoic dinosaurs
<p><span>Teeth evolved early in vertebrate evolution, and their morphology reflects important specializations in diet and ecology among species. The toothless jaws (edentulism) in extant birds likely </span><span><span>co</span></span><span><span>evolved</span> <span>with beak keratin, which functionally replaced teeth. However, extinct dinosaurs lost teeth multiple times independently and exhibited great variation in toothrow distribution and beak-like keratin structures. Here, we use facial jawbone surface texture as a proxy for </span><span>rostral keratin covering and phylogenetic comparative models to test for the influence of facial keratin on toothrow distribution in Mesozoic dinosaurs. We find that the evolution of </span><span>rostral</span><span> keratin covering explains partial toothrow reduction but not jaw </span><span>toothlessness</span><span>. Toothrow reduction preceded the evolution of </span><span>rostral</span><span> keratin cover in theropods. Non-theropod dinosaurs evolved continuous toothrows despite </span><span>rostral</span><span> keratin cover (e.g., some ornithischians and sauropodomorphs). We also show that </span><span>rostral</span><span> keratin cover did not significantly increase the evolutionary rate of tooth loss, which further delineates the antagonistic relationship between these structures. Our results suggest that the evolution of </span><span>rostral</span><span> keratin had a limited effect on suppressing tooth development</span><span>.</span><span> <span>Independent changes in jaw development may have facilitated further tooth loss.</span></span> <span>Furthermore, the evolution of strong chemical digestion, a gizzard, and a dietary shift to omnivory or herbivory </span><span>likely </span><span>alleviated</span> <span>selective pressure</span><span>s</span><span> for tooth development.</span><span><span> </span></span></span></p>
Rapid divergent evolution of internal female genitalia and the coevolution of male genital morphology revealed by micro-computed tomography
<p>Animal genitalia are thought to evolve rapidly and divergently in response to sexual selection. Studies of genital evolution have focused largely on male genitalia, with our understanding of female genital evolution relatively limited. The paucity of work on female genital morphology is likely due to problems faced in quantifying shape variation, due to their composition and accessibility. Here we use a combination of micro-computed tomography, landmark-free shape quantification, and phylogenetic analysis to quantify the rate of female genital shape evolution among 29 species of Antichiropus millipedes, and the coevolution of male genitalia. We found significant variation in female and male genital shape among species. While male genital shape showed significant phylogenetic signal, female genital shape did not. Male genital shape was found to be evolving 1.2 times faster than female genital shape. Female and male genital shapes exhibited strongly correlated evolution, indicating that genital shape changes in one sex are associated with corresponding changes in the genital shape of the other sex. This study adds novel insight into our growing understanding of how female genitalia can evolve rapidly and divergently and highlights the advantages of three-dimensional techniques and multivariate analyses in studies of female genital evolution.</p>
Ectopical expression of bacterial collagen-like protein supports its role as adhesin in host-parasite coevolution
<div> <div> <div> <div> <p>For a profound understanding of antagonistic coevolution, it is necessary to identify the coevolving genes. The bacterium Pasteuria and its host, the microcrustacean Daphnia, are a well-characterized paradigm for co-evolution, but the underlying genes remain largely unknown. A genome-wide association study suggested a Pasteuria collagen-like protein 7 (Pcl7) as a candidate mediating parasite attachment and driving its coevolution with the host. Since Pasteuria ramosa cannot currently be genetically manipulated, we used Bacillus thuringiensis to express a fusion protein of a Pcl7 carboxy- terminus from P. ramosa and the amino-terminal domain of a B. thuringiensis collagen-like protein (CLP). Mutant B. thuringiensis (Pcl7-Bt) spores but not wild-type B. thuringiensis (WT-Bt) spores, attached to the same site of susceptible hosts as P. ramosa. Furthermore, Pcl7-Bt spores attached readily to susceptible host genotypes, but only slightly to resistant host genotypes. These findings indicated that the fusion protein was properly expressed and folded and demonstrated that indeed the C-terminus of Pcl7 mediates attachment in a host genotype-specific manner. These results provide strong evidence for the involvement of a CLP in the coevolution of Daphnia and P. ramosa and open new avenues for genetic epidemiological studies of host–parasite interactions.</p> </div> </div> </div> </div>
Coevolution of relative brain size and life expectancy in parrots
<p><span><span><span><span>Previous studies have demonstrated a correlation between longevity and brain size in a variety of taxa. Little research has been devoted to understanding this link in parrots; yet parrots are well-known for both their exceptionally long lives and cognitive complexity. We employed a large-scale comparative analysis that investigated the influence of brain size and life history variables on longevity in parrots. Specifically, we addressed two hypotheses for evolutionary drivers of longevity: the <em>Cognitive Buffer Hypothesis</em>, which proposes that increased cognitive abilities enable longer life spans, and the <em>Expensive Brain Hypothesis</em>, which holds that increases in life span are caused by prolonged developmental time of, and increased parental investment in, large-brained offspring<em>. </em>We estimated life expectancy from detailed zoo records for 133,818 individuals across 244 parrot species. Using a principled Bayesian approach that addresses data uncertainty and imputation of missing values, we found a consistent correlation between relative brain size and life expectancy in parrots. This correlation was best explained by a direct effect of relative brain size. Notably, we found no effects of developmental time, clutch size, or age at first reproduction. Our results suggest that selection for enhanced cognitive abilities in parrots have in turn promoted longer lifespans.</span></span></span></span></p>
The Community Coevolution Model with application to the study of evolutionary relationships between genes based on phylogenetic profiles
<p>Organismal traits can evolve in a coordinated way, with correlated patterns of gains and losses reflecting important evolutionary associations. Discovering these associations can reveal important information about the functional and ecological linkages among traits. Phylogenetic profiles treat individual genes as traits distributed across sets of genomes and can provide a fine-grained view of the genetic underpinnings of evolutionary processes in a set of genomes. Phylogenetic profiling has been used to identify genes that are functionally linked, and to identify common patterns of lateral gene transfer in microorganisms. However, comparative analysis of phylogenetic profiles and other trait distributions should take into account the phylogenetic relationships among the organisms under consideration.</p> <p>Here we propose the Community Coevolution Model (CCM), a new coevolutionary model to analyze the evolutionary associations among traits, with a focus on phylogenetic profiles. In the CCM, traits are considered to evolve as a community with interactions, and the transition rate for each trait depends on the current states of other traits. Surpassing other comparative methods for pairwise trait analysis, CCM has the additional advantage of being able to examine multiple traits as a community to reveal more dependency relationships. We also develop a simulation procedure to generate phylogenetic profiles with correlated evolutionary patterns that can be used as benchmark data for evaluation purposes.</p> <p>A simulation study demonstrates that CCM is more accurate than other methods including the Jaccard Index and three tree-aware methods. The parameterization of CCM makes the interpretation of the relations between genes more direct, which leads to Darwin's scenario being identified easily based on the estimated parameters. We show that CCM is more efficient and fits real data better than other methods resulting in higher likelihood scores with fewer parameters. An examination of 3786 phylogenetic profiles across a set of 659 bacterial genomes highlights linkages between genes with common functions, including many patterns that would not have been identified under a non-phylogenetic model of common distribution. We also applied the CCM to 44 proteins in the well-studied Mitochondrial Respiratory Complex I and recovered associations that mapped well onto the structural associations that exist in the complex.</p>
Combining GWAS and population genomic analyses to characterize coevolution in a legume-rhizobia symbiosis
<p>The mutualism between legumes and rhizobia is clearly the product of past coevolution. However, the nature of ongoing evolution between these partners is less clear. To characterize the nature of recent coevolution between legumes and rhizobia, we used population genomic analysis to characterize selection on functionally annotated symbiosis genes as well as on symbiosis gene candidates identified through a two-species association analysis. For the association analysis, we inoculated each of 202 accessions of the legume host <em>Medicago truncatula</em> with a community of 88 <em>Ensifer meliloti</em> strains. Multi-strain inoculation, which better reflects the ecological reality of rhizobial selection in nature than single-strain inoculation, allows strains to compete for nodulation opportunities and host resources and for hosts to preferentially form nodules and provide resources to some strains. We found extensive host by symbiont, <em>i.e.</em>, genotype-by-genotype, effects on rhizobia fitness and some annotated rhizobia genes bear signatures of recent positive selection. However, neither genes responsible for this variation nor annotated host symbiosis genes are enriched for signatures of either positive or balancing selection. This result suggests that stabilizing selection dominates selection acting on symbiotic traits and that variation in these traits is under mutation-selection balance. Consistent with the lack of positive selection acting on host genes, we found that among-host variation in growth was similar whether plants were grown with rhizobia or N-fertilizer, suggesting that the symbiosis may not be a major driver of variation in plant growth in multi-strain contexts.</p>
Sexually antagonistic coevolution of the male nuptial gift and female feeding behaviour in decorated crickets
<p>The evolution of nuptial gifts has traditionally been considered a harmonious affair, providing benefits to both mating partners. There is growing evidence, however, that receiving a nuptial gift can be actively detrimental to the female.<strong> </strong>In decorated crickets (<em>Gryllodes sigillatus</em>), males produce a gelatinous spermatophylax that enhances sperm transfer but provides little nutritional benefit and hinders female post-copulatory mate choice. Here, we examine the sexually antagonistic coevolution of the spermatophylax and the female feeding response to this gift in <em>G. sigillatus</em> maintained in experimental populations with either a male-biased or female-biased adult sex ratio. After 25 generations, males evolving in male-biased populations produced heavier spermatophylaxes with a more manipulative combination of free amino acids than those evolving in female-biased populations. Moreover, when the spermatophylax originated from the same selection regime, females evolving in male-biased populations always had shorter feeding durations than those evolving in female-biased populations indicating the evolution of greater resistance.<strong> </strong>Across populations, female feeding duration increased with the mass and manipulative combination of free amino acids in the spermatophylax suggesting sexually antagonistic coevolution.<strong> </strong>Collectively, our work demonstrates a key role for interlocus sexual conflict and sexually antagonistic coevolution in the mating system of<em> G. sigillatus</em>.</p>
Data and model output for "Evidence of subsurface control on the coevolution of hillslope morphology and runoff generation"
<p>Data, model output, and scripts supporting the manuscript:</p> <p>Litwin, D. G., & Harman, C. J. (2024) Evidence of subsurface control on the coevolution of hillslope morphology and runoff generation. <em>Water Resources Research</em>, 60, e2024WR037301. https://doi.org/10.1029/2024WR037301</p>
A geographic mosaic of coevolution between Eurosta solidaginis (Fitch) and its host plant tall goldenrod Solidago altissima (L.)
<p>A geographic mosaic of coevolution has produced local reciprocal adaptation in tall goldenrod, <i>Solidago altissima</i> (L.), and the goldenrod ball gall fly, <i>Eurosta solidaginis</i> (Fitch 1855). The fly is selected to induce gall diameters that minimize mortality from natural enemies, and the plant is selected to limit gall growth that reduces plant fitness. We conducted a double reciprocal transplant experiment where <i>S. altissima</i> and <i>E. solidaginis</i> from three sites were grown in gardens at each site to partition the gall morphology variation into fly genotype, plant genotype, and the environment components. The host plant gall diameter induced by each <i>E. solidaginis</i> population was adapted to inhibit local natural enemies from ovipositing on or consuming enclosed larvae. Reciprocally, increasing the gall size induced by the local fly population increased the resistance of the local plant host population to gall growth. Differences among sites in natural enemies produced a mosaic of hotspots of coevolutionary arms races between flies selecting for greater gall diameter and plants for smaller diameters, and coldspots where there is no selection on plant or fly for a change in gall diameter. In contrast, the geographic variations of gall length and gall shape were not due to coevolutionary interactions.</p>
Bacteria-phage coevolution with a seed bank
<p>Dormancy is an adaptation to living in fluctuating environments. It allows individuals to enter a reversible state of reduced metabolic activity when challenged by unfavorable conditions. Dormancy can also influence species interactions by providing organisms with a refuge from predators and parasites. Here we test the hypothesis that, by generating a seed bank of protected individuals, dormancy can modify the patterns and processes of antagonistic coevolution. We conducted a factorially designed experiment where we passaged a bacterial host (<em>Bacillus subtilis</em>) and its phage (SPO1) in the presence versus absence of a seed bank consisting of dormant endospores. Owing in part to the inability of phages to attach to spores, seed banks stabilized population dynamics and resulted in minimum host densities that were 30-fold higher compared to bacteria that were unable to engage in dormancy. By supplying a refuge to phage-sensitive strains, we show that seed banks retained phenotypic diversity that was otherwise lost to selection. Dormancy also stored genetic diversity. After characterizing allelic variation with pooled population sequencing, we found that seed banks retained twice as many host genes with mutations, whether phages were present or not. Based on mutational trajectories over the course of the experiment, we demonstrate that seed banks can dampen bacteria-phage coevolution. Not only does dormancy create structure and memory that buffers populations against environmental fluctuations, it also modifies species interactions in ways that can feed back onto the eco-evolutionary dynamics of microbial communities. </p>
The role of indirect effects in coevolution along the mutualism-antagonism continuum: data and code
<p>This repository contains the data described in "The role of indirect effects in coevolution along the mutualism-antagonism continuum" and the code used to generate it. </p>
NGS data from: Deploying synthetic coevolution and machine learning to engineer protein-protein interactions
<p>Fine-tuning of protein-protein interactions occurs naturally through coevolution, but this process is difficult to recapitulate in the laboratory. We describe a synthetic platform for protein-protein coevolution that can isolate matched pairs of interacting muteins from complex libraries. This large dataset of coevolved complexes<span class="Apple-converted-space"> </span>drove a systems-level analysis of molecular recognition between Z domain-affibody pairs spanning a wide range of structures, affinities, cross-reactivities, and orthogonalities, and captured a broad spectrum of coevolutionary networks. Furthermore, we harnessed pre-trained protein language models to expand, <em>in silico</em>, the amino acid diversity of our coevolution screen, predicting remodeled interfaces beyond the reach of the experimental library. The integration of these approaches provides a means of generating protein complexes with diverse molecular recognition properties as tools for biotechnology and synthetic biology.</p>
Sex-specific effects of antagonistic coevolution: Insights from an insect host and a bacterial pathogen coevolution system
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In vivo microbial coevolution favours host protection and plastic downregulation of immunity
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Data from: Coevolution of Drosophila-type timeless with partner clock proteins
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Data from: The coevolution of male and female genitalia in a mammal: a quantitative genetic insight
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Female-driven intersexual coevolution in beetle genitalia
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The coevolution of rostral keratin cover and toothrow distribution in Mesozoic dinosaurs
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