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21 results for “evolution of symbiosis”
Microbial warfare and the evolution of symbiosis
<p>Cooperative symbionts enable their hosts to exploit a diversity of environments. A low genetic diversity (high relatedness) between the symbionts within a host is thought to favour cooperation by reducing conflict within the host. However, hosts will not be favoured to transmit their symbionts in costly ways that increase relatedness, unless this also provides an immediate fitness benefit to the host. We suggest that costly antimicrobial warfare, with compounds such as bacteriocins, could provide a relatively universal reason for why hosts would gain a benefit from increasing the relatedness between bacterial symbionts. We theoretically test this hypothesis with a simple illustrative model that examines whether hosts should manipulate relatedness, and an individual-based simulation, where host control evolves in a structured population. We find that hosts can be favoured to manipulate relatedness, to reduce conflict between symbionts via this immediate reduction in symbiont warfare.</p>
Microbial warfare and the evolution of symbiosis
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Electronic supplementary information: Independent and adaptive evolution of phenotypic novelties is driven by coral symbiosis in barnacle larvae
<p class="Standard">The invasion of novel habitats is recognized as a major promotor of adaptive trait evolution in animals. We tested whether similar ecological niches entail independent and adaptive evolution of key phenotypic structures related to larval host invasion in distantly related taxa. We use disparately related clades of coral barnacles as our model system (Acrothoracica: <i>Berndtia</i> and Thoracica: Pyrgomatidae). We analyze the larval antennular phenotypes and functional morphologies facilitating host invasion. Extensive video recordings show that coral host invasion is carried out exclusively by cypris larvae with spear-shaped antennules. These first exercise a series of complex probing behaviors followed by repeated antennular penetration of the soft host tissues, which subsequently facilitates permanent invasion. Phylogenetic mapping of larval form and function related to niche invasion in 99 species of barnacles (Thecostraca) compellingly shows that the spear-phenotype is uniquely associated with corals and penetrative behaviors. These features evolved independently in the two coral barnacle clades and from ancestors with fundamentally different antennular phenotypes. The larval host invasion system in coral barnacles likely evolved adaptively across millions of years for overcoming challenges associated with invading and entering demanding coral hosts.</p> <p class="Standard"> </p> <p class="Standard"><i>Key words: </i>adaptive host invasion, larval phenotypes, coral barnacle, barnacle phylogeny</p>
Impact of model assumptions on the inference of the evolution of ectomycorrhizal symbiosis in fungi
<p>Ectomycorrhiza (ECM) is a symbiotic relation between plant and fungi that is essential for nutrient uptake of many stand forming trees. There are two conflicting views about the evolution of ECM in fungi suggesting (1) relatively few transitions to ECM followed by reversals to non-ECM, or (2) many independent origins of ECM and no reversals. In this study, we compare these, and other, hypotheses and test the impact of different models on inference. We assembled a dataset of five marker gene sequences (nuc58, nucLSU, nucSSU, rpb1, and rpb2) and 2,174 fungal taxa covering the three subphyla: Agaricomycotina, Mucoromycotina and Pezizomycotina. The fit of different models, including models with variable rates in clades or through time, to the pattern of ECM fungal taxa was tested in a Bayesian framework, and using AIC and simulations. We find that models implementing variable rates are a better fit than models without rate shift, and that the conclusion about the relative rate between ECM and non-ECM depend largely on whether rate shifts are allowed or not. We conclude that standard constant-rate ancestral state reconstruction models are not adequate for the analysis of the evolution of ECM fungi, and may give contradictory results to more extensive analyses. </p>
Microsatellite genotype data from: Male-biased dispersal in a fungus-gardening ant symbiosis (Matthews et al, Ecology and Evolution)
<p>For nearly all organisms, dispersal is a fundamental life history trait that can shape their ecology and evolution. Variation in dispersal capabilities within a species exists and can influence population genetic structure and ecological interactions. In fungus-gardening (attine) ants, co-dispersal of ants and mutualistic fungi is crucial to the success of this obligate symbiosis. Female-biased dispersal (and gene flow) may be favored in attines because virgin queens carry the responsibility of dispersing the fungi, but a paucity of research has made this conclusion difficult. Here, we investigate dispersal of the fungus-gardening ant <i>Trachymyrmex septentrionalis</i> using a combination of maternally- (mitochondrial DNA) and biparentally-inherited (microsatellites) markers. We found three distinct, spatially isolated mitochondrial DNA haplotypes; two were found in the Florida panhandle and the other in the Florida peninsula. In contrast, biparental markers illustrated significant gene flow across this region and minimal spatial structure. The differential patterns uncovered from mitochondrial DNA and microsatellite markers suggest that most long-distance ant dispersal is male-biased and that females (and concomitantly the fungus) have more limited dispersal capabilities. Consequently, the limited female dispersal is likely an important bottleneck for the fungal symbiont. This bottleneck could slow fungal genetic diversification, which has significant implications for both ant hosts and fungal symbionts regarding population genetics, species distributions, adaptive responses to environmental change, and coevolutionary patterns.</p>
Convergent evolution of NFP-facilitated root nodule symbiosis
<p># NFP</p> <p>Scripts and data associated with the manuscript "Convergent evolution of NFP-facilitated root nodule symbiosis."</p> <p>## 00_sequences<br>This directory contains NFP/LYR homologs and annotations.</p> <p>## 02_alignments<br>This directory contains NFP alignments</p> <p>## 03_trees<br>This directory contains gene trees and species tree guides for the analyses.</p> <p>## 04_reconciliation<br>This directory contains notung files and figures for the gene tree reconciliation analysis</p> <p>## 05_synteny<br>This directory contains files for the synteny analyses. The base directory contains circos plots and a subdirectory `Synteny.2.2020` containing scripts and summary output as well as the following:<br>### Results_Apr01.zip<br>Summary of synteny results<br>### csvs.zip<br>An archive containing all csvs in the analysis.<br>### fastas.zip<br>synteny analysis - chr 5 v 8.zip<br>### tsvs.zip<br>An archive containing all csvs in the analysis.<br>### blasts.zip<br>An archive containing blast results.<br>### coords.zip<br>An archive containing genome coordinate files.<br>### gffs.zip<br>An archive containing GFF annotations.<br>### gff3s.zip<br>An archive containing GFF annotations.<br>### imgs.zip<br>An archive containing figure files used for preparing the manuscript.<br> <br>## figs<br>This directory contains figure files used for preparing the manuscript.</p> <p>## Scripts_used_CF<br>This directory contains submission and shell scripts used to conduct the analyses.</p>
The evolution of ectomycorrhizal symbiosis in the Late Cretaceous is a key driver of explosive diversification in Agaricomycetes
<p>Ectomycorrhizal (EcM) symbiosis is one of the most ubiquitous and important plant–microbe interactions in forest ecosystems. Coevolutionary interactions often create new ecological opportunities for explosive diversification. It remains unclear why the evolution of EcM fungi did not necessarily increase ecological opportunities for explosive diversification. This study aims to reveal the driving mechanism of the explosive diversification in the fungal class Agaricomycetes, specifically by testing whether the evolution of EcM symbiosis in the Late Cretaceous increased ecological opportunities. Molecular phylogenies of Agaricomycetes inferred from fragments of 89 single-copy genes indicate that the unidirectional evolution of EcM symbiosis occurred multiple times, ranging in date from the early Triassic to the early Paleogene. However, five analyses for estimating net diversification rates (speciation rates minus extinction rates) suggest that the explosive diversification occurred only at the stem EcM fungal clades diverging in the late Cretaceous, coinciding with the rapid diversification of EcM angiosperms. The present findings suggest that the evolution of EcM symbiosis, supposedly with coevolving EcM angiosperms, in the Late Cretaceous was the key drive of the explosive diversification in Agaricomycetes.</p>
Electronic supplementary information: Independent and adaptive evolution of phenotypic novelties is driven by coral symbiosis in barnacle larvae
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The evolution of ectomycorrhizal symbiosis in the Late Cretaceous is a key driver of explosive diversification in Agaricomycetes
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Microsatellite genotype data from: Male-biased dispersal in a fungus-gardening ant symbiosis (Matthews et al, Ecology and Evolution)
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Impact of model assumptions on the inference of the evolution of ectomycorrhizal symbiosis in fungi
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Experimental evolution of virulence and associated traits in a Drosophila melanogaster – Wolbachia symbiosis
<p>Evolutionary theory predicts that vertically transmitted symbionts are selected for low virulence, as their fitness is directly correlated to that of their host. In contrast with this prediction, the <em>Wolbachia</em> strain <em>w</em>MelPop drastically reduces its <em>Drosophila melanogaster</em> host lifespan at high rearing temperatures. It is generally assumed that this feature is maintained because the <em>D. melanogaster</em>–<em>w</em>MelPop symbiosis is usually not exposed to environmental conditions in which the symbiont is virulent. To test this hypothesis, we submitted <em>w</em>MelPop-infected <em>D. melanogaster</em> lines to 17 generations of experimental evolution at a high temperature, while enforcing late reproduction. The fly survival was measured at different time points, as well as two traits that have been proposed to be causally responsible for <em>w</em>MelPop virulence: its relative density and the mean number of octomom copies present in its genome. We hypothesised that these conditions would select for a reduced <em>w</em>MelPop virulence, a reduced <em>w</em>MelPop density, and a reduced octomom copy number. Our results indicate that density, octomom copy number and virulence are correlated. However, contrary to our expectations, we could not detect any reduction in virulence during the course of evolution. We discuss the significance of our results with respect to the evolutionary causes of <em>w</em>MelPop virulence and propose that intra-host selection could explain this conundrum.</p>
Supplementary data for: Convergent reductive evolution of cyanobacteria in symbiosis with Dinophysiales dinoflagellates
<p>Supplementary data for phylogenomic analysis in "<strong>Convergent reductive evolution of cyanobacteria in symbiosis with Dinophysiales dinoflagellates</strong>" by Nakayama, T., Nomura, M., Yabuki, A., Shiba, K., Inaba, K., & Inagaki, Y. (<a href="https://www.nature.com/articles/s41598-024-63502-0">https://www.nature.com/articles/s41598-024-63502-0</a>; <a href="https://doi.org/10.1101/2024.01.11.574452">https://doi.org/10.1101/2024.01.11.574452</a>).</p> <p>The text file <code>CregCyn_phylogenomic_tree.newick</code> contains a newick formatted phylogenomic tree shown in Figure 2 of the paper. Note that the tree is unrooted.<br>The compressed file <code>phylogenomic_analysis_dataset.tar.gz</code> contains the following directories and files.</p> <ul> <li><code>concatenated_dataset.fasta </code>: dataset used for the phylogenomic analysis, constructed by combining 143 protein alignments.</li> <li><code>single_protein_datasets</code>: directory containing each orthologous protein sequence from which the concatenated dataset was derived.<br>It also contains the following subdirectories. <ul> <li><code>original_sequences</code>: contains the multi-FASTA files of the original sequences for each orthologous protein.</li> <li><code>multiple_alignments</code>: contains multiple alignments for each orthologous protein.</li> <li><code>trimmed_alignments</code>: contains multiple alignments for each protein, with positions not suitable for analysis removed. These files are combined into <code>single_protein_dataset.fasta</code>.</li> </ul> </li> </ul>
High rate of gene family evolution in close proximity to the origin of ectomycorrhizal symbiosis in Inocybaceae
<p>Annotations, aligned rthologoious gene sets and CAFE outputs used in the article "High rate of gene family evolution in close proximity to the origin of ectomycorrhizal symbiosis in Inocybaceae."</p>
Evolution of phenotypic polymorphism in symbiont-pairing in plant-fungal symbiosis
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Data from: Mutualism persistence and abandonment during the evolution of the mycorrhizal symbiosis
Mutualistic symbioses with mycorrhizal fungi are widespread in plants. The majority of plant species associate with arbuscular mycorrhizal (AM) fungi. By contrast, the minority associate with ectomycorrhizal (EM) fungi, have abandoned the symbiosis and are nonmycorrhizal (NM), or engage in an intermediate, weakly AM symbiosis (AMNM). To understand the processes that maintain the mycorrhizal symbiosis or cause its loss, we reconstructed its evolution using a ∼3,000-species seed plant phylogeny integrated with mycorrhizal state information. Reconstruction indicated that the common ancestor of seed plants most likely associated with AM fungi and that the EM, NM, and AMNM states descended from the AM state. Direct transitions from the AM state to the EM and NM states were infrequent and generally irreversible, implying that natural selection or genetic constraint could promote stasis once a particular state evolved. However, the evolution of the NM state was more frequent via an indirect pathway through the AMNM state, suggesting that weakening of the AM symbiosis is a necessary precursor to mutualism abandonment. Nevertheless, reversions from the AMNM state back to the AM state were an order of magnitude more likely than transitions to the NM state, suggesting that natural selection favors the AM symbiosis over mutualism abandonment.
Data from: Mutualism persistence and abandonment during the evolution of the mycorrhizal symbiosis
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Stepwise evolution of root nodule symbiosis
GEO Series GSE264606. Elaeagnus umbellata; Coriaria nepalensis; Alnus trabeculosa; Populus deltoides x Populus x canadensis; Chamaecrista pumila; Medicago truncatula; Mimosa pudica. 37 samples. Type: Other; Expression profiling by high throughput sequencing.
The evolution of facultative symbiosis in corals
GEO Series GSE289546. Acropora millepora; Stylophora pistillata; Oculina patagonica. 14 samples. Type: Expression profiling by high throughput sequencing.
Stepwise evolution of root nodule symbiosis [RNA-seq]
GEO Series GSE264605. Elaeagnus umbellata; Coriaria nepalensis; Alnus trabeculosa; Populus deltoides x Populus x canadensis; Mimosa pudica; Chamaecrista pumila. 35 samples. Type: Expression profiling by high throughput sequencing.
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Allen Brain Atlas
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DANDI Archive for NWB datasets
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International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.