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15 results for “colonization success”
Input data and Supplementary Results for "Turnover in life-strategies recapitulates marine microbial succession colonizing model particles"
<p><strong>README</strong></p> <p>This page contains processed input data used for downstream analysis and some Supplementary Results for the paper:</p> <p>Pascual-García, A., Schwartzman, J., Enke, T.N., Iffland-Stettner, A., Cordero, O.X., Bonhoeffer, S., Turnover in life-strategies recapitulates marine microbial succession colonizing model particles (2022).</p> <p> </p> <p><strong>Input data</strong></p> <p> </p> <ul> <li> <p>File <em>“count_table.ESV.biom”</em>: Table containing the abundance of each Exact Sequence Variant (ESV) in the different samples (biom format).</p> </li> <li> <p>File <em>“count-table_</em><em>metagenomes</em><em>_KEGGs.L3.spf”</em>. Table containing the abundances of genes found in the shotgun metagenomics experiments annotated in KEGG and then aggregated into classes according to the finest classification in KEGG's hierarchy (level 3). This is a tsv-formatted file that can be directly used in STAMP to perform statistical analysis (spf format).</p> </li> <li> <p>File <em>“count-table_</em><em>PICRUST2</em><em>_KEGGs.L3.spf</em>”. Table containing the abundances of genes predicted with PICRUSt v2. These genes were annotated in KEGG and aggregated into classes according to the finest hierarchy in KEGG (level 3). This is a tsv-formatted file that can be directly used in STAMP to perform statistical analysis (spf format).</p> </li> <li> <p>File <em>“count-table_Isolates_KEGGs.L3.spf</em>”. Table containing the abundances of genes found in the isolates genomes that were annotated in KEGG and aggregated into classes according to the finest classification in KEGG's hierarchy (level 3). This is a tsv-formatted file that can be directly used in STAMP to perform statistical analysis (spf format).</p> </li> <li> <p>File <em>“samples_metadata.tsv”</em>. Metadata table describing the samples.</p> </li> <li> <p>File <em>“isolates_metadata.tsv”.</em> Metadata table describing the isolates, it includes shallow phylogenetic levels and a categorical identifier describing the environmental preference estimated for the ESV having a 100% sequence identity with a ZINB-GLM.</p> </li> <li> <p>File <em>“sequences.ESV.</em><em>fasta</em><em>”.</em> File containing the Exact Sequence Variants fasta.</p> </li> </ul> <p><strong>Supplementary Materials</strong></p> <p> </p> <ul> <li> <p>File <em>“qiime2_visualizations.zip”</em>. A file containing visualizations compatible with the qiime2 viewer (simply drag and drop the file in <a href="https://view.qiime2.org/">https://view.qiime2.org/</a>) for each sample or combination of samples, labelled as `$substrate.$medium.$replicate`, where `$medium = {Beads, Seawater}` and `$replicate = {A,B,C}`. If the label is not present for one field, it means that all samples are aggregated for that field e.g.:</p> <ul> <li> <p>“<em>count_table.ESV.Chitosan.Beads.A.bar-plots.</em><em>qzv”</em> Contains the replicate experiment A for communities on the synthetic beads in chitosan.</p> </li> <li> <p>“<em>count_table.ESV.Chitosan.bar-plots.</em><em>qzv”</em> Contains all samples in chitosan (both seawater communities and the three replicates of communities on the beads).</p> </li> </ul> </li> <li> <p>File <em>“README.odt”</em>. This readme in libreoffice format.</p> </li> <li> <p>File <em>“</em><em>Genome_deposition_information.xlsx”. </em> NCBI identifiers for the isolates’ genomes.</p> </li> <li> <p>File "barcodes_to_samples_MGRAST.xlsx". Contains the barcodes of each sample and its metadata as it was deposited in MG-RAST. In a second tab, there is a subset of samples with a low number of reads that MG-RAST analyzed together, generating a single entry (termed "mixed").</p> </li> <li> <p>Access to raw an processed metagenomes and analysis are provided through MG-RAST following [this link](<a href="https://www.mg-rast.org/mgmain.html?mgpage=project&project=mgp85635">https://www.mg-rast.org/mgmain.html?mgpage=project&project=mgp85635</a>).</p> <ul> <li> <p>As of May 30th, 2022, there are two issues with the dataset in MG-RAST which are out of our scope to solve. We will report any update here. The first problem is related to the entry TCCTGAGC-GTAAGGAG-s_2_, which does not load in MG-RAST. These are very low samples and were discarded in most analyses. In addition, you will find in the metadata 17 metagenomes that do not belong to our project.</p> </li> </ul> </li> </ul>
Data from: Genomic signature of successful colonization of Eurasia by the allopolyploid shepherd's purse (Capsella bursa-pastoris)
Polyploidization is a dominant feature of flowering plant evolution. However, detailed genomic analyses of the inter-population diversification of polyploids following genome duplication are still in their infancy, mainly because of methodological limits, both in terms of sequencing and computational analyses. The shepherd's purse (Capsella bursa-pastoris) is one of the most common weed species in the world. It is highly self-fertilizing, and recent genomic data indicate that it is an allopolyploid, resulting from hybridization between the ancestors of the diploid species Capsella grandiflora and Capsella orientalis. Here, we investigated the genomic diversity of C. bursa-pastoris, its population structure and demographic history, following allopolyploidization in Eurasia. To that end, we genotyped 261 C. bursa-pastoris accessions spread across Europe, the Middle East and Asia, using genotyping-by-sequencing, leading to a total of 4,274 SNPs after quality control. Bayesian clustering analyses revealed three distinct genetic clusters in Eurasia: one cluster grouping samples from Western Europe and Southeastern Siberia, the second one centered on Eastern Asia and the third one in the Middle East. Approximate Bayesian computation (ABC) supported the hypothesis that C. bursa-pastoris underwent a typical colonization history involving low gene flow among colonizing populations, likely starting from the Middle East towards Europe and followed by successive human-mediated expansions into Eastern Asia. Altogether, these findings bring new insights into the recent multistage colonization history of the allotetraploid C. bursa-pastoris and highlight ABC and genotyping-by-sequencing data as promising but still challenging tools to infer demographic histories of selfing allopolyploids.
An interaction between host and microbe genotypes determines colonization success of a key bumble bee gut microbiota member
<p><span>There has been a proliferation of studies demonstrating an organism's health is influenced by its microbiota. However, factors influencing beneficial microbe colonization and the evolution of these relationships remain understudied relative to host-pathogen interactions. Vertically transmitted beneficial microbes are predicted to show high levels of specificity in colonization, including genotype matching, which may transpire through coevolution. We investigate how host and bacterial genotypes influence colonization of a core coevolved microbiota member in bumble bees. The hindgut colonizing </span><i>Snodgrassella alvi</i><span> confers direct benefits, but, as an early colonizer, also facilitates the further development of a healthy microbiota. Due to predominantly vertical transmission promoting tight evolution between colonization factors of bacteria and host lineages, we predict that genotype-by-genotype interactions will determine successful colonization. Germ-free adult bees from seven bumble bee colonies (host genotypic units) were inoculated with one of six genetically distinct strains of </span><i>S. alvi</i><span>. Subsequent colonization within host-genotype and microbe-genotype combinations ranged from zero to one hundred percent, and an interaction between host and microbe genotypes determined colonization success. This novel finding of a genotype-by-genotype interaction determining colonization in an animal host-beneficial microbe system has implications for the ecological and evolutionary dynamics of host and microbe,</span><i> </i><span>including associated host-fitness benefits. </span></p>
Data from: Hybridization alters early life-history traits and increases plant colonization success in a novel region
Hybridization is hypothesized to promote invasiveness, but empirical tests comparing the performance of hybrid versus parental taxa in novel regions are lacking. We experimentally compared colonization ability of populations of wild radish (Raphanus raphanistrum) versus populations of advanced-generation hybrids between wild and cultivated radish (R. sativus) in a southeast Texas pasture, well beyond the known invasive range of hybrid radish. We also manipulated the strength of interspecific competition to better generalize across variable environments. In both competitive environments, hybrid populations produced at least three times more seeds than wild radish populations, a distinction that was driven by greater hybrid seedling emergence, earlier hybrid emergence and more hybrid seedlings surviving to flower, rather than by greater individual fecundity. Flowering duration in hybrids was less negatively affected by competition than it was in wild radishes, while early emergence was associated with subsequent high seed output in both biotypes. Our data show that hybridization can enhance colonization success in a novel region, and, by comparison with previous studies, that the life-history traits enhancing hybrid success can differ across regions, even for lineages originating from the same hybridization event. These results imply a much larger arena for hybrid success than previously appreciated.
Data from: Invasion success in polyploids: the role of inbreeding in the contrasting colonization abilities of diploid versus tetraploid populations of Centaurea stoebe s.l
As a consequence of founder effects, inbreeding can hamper colonization success: First, in species with self-incompatibility controlled by an S-locus, inbreeding may decrease cross-compatibility, mainly due to the sharing of identical S-alleles between closely related mating partners. Secondly, inbreeding can reduce fitness of inbred relative to outbred offspring (i.e. inbreeding depression). Polyploids often show reduced inbreeding depression compared to diploids, which may contribute to the overrepresentation of polyploids among invasive species. This is the first study that tests how the effects of inbreeding differ between geocytotypes (i.e. ploidy levels within a given range). Our model organism, Centaurea stoebe, is strictly self-incompatible and comprises three geocytotypes: diploids are more frequent than tetraploids in the native range, while only tetraploids occur in the invasive range. We conducted a breeding experiment (sib-mating vs. outcrossing) with 14 native diploid, 13 native tetraploid and 15 invasive tetraploid populations. We recorded cross-compatibility and estimated a cumulative index for offspring fitness. Since frequent inbreeding can result in purging of genetic load responsible for inbreeding depression, our analyses included a metric for within-population relatedness, based on eight microsatellite markers, to assess the effect of purging. Inbreeding was found to reduce cross-compatibility, which was similarly pronounced in diploids and tetraploids. It also caused inbreeding depression in cumulative fitness, which was significant in diploids but not in tetraploids. No evidence of purging was observed as inbred fitness was not affected by within-population relatedness. Synthesis. Our results provide new insights into the contrasting invasion success of the cytotypes of C. stoebe. As the effects of cross-compatibility and purging were comparable between cytotypes, both processes can be ruled out to affect the colonization success of diploids versus tetraploids. Our findings are consistent with the hypothesis that polyploidy increases the masking of recessive mutations, which maintains high fitness in inbred tetraploids and may thus facilitate colonization of new ranges. We highlight that reduced inbreeding depression may add to previously acknowledged advantages of polyploids in range expansions, a mechanism that may hitherto have been underestimated due to a lack of data on variation in inbreeding depression across geocytotypes.
Distribution. Natural distribution now restricted to West and East Franklin Is, Nuyts Archipelago, South Australia. From 1990, successful introductions (assisted colonization) from there to Salutation I, W Western Australia, and to Reevesby I and Saint Peter I, South Australia; also reintroduced to predator-exclosures at Mt Gibson Sanctuary, Western Australia, Arid Recovery Reserve, Roxby Downs, South Australia, and Scotia Sanctuary, New South Wales. Attempted reintroduction to Faure I, Western Australia, failed. in Muridae
Distribution. Natural distribution now restricted to West and East Franklin Is, Nuyts Archipelago, South Australia. From 1990, successful introductions (assisted colonization) from there to Salutation I, W Western Australia, and to Reevesby I and Saint Peter I, South Australia; also reintroduced to predator-exclosures at Mt Gibson Sanctuary, Western Australia, Arid Recovery Reserve, Roxby Downs, South Australia, and Scotia Sanctuary, New South Wales. Attempted reintroduction to Faure I, Western Australia, failed.
Data from: Genomic signature of successful colonization of Eurasia by the allopolyploid shepherd’s purse (Capsella bursa-pastoris)
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An interaction between host and microbe genotypes determines colonization success of a key bumble bee gut microbiota member
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Data from: Hybridization alters early life-history traits and increases plant colonization success in a novel region
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Data from: Asymmetric dispersal and colonization success of Amazonian plant-ants queens
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Data from: Reproductive success of captively bred and naturally spawned Chinook salmon colonizing newly accessible habitat
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Data from: Invasion success in polyploids: the role of inbreeding in the contrasting colonization abilities of diploid versus tetraploid populations of Centaurea stoebe s.l
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Data from: Role of propagule pressure in colonization success: disentangling the relative importance of demographic, genetic and habitat effects
High propagule pressure is arguably the only consistent predictor of colonization success. More individuals enhance colonization success because they aid in overcoming demographic consequences of small population size (e.g. stochasticity and Allee effects). The number of founders can also have direct genetic effects: with fewer individuals, more inbreeding and thus inbreeding depression will occur, whereas more individuals typically harbour greater genetic variation. Thus, the demographic and genetic components of propagule pressure are interrelated, making it difficult to understand which mechanisms are most important in determining colonization success. We experimentally disentangled the demographic and genetic components of propagule pressure by manipulating the number of founders (fewer or more), and genetic background (inbred or outbred) of individuals released in a series of three complementary experiments. We used Bemisia whiteflies and released them onto either their natal host (benign) or a novel host (challenging). Our experiments revealed that having more founding individuals and those individuals being outbred both increased the number of adults produced, but that only genetic background consistently shaped net reproductive rate of experimental populations. Environment was also important and interacted with propagule size to determine the number of adults produced. Quality of the environment interacted also with genetic background to determine establishment success, with a more pronounced effect of inbreeding depression in harsh environments. This interaction did not hold for the net reproductive rate. These data show that the positive effect of propagule pressure on founding success can be driven as much by underlying genetic processes as by demographics. Genetic effects can be immediate and have sizable effects on fitness.
Data from: Role of propagule pressure in colonization success: disentangling the relative importance of demographic, genetic and habitat effects
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Additional information for Biofilm colonization and succession in a full-scale partial nitritation-anammox moving bed biofilm reactor
<p>Here we include additional files for Suarez <em>et al</em>. <strong>Biofilm colonization and succession in a full-scale partial nitritation-anammox moving bed biofilm reactor</strong></p> <p>Files included here:</p> <ul> <li><strong>MAG_annotations_EUK.tsv</strong>. Genome annotation of eukaryotic MAGs made with eggnog-mapper v2.1.9. </li> <li><strong>MAG_annotations_PROK.tsv</strong>. Genome annotation of bacterial and Archaeal MAGs made with eggNOG-mapper v2.1.9</li> </ul> <p>Metagenome reads and MAGs have been deposited at the European Nucleotide Archive (ENA) under accession PRJEB58181.</p>
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