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Data from: Age-specific induction of mutant p53 drives clonal hematopoiesis and acute myeloid leukemia in adult mice
<p>The investigation of the mechanisms behind p53 mutations in acute myeloid leukemia (AML) has been limited by the lack of suitable mouse models, which historically have resulted in lymphoma rather than leukemia. This study introduces two new AML mouse models. One model induces mutant p53 and <em>Mdm2</em> haploinsufficiency in early development, showing the role of Mdm2 in myeloid-biased hematopoiesis and AML predisposition, independent of p53. The second model mimics clonal hematopoiesis by inducing mutant p53 in adult hematopoietic stem cells, demonstrating that the timing of p53 mutation determines AML versus lymphoma development. In this context, age-related changes in hematopoietic stem cells (HSCs), collaborates with mutant p53 to predispose towards myeloid transformation rather than lymphoma development. Our study unveils new insights into the cooperative impact of HSC age, <em>Trp53</em> mutations and <em>Mdm2</em> haploinsufficiency on clonal hematopoiesis and the development of myeloid malignancies.</p>
Gene-collapsing analysis of clonal haematopoiesis in 136,401 Admixed Americans and 416,118 Europeans
<p>We performed gene-collapsing (gene burden) analysis of germline genetic variants identified from whole-exome sequencing (WES) to identify novel inherited genetic determinants of clonal haematopoiesis (CH). Here, we provide the summary statistics from CH gene-collapsing analysis performed on Admixed Americans recruited to the Mexico City Prospective Study (MCPS), Europeans recruited to the United Kingdom Biobank (UKB), and cross-ancestry meta-analysis of Admixed Americans and Europeans. Analyses was performed with <span>Fisher'</span>s exact test (for MCPS and UKB analysis) and Cochran–Mantel–Haenszel test (for meta-analysis).</p>
Data for Isotype-aware Inference of B cell Clonal Lineage Trees from Single-cell Sequencing Data
<p>This is the accompanying data to the manuscript titled<em> Isotype-aware Inference of B cell Clonal Lineage Trees from Single-cell Sequencing Data</em>. To reproduce the TRIBAL output please use this <a href="https://doi.org/10.5281/zenodo.12741290">code repository</a> as the arguments and codebase may have changed since release. </p>
CLONALITY CONTRIBUTES TO THE SPREAD OF AVRAINVILLEA LACERATA (BRYOPSIDALES, CHLOROPHYTA) IN HAWAIʻI
<p>The excel file includes all multilocus genotypes. The first sheet includes all raw multilocus genotypes prior to allele dosage estimation. The second sheet is in GenAPoPop format and includes all multilocus genotypes after allele dosage correction using allele peak height. </p> <p>Population acronyms:</p> <p>ewaA – ʻEwa Beach, Lagoon East</p> <p>mlb – Maunalua Bay</p> <p>ewaB – ʻEwa Beach, Kaloi</p> <p>The code for each individual sampled during 2018, 2019, and 2021 is Av_sample # (01-260).</p> <p>The code for each individual sampled during 2022 is Av_3-digit sample # (001-040).</p> <p>The code for each individual sampled during 2023 is Av mound #_H holdfast #_B blade #.</p> <p> </p> <p>This project was supported by Alabama Academy of Science student research award (to BMT), the Phycological Society of America Grant In Aid of Research (to BMT), the UAB Graduate Student Government (GSG) Professional Development and Travel Award (to BMT), the UAB Harold Martin Outstanding Student Development Award (to BMT), CLONIX-2D (ANR-18-CE32-0001 to SS and SAKH), start-up funds from the College of Arts and Sciences at UAB (to SAKH and MLH), the National Science Foundation (NSF) DEB-2113745 (to SAKH), and National Fish and Wildlife Foundation (#74235 to SAKH and HLS). SAKH was supported by the NSF CAREER award DEB-2141971 and the Norma Lang Early Career Fellowship from the Phycological Society of America.</p>
Transgenerational effects of mycorrhiza are stronger in sexual than in clonal offspring of Fragaria vesca and are partly adaptive (dataset)
Open the record for dataset details and reuse information.
Table 2 in Clonal mechanisms that matter in Agave fourcroydes and A. sisalana invasions in drylands: implications for their management
<p><b>Table 2.</b> Standardized coefficients of the best-fitting Generalized Linear Mixed Models (GLMMs) explaining bulbil rooting success under the monitored conditions (natural conditions, and experimental plots). Three predictor variable types were considered (intrinsic mother plant and bulbil traits, and extrinsic bulbil traits). Species identity and plots were included as random factors. The best model was ranked according to AIC (Akaike Information Criterion) value (See also Table S5). Non-data cells indicate variables not included in a particular model.</p><table><tbody><tr><th></th><th>Intrinsic mother plant Extrinsic bulbil Extrinsic bulbil</th><th>Random factor</th></tr></tbody><tbody><tr><th>Sets of bulbils data</th><td>Intercept</td><td>traits Rosette Scape diameter height</td><td>traits Height</td><td>traits Position Buried</td><td>significance Species Plot identity</td></tr><tr><th>Monitored under natural conditions</th><td>0.936***</td><td>−0.064</td><td>0.034</td><td></td><td>0.799***</td><td>ns</td><td></td></tr><tr><th>Greenhouse plots</th><td>−3.805***</td><td></td><td></td><td>0.835***</td><td>3.427***</td><td>ns</td><td>ns</td></tr><tr><th>Natural conditions plots</th><td>−0.481***</td><td>0.124</td><td></td><td></td><td>1.897***</td><td>ns</td><td>ns</td></tr></tbody></table><p>Significance: *** <i>p-values</i> <0.001. ns: no significance</p>
Table 1 in Clonal mechanisms that matter in Agave fourcroydes and A. sisalana invasions in drylands: implications for their management
<p><b>Table 1.</b> Sampling goals, work stages and summary of data collected.</p><table><tbody><tr><th>Sampling goal</th><th>Phenology of flowering and bulbils and production of basal shoots</th><th>Estimation of bulbil production*</th><th>Estimation of shoot production from rhizomes</th><th>Estimation of rooting rates of bulbils under natural conditions</th><th>Estimation of the rooting rates of bulbils in experimental plots (greenhouse and natural conditions)*</th><th>Phenology of shoots production and rate of establishment of new individuals (rooted bulbils vs shoots from rhizomes)</th></tr></tbody><tbody><tr><th>Sampling unit</th><td>60 individuals (30 from Agave fourcroydes and 30 from | <i>A. sisalana</i>)</td><td>60 individuals (30 from Agave fourcroydes and 30 from <i>A. sisalana</i>)</td><td>8 individuals (4 from Agave fourcroydes, 4 from <i>A. sisalana</i>)</td><td>1,184 bulbils (582 from Agave fourcroydes, 602 from <i>A. sisalana</i>; 590 from early fall, 594 from late fall)</td><td>1,440 bulbils, 24 <i>from each of 60</i> individuals (30 from <i>Agave fourcroydes</i>, and 30 from <i>A. sisalana</i>)</td><td>10 plots 10 × 10 m</td></tr><tr><th>Monitored individual nature</th><td>Reproductive individuals with incipient floral scapes emerging from the rosette</td><td>Reproductive individuals with floral scapes at the stage of maximum bulbils production</td><td>Juvenile, i.e., prominent but not reproductive individuals</td><td>Mature bulbils fallen from the floral scapes</td><td>Mature bulbils fallen from the floral scapes</td><td>New young individuals</td></tr><tr><th>Traits measured</th><td>Height and</td><td>Height and</td><td>Number of</td><td>Height (cm)</td><td>Height (cm)</td><td>Origin: from</td></tr><tr><td>diameter of the rosette (cm) Height and</td><td>diameter of the rosette (cm) Height and</td><td>rhizomes Number of emerged shoots</td><td>Diameter (cm) Number of leaves</td><td>Diameter (cm) Number of leaves</td><td>rhizomes or rooted bulbils Presence of</td></tr><tr><td>diameter of the floral scape (cm)</td><td>diameter of the floral scape (cm)</td><td>from rhizomes</td><td>Number of preformed roots</td><td>Number of preformed roots</td><td>contractile roots</td></tr><tr><td>Number of scape branches</td><td>Number of bulbils by scape branches</td><td></td><td>Position (vertical or horizontal)</td><td>Rooted</td><td></td></tr><tr><td>% of branches with floral buds</td><td>Number of fallen bulbils</td><td></td><td>Buried or not</td><td></td><td></td></tr><tr><td>% of branches with flowers</td><td></td><td></td><td>Rooted</td><td></td><td></td></tr><tr><th>% of branches with bulbils</th></tr><tr><th>% of branches with fruits</th></tr><tr><th>% of branches with fallen bulbils</th></tr><tr><th>Number of basal shoots (born directly from the rosette)</th></tr><tr><th>Monitoring dates and frequency</th><td>February 2015– May 2016 (monthly)</td><td>October 2015</td><td>May–July 2015</td><td>October 2015– October 2016 (monthly)</td><td>January 2016– May 2016</td><td>February 2015– February 2016 (monthly)</td></tr></tbody></table><p>* The individuals selected for these two studies were the same.</p>
Stronger transgenerational plasticity in clonal compared to sexual offspring of Fragaria vesca: effects of drought, elevated temperature and CO2 conditions
<div>The dataset contains phenotypic data of woodland strawberry (<em>Fragaria vesca</em>) regarding its reproductive strategy, as well as climate and water availability for both parental and offspring generations.</div> <div> </div> <div><u>F1StatGPT.csv</u>: Table containing Ramet Number at Harvest, Fruit Number at Harvest, Ramet Biomass, Offspring Ramet Biomass, and Total Biomass.</div> <div><u>StomataStatGPT.csv:</u> Table containing Number of Stomata per mm² and Stomata Size.</div>
Genotype data not consistent with clonal transmission of sea turtle fibropapillomatosis or goldfish schwannoma
<p>Recent<b> </b>discoveries of transmissible cancers in multiple bivalve species suggest that direct transmission of cancer cells within species may be more common than previously thought, particularly in aquatic environments. Fibropapillomatosis occurs with high prevalence in green sea turtles (Chelonia mydas) and the geographic range of disease has increased since fibropapillomatosis was first reported in this species. Widespread incidence of schwannomas, benign tumours of Schwann cell origin, reported in aquarium-bred goldfish (Carassius auratus), suggest an infectious aetiology. We investigated the hypothesis that cancers in these species arise by clonal transmission of cancer cells. Through analysis of polymorphic microsatellite alleles, we demonstrate concordance of host and tumour genotypes in diseased animals. These results imply that the tumours examined arose from independent oncogenic transformation of host tissue and were not clonally transmitted. Further, failure to experimentally transmit goldfish schwannoma via water exposure or inoculation suggest that this disease is unlikely to have an infectious aetiology.</p>
Data - Attack of the clones: population genetics reveals clonality of Colletotrichum lupini, the causal agent of lupin anthracnose
<p><em>Colletotrichum lupini</em>, causing lupin anthracnose, is one of the worst pathogens to lupin cultivation worldwide. Understanding its population structure and evolutionary potential is crucial to design successful disease management strategies. The objective of this study was to employ population genetics to investigate the genetic diversity, evolutionary dynamics and molecular basis of host-speciation of this notorious lupin pathogen. A collection of globally representative <em>C. lupini </em>isolates was genotyped through triple digest restriction-site associated DNA sequencing (3D-RADseq), resulting in a dataset of unparalleled resolution. Phylogenetic and structural analysis could distinguish four (I – IV) independent lineages. The strong population structure, low recombination rate and slow linkage decay strongly indicate that <em>C. lupini</em> reproduces clonally. Different morphologies and virulence patterns on white and Andean lupin were observed between and within clonal lineages. Lineage II isolates were shown to have a mini chromosome which was also partly present in lineage III and IV, but not in lineage I isolates. Variation in the presence of this mini-chromosome could indicate a function related to virulence or host-speciation. All four lineages were present in the South American Andes region, which is concluded to be the center of origin of this species. Only members of lineage II have been found outside South America since the 1990s, indicating it as the current pandemic population. As a seed-borne pathogen, <em>C. lupini</em> has mainly spread through infected but symptomless seeds, stressing the importance of phytosanitary measures to prevent future outbreaks of strains that are yet confined to South America.</p>
Genet dynamics and its variation among genets of a clonal plant Convallaria keiskei
<p><span>In clonal plant populations, a number of genetically identical ramets form a genet. While coexisting ramets potentially perform independently, their behaviours not only depend on ages and sizes but are also constrained by genetic background. In this study, genet dynamics and its variability among neighbouring genets were investigated based on the ramet demography of each genet in <em>Convallaria</em> <em>keiskei</em>. Genet dynamics were first formulated as a matrix model with the two components of clonal growth (clonal reproduction) and survival-transitions between ramet size classes. Then, a statistical estimation of the matrix elements was established using three datasets: aboveground demographic censuses, belowground directional rhizomatous connections and genetic identification of ramets. Finally, genet growth rates reflecting both the changes of clonal growth and ramet size growth were estimated and compared for fundamental demographic elements among genets. Over three years of aboveground annual censuses of a 28 × 2 m plot, 2,021 ramets were identified as belonging to 28 genotypes. Belowground excavation detected 515 clonal fragments. Genet growth rate of three dominant genets varied with medians of 1.13, 1.02 and 1.05; 95% credible intervals of the posterior distributions did not overlap between the genet with the largest median and the others. The variation was caused primarily by differences in clonal growth rather than survival-transitions between size classes. Clonal growth by branching was rarer than at the tips but contributed to the maintenance of the genet. Therefore, both clonal growth frequencies and connecting patterns of ramets caused the variation of genet dynamics and established genets persist for a long time through the positive growth rates, which would contribute to maintaining a population. We also conclude that fundamental demographic elements relating to clonal growth traits (the features of individual genets) strongly impact genet dynamics.</span></p>
[Data S2] Microbiota dictate T cell clonal selection to augment graft-vs-host disease after stem cell transplantation
<p><strong>Data</strong> <strong>S2. GLIPH2 hits for all recipient pairs amongst B6 to B6D2F1 transplants with or without antibiotic exposure and 900cGy vs. 1300cGy TBI conditioning. </strong>For all TCRs within each recipient pair (12 mice total, 66 pairs for spleen; 15 pairs for SILP analysis), GLIPH2 specificity groups are generated as described in methods.</p>
[Data S1] Microbiota dictate T cell clonal selection to augment graft-vs-host disease after stem cell transplantation
<p><strong>Data S1. ALICE hits for all recipient pairs amongst B6 to B6D2F1 transplants with or without antibiotic exposure and 900cGy vs. 1300cGy TBI conditioning. </strong>For each recipient pair (12 mice total, 66 pairs for spleen; 15 pairs for SILP analysis), all ALICE hits generated as described in methods.</p>
[Github Sample Dataset] Microbiota dictate T cell clonal selection to promote graft-vs-host disease after stem cell transplantation
<p>[Github Sample Dataset]. This is an accompanying data set for the github repository "<em>https://github.com/acyeh-lab/2023/tree/main/tcr-simulation" referred to in "</em>Non-genetic determinants of clonotypic T cell expansion following stem cell transplantation" by Yeh AC et al.</p>
Clonally related, Notch-differentiated spinal neurons integrate into distinct circuits EPhys raw data
<p>Shared lineage has diverse effects on patterns of neuronal connectivity. In mammalian cortex, excitatory sister neurons assemble into shared microcircuits, whereas throughout the <em>Drosophila</em> nervous system, Notch-differentiated sister neurons diverge into distinct circuits. Notch-differentiated sister neurons have been observed in vertebrate spinal cord and cerebellum, but whether they integrate into shared or distinct circuits remains unknown. Here we evaluate the connectivity between sister V2a/b neurons in the zebrafish spinal cord. Using an <em>in</em> <em>vivo</em> labeling approach, we identified pairs of sister V2a/b neurons born from individual Vsx1+ progenitors and observed that they have similar axonal trajectories and proximal somata. However, paired whole-cell electrophysiology and optogenetics revealed that sister V2a/b neurons receive input from distinct presynaptic sources, do not communicate with each other, and connect to largely distinct targets. These results resemble the divergent connectivity in <em>Drosophila</em> and represent the first evidence of Notch-differentiated circuit integration in a vertebrate system.</p>
Klebsiella pneumonia in Sudan: Multidrug Resistance, Poly-clonal Dissemination and Virulence
<p>Minimum spanning tree (MST) of 84 <em>K. pneumoniae</em> by hospital information. Ridom SeqSphere+ MST for 84 samples based on 2358 columns, pairwise ignoring missing values, logarithmic scale. Cluster distance threshold: 15. Isolates grouped by colour indicating the different hospitals . Samples were collected from five different hospitals, 37 different STs were identified, in addition to 14 transmission clusters, represented by shaded nodes and arrows. Numbers between the nodes indicate the number of allelic differences.</p>
Data from: Effective population size in a partially clonal plant is not predicted by the number of genetic individuals
<p>Estimating effective population size (<em>N</em><sub>e</sub>) is important for theoretical and practical applications in evolutionary biology and conservation. Nevertheless, estimates of <em>N</em><sub>e</sub> in organisms with complex life-history traits remain scarce because of the challenges associated with estimation methods. Partially clonal plants capable of both vegetative (clonal) growth and sexual reproduction are a common group of organisms for which the discrepancy between the apparent number of individuals (ramets) and the number of genetic individuals (genets) can be striking, and it is unclear how this discrepancy relates to <em>N</em><sub>e</sub>.</p> <p>In this study, we analysed two populations of the orchid <em>Cypripedium calceolus</em> to understand how the rate of clonal vs. sexual reproduction affected <em>N</em><sub>e</sub>. We genotyped >1,000 ramets at microsatellite and SNP loci, and estimated contemporary <em>N</em><sub>e</sub> with the linkage disequilibrium method, starting from the theoretical expectation that variance in reproductive success among individuals caused by clonal reproduction and by constraints on sexual reproduction would lower <em>N</em><sub>e</sub>. We considered factors potentially affecting our estimates, including different marker types and sampling strategies, and the influence of pseudoreplication in genomic datasets on <em>N</em><sub>e</sub> confidence intervals. The magnitude of <em>N</em><sub>e</sub>/<em>N</em><sub>ramets </sub>and <em>N</em><sub>e</sub>/<em>N</em><sub>genets</sub> ratios we provide may be used as reference points for other species with similar life-history traits. Our findings demonstrate that <em>N</em><sub>e</sub> in partially clonal plants cannot be predicted based on the number of genets generated by sexual reproduction, because demographic changes over time can strongly influence <em>N</em><sub>e</sub>. This is especially relevant in species of conservation concern, in which population declines may not be detected by only ascertaining the number of genets.</p>
Code and Output data associated with M.E. Orive, M, Barfield, R.D. Holt. Partial clonality expands the opportunity for spatial adaptation. Submitted to The American Naturalist.
<p>This contains the source code, all output files and sample input files used to create the graphs in the manuscript " M.E. Orive, M, Barfield, R.D. Holt. Partial clonality expands the opportunity for spatial adaptation," submitted to The American Naturalist. The readme.rtf file summarizes the manuscript, lists all code files and output files, and explains the output file format and which output data was used, organized by figure number.</p>
Conditional indirect genetic effects of caregivers on brood in the clonal raider ant
<p>Caregivers shape the rearing environment of their young. Consequently, offspring traits are influenced by the genes of their caregivers via indirect genetic effects (IGEs). However, the extent to which IGEs are modulated by environmental factors, other than the genotype of social partners (i.e., intergenomic epistasis), remains an open question. Here we investigate how broods are influenced by the genotype of their caregivers in the clonal raider ant, <em>Ooceraea biroi</em>, a species in which the genotype, age, and number of both caregivers and brood can be experimentally controlled. First, we used four clonal lines to establish colonies that differed only in the genotype of caregivers and measured effects on foraging activity, as well as IGEs on brood phenotypes. In a second experiment, we tested whether these IGEs are conditional on the age and number of caregivers. We found that caregiver genotype affected the feeding and foraging activity of colonies, and influenced the rate of development, survival, body size, and caste fate of brood. Caregiver genotype interacted with other factors to influence the rate of development and survival of brood, demonstrating that IGEs can be conditional. Thus, we provide an empirical example of phenotypes being influenced by IGE-by-environment interactions beyond intergenomic epistasis, highlighting that IGEs of caregivers/parents are alterable by factors other than their brood's/offspring's genotype.</p>
Data from: Maintenance and expansion of genetic and trait variation following domestication in a clonal crop: Enset tGBS individual genotype data
<p class="MsoNormal">Clonal propagation enables favourable crop genotypes to be rapidly selected and multiplied. However, the absence of sexual propagation can lead to low genetic diversity and accumulation of deleterious mutations, which may eventually render crops less resilient to pathogens or environmental change. To better understand this trade-off, we characterise the domestication and contemporary genetic diversity of Enset (<em>Ensete ventricosum</em>), an indigenous African relative of bananas (<em>Musa</em>) and principal starch staple for 20 million Ethiopians. Wild enset is strictly sexually outcrossing, but in cultivation is propagated clonally and associated with diversification and specialisation into hundreds of named landraces. We applied tGBS sequencing to generate genome-wide genotypes for 192 accessions from across enset's cultivated distribution, and surveyed 1340 farmers on enset agronomic traits. Overall, reduced heterozygosity in the domesticated lineage was consistent with a domestication bottleneck that retained 37% of wild diversity. However, an excess of putatively deleterious missense mutations at low frequency present as heterozygotes suggested accumulation of mutational load in clonal domesticated lineages. Our evidence indicates that the major domesticated lineages initially arose through historic sexual recombination associated with a domestication bottleneck, followed by amplification of favourable genotypes through an extended period of clonal propagation. Among domesticated lineages we found significant phylogenetic signal for multiple farmer-identified food, nutrition and disease resistance traits and little evidence of contemporary recombination. Development of future-climate adapted genotypes may require crop breeding, but outcrossing risks exposing deleterious alleles as homozygotes. This trade-off may partly explain the ubiquity and persistence of clonal propagation over recent centuries of comparative climate stability.</p>
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Allen Brain Atlas
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Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
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