Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
252
datasets available to search
ShareScore release 0.9.0
Dataset results
252 results for “plant evolution”
Code and data for: The evolution of ontogenetic decision-making in the wood of a clade of tropical plants
<p>Code and data for reproducing the analysis from the manuscript "The evolution of ontogenetic "decision-making" in the wood of a clade of tropical plants". Data includes raw and curated data from cell lineages derived from wood progenitor cells. Python code is provided to generate virtual wood cell lineages using L-systems. It also provides code to determine number of words at different k-mer lengths and to estimate Shannon-Entropy and Lempel-Ziv values, from the coded cell lineages. R code is provided to generate the plots and to adjust linear models of the maximum number of words based on total number of coded cells and mean cell lineage length.</p>
Data for: Microbe-induced plant resistance alters aphid inter-genotypic competition leading to rapid evolution with consequences for plant growth and aphid abundance
<p>Plants and insect herbivores are two of the most diverse multicellular groups in the world, and both are strongly influenced by interactions with the belowground soil microbiome. Effects of reciprocal rapid evolution on ecological interactions between herbivores and plants have been repeatedly demonstrated, but it is unknown if (and how) the soil microbiome could mediate these eco-evolutionary processes on a shared host plant. We tested the role of a plant-beneficial soil bacterium (<em>Acidovorax radicis</em>) in altering eco-evolutionary interactions between different aphid genotypes (Sitobion avenae; genotypes Sickte and Fescue) feeding on barley (<em>Hordeum vulgare</em>). We measured fecundity, longevity and population growth of two aphid genotypes reared separately or together (population mixture) on three different barley varieties that were inoculated with or without <em>A. radicis</em>. Results showed that across all plant varieties <em>A. radicis</em> increased plant growth and suppressed aphid populations via reduced longevity and fecundity. The strength of effect was dependent on aphid genotype and barley variety, while the direction of effect was altered by aphid population mixture. Using Lotka-Volterra modelling, we demonstrated that while <em>A. radicis</em> inoculation decreased growth rates for both aphid genotypes it increased the competitiveness of one genotype against the other. In general, in the presence of <em>A. radicis</em>, the Fescue aphid genotype became more inhibitory of Sickte aphids, while Sickte aphids facilitated the growth of Fescue aphids. Our work demonstrates that plant rhizosphere microbiomes exert community-level influences by mediating eco-evolutionary interactions between herbivores and host plants. By altering competitive interaction outcomes among aphids and thus impacting processes such as rapid evolution, soil microbes contribute to the short- and long-term structure and functioning of terrestrial habitats.</p>
Implications of the three-dimensional chromatin organization for genome evolution in a fungal plant pathogen
<p><span>The spatial organization of eukaryotic genomes is linked to their biological functions, although it is not clear how this impacts the overall evolution of a genome. Here, we uncover the three-dimensional (3D) genome organization of the phytopathogen <em>Verticillium dahliae</em>,<em> </em>known to possess distinct genomic regions, designated adaptive genomic regions (AGRs), enriched in transposable elements and genes that mediate host infection. Short-range DNA interactions form clear topologically associating domains (TADs) with gene-rich boundaries that show reduced levels of gene expression and reduced genomic variation. Intriguingly, TADs are less clearly insulated in AGRs than in the core genome. At a global scale, the genome contains bipartite long-range interactions, particularly enriched for AGRs and more generally containing segmental duplications. Notably, the patterns observed for <em>V. dahliae </em>are also present in other <em>Verticillium</em> species. Thus, our analysis links 3D genome organization to evolutionary features conserved throughout the <em>Verticillium</em> genus.</span></p>
Host developmental stages shape the evolution of a plant RNA virus
<p>Datasets used in the generation of figures 1 and 2 of:</p> <p>Melero, I., González, R., Elena, S.F. 2022. Host developmental stages shape the evolution of a plant RNA Virus. Philos. Trans. R. Soc. B doi: 10.1098/rtsb.2022.0005</p>
Data from: How important are functional and developmental constraints on phenotypic evolution? An empirical test with the stomatal anatomy of flowering plants
<p>Quantifying the relative contribution of functional and developmental constraints on phenotypic variation is a longstanding goal of macroevolution, but it is often difficult to distinguish different types of constraints. Alternatively, selection can limit phenotypic (co)variation if some trait combinations are generally maladaptive. The anatomy of leaves with stomata on both surfaces (amphistomatous) presents a unique opportunity to test the importance of functional and developmental constraints on phenotypyic evolution. The key insight is that stomata on each leaf surface encounter the same functional and developmental constraints, but potentially different selective pressures because of leaf asymmetry in light capture, gas exchange, and other features. Independent evolution of stomatal traits on each surface implies that functional and developmental constraints alone likely do not explain trait covariance. Packing limits on how many stomata can fit into a finite epidermis and cell-size-mediated developmental integration are hypothesized to constrain variation in stomatal anatomy. The simple geometry of the planar leaf surface and knowledge of stomatal development makes it possible to derive equations for phenotypic (co)variance caused by these constraints and compare them with data. We analyzed evolutionary covariance between stomatal density and length in amphistomatous leaves from 236 phylogenetically independent contrasts using a robust Bayesian model. Stomatal anatomy on each surface diverges partially independently, meaning that packing limits and developmental integration are not sufficient to explain phenotypic (co)variation. Hence, (co)variation in ecologically important traits like stomata arises in part because there is a limited range of evolutionary optima. We show how it is possible to evaluate the contribution of different constraints by deriving expected patterns of (co)variance and testing them using similar but separate tissues, organs, or sexes.</p>
Data and reproducible code for Honor et al: Direct and indirect fitness effects of competition limit evolution of allelopathy in an invading plant
<p><span>Upon introduction to new continents, invading species encounter novel communities of consumers, pathogens, and competitors. Both phenotypic plasticity and rapid evolution can facilitate adaptation across these heterogenous communities, facilitating further invasion. However, the rate and extent of adaptive evolution on contemporary timescales can be constrained by phenotypic plasticity and limits imposed by genetic co-variation for traits under selection.</span></p> <p><span>We measured phenotypic plasticity and quantified genetic co-variation for growth, competition, and fitness among </span>23 naturally inbred seed families <span>of <em>Alliaria petiolata</em> (garlic mustard) </span>collected across its invasive range in eastern North America. After growing a self-pollinated generation in a uniform common garden to reduce maternal effects, we reared second-generation plants in a <span>two-year greenhouse and field experiment with naïve soil from an uninvaded habitat. W</span>e measured selection gradients and lifetime fitness when reared alone, with an intraspecific competitor, and under interspecific competition with naïve <em>Acer saccharum </em>(sugar maple) saplings.</p> <p>Total glucosinolate production was strongly correlated with the production of chlorophyll a (Chl a) (<em>R<sup>2</sup></em> = 0.45) such that first principal component (PC1) accounted for 84% of variation in these two traits. Furthermore, PC1 exhibited high plasticity across growing environments (p < 0.001) with limited broad-sense heritability (<em>H<sup>2</sup> </em>= 2.91; p = 0.08). In contrast, investment in glucosinolate production relative to Chl a (PC2) was significantly heritable (<em>H</em><sup><em>2</em> </sup>=16.91, p < 0.001) with minimal plasticity across treatments. Causal analysis revealed that plastic variation for higher Chl a + glucosinolate production (PC1) had an indirect positive effect on A. petiolata fitness via a direct, negative effect on <em>A. saccharum</em> performance. In contrast, heritable variation for higher glucosinolate investment (PC2) had a direct, positive effect on <em>A. saccharum</em> performance and an indirect negative effect on A. petiolata fitness. </p> <p>Applying causal inference, we find that evolution of allelopathy in <em>A. petiolata</em> has been constrained by (i) a lack of genetic variation, (ii) selection against glucosinolate investment under interspecific competition, and (iii) phenotypic plasticity. These factors limit adaptive evolution but maintain fitness during population growth as plants switch from interspecific to intraspecific competition during invasion.</p>
Data from: The sequential direct and indirect effects of mountain uplift, climatic niche and floral trait evolution on diversification dynamics in an Andean plant clade
<p><span>Why and how organismal lineages radiate is commonly studied through either assessing abiotic factors (biogeography, geomorphological processes, climate) or biotic factors (traits, interactions). Despite increasing awareness that both abiotic and biotic processes may have important joint effects on diversification dynamics, few attempts have been made to quantify the relative importance and timing of these factors, and their potentially interlinked direct and indirect effects, on lineage diversification.</span></p> <p><span>We here combine assessments of historical biogeography, geomorphology, climatic niche, vegetative and floral trait evolution to test whether these factors jointly, or in isolation, explain diversification dynamics of a Neotropical plant clade (Merianieae, Melastomataceae). After estimating ancestral areas and disparification over time in climate and trait space, we employ Phylogenetic Path Analyses as a synthesis tool to test eleven hypotheses on the individual direct and indirect effects of these factors on diversification rates.</span></p> <p><span>We find strongest support for interlinked effects of colonization of the uplifting Andes during the mid-Miocene and rapid abiotic climatic niche evolution in explaining a burst in diversification rate in Merianieae. Within Andean habitats, later disparification in floral trait space allowed for the exploitation of wider pollination niches (i.e., shifts from bee to vertebrate pollinators), but did not affect diversification rates. Our approach of including both vegetative and floral trait evolution, rare in assessments of plant diversification in general, highlights important pre-adaptations to mountain colonization, specifically woody habit and larger flowers. Overall, and in concert with the idea that ecological opportunity is a key element of evolutionary radiations, our results suggest that a combination of rapid niche evolution and pre-adapted traits were critical for the exploitation of newly available niche space in the Andes in the mid-Miocene. Further, our results emphasize the importance of incorporating both abiotic and biotic factors into the same analytical framework if we aim to quantify the relative and interlinked effects of these processes on diversification.</span></p>
Data from: Soil microbes influence the ecology and evolution of plant plasticity
Open the record for dataset details and reuse information.
Data from: How important are functional and developmental constraints on phenotypic evolution? An empirical test with the stomatal anatomy of flowering plants
Open the record for dataset details and reuse information.
Data from: Herbicidal interference: Glyphosate drives both the ecology and evolution of plant-herbivore interactions
Open the record for dataset details and reuse information.
Data from: The sequential direct and indirect effects of mountain uplift, climatic niche and floral trait evolution on diversification dynamics in an Andean plant clade
Open the record for dataset details and reuse information.
Data and reproducible code for Honor et al: Direct and indirect fitness effects of competition limit evolution of allelopathy in an invading plant
Open the record for dataset details and reuse information.
Data for: Predicting the contribution of single trait evolution to rescuing a plant population from demographic impacts of climate change
Open the record for dataset details and reuse information.
Code and data for: The evolution of ontogenetic decision-making in the wood of a clade of tropical plants
Open the record for dataset details and reuse information.
Data for: Microbe-induced plant resistance alters aphid inter-genotypic competition leading to rapid evolution with consequences for plant growth and aphid abundance
Open the record for dataset details and reuse information.
Historical biogeography of Vochysiaceae reveals an unexpected perspective of plant evolution in the Neotropics
<p>PREMISE OF THE STUDY: Despite the fast pace of exploration of the patterns and processes influencing Neotropical plant hyperdiversity, taxa explored are mostly from large groups that are widely distributed, morphologically diverse or economically important. Vochysiaceae is an example of an undersampled taxon, providing an excellent system for investigating Neotropical biogeography. We present a phylogenomic-based hypothesis of species relationships in Vochysiaceae to investigate its evolutionary history through space and time.</p> <p>METHODS: We inferred a phylogeny for 122 species from Vochysiaceae and seven other families of Myrtales. Fossils from four myrtalean families were used to estimate the divergence times within Vochysiaceae. Historical biogeography was estimated using ancestral range probabilities and stochastic mapping.</p> <p>KEY RESULTS: Monophyly of all genera was supported except Qualea, which was split by Ruizterania into two clades. Vochysiaceae originated roughly 100 million years ago (Mya), splitting into an Afrotropical and a Neotropical lineage ca. 50 Mya, and its ancestral range is in the area currently occupied by the Cerrado.</p> <p>CONCLUSIONS: The most recent common ancestor of Vochysiaceae + Myrtaceae had a West Gondwanan distribution, supporting a South American + African ancestral range of Vochysiaceae. On a global scale, geographic range reduction was the principal biogeographical event. At a finer scale, initial range reduction was also important and the Cerrado region was the most ancestral area with multiple colonization events to the Amazon, Central America and the Atlantic Forest. Colonization events occurred from open areas to forest vegetation providing an unusual finding regarding evolution of plants in the Neotropics.</p>
Widespread recombination suppression facilitates plant sex chromosome evolution
<p>Classical models suggest that recombination rates on sex chromosomes evolve in a stepwise manner to localize sexually antagonistic variants in the sex in which they are beneficial, thereby lowering rates of recombination between X and Y chromosomes. However, it is also possible that sex chromosome formation occurs in regions with pre-existing recombination suppression. To evaluate these possibilities, we constructed linkage maps and a chromosome-scale genome assembly for the dioecious plant <i>Rumex hastatulus</i>. This species has a polymorphic karyotype with a young neo-sex chromosome, resulting from a Robertsonian fusion between the X chromosome and an autosome, in part of its geographical range. We identified the shared and neo-sex chromosome using comparative genetic maps of the two cytotypes. We found that sex-linked regions of both the ancestral and the neo-sex chromosome are embedded in large regions of low recombination. Furthermore, our comparison of the recombination landscape of the neo-sex chromosome to its autosomal homologue indicates that low recombination rates preceded sex linkage. These patterns are not unique to the sex chromosomes; all chromosomes were characterized by massive regions of suppressed recombination spanning most of each chromosome. This represents an extreme case of the periphery-biased recombination seen in other systems with large chromosomes. Across all chromosomes, gene and repetitive sequence density correlated with recombination rate, with patterns of variation differing between repetitive element type. Our findings suggest that ancestrally low rates of recombination may facilitate the formation and subsequent evolution of heteromorphic sex chromosomes.</p>
Data from: Living in the city: urban environments shape the evolution of a native annual plant
Urban environments are warmer, have higher levels of atmospheric CO2, and altered patterns of disturbance and precipitation than nearby rural areas. These differences can be important for plant growth and are likely to create distinct selective environments. We planted a common garden experiment with seeds collected from natural populations of the native annual plant Lepidium virginicum, growing in five urban and nearby rural areas in the northern United States to determine whether and how urban populations differ from those from surrounding rural areas. When grown in a common environment, plants grown from seeds collected from urban areas bolted sooner, grew larger, had fewer leaves, had an extended time between bolting and flowering, and produced more seeds than plants grown from seeds collected from rural areas. Interestingly, the rural populations exhibited larger phenotypic differences from one another than urban populations. Surprisingly, genomic data revealed that the majority of individuals in each of the urban populations were more closely related to individuals from other urban populations than they were to geographically proximate rural areas – the one exception being urban and rural populations from New York which were nearly identical. Taken together our results suggest that selection in urban environments favors different traits than selection in rural environments and that these differences can drive adaptation and shape population structure.
Novel plant-microbe interactions: rapid evolution of a legume-rhizobium mutualism in restored prairies
1. When plants colonize new habitats, the novel interactions they form with new mutualists or enemies can immediately affect plant performance. These novel interactions also may provoke rapid evolutionary responses and can be ideal scenarios for investigating how species interactions influence plant evolution. 2. To explore how mutualists influence the evolution of colonizing plant populations, we capitalized on an experiment in which two former agricultural fields were seeded with identical prairie seed mixes in 2010. Six years later, we compared how populations of the legume Chamaecrista fasciculata from these sites and their original (shared) source population responded to nitrogen-fixing rhizobia from the restoration sites in a greenhouse reciprocal cross-inoculation experiment. 3. We found that the two populations differed both from their original source population and from each other in the benefits they derive from rhizobia, that one population has evolved reduced allocation to rhizobia (i.e., forms fewer rhizobium-housing nodules). 4. Synthesis. Our results suggest that these plant populations have evolved different ways of interacting with rhizobia, potentially in response to differences in rhizobium quality between sites. Our study illustrates how microbial mutualists may shape plant evolution in new environments and highlights how variation in microbial mutualists potentially may select for different evolutionary strategies in plant hosts.
Data from: Combining experimental evolution and genomics to understand how seed beetles adapt to a marginal host plant
<p>Genes that affect adaptive traits have been identified, but our knowledge of the genetic basis of adaptation in a more general sense (across multiple traits) remains limited. We combined population-genomic analyses of evolve and resequence experiments, genome-wide association mapping of performance traits, and analyses of gene expression to fill this knowledge gap, and shed light on the genomics of adaptation to a marginal host (lentil) by the seed beetle <em>Callosobruchus maculatus</em>. Using population-genomic approaches, we detected modest parallelism in allele frequency change across replicate lines during adaptation to lentil. Mapping populations derived from each lentil-adapted line revealed a polygenic basis for two host-specific performance traits (weight and development time), which had low to modest heritabilities. We found less evidence of parallelism in genotype-phenotype associations across these lines than in allele frequency changes during the experiments. Differential gene expression caused by differences in recent evolutionary history exceeded that caused by immediate rearing host. Together, the three genomic data sets suggest that genes affecting traits other than weight and development time are likely to be the main causes of parallel evolution, and that detoxification genes (especially cytochrome P450s and beta-glucosidase) could be especially important for colonization of lentil by <em>C. maculatus</em>.</p>
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
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.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
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.