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120 results for “plant phenotyping”
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 from: Population divergence in heat and drought responses of a coastal plant: from metabolic phenotypes to plant morphology and growth
<p>This dataset supports the article "Population divergence in heat and drought responses of a coastal plant: from metabolic phenotypes to plant morphology and growth", which is under minor revision in Journal of Experimental Botany. The study addresses the combined effects of and plant population origin, drought and heat stress on plant growth, plant morphology and the leaf metabolome. The data were assessed in Northern and Southern European individuals of <em>Cakile maritma</em> (See Rocket). An R-script containing all statistical analyses that have been implemented with these data is also provided.</p>
Data from: How important are functional and developmental constraints on phenotypic evolution? An empirical test with the stomatal anatomy of flowering plants
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Unveiling the genetic networks: Exploring the dynamic interaction of photosynthetic phenotypes in woody plants across varied light gradients
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Data from: Testing the evolutionary potential of an alpine plant: Phenotypic plasticity in response to growth temperature outweighs parental environmental effects and other genetic causes of variation
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Data from: Population divergence in heat and drought responses of a coastal plant: from metabolic phenotypes to plant morphology and growth
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Long-term experimental drought alters floral scent and pollinator visits in a Mediterranean plant community despite overall limited impacts on plant phenotype and reproduction
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Phenotypic divergence of traits that mediate antagonistic and mutualistic interactions between island and continental populations of the tropical plant, Tribulus cistoides (Zygophyllaceae)
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Contrasting effects of two phenotypes of an alpine cushion plant on understory species drive community assembly
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Data from: Floral scents of a deceptive plant are hyperdiverse and under population-specific phenotypic selection
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Data from: Linking divergence in phenotypic selection on floral traits to divergence in local pollinator assemblages in a pollination-generalized plant
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Phenotypic and genotypic divergence of plant-herbivore interactions along an urbanization gradient
<p class="MsoNormal"><span>Urban environments provide challenging conditions for species survival, including increased temperatures, drought, and pollution. Species can deal with these conditions through evolution across generations or the immediate expression of phenotypic plasticity. The resulting phenotypic changes are key to the performance of species and their interactions with other species in the community. We here document patterns of herbivory in <em>Arabidopsis thaliana</em> along a rural-urban gradient, and tested the genetic background and ecological consequences of traits related to herbivore resistance. Aphid densities increased with urbanization levels along the gradient while plant size did not change. Offspring of urban mothers, raised under common garden conditions, were larger and had a decreased trichome density and seed set but a higher caterpillar (<em>Pieris brassicae</em>) tolerance. In contrast, no urban evolution was detected for defenses against aphids (<em>Myzus persicae</em>). Aphids reduced seed set more strongly in urban offspring, but this effect disappeared in second-generation plants. In general, urban adaptations as expressed in size and caterpillar tolerance were found, but these adaptations were associated with smaller inflorescences. The maternal effect on the response of seed set to aphid feeding demonstrates the relevance of intergenerational plasticity as a direct ecological consequence of herbivory. Our study demonstrates that the urban environment interacts with the plant's genotype and the extended phenotype as determined by ecological interactions.</span></p>
Unraveling the roles of genotype and environment in the expression of plant defense phenotypes
<p>1. Phenotypic variability results from interactions between genotype and environment and is a major driver of ecological and evolutionary interactions. Measuring the relative contributions of genetic variation, the environment, and their interaction to phenotypic variation remains a fundamental goal of evolutionary ecology.</p> <p>2. In this study, we assess the question: How do genetic variation and local environmental conditions interact to influence phenotype within a single population? We explored this question using seed from a single population of common milkweed, <i>Asclepias syriaca</i>, in northern Michigan. We first measured resistance and resistance traits of 14 maternal lines in two common garden experiments (field and greenhouse) to detect genetic variation within the population. We carried out a reciprocal transplant experiment with three of these maternal lines to assess effects of local environment on phenotype. Finally, we compared the phenotypic traits measured in our experiments with the phenotypic traits of the naturally-growing maternal genets to be able to compare relative effect of genetic and environmental variation on naturally-occurring phenotypic variation. We measured defoliation levels, arthropod abundances, foliar cardenolide concentrations, foliar latex exudation, foliar carbon and nitrogen concentrations, and plant growth.</p> <p>3. We found a striking lack of correlation in trait expression of the maternal lines between the common gardens, or between the common gardens and the naturally-growing maternal genets, suggesting that environment plays a larger role in phenotypic trait variation of this population. We found evidence of significant genotype-by-environment interactions for all traits except foliar concentrations of nitrogen and cardenolide. Milkweed resistance to chewing herbivores was associated more strongly with the growing environment. We observed no variation in foliar cardenolide concentrations among maternal lines but did observe variation among maternal lines in foliar latex exudation.</p> <p>4. Overall, our data reveal powerful genotype-by-environment interactions on the expression of most resistance traits in milkweed.</p>
Study of the genetic and phenotypic variation among wild and cultivated clary sages provides interesting avenues for breeding programs of a perfume, medicinal and aromatic plant
<p>A road-map of the genetic and phenotypic diversities in both crops and their wild-related species can help identifying valuable genetic resources for further crop breeding. The clary sage (<em>Salvia sclarea L.</em>), a perfume, medicinal and aromatic plant, is used for sclareol production and ornamental purposes. Despite its wide use in the field of cosmetics, the phenotypic and genetic diversity of wild and cultivated clary sage remains to be explored. We characterized the genetic and phenotypic variation of a collection of six wild <em>S. sclarea</em> populations from Croatia, sampled along an altitudinal gradient, and of populations of three <em>S. sclarea</em> cultivars. We showed low level of genetic diversity for the two <em>S. sclarea</em> traditional cultivars used for essential oil production and for ornamental purposes, respectively. In contrast, a recent cultivar resulting from new breeding methods, which involve hybridizations among several genotypes rather than traditional recurrent selection and self-crosses over time, showed high genetic diversity. We also observed a marked phenotypic differentiation for the ornamental clary sage compared with other cultivated and wild clary sages. Instead, the two cultivars used for essential oil production, a traditional and a recent, respectively, were not phenotypically differentiated from the wild Croatian populations. Our results also featured some wild populations with high sclareol content and early-flowering phenotypes as good candidates for future breeding programs. This study opens up perspectives for basic research aiming at understanding the impact of breeding methods on clary sage evolution, and highlights interesting avenues for clary breeding programs.</p>
Data From: Evolution of woody plants to the land‐sea interface: The atypical genomic features of mangroves with atypical phenotypic adaptation
<p><span>How plants adapt and diverge in extreme environments is a key question of plant evolution and ecology. Mangrove invasion of intertidal environments is facilitated by adaptive phenotypes such as aerial roots, salt-secreting leaf, and viviparity, and genomic mechanisms including whole genome duplication and transposable element number reduction. However, a number of mangroves lack these typical phenotypes. The question we ask is whether these phenotypically atypical mangroves also have distinct genomic features? The sibling mangrove species <em>Lumnitzera littorea</em> and <em>Lumnitzera racemosa</em> provide a model to study this question. We sequenced and assembled their genomes to chromosome level, together with a closely related species <em>Combretum micranthum</em>. While most mangroves have small genomes, the genomes of both <em>Lumnitzera </em>species are large (1443 and 1317 Mb) and carry a high proportion of repeat sequences (~75%). Moreover, <em>Lumnitzera</em> species have not undergone post-gamma whole-genome duplications. Their genome size increased mainly due to the expansion of repeat sequences in their ancestors. However, <em>Lumnitzera </em>genomes have reduced transposable elements by constraining the proliferation of new LTR-RTs. Meanwhile, the two species have more gene families contracted than expanded, and some gene families with reversed size change may underlie their differentiation in root morphology and local distribution. We identified 86 chromosomal inversions, five of which are measured between 6.5 and 12.8 megabases. A number of genes located in these inversions function in pigment biosynthesis, a process likely involved in flower color differentiation between the <em>Lumnitzera </em>species. We conclude that the mangroves with atypical phenotypes also have atypical genomic evolution.</span></p>
Spatial phylogenetic and phenotypic patterns reveal ontogenetic shifts in ecological processes of plant community assembly
The analysis of spatial phylogenetic and phenotypic structure of plant communities provides insight into the underlying processes and interactions governing their assembly, and how these may change during plant ontogeny. We used point pattern analysis to find out if saplings and adult plants are surrounded by phylogenetically and phenotypically more similar or dissimilar neighbours than expected by chance, and whether these associations change from the sapling to the adult stage. To this end, we combined information on the phylogenetic structure and eight phenotypic traits of 15 woody plant species in two Mediterranean mixed forests of southeastern Spain. At the community level, we found that the sapling bank at both sites did not show phylogenetic or phenotypic spatial patterns, but adults showed phylogenetic clustering (i.e., heterospecific neighbours were more similar than expected). At the species level, we found frequently repulsive patterns in the sapling bank of less abundant species (i.e., heterospecific sapling or adult neighbours were more dissimilar than expected) in both, phylogenetic and phenotypic analyses. For the adult stage, we found phylogenetic attraction (i.e., more similar neighbours) in just one species and phenotypic clustering in four species. The processes driving the assembly of the communities of saplings and adults leave detectable signals in the spatial phylogenetic and phenotypic structure of our two forest communities. Our findings reinforce the existence of ontogenetic shifts in the mechanisms involved in plant community assembly. Facilitation between phylogenetically distant and phenotypically divergent species favours the recruitment of less abundant species. However, processes acting later in the ontogeny ameliorate the competition between close relatives and determine the spatial structure of adult plants. Nevertheless, the role of phenotype in shaping adult-adult interactions was context- and trait-dependent. The use of spatial point pattern analysis allowed a nuanced interpretation of the phylogenetic and phenotypic structures of the plant community.
Depicting the phenotypic space of the annual plant Diplotaxis acris in hyper-arid deserts
<p class="CxSpFirst">The phenotypic space encompasses the assemblage of trait combinations yielding well-suited integrated phenotypes. At the population level, understanding phenotypic space structure requires the quantification of among- and within-population variation in traits and the correlation pattern among them. Here, we studied the phenotypic space of the annual plant <i>Diplotaxis acris</i> occurring in hyper-arid deserts. Given the advance of warming and aridity in vast regions occupied by drylands, <i>D. acris</i> can indicate the successful evolutionary trajectory that many other annual plant species may follow in expanding drylands. To this end, we conducted a greenhouse experiment with 176 <i>D. acris</i> individuals from five Saudi populations to quantify the genetic component of variation in architectural and life-history traits. We found low among-population divergence but high among-individual variation in all traits. In addition, all traits showed a high degree of genetic determination in our study experimental conditions. We did not find significant effects of recruitment and fecundity on fitness. Finally, all architectural traits exhibited a strong correlation pattern among them, whereas for life-history traits, only higher seed germination implied earlier flowering. Seed weight appeared to be an important trait in <i>D. acris</i>, as individuals with heavier seeds tended to advance flowering and have a more vigorous branching pattern, which led to higher fecundity. Population divergence in <i>D. acris</i> might be constrained by the severity of the hyper-arid environment, but populations maintain high among-individual genetic variation in all traits. Furthermore, <i>D. acris</i> showed phenotypic integration for architectural traits and, to a lesser extent, for life-history traits. Overall, we hypothesize that <i>D. acris</i> may be fine-tuned to its demanding extreme environments. Evolutionary speaking, annual plants facing increasing warming, aridity and environmental seasonality might modify their phenotypic spaces towards new phenotypic configurations strongly dominated by correlated architectural traits enhancing fecundity and seed-related traits advancing flowering time.</p>
Data from: Associations between developmental stability, canalization and phenotypic plasticity in plants with temporally heterogeneous environmental experience
<p>We subjected eight plant species to a first round of alternating inundation and drought vs. constantly moderate water treatments and a second round of water conditions. Fluctuating asymmetry (FA), intra- and inter-individual variations (CV<sub>intra</sub> and CV<sub>inter</sub>), and plasticity in traits were measured and correlations between variables were calculated for each species. Early temporally heterogeneous experience decreased the leaf size of half of the species, but had complex effects on leaf fluctuating asymmetry (FA) and inter-individual variation (CV<sub>inter</sub>) in traits immediately or in late conditions, with little effects on intra-individual variation (CV<sub>intra</sub>). There were several positive correlations between FA and CV<sub>inter</sub>, while there were correlations between CV<sub>inter</sub> and plasticity in early treatments, but negative ones in late treatments.</p>
Data from de Vega et al_Flora "Host-driven phenotypic and phenological differentiation in sympatric races of a parasitic plant" [Dataset]
<p>Data from de Vega et al_Flora "Host-driven phenotypic and phenological differentiation in sympatric races of a parasitic plant"</p>
Plant-phenotypic changes induced by parasitoid ichnoviruses enhance the performance of both unparasitized and parasitized caterpillars
<p>There is increasing awareness that interactions between plants and insects can be mediated by microbial symbionts. Nonetheless, evidence showing that symbionts associated with organisms beyond the second trophic level affect plant-insect interactions are restricted to a few cases belonging to parasitoid-associated bracoviruses. Insect parasitoids harbor a wide array of symbionts which, like bracoviruses, can be injected into their herbivorous hosts to manipulate their physiology and behavior. Yet, the function of these symbionts in plant-based trophic webs remains largely overlooked.</p> <p>Here we provide the first evidence of a parasitoid-associated symbiont belonging to the group of ichnoviruses which affects the strength of plant-insect interactions. A comparative proteomic analysis shows that, upon parasitoid injection of calyx fluid containing ichnovirus particles, the composition of salivary glands of caterpillars changes both qualitatively (presence of two viral-encoded proteins) and quantitatively (abundance of several caterpillar-resident enzymes, including elicitors such as glucose oxidase). In turn, plant phenotypic changes triggered by the altered composition of caterpillar oral secretions affect the performance of herbivores. Ichnovirus manipulation of plant responses to herbivory leads to benefits for their parasitoid partners in terms of reduced developmental time within the parasitized caterpillar. Interestingly, plant-mediated ichnoviruses-induced effects also enhance the performances of unparasitized herbivores which in natural conditions may feed alongside parasitized ones. We discuss these findings in the context of ecological costs imposed to the plant by the viral symbiont of the parasitoid. Our results provide intriguing novel findings about the role played by carnivore-associated symbionts on plant-insect-parasitoid systems and underline the importance of placing mutualistic associations in an ecological perspective.</p>
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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.