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408 results for “Plant population”
Data from: Bayesian quantification of ecological determinants of outcrossing in natural plant populations: computer simulations and the case study of biparental inbreeding in English yew
The mating system is a central parameter of plant biology because it shapes their ecological and evolutionary properties. Therefore, determining ecological variables that influence the mating system is important for a deeper understanding of the functioning of plant populations. Here, using old concepts and recent statistical developments, we propose a new statistical tool to make inferences about ecological determinants of outcrossing in natural plant populations. The method requires co-dominant genotypes of seeds collected from maternal plants within different locations. Using extensive computer simulations, we demonstrated that the method is robust to the issues expected for real-world data, including the Wahlund effect, inbreeding and genotyping errors such as allele dropout and allele misclassification. Furthermore, we showed that the estimates of ecological effects and outcrossing rates can be severely biased if genotyping errors and genetic differentiation are not treated explicitly. Application of the new method to the case study of a dioecious tree (Taxus baccata) allowed revealing that female trees that grow in lower local densities have a greater tendency towards mating with relatives. Moreover, we also demonstrated that biparental inbreeding is higher in populations that are characterised by a longer mean distance between trees and a smaller mean trunk perimeter. We found these results to agree with both the theoretical predictions and the history of English yew.
Data from: Plasticity of plant defense and its evolutionary implications in wild populations of Boechera stricta
Phenotypic plasticity is thought to impact evolutionary trajectories by shifting trait values in a direction that is either favored by natural selection ("adaptive plasticity") or disfavored ("nonadaptive" plasticity). However, it is unclear how commonly each of these types of plasticity occurs in natural populations. To answer this question, we measured glucosinolate defensive chemistry and reproductive fitness in over 1,500 individuals of the wild perennial mustard Boechera stricta, planted in four common gardens across central Idaho, USA. Glucosinolate profiles—including total glucosinolate concentration as well as the relative abundances and overall diversity of different compounds—were strongly plastic both among habitats and within habitats. Patterns of glucosinolate plasticity varied greatly among genotypes. Plasticity among sites was predicted to affect fitness in 27.1% of cases; more often than expected by chance, glucosinolate plasticity increased rather than decreased relative fitness. In contrast, we found no evidence for within-habitat selection on glucosinolate reaction norm slopes (i.e., plasticity along a continuous environmental gradient). Together, our results indicate that glucosinolate plasticity may improve the ability of B. stricta populations to persist after migration to new habitats.
Rapid adaptation (or not) in restored plant populations
<p>Mismatches between the traits of a colonizing population and a novel habitat can generate strong selection, potentially resulting in rapid adaptation. However, for most colonization events, it can be difficult to detect rapid adaptation or distinguish it from non-adaptive evolutionary changes. Here I take advantage of a replicated prairie restoration experiment to compare recently established plant populations in two closely-located restored prairies to each other and to their shared source population to test for rapid adaptation. Using a reciprocal transplant experiment six years after the populations were established, I found that one restored plant population showed evidence of adaptation, outperforming the other restored population when grown at its home site. In contrast, I detected no evidence for adaptation at the other site. These findings demonstrate that while rapid adaptation can occur in colonizing plant populations, it may not be the rule. Better understanding of when adaptation may or may not occur in these contexts may help us use evolution to our advantage, potentially improving establishment of desirable species in restored habitats.</p>
Data from: Early snowmelt projected to cause population decline in a subalpine plant
How climate change influences the dynamics of plant populations is not well understood, as few plant studies have measured responses of vital rates to climatic variables and modeled the impact on population growth. I used 25 years of demographic data to analyze how survival, growth, and fecundity respond to date of spring snow melt for a subalpine plant. Fecundity was estimated by seed production (over 15 years) and also divided into flower number, fruit set, seeds per fruit, and escape from seed predation. Despite no apparent effects on flower number, plants produced more seeds in years with later snowmelt. Survival and probability of flowering were reduced by early snow melt in the previous year. Based on demographic models, earlier snowmelt with warming is expected to lead to negative population growth, driven especially by changes in seedling establishment and seed production. These results provide a rare example of how climate change is expected to influence the dynamics of a plant population. They furthermore illustrate the potential for strong population impacts even in the absence of more commonly reported visual signs, such as earlier blooming or reduced floral display in early melting years.
Patterns of pollen dispersal and mating in a population of the clonal plant Sagittaria latifolia
<p>1) Increased plant size is generally expected to have negative consequences for mating by increasing pollen transfer between flowers of the same plant. Such geitonogamous self-pollination would then reduce sexual fitness through both female and male function. However, recent theoretical work has indicated that when plants grow clonally, the outward expansion of plants caused by clonal growth might have positive effects on siring without substantially increasing rates of self-pollination.</p> <p>2) We investigated patterns of pollen dispersal, selfing, and siring in a monoecious population of the clonal plant <em>Sagittaria latifolia</em>, in which clones varied in size and the extent of intermingling with other clones. A spatially-explicit statistical model based on the inferred pollen-dispersal kernel was constructed to examine the mechanisms underlying observed mating patterns.</p> <p>3) Pollen dispersal typically occurred over distances that exceeded the spatial extent of clones. There was a positive association between clone size (measured as the number of ramets per genet) and the likelihood that clones were intermingled with the shoots of other clones. Together, these patterns of pollen dispersal and clonal intermingling resulted in a weak positive association between clone size and selfing rates and a strong positive association between clone size and outcross siring success. These patterns were replicated in the spatially-explicit model, indicating that the intermingling of clones is an important determinant of mating patterns in this population.</p> <p>4) Synthesis. Our study provides the first examination of the pollen dispersal kernel for a clonal plant. It is the first study providing empirical support for model predictions that potentially negative effects of increased selfing in large clones might be offset by increased siring success. This implies that the negative consequences of becoming large do not necessarily apply to clonal plants.</p>
Supplementary Material for Frontiers Plant Genetics and Genomics 'Novel R tools for analysis of genome-wide population genetic data with emphasis on clonality'
<p>Authors</p> <p>Zhian N. Kamvar, Jonah C. Brooks, and Niklaus J. Grünwald</p>
Summary statistics of North American plant populations
<p>Summary statistics of North American plant populations calculated by using the microsatellites of invasive and native species from multiple studies. The packages “hierfstat” (Goudet and Jombart, 2015), “vegan” (Oksanen <em>et al.</em>, 2017) and “sp” (Pebesma and Bivand, 2005; Bivand <em>et al.</em>, 2013) were used in RStudio to calculate the averaged heterozygosity over all subpopulations (<em>H</em><sub>S</sub>), the proportion of genetic variation due to differences among populations (<em>F</em><sub>ST</sub>p), the degree of non-random mating within subpopulations (<em>F</em><sub>IS</sub>) and the correlation between geographic and genetic distance (<em>r)</em>. STRUCTURE (Pritchard <em>et al.</em>, 2000) was used to calculate the number of genetic clusters (<em>K)</em> (5 iterations, burnin length 1000, 10000 MCMC reps after burnin). STRUCTURE HARVESTER (Earl & vonHoldt, 2012) was consulted to determine Evanno’s ΔK (Evanno <em>et al.</em>, 2005).</p>
QTL mapping for seedling and adult plant resistance to stripe and leaf rust in two winter wheat populations
<p><span>The two recombinant inbred lines (RIL) populations developed by crossing Almaly × Avocet S (206 RILs) and Almaly × Anza (162 RILs) were used to detect the novel genomic regions associated with adult plant resistance (APR) and seedling or all-stage resistance (ASR) to yellow rust (YR) and leaf rust (LR). Both the populations were evaluated for YR APR in two environments (2018 and 2019) and LR APR in three environments (2018, 2019, and 2020) in the Anza population and two environments (2018 and 2019) in the Avocet population; both the populations were phenotyped for one environment during 2020 for LR and YR ASR and genotyped using high throughput DArTseq technology. A set of 51 QTLs including 22 for YR APR, nine for LR APR, nine for YR ASR, and 11 for LR ASR were identified. Also, a set of 13 stable QTLs including nine QTLs (<em>QYR-APR-2A.1, QYR-APR-2A.2, QYR-APR-4D.2, QYR-APR-1B, QYR-APR-2B.1, QYR-APR-2B.2, QYR-APR-3D, QYR-APR-4D.1, </em>and<em> QYR-APR-4D.2</em>) for YR APR and four QTLs (<em>QLR-APR-4A, QLR-APR-2B, QLR-APR-3B, </em>and<em> </em></span><em>QLR-APR-5A.2</em>) <span>for LR APR were identified. </span><span>In silico analysis revealed that the key putative candidate genes such as <em>Cytochrome P450</em></span><em><span>, Protein kinase-like domain superfamily</span><span>, Zinc-binding ribosomal protein</span><span>, SANT/Myb domain</span><span>, WRKY transcription factor</span><span>, Nucleotide-sugar transporter,</span></em><span> and <em>NAC</em> </span><em><span>domain superfamily</span></em><span> were in the QTL regions and involved in the regulation of host response towards the pathogen infection. </span><span>The stable QTLs identified in this study are useful for developing rust-resistant varieties through marker-assisted selection (MAS).</span></p>
Data from: Quantifying the impacts of management and herbicide resistance on regional plant population dynamics in the face of missing data
<p>A key challenge in the management of populations is to quantify the impact of interven-tions in the face of environmental and phenotypic variability. However, accurate estima-tion of the effects of management and environment, in large-scale ecological research is often limited by the expense of data collection, the inherent trade-off between quality and quantity, and missing data.</p> <p>In this paper we develop a novel modelling framework, and demographically informed imputation scheme, to comprehensively account for the uncertainty generated by miss-ing population, management, and herbicide resistance data. Using this framework and a large dataset (178 sites over 3 years) on the densities of a destructive arable weed (Alo-pecurus myosuroides) we investigate the effects of environment, management, and evolved herbicide resistance, on weed population dynamics.</p> <p>In this study we quantify the marginal effects of a suite of common management prac-tices, including cropping, cultivation, and herbicide pressure, and evolved herbicide re-sistance, on weed population dynamics.</p> <p>Using this framework, we provide the first empirically backed demonstration that herbi-cide resistance is a key driver of population dynamics in arable weeds at regional scales. Whilst cultivation type had minimal impact on weed density, crop rotation, and earlier cultivation and drill dates consistently reduced infestation severity.</p> <p>Synthesis and applications: As we demonstrate that high herbicide resistance levels can produce extremely severe weed infestations, monitoring of herbicide resistance is a pri-ority for famers across western Europe. Furthermore, developing non chemical control methods is essential to control current weed populations, and prevent further resistance evolution. We recommend that planning interventions that center on crop rotation and incorporate spring sewing and cultivation to provide the best reductions in weed densi-ties. More generally, by directly accounting for missing data our framework permits the analysis of management practices with data that would otherwise be severely compro-mised.</p>
Plant size, latitude, and phylogeny explain within-population variability in herbivory
<p>Interactions between plants and herbivores are central in most ecosystems, but their strength is highly variable. The amount of variability within a system is thought to influence most aspects of plant-herbivore biology, from ecological stability to plant defense evolution. Our understanding of what influences variability, however, is limited by sparse data. We collected standardized surveys of herbivory for 503 plant species at 790 sites across 116° of latitude. With these data, we show that within-population variability in herbivory increases with latitude, decreases with plant size, and is phylogenetically structured. Differences in the magnitude of variability are thus central to how plant-herbivore biology varies across macroscale gradients. We argue that increased focus on interaction variability will advance understanding of patterns of life on Earth.</p>
Data from: Combining the resurrection approach with transplant experiments to investigate adaptation of plant populations to environmental change
<p>Recent climatic changes, such as more frequent droughts and heatwaves, can lead to rapid evolutionary adaptations in plant populations. Such rapid evolution can be investigated using the resurrection approach by comparing plants raised from stored ancestral and contemporary seeds from the same population. This approach has so far only been used in common garden experiments, allowing it to reveal genetic differentiation but not adaptation. In this study, we performed a novel approach by testing for evolutionary adaptation in natural plant populations using a resurrection study in combination with in situ transplantations. We cultivated seedlings from ancestors (23–26 years old) and contemporary descendants of three perennial species (<em>Melica ciliata, Leontodon hispidus</em> and <em>Clinopodium vulgare</em>) from calcareous grasslands in the greenhouse and transplanted them back to their collection sites. In addition, we sowed seeds of ancestors and descendants of two species (<em>L. hispidus</em> and <em>C. vulgare</em>) to the collection sites in order to investigate germination rates. In transplanted <em>M. ciliata</em> seedlings, we observed lower mortality and larger plant size in descendants compared to ancestors. This indicates that descendants are better adapted than ancestors to the current environmental conditions, which proved to be exceptionally hot and dry during the study period. Descendants of <em>C. vulgare</em> seedlings tended to be smaller and descendants of <em>L. hispidus</em> seedlings produced fewer leaves compared to their ancestors in their contemporary environmental conditions. In <em>C. vulgare</em> and <em>L. hispidus</em>, we found evolution towards faster germination, and especially descendant seeds of <em>C. vulgare</em> were better adapted to the unfavourable conditions during the experimental period. Concluding, we demonstrate that our novel approach to combine resurrection ecology with transplant experiments is a promising avenue to rigorously test for evolutionary adaptations in changing environments.</p>
Data from: Plant-soil microbe feedbacks depend on distance and ploidy in a mixed cytotype population of Larrea tridentata
<p><strong>Premise of the study</strong></p> <p>Theory predicts that mixed ploidy populations should be short-lived due to strong fitness disadvantages for the rare ploidy. However, mixed ploidy populations are common, suggesting that the fitness costs for rare ploidies are counterbalanced by ecological benefits that emerge when rare. We investigated whether differences in ecological interactions with soil microbes help to maintain a tetraploid-hexaploid population of <em>Larrea tridentata </em>(creosote bush) in the Sonoran Desert, California, USA, where prior work documented ploidy-specific root-associated microbes.</p> <p><strong>Methods</strong></p> <p>We used a plant-soil feedback (PSF) experiment to test whether host-specific soil microbes can alter the outcomes of intra-ploidy vs. inter-ploidy competition. Host-specific soil microbes can build up over time; thus, distance from a host plant can affect the fitness of nearby plants.</p> <p><strong>Key results</strong></p> <p>Seedlings grown in soils from near plants of a different ploidy produced greater biomass relative to seedlings grown in soils from near plants of the same ploidy. Moreover, seedlings grown in soils from near plants of a different ploidy produced greater biomass than those grown in soils from further away from plants of a different ploidy. This suggests the ecological consequences of PSF may facilitate the persistence of mixed ploidy populations.</p> <p><strong>Conclusions</strong></p> <p>This is the first evidence, to our knowledge, consistent with plant-soil microbe feedback as a viable mechanism to maintain the coexistence of multiple ploidy levels in a single population.</p>
Data for: Shifts in plant-invertebrate interactions between wild and ex-situ conservation populations of a critically endangered tree
<p>Ex-situ conservation is an effective approach to prevent the extinction of endangered species. Biotic interactions (eg herbivory and pollination) are critical to ex-situ conservation success, including plant establishment, survival, and reproduction. However, shifts in biotic interactions between wild and ex-situ populations are still poorly understood. We compared herbivory and pollination characteristics between the only wild population (WP) and three ex-situ populations (LP, local population, nearby WP; NP, north population, ca. 850 km; and SP, south population, ca. 750 km) of a critically endangered tree species (<em>Sinojackia huangmeiensis</em>) to explore the latitudinal changes in plant-invertebrate interactions. Larvae of the Limacodidae family were the dominant herbivores in WP, LP, and NP, while the only herbivore observed in SP was a snail. Compared to WP, the leaf herbivory rate was unchanged in LP but decreased in NP and SP. Leaf defense traits (total phenols, tannins, leaf thickness, and leaf dry matter content) increased or remained unchanged in the three ex-situ populations. A pollinator (<em>Apis cerana</em>) of <em>S. huangmeiensis</em> was present in the four populations. NP and SP lacked some pollinators that were found in both WP and LP, but they shared one pollinator that was not observed in WP and LP. The pollinator visiting frequency increased in SP, while it did not change significantly in LP and NP. Synthesis and applications: Our results suggested that both herbivory and pollination of <em>S. huangmeiensis</em> changed in ex-situ populations, with complete or partial changes in herbivores, leaf herbivory rate, pollinators, pollinator visiting frequency, and fruit set in the two distant ex-situ populations. This work provides a unique empirical study of shifts in both antagonistic and mutualistic biotic interactions between wild and ex-situ populations. We emphasized that it is essential to integrate herbivore and pollinator management in future ex-situ conservation of plant species.</p>
Data from: Pace and parity predict short-term persistence of small plant populations
<p>Life history traits are used to predict asymptotic odds of extinction from dynamic conditions. Less is known about how life history traits interact with stochasticity and population structure of finite populations to predict near-term odds of extinction. Through empirically parameterized matrix population models, we study the impact of life history (reproduction, pace), stochasticity (environmental, demographic), and population history (existing, novel) on the transient population dynamics of finite populations of plant species. Among fast and slow pace and either uniform or increasing reproductive intensity or short or long reproductive lifespan, slow, semelparous species are at the greatest risk of extinction. Long reproductive lifespans buffer existing populations from extinction while the odds of extinction of novel populations decreases when reproductive effort is uniformly spread across the reproductive lifespan. Our study highlights the importance of population structure, pace, and two distinct aspects of parity for predicting near-term odds of extinction. </p>
Azole resistance mechanisms and population structure of Aspergillus fumigatus on retail plant products
<p><em>Aspergillus fumigatus </em>is a ubiquitous saprotroph and human-pathogenic fungus that is life-threatening to the immunocompromised. Triazole-resistant <em>A. fumigatus</em><em> </em>was found in patients without prior treatment with azoles, leading researchers to conclude that resistance had developed in agricultural environments where azoles are used against plant pathogens. Previous studies have documented azole-resistant <em>A. fumigatus </em>across agricultural environments, but few have looked at retail plant products. Our objectives were to determine if azole-resistant <em>A. fumigatus </em>is prevalent<em> </em>in retail plant products produced in the United States (U.S.), as well as to identify the resistance mechanism(s) and population genetic structure of these isolates. Five hundred twenty-five isolates were collected from retail plant products and screened for azole resistance. Twenty-four isolates collected from compost, soil, flower bulbs, and raw peanuts were pan-azole resistant. Resistant isolates had the TR<sub>34</sub>/L98H, TR<sub>46</sub>/Y121F/T289A, G448S, and H147Y <em>cyp51A </em>alleles, all known to underly pan-azole resistance, as well as WT alleles, suggesting that non-cyp51A-mechanisms contribute to pan-azole resistance in some isolates. Minimum spanning networks showed two lineages containing isolates with TR alleles or the F46Y/M172V/E427K allele, and discriminant analysis of principle components (DAPC) identified three primary clusters. This is consistent with previous studies detecting three clades of <em>A. fumigatus</em> and identifying pan-azole-resistant isolates with TR alleles in a single clade. We found pan-azole resistance in U.S. retail plant products, particularly compost and flower bulbs, which indicates the risk of exposure to these products for susceptible populations and that highly resistant isolates are likely distributed worldwide on these products.</p>
Inter- and intraspecific selection in alien plants: how population growth, functional traits and climate responses change with residence time
<p><strong>Aim: </strong>When alien species are introduced to new ranges, climate or trait mismatches may initially constrain their population growth. However, inter- and intraspecific selection in the new environment should cause population growth rates to increase with residence time. Using a species-for-time approach, we test whether with increasing residence time (a) negative effects of climatic mismatches between the species' new and native range on population growth weaken, and (b) functional traits converge towards values that maximize population growth in the new range.</p> <p><strong>Location:</strong> Germany.</p> <p><strong>Time period: </strong>12,000 years BP to present.</p> <p><strong>Major taxa studied: </strong>46 plant species of the Asteraceae family.</p> <p><strong>Methods:</strong> We set up a common-garden mesocosm-experiment using annual plant species with a wide range of residence times (7-12,000 years) and followed their population dynamics over two years. We calculated climatic distance between the common garden and the species' native range. We also measured key functional traits of each species to analyse trait-demography relationships and test trait convergence with increasing residence time.</p> <p><strong>Results: </strong>We found no support for the hypothesis that negative effects of climatic mismatches on population growth weaken with residence time. However, seed mass had a clear negative effect on population growth. As expected under such strong directional selection between or within species, increasing residence time led seed mass to converge to low values that increase population growth. Accordingly, population growth tended to increase with residence time.</p> <p><strong>Main conclusions: </strong>We identify trait but not climatic mismatches as important constraints on population growth of invaders. Understanding how inter- and intraspecific selection shapes functional traits of alien species should improve the predictability of future invasions and help understanding limits to the population growth and spread of invaders already present. In a broader context, this study contributes to the conceptual integration of invasion biology with community, functional, and population ecology.</p>
The population genetics of adaptation through copy-number variation in a fungal plant pathogen
<p>Supplementary Tables S1-S8 for the manuscript "The population genetics of adaptation through copy-number variation in a fungal plant pathogen"</p>
Older populations of the invader Solidago canadensis exhibit stronger positive plant-soil feedbacks and competitive ability in China
<p><strong>PREMISE</strong></p> <p>The enemy release hypothesis predicts that release from natural enemies, including soil-borne pathogens, liberates invasive plants from a negative regulating force. Nevertheless, invasive plants may acquire novel enemies and mutualists in the introduced range, which may cause variable effects on invader growth. However, how soil microorganisms may influence competitive ability of invasive plants along invasion chronosequences has been little explored.</p> <p><strong>METHODS</strong></p> <p>Using the invasive plant <em>Solidago canadensis</em>, we tested whether longer residence times are associated with stronger negative plant-soil feedbacks and thus weaker competitive abilities at the individual level. We grew S. canadensis individuals from 36 populations with different residence times in competition versus no competition and in three different types of soils: (1) conspecific rhizospheric soils, (2) soil from uninvaded patches, and (3) sterilized soil. For our competitor treatments, we constructed synthetic communities of four native species <em>Bidens parviflora, Solanum nigrum, Kalimeris indica,</em> and <em>Mosla scabra</em>, which naturally co-occur with <em>S. canadensis</em> in the field.</p> <p><strong>RESULTS</strong></p> <p>Solidago canadensis populations with longer residence times experienced stronger positive plant-soil feedbacks and had greater competitive responses (i.e., produced greater above-ground biomass and grew taller) in conspecific rhizospheric soils than in sterilized and uninvaded soils. Moreover, <em>S. canadensis</em> from older populations significantly suppressed above-ground biomass of the native communities in rhizospheric and uninvaded soils but not in sterilized soil.</p> <p><strong>CONCLUSIONS</strong></p> <p>The present results suggest that older populations of <em>S. canadensis</em> experience stronger positive plant-soil feedback, which may enhance their competitive ability against native plant communities. </p>
Figure 1 in Within-plant distribution and rapid assessment of sugarcane rust mite population on sugarcane canopy
Figure 1 Mites appearances in visual direct count (left) and imprinting techniques (right).
Downscaling mutualistic networks from species to individuals reveals consistent interaction niches and roles within plant populations.
<p>Repository containing dataset and code for the manuscript entitled <em>Downscaling mutualistic networks from species to individuals reveals consistent interaction niches and roles within plant populations</em>.</p> <p>For this study, we compiled 46 empirical individual-based networks on plant-animal seed dispersal mutualism, encompassing 1037 plant individuals across 29 species from various regions. We compare the structure of individual-based networks to that of species-based networks and by extending the niche concept to interaction assemblages, we explore levels of individual plant specialization. We examine how individual variation influences network structure and how plant individuals "explore" the interaction niche of the population.</p> <p>Please refer to <strong>makefile.R</strong> for project outline, explanation and codes used, and to the <strong>README</strong> in networks folder for data structure and compilation.</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)
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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.