Find research datasets worth reusing

Data from: Genome-wide search for quantitative trait loci controlling important plant and flower traits in petunia using an interspecific recombinant inbred population of Petunia axillaris and Petunia exserta

A major bottleneck in plant breeding has been the much limited genetic base and much reduced genetic diversity in domesticated, cultivated germplasm. Identification and utilization of favorable gene loci or alleles from wild or progenitor species can serve as an effective approach to increasing genetic diversity and breaking this bottleneck in plant breeding. This study was conducted to identify quantitative trait loci (QTL) in wild or progenitor petunia species that can be used to improve important horticultural traits in garden petunia. An F7 recombinant inbred population derived between Petunia axillaris and P. exserta was phenotyped for plant height, plant spread, plant size, flower counts, flower diameter, flower length, and days to anthesis, in Florida in two consecutive years. Transgressive segregation was observed for all seven traits in both years. The broad-sense heritability estimates for the traits ranged from 0.20 (days to anthesis) to 0.62 (flower length). A genome-wide genetic linkage map consisting 368 single nucleotide polymorphism bins and extending over 277 cM was searched to identify QTL for these traits. Nineteen QTL were identified and localized to five linkage groups. Eleven of the loci were identified consistently in both years; several loci explained up to 34.0% and 24.1% of the phenotypic variance for flower length and flower diameter, respectively. Multiple loci controlling different traits are co-localized in four intervals in four linkage groups. These intervals contain desirable alleles that can be introgressed into commercial petunia germplasm to expand the genetic base and improve plant performance and flower characteristics in petunia.

opencc-zeroDec 2016View details →

Data from: Repeated evolution of vertebrate pollination syndromes in a recently diverged Andean plant clade

While specialized interactions, including those involving plants and their pollinators, are often invoked to explain high species diversity, they are rarely explored at macroevolutionary scales. We investigate the dynamic evolution of hummingbird and bat pollination syndromes in the centropogonid clade (Lobelioideae: Campanulaceae), an Andean-centered group of ∼550 angiosperm species. We demonstrate that flowers hypothesized to be adapted to different pollinators based on flower color fall into distinct regions of morphospace, and this is validated by morphology of species with known pollinators. This supports the existence of pollination syndromes in centropogonids, an idea corroborated by ecological studies. We further demonstrate that hummingbird pollination is ancestral, and that bat pollination has evolved ∼13 times independently, with ∼11 reversals. This convergence is associated with correlated evolution of floral traits within selective regimes corresponding to pollination syndrome. Collectively, our results suggest that floral morphological diversity is extremely labile, likely resulting from selection imposed by pollinators. Finally, even though this clade's rapid diversification is partially attributed to their association with vertebrate pollinators, we detect no difference in diversification rates between hummingbird- and bat-pollinated lineages. Our study demonstrates the utility of pollination syndromes as a proxy for ecological relationships in macroevolutionary studies of certain species-rich clades.

opencc-zeroMar 2020View details →

Optical traits perform equally well as directly-measured functional traits in explaining the impact of an invasive plant on litter decomposition

1. Functional traits can help elucidate and predict the impact of invasive plant species on ecosystem functioning. Yet, this approach requires comprehensive and labor-intensive trait collection campaigns, covering intraspecific trait variation of both the invader and native species in the invaded community. One potential way to overcome these logistic constraints is using hyperspectral remote sensing technology to efficiently quantify functional trait values. Although such spectrally derived or 'optical' traits are known to closely link to directly-measured functional traits, little research has explored how well these optical traits perform in assessing invader-induced ecosystem impact. 2. Here, we explored the trait-mediated impact of the invasive Rosa rugosa on litter decomposition and evaluated whether optical traits perform equally well as directly-measured traits in predicting litter decomposition variation. We collected data on species-specific functional traits, leaf hyperspectral reflectance and standardized 'tea bag index' litter decomposition across 25 invaded and 25 uninvaded coastal grassland plots. The selected traits were all potentially related to litter decomposition and covered the leaf economics spectrum, additional leaf structural components and competitive ability. Optical traits were quantified through a combination of a physical radiative transfer model inversion and vegetation indices calculations. 3. Invasion significantly increased the stabilization factor, i.e. the amount of resulting recalcitrant litter. Invader impact on litter decomposition could be entirely explained by changes it induced in the functional traits of the native community, rather than by the invader's traits itself. More specifically, the invader pushed the invaded community towards traits associated with high litter quality. Optical traits performed equally well as directly-measured traits in explaining the invasion impact on the stabilization factor (R2= 41.9% vs. 38.5%). Furthermore, the interpretation of the results based on optical traits resulted in a similar functional understanding of the invader impact. 4. Synthesis: Our results indicate the potential of hyperspectral data to explain changes in ecosystem functioning. The combination of radiative transfer models and vegetation indices allowed to extract all relevant trait information from the hyperspectral data. This framework thus presents a practical short-cut to assess relevant leaf traits, requiring only a limited amount of field trait measurements.

opencc-zeroDec 2018View details →

Data from: Contingency rules for pathogen competition and antagonism in a genetically based, plant defense hierarchy

1. Plant defense against pathogens includes a range of mechanisms, including, but not limited to, genetic resistance, pathogen-antagonizing endophytes, and pathogen competitors. The relative importance of each mechanism can be expressed in a hierarchical view of defense. Several recent studies have shown that pathogen antagonism is inconsistently expressed within the plant defense hierarchy. Our hypothesis is that the hierarchy is governed by contingency rules that determine when and where antagonists reduce plant disease severity. 2. Here, we investigated whether pathogen competition influences pathogen antagonism using Populus as a model system. In three independent field experiments, we asked whether competition for leaf mesophyll cells between a Melampsora rust pathogen and a microscopic, eriophyid mite affects rust pathogen antagonism by fungal leaf endophytes. The rust pathogen has an annual, phenological disadvantage in competition with the mite because the rust pathogen must infect its secondary host in spring before infecting Populus. We varied mite-rust competition by utilizing Populus genotypes characterized by differential genetic resistance to the two organisms. We inoculated plants with endophtyes and allowed mites and rust to infect plants naturally. 3. Two contingency rules emerged from the three field experiments: 1) pathogen antagonism by endophytes can be preempted by host genes for resistance that suppress pathogen development, and 2) pathogen antagonism by endophtyes can secondarily be preempted by competitive exclusion of the rust by the mite. 4. Synthesis: Our results point to a Populus defense hierarchy with resistance genes on top, followed by pathogen competition, and finally pathogen antagonism by endophytes. We expect these rules will help to explain the variation in pathogen antagonism that is currently attributed to context dependency.

Data from: Adaptive diversification of growth allometry in the plant Arabidopsis thaliana

Seed plants vary tremendously in size and morphology. However, variation and covariation between plant traits may at least in part be governed by universal biophysical laws and biological constants. Metabolic Scaling Theory (MST) posits that whole-organismal metabolism and growth rate are under stabilizing selection that minimizes the scaling of hydrodynamic resistance and maximizes the scaling of resource uptake. This constrains variation in physiological traits and in the rate of biomass accumulation, so that they can be expressed as mathematical functions of plant size with near constant allometric scaling exponents across species. However, observed variation in scaling exponents questions the evolutionary drivers and the universality of allometric equations. We have measured growth scaling and fitness traits of 451 Arabidopsis thaliana accessions with sequenced genomes. Variation among accessions around the scaling exponent predicted by MST correlated with relative growth rate, seed production and stress resistance. Genomic analyses indicate that growth allometry is affected by many genes associated with local climate and abiotic stress response. The gene with the strongest effect, PUB4, has molecular signatures of balancing selection, suggesting that intraspecific variation in growth scaling is maintained by opposing selection on the trade-off between seed production and abiotic stress resistance. Our findings support a core MST prediction and suggest that variation in allometry contributes to local adaptation to contrasting environments. Our results help reconcile past debates on the origin of allometric scaling in biology, and begin to link adaptive variation in allometric scaling to specific genes.

Data from: Spatial heterogeneity in species composition constrains plant community responses to herbivory and fertilization

Environmental change can result in substantial shifts in community composition. The associated immigration and extinction events are likely constrained by the spatial distribution of species. Still, studies on environmental change typically quantify biotic responses at single spatial (time series within a single plot) or temporal (spatial beta-diversity at single time points) scales, ignoring their potential interdependence. Here, we use data from a global network of grassland experiments to determine how turnover responses to two major forms of environmental change – fertilization and herbivore loss – are affected by species pool size and spatial compositional heterogeneity. Fertilization led to higher rates of local extinction whereas turnover in herbivore exclusion plots was driven by species replacement. Overall, sites with more spatially heterogeneous composition showed significantly higher rates of annual turnover, independent of species pool size and treatment. Taking into account spatial biodiversity aspects will therefore improve our understanding of consequences of global and anthropogenic change on community dynamics.

opencc-zeroDec 2018View details →

Data from: Fire, grazing, and climate shape plant-grasshopper interactions in a tallgrass prairie

1. Species interactions are integral to ecological community function and the structure of species interactions has repercussions for the consequences of species extinctions. Few studies have examined the role of environmental factors in controlling species interaction networks across time. 2. We examined variation in plant-grasshopper network structural properties in response to three major grassland drivers: periodic fire, ungulate grazing and climate. 3. We sequenced a plant barcoding gene from extracted grasshopper gut contents to characterize diets of 26 grasshopper species. Resulting grasshopper species' diets were combined with long-term plant and grasshopper surveys to assemble plant-grasshopper networks across 13-19 years for 6 watersheds subjected to varying fire and grazing treatments. 4. Network modularity, generality, and predicted grasshopper community robustness to plant species loss all increased in grazed watersheds. Temperature decreased predicted grasshopper community robustness to plant species loss. 5. Grasshopper communities were found to be vulnerable to climatic warming due to host plant loss. However, intermediate disturbance from ungulate grazers may maintain grasshopper diversity and buffer community robustness to species loss. Our results suggest that climate and disturbance shape the structure of ecological interaction networks and thus have many indirect effects on species persistence though direct effects on interaction partners.

opencc-zeroMay 2020View details →

Data from: Protection of pepper plants from drought by microbacterium sp. 3J1 by modulation of the plant's glutamine and α-ketoglutarate content: a comparative metabolomics approach

Desiccation-tolerant plants are able to survive for extended periods of time in the absence of water. The molecular understanding of the mechanisms used by these plants to resist droughts can be of great value for improving drought tolerance in crops. This understanding is especially relevant in an environment that tends to increase the number and intensity of droughts. The combination of certain microorganisms with drought-sensitive plants can improve their tolerance to water scarcity. One of these bacteria is Microbacterium sp. 3J1, an actinobacteria able to protect pepper plants from drought. In this study, we supplemented drought-tolerant and drought-sensitive plant rhizospheres with Microbacterium sp. 3J1 and analyzed their proteomes under drought to investigate the plant-microbe interaction. We also compare this root proteome with the proteome found in desiccation-tolerant plants. In addition, we studied the proteome of Microbacterium sp. 3J1 subjected to drought to analyze its contribution to the plant-microbe interaction. We describe those mechanisms shared by desiccation-tolerant plants and sensitive plants protected by microorganisms focusing on protection against oxidative stress, and production of compatible solutes, plant hormones, and other more specific proteins.

opencc-zeroDec 2019View details →

Biotic and anthropogenic forces rival climatic/abiotic factors in determining global plant population growth and fitness

Multiple, simultaneous environmental changes, in climatic/abiotic factors, in interacting species, and in direct human influences, are impacting natural populations and thus biodiversity, ecosystem services, and evolutionary trajectories. Determining whether the magnitudes of the population impacts of abiotic, biotic, and anthropogenic drivers differ, accounting for their direct effects and effects mediated through other drivers, would allow us to better predict population fates and design mitigation strategies. We compiled 644 paired values of the population growth rate (lambda) from high and low levels of an identified driver from demographic studies of terrestrial plants. Among abiotic drivers, natural disturbance (not climate), and among biotic drivers, interactions with neighboring plants had the strongest effects on lambda. However, when drivers were combined into the three main types, their average effects on lambda did not differ. For the subset of studies that measured both the average and variability of the driver, lambda was more sensitive to one standard deviation of change in abiotic drivers relative to biotic drivers, but sensitivity to biotic drivers was still substantial. Similar impact magnitudes for abiotic/biotic/anthropogenic drivers holds for plants of different growth forms, for different latitudinal zones, and for biomes characterized by harsher or milder abiotic conditions, suggesting that all three drivers have equivalent impacts across a variety of contexts. Thus the best available information about the integrated effects of drivers on all demographic rates provides no justification for ignoring drivers of any of these three types when projecting ecological and evolutionary responses of populations and of biodiversity to environmental changes.

opencc-zeroDec 2016View details →

Data from: Parallel Pleistocene amphitropical disjunctions in a parasitic plant and its host

PREMISE OF THE STUDY: Aphyllon is a clade of holoparasites that includes closely related North American and South American species parasitic on Grindelia. Both Aphyllon (Orobanchaceae) and Grindelia (Asteraceae) have amphitropical disjunctions between North America and South America; however, the timing of these patterns and the processes to explain them are unknown. METHODS: Chronograms for the Orobanchaceae and Grindelia and their relatives were constructed using fossil and secondary calibration points, one of which was based on the inferred timing of horizontal gene transfer from a papilionoid legume into the common ancestor of Orobanche and Phelipanche. Elevated rates of molecular evolution in the Orobanchaceae have hindered efforts to determine reliable divergence time estimates in the absence of a fossil record. However, using a horizontal gene transfer event as a secondary calibration overcomes this limitation. These chronograms were used to reconstruct the biogeography of Aphyllon, Grindelia, and relatives using a DEC+J model implemented in RevBayes. KEY RESULTS: Aphyllon had two amphitropical dispersals from North America to South America, while Grindelia had a single dispersal. The dispersal of the Aphyllon lineage that is parasitic on Grindelia (0.40 Ma) took place somewhat after Grindelia began to diversify in South America (0.93 Ma). Using a secondary calibration based on horizontal gene transfer, we infer more recent divergence dates of holoparasitic Orobancheae than previous studies. CONCLUSIONS: Parallel host–parasite amphitropical disjunctions in Grindelia and Aphyllon illustrate one means by which ecological specialization may result in nonindependent patterns of diversity in distantly related lineages. Although Grindelia and Aphyllon both dispersed to South America recently, Grindelia appears to have diversified more extensively following colonization. More broadly, recent Pleistocene glaciations probably have also contributed to patterns of diversity and biogeography of temperate northern hemisphere Orobancheae. We also demonstrate the utility of using horizontal gene transfer events from well-dated clades to calibrate parasite phylogenies in the absence of a fossil record.

opencc-zeroJun 2021View details →

Native plant species show evolutionary responses to invasion by Parthenium hysterophorus in an African savanna

Invasive plant species often competitively displace native plant species but some populations of native plant species can evolve adaptation to competition from invaders and persist in invaded habitats. However, studies are lacking that examine how variation in abiotic conditions in invaded landscapes may affect fitness of native plants that have adapted to compete with invasive plants. I tested whether invasion by Parthenium hysterophorus in an African savanna may have selected for native plant individuals with greater competitive ability than conspecific naïve natives in nutrient-rich and mesic soil conditions. I compared vegetative growth and seed yields of invader-experienced and conspecific naïve native individuals. Invader-experienced natives grew shorter than naïve natives regardless of growth conditions. Nevertheless, the two groups of native plants also exhibited treatment-specific differences in competitive ability. Invader-experienced natives displayed plasticity in seed yield under drought treatment, while naïve natives did not. Moreover, drought treatment enhanced competitive effects of invader-experienced natives on P. hysterophorus, while nutrient enrichment relaxed competitive effects of experienced natives on the invader. The results suggest that P. hysterophorus may have selected for shorter native plant genotypes that also exhibit plasticity in competitive ability under drought conditions.

opencc-zeroOct 2019View details →

Data from: Host plant-related genomic differentiation in the European cherry fruit fly, Rhagoletis cerasi (L., 1758) (Diptera: Tephritidae)

Elucidating the mechanisms and conditions facilitating the formation of biodiversity are central topics in evolutionary biology. A growing number of studies imply that divergent ecological selection may often play a critical role in speciation by counteracting the homogenising effects of gene flow. Several examples involve phytophagous insects, where divergent selection pressures associated with host plant shifts may generate reproductive isolation, promoting speciation. Here, we use ddRADseq to assess the population structure and to test for host-related genomic differentiation in the European cherry fruit fly, Rhagoletis cerasi (L., 1758) (Diptera: Tephritidae). This tephritid is distributed throughout Europe and western Asia, and has adapted to two different genera of host plants, Prunus spp. (cherries) and Lonicera spp. (honeysuckle). Our data imply that geographic distance and geomorphic barriers serve as the primary factors shaping genetic population structure across the species range. Locally, however, flies genetically cluster according to host plant, with consistent allele frequency differences displayed by a subset of loci between Prunus and Lonicera flies across four sites surveyed in Germany and Norway. These 17 loci display significantly higher FST values between host plants than others. They also showed high levels of linkage disequilibrium within and between Prunus and Lonicera flies, supporting host-related selection and reduced gene flow. Our findings support the existence of sympatric host races in R. cerasi embedded within broader patterns of geographic variation in the fly, similar to the related apple maggot, Rhagoletis pomonella, in North America.

opencc-zeroDec 2020View details →

Plant traits of grass and legume species for flood resilience and N2O mitigation

Flooding threatens the functioning of managed grasslands by decreasing primary productivity and increasing nitrogen losses, notably as the potent greenhouse gas nitrous oxide (N2O). Sowing species with traits that promote flood resilience and mitigate flood-induced N2O emissions within these grasslands could safeguard their productivity while mitigating nitrogen losses. We tested how plant traits and resource acquisition strategies could predict flood resilience and N2O emissions of 12 common grassland species (eight grasses and four legumes) grown in field soil in monocultures in a 14-week greenhouse experiment. We found that grasses were more resistant to flooding, while legumes recovered better. Resource-conservative grass species had higher resistance, while resource-acquisitive grasses species recovered better. Resilient grass and legume species lowered cumulative N2O emissions. Grasses with lower inherent leaf and root δ13C (and legumes with lower root δ13C) lowered cumulative N2O emissions during and after the flood. Our results highlight the differing responses of grasses with contrasting resource acquisition strategies, and of legumes to flooding. Combining grasses and legumes based on their traits and resource acquisition strategies could increase the flood-resilience of managed grasslands, and their capability to mitigate flood-induced N2O emissions.

Data from: Plant diversity and density predict belowground diversity and function in an early successional alpine ecosystem

Despite decades of interest, few studies have provided evidence supporting theoretical expectations for coupled relationships between aboveground and belowground diversity and ecosystem functioning in non-manipulated naturalecosystems. We characterized plant species richness and density, soil bacterial, fungal and eukaryotic species richness and phylogenetic diversity (using 16S, ITS, and 18S gene sequencing), and ecosystem function (levels of soil C and N, and rates of microbial enzyme activities) along a natural gradient in plant richness and density in high-elevation, C-deficient soils to examine the coupling between above- and belowground systems. Overall, we observed a strong positive relationship between aboveground (plant richness and density) and belowground (bacteria, fungi, and non-fungal eukaryotes) richness. In addition to the correlations between plants and soil communities, C and N pools, and rates of enzyme activities increased as plant and soil communities became richer and more diverse. Our results suggest that the theoretically expected positive correlation between above- and belowground communities does exist in natural systems, but may be undetectable in late successional ecosystems due to the buildup of legacy organic matter that results in extremely complex belowground communities. In contrast, microbial communities in early successional systems, such as the system described here, are more directly dependent on contemporary inputs from plants and therefore are strongly correlated with plant diversity and density.

opencc-by-4.0Jun 2021View details →

zenodo36/100

D4.3 Assessment of DRALOD drying plant performance data set dryer march 2021

Data and meta-data for dryer operation March 2021

Data from: Trophic level and basal resource use of soil animals are hardly affected by local plant associations in abandoned arable land

Stable isotope composition of plants and soil animals in abandoned arable land Dataset provides raw data on stable isotope composition of C and N of plants and soil meso- and macrofauna. Dominating animal groups were collected in arable fallow systems 3 and 14-16 years after abandonment. Animals were sampled from the rhizosphere of three plant species of different functional groups: a legume (Medicaco sativa), a non-legume herb (Taraxacum officinale) and a grass (Bromus sterilis). More information can be found in the associated paper.

Location and plant spacing affect biomass yield and nutritional value of pigeon pea forage

An experiment was conducted to evaluate the effects of row spacing (RS) and interplant spacing (IPS) on the yield of total biomass, leaf, and edible twigs, and nutritive value of pigeon pea,(Cajanus cajan L. Millsp.) at three locations in the Rift Valley area of Ethiopia, using a randomized completed block design with three replications in 3 × 3 factorial arrangement; three RS ( 25, 50, and 75 cm) and three IPS (15, 30, and 45 cm). Row spacing × IPS of 25 × 30 cm and 50 × 15 cm, gave greater total biomass yield than the other RS and IPS combinations. A similar result was found for edible plant yield. At Hawassa the greater leaf CP was found for the wider IPS of 45 cm than the narrower IPS of 30 cm (318 Vs. 303 g kg-1 ). At Wondo-Genet, the greater leaf in vitro digestible organic matter (597 Vs. 582 g kg-1 ) was found for the wider RS of 75 cm than narrower RS. Similar to leaf, a better nutritional value of edible twigs was found for a wider RS and IPS than narrower RS and IPS at Hawassa and Wondo-Genet. In contrast at Aliyu-Amab, a better nutritional value of edible twigs was found for narrower RS and IPS than the wider spacing. Thus, it can be concluded that RS × IPS of 25 × 30 cm or 50 × 15 cm are advisable for pigeon pea forage production.

Data from: Chemical novelty facilitates herbivore resistance and biological invasions in some introduced plant species

Ecological release from herbivory due to chemical novelty is commonly predicted to facilitate biological invasions by plants, but has not been tested on a community scale. We used metabolomics based on mass spectrometry molecular networks to assess the novelty of foliar secondary chemistry of 15 invasive plant species compared to 46 native species at a site in eastern North America. Locally, invasive species were more chemically distinctive than natives. Among the 15 invasive species, the more chemically distinct were less preferred by insect herbivores and less browsed by deer. Finally, an assessment of invasion frequency in 2,505 forest plots in the Atlantic coastal plain revealed that, regionally, invasive species that were less preferred by insect herbivores, less browsed by white-tailed deer, and chemically distinct relative to the native plant community occurred more frequently in survey plots. Our results suggest that chemically-mediated release from herbivores contributes to many successful invasions.

Evolutionary changes in an invasive plant support the defensive role of plant volatiles

It is increasingly evident that plants interact with their outside world through the production of volatile organic compounds, but whether the volatiles have evolved to serve in plant defense is still a topic of considerable debate. Unharmed leaves constitutively release small amounts of volatiles, but when the leaves are damaged by herbivorous arthropods, they emit substantially more volatiles. These herbivore-induced plant volatiles (HIPVs) attract parasitoids and predators that kill insect herbivores, and this can benefit the plants. As yet, however, there is no tangible evolutionary evidence that this tritrophic interplay contributes to the selection forces that have shaped the volatile emissions of plants. With this in mind, we investigated the evolutionary changes in volatile emissions in invasive common ragwort and the respective defensive roles of its constitutive and inducible volatiles. This Eurasian plant has invaded other continents, where it evolved for many generations in the absence of specialized herbivores and their natural enemies. We found that, compared to native ragworts, invasive plants release higher levels of constitutive volatiles but considerably lower levels of herbivore-induced volatiles. As a consequence, invasive ragwort is more attractive to a specialist moth but avoided by an unadapted generalist moth. Importantly, conforming to the indirect defense hypothesis, a specialist parasitoid was much more attracted to caterpillar-damaged native ragwort, which was reflected in higher parasitism rates in a field trial. The evolution of foliar volatile emissions appears to be indeed driven by their direct and indirect roles in defenses against insects.