Efficient Recycled Algorithms for Quantitative Trait Models on Phylogenies.
ABSTRACT: We present an efficient and flexible method for computing likelihoods for phenotypic traits on a phylogeny. The method does not resort to Monte Carlo computation but instead blends Felsenstein's discrete character pruning algorithm with methods for numerical quadrature. It is not limited to Gaussian models and adapts readily to model uncertainty in the observed trait values. We demonstrate the framework by developing efficient algorithms for likelihood calculation and ancestral state reconstruction under Wright's threshold model, applying our methods to a data set of trait data for extrafloral nectaries across a phylogeny of 839 Fabales species.
Project description:Extrafloral nectaries are a defence trait that plays important roles in plant-animal interactions. Gossypium species are characterized by cellular grooves in leaf midribs that secret large amounts of nectar. Here, with a panel of 215 G. arboreum accessions, we compared extrafloral nectaries to nectariless accessions to identify a region of Chr12 that showed strong differentiation and overlapped with signals from GWAS of nectaries. Fine mapping of an F2 population identified GaNEC1, encoding a PB1 domain-containing protein, as a positive regulator of nectary formation. An InDel, encoding a five amino acid deletion, together with a nonsynonymous substitution, was predicted to cause 3D structural changes in GaNEC1 protein that could confer the nectariless phenotype. mRNA-Seq analysis showed that JA-related genes are up-regulated and cell wall-related genes are down-regulated in the nectary. Silencing of GaNEC1 led to a smaller size of foliar nectary phenotype. Metabolomics analysis identified more than 400 metabolites in nectar, including expected saccharides and amino acids. The identification of GaNEC1 helps establish the network regulating nectary formation and nectar secretion, and has implications for understanding the production of secondary metabolites in nectar. Our results will deepen our understanding of plant-mutualism co-evolution and interactions, and will enable utilization of a plant defence trait in cotton breeding efforts.
Project description:Ant guards protect plants from herbivores, but can also hinder pollination by damaging reproductive structures and/or repelling pollinators. Natural selection should favour the evolution of plant traits that deter ants from visiting flowers during anthesis, without waiving their defensive services. The Distraction Hypothesis posits that rewarding ants with extrafloral nectar could reduce their visitation of flowers, reducing ant-pollinator conflict while retaining protection of other structures.We characterised the proportion of flowers occupied by ants and the number of ants per flower in a Mexican ant-plant, Turnera velutina. We clogged extrafloral nectaries on field plants and observed the effects on patrolling ants, pollinators and ants inside flowers, and quantified the effects on plant fitness. Based on the Distraction Hypothesis, we predicted that preventing extrafloral nectar secretion should result in fewer ants active at extrafloral nectaries, more ants inside flowers and a higher proportion of flowers occupied by ants, leading to ant-pollinator conflict, with reduced pollinator visitation and reduced plant fitness.Overall ant activity inside flowers was low. Preventing extrafloral nectar secretion through clogging reduced the number of ants patrolling extrafloral nectaries, significantly increased the proportion of flowers occupied by ants from 6.1% to 9.7%, and reduced plant reproductive output through a 12% increase in the probability of fruit abortion. No change in the numbers of ants or pollinators inside flowers was observed. This is the first support for the Distraction Hypothesis obtained under field conditions, showing ecological and plant fitness benefits of the distracting function of extrafloral nectar during anthesis. Synthesis. Our study provides the first field experimental support for the Distraction Hypothesis, suggesting that extrafloral nectaries located close to flowers may bribe ants away from reproductive structures during the crucial pollination period, reducing the probability of ant occupation of flowers, reducing ant-pollinator conflict and increasing plant reproductive success.
Project description:Mite domatia are small structures on the underside of plant leaves that provide homes for predacious or fungivorous mites. In turn, mites inhabiting domatia defend the plant by consuming leaf herbivores and pathogens, which can result in a domatia-mediated, plant-mite defence mutualism. Several recent studies have suggested that plants receive enhanced benefits when they provide a foliar food source, such as sugars secreted from extrafloral nectaries, to mite mutualists alongside mite domatia. However, the effect of foliar sugar on reducing leaf pathogen load via domatia-inhabiting mites has not been directly investigated.To fill this gap, the links between foliar sugar addition, domatia-inhabiting mite abundance, and pathogen load were experimentally evaluated in wild grape. Furthermore, because the proposed combined benefits of providing food and housing have been hypothesized to select for the evolutionary correlation of extrafloral nectaries and domatia across plant lineages, a literature survey aimed at determining the overlap of mite domatia and extrafloral nectaries across plant groups was also conducted.It was found that leaves with artificial addition of foliar sugar had 58-80 % more mites than leaves without foliar sugar addition, and that higher mite abundances translated to reduced powdery mildew (Erysiphe necator) loads on leaves. It was found that mite domatia and extrafloral nectaries occur non-randomly in the same clades across Eudicots. Genera with both traits are reported to highlight candidate lineages for future studies.Together, the results demonstrate that foliar sugar can indeed enhance the efficacy of domatia-mediated plant-mite mutualisms, and suggest that this synergism has the potential to influence the co-distribution of foliar nectar and mite domatia across plants.
Project description:Comparative RNA-Seq study of expression in Phaseolus vulgaris nectaries Overall design: RNA-seq of extrafloral nectaries, floral nectaries and leaf tissue from Phaseolus vulgaris cv Blue Lake 274.
Project description:To identify the genes encoding the defense proteins and gain a deeper insight into the Ptt nectary transcriptom, poplar DNA microarrays (Affymetrix) were hybridized with RNA of extrafloral nectaries and nectary-free leaf sections Many plant species grow extrafloral nectaries and produce nectar to attract carnivore arthropods as defenders against herbivores. We studied in Populus how insect feeding feeds back on nectary development and activity. Two nectary types evolved with Populus trichocarpa (Ptr) and P. tremula x P. tremuloides (Ptt) were studied from their ecology down to the genes and molecules. 3 samples of leaves and 3 of nectaries from P. tremula tremuloides field-culture
Project description:Phylogeny reflects genetic and phenotypic traits in Bacteria and Archaea. The phylogenetic conservatism of microbial traits has prompted the application of phylogeny-based algorithms to predict unknown trait values of extant taxa based on the traits of their evolutionary relatives to estimate, for instance, rRNA gene copy numbers, gene contents or tolerance to abiotic conditions. Unlike the 'macrobial' world, microbial ecologists face scenarios potentially compromising the accuracy of trait reconstruction methods, as, for example, extremely large phylogenies and limited information on the traits of interest. We review 990 bacterial and archaeal traits from the literature and support that phylogenetic trait conservatism is widespread through the tree of life, while revealing that it is generally weak for ecologically relevant phenotypic traits and high for genetically complex traits. We then perform a simulation exercise to assess the accuracy of phylogeny-based trait predictions in common scenarios faced by microbial ecologists. Our simulations show that ca. 60% of the variation in phylogeny-based trait predictions depends on the magnitude of the trait conservatism, the number of species in the tree, the proportion of species with unknown trait values and the mean distance in the tree to the nearest neighbour with a known trait value. Results are similar for both binary and continuous traits. We discuss these results under the light of the reviewed traits and provide recommendations for the use of phylogeny-based trait predictions for microbial ecologists.
Project description:To identify the genes encoding the defense proteins and gain a deeper insight into the Ptt nectary transcriptom, poplar DNA microarrays (Affymetrix) were hybridized with RNA of extrafloral nectaries and nectary-free leaf sections Many plant species grow extrafloral nectaries and produce nectar to attract carnivore arthropods as defenders against herbivores. We studied in Populus how insect feeding feeds back on nectary development and activity. Two nectary types evolved with Populus trichocarpa (Ptr) and P. tremula x P. tremuloides (Ptt) were studied from their ecology down to the genes and molecules. Overall design: 3 samples of leaves and 3 of nectaries from P. tremula tremuloides field-culture
Project description:In September 2013, we discovered sooty mould growing on kenaf with the extrafloral nectaries in Iksan, Korea and identified the causative fungus as Leptoxyphium kurandae based on morphological characteristics and phylogenetic analyses. This is the first report of sooty mould caused by L. kurandae on kenaf in Korea and globally.
Project description:Upland cotton (Gossypium hirsutum L.) produces terpenoid aldehydes (TAs) that protect the plant from microbial and insect infestations. Foliar TAs include plus (+)- and minus (-)-gossypol, hemigossypolone, and heliocides. To examine foliar TAs' response to physical wounding, the four TA derivatives of a fully glanded G. hirsutum variety JACO GL were quantified by ultra-high performance liquid chromatography. The results show that foliar heliocides increased by 1.7-fold in younger leaves after wounding. While the hemigossypolone level was not affected by the physical wounding, the level of heliocides was significantly increased up to 1.8-fold in the younger leaves. Upland cotton accumulates concentrated carbohydrates, amino acids, and fatty acids in foliar extrafloral nectar (EFN) to serve as a nutrient resource, which attracts both beneficial insects and damaging pests. To better understand the nectar physiology, particularly to determine the temporal dynamics of EFN metabolites in response to the wounding, a gas chromatograph-mass spectrometer (GC-MS) was used to perform metabolic profiling analyses of a G. hirsutum variety Deltapine 383 that has fully developed extrafloral nectaries. A total of 301 compounds were monitored, specifically 75 primary metabolites, two secondary metabolites and 224 unidentified compounds. The physical wounding treatment changed the EFN composition and lowered overall production. The accumulation of 30 metabolites was altered in response to the wounding treatment and threonic acid levels increased consistently. GC-MS combined with Kovat's analysis enabled identification of EFN secondary metabolites including furfuryl alcohol and 5-hyrdomethoxyfurfural, which both have antioxidant and antimicrobial properties that may protect the nectar against microbial pathogens. This study provides new insights into the wounding response of cotton plants in terms of cotton metabolites found in leaf glands and extrafloral nectar as well as highlighting some protective functions of secondary metabolites produced in foliar glands and extrafloral nectaries.
Project description:Extrafloral (EF) nectaries recruit carnivorous arthropods that protect plants from herbivory, but they can also be exploited by nectar thieves. We studied the opportunistic, targeted predation (and destruction) of EF nectaries by insects, and the localized chemical defences that plants presumably use to minimize this effect. In field and laboratory experiments, we identified insects that were possibly responsible for EF nectary predation in Vicia faba (fava bean) and determined the extent and accuracy of the feeding damage done to the EF nectaries by these insects. We also performed biochemical analyses of plant tissue samples in order to detect microscale distribution patterns of chemical defences in the area of the EF nectary. We observed selective, targeted feeding on EF nectaries by several insect species, including some that are otherwise not primarily herbivorous. Biochemical analyses revealed high concentrations of l-3,4-dihydroxyphenylalanine, a non-protein amino acid that is toxic to insects, near and within the EF nectaries. These results suggest that plants allocate defences to the protection of EF nectaries from predation, consistent with expectations of optimal defence theory, and that this may not be entirely effective, as insects limit their exposure to these defences by consuming only the secreting tissue of the nectary.