MOTIVATION Inferring species phylogenies with a history of gene losses and duplications is a challenging and an important task in computational biology. This problem can be solved by duplication-loss models in which the primary step is to reconcile a rooted gene tree with a rooted species tree. Most modern methods of phylogenetic reconstruction (from sequences) produce unrooted gene trees. This...

Raspberries (Rubus spp.) exhibit a unique rooting process that is initiated from the stem apex of primocane, conferring an unusual asexual mode of reproduction to this plant. However, the full complement of genes involved in this process has not been identified. To this end, the present study analyzed the transcriptomes of the Rubus primocane and floricane stem apex at three developmental stage...

The root of a phylogenetic tree is fundamental to its biological interpretation, but standard substitution models do not provide any information on its position. Here, we describe two recently developed models that relax the usual assumptions of stationarity and reversibility, thereby facilitating root inference without the need for an outgroup. We compare the performance of these models on a c...

UNLABELLED PREMISE OF THE STUDY Wild-boar soil disturbance (i.e., rooting) increases the abundance of some species of geophytes (i.e., plants with underground renewal buds) in upland meadows. However, the mechanisms that could lead to such enhanced prevalence remain unexplored. • METHODS We analyzed the effects of wild-boar disturbance on the size, nutrient (N, P, K, C, and total ash), and...

This paper addresses the problem of peak-to-average power ratio (PAPR) in orthogonal frequency division multiplexing (OFDM) systems. It also introduces a new PAPR reduction technique based on adaptive square-rooting (SQRT) companding process. The SQRT process of the proposed technique changes the statistical characteristics of the OFDM output signals from Rayleigh distribution to Gaussian-like ...

Vegetative shoot-based propagation of plants, including mass propagation of elite genotypes, is dependent on the development of shoot-borne roots, which are also called adventitious roots. Multiple endogenous and environmental factors control the complex process of adventitious rooting. In the past few years, we have shown that the auxin response factors ARF6 and ARF8, targets of the microRNA m...

Background and Aims The genetic basis of increased rooting below the plough layer, post-anthesis in the field, of an elite wheat line (Triticum aestivum 'Shamrock') with recent introgression from wild emmer (T. dicoccoides), is investigated. Shamrock has a non-glaucous canopy phenotype mapped to the short arm of chromosome 2B (2BS), derived from the wild emmer. A secondary aim was to determine ...

The potential of slow phase chlorophyll fluorescence (CF) to predict the physiological status of Pelargonium propagules (seven varieties in 28 different batches) post shipment or post simulated shipment was evaluated. The rooting ability of the cuttings was recorded and used to confirm the results from the CF data. The use of cardboard versus polystyrene packaging and the inclusion of two treat...

Root traits influence the amount of water and nutrient absorption, and are important for maintaining crop yield under drought conditions. The objectives of this research were to characterize variability of root traits among spring wheat genotypes and determine whether root traits are related to shoot traits (plant height, tiller number per plant, shoot dry weight, and coleoptile length), region...

The placement of the root node in a phylogeny is fundamental to characterizing evolutionary relationships. The root node of bee phylogeny remains unclear despite considerable previous attention. In order to test alternative hypotheses for the location of the root node in bees, we used the F1 and F2 paralogs of elongation factor 1-alpha (EF-1α) to compare the tree topologies that result when usi...