We establish universality and ultra-homogeneity of (U,uGH), the collection of all compact ultrametric spaces endowed with the so-called Gromov-Hausdorff ultrametric. This result also gives rise to a ...novel construction of the so-called R-Urysohn universal ultrametric space for each countable subset R⊂R≥0 containing 0.
10 primers each of random amplified polymorphic DNA (RAPD), inter-simple sequence repeats (ISSR), inter primer binding site (iPBS) and start codon targeted (SCoT) were used to analyze genetic ...polymorphism and relationship between 50 genotypes of 5 economical important native bamboos (Bambusa cacharensis, B. mizorameana, Dendrocalamus manipureanus, D. hamiltonii and D. sikkimensis) of North-East India. The 40 different primers generated 111, 115, 116 and 138 polymorphic bands for RAPD, ISSR, iPBS and SCoT markers respectively. The comparative analysis of 4 marker systems based on polymorphic information content (PIC), effective multiplex ratio (EMR) and marker index (MI) values showed SCoT to be more informative with higher discriminating power than the other three markers. The correlation value (r) as determined by the Mantel test ranged from 0.60 (SCoT and RAPD) to 0.83 (iPBS and ISSR) indicating a high positive correlation between the markers. The close correspondence between the genetic matrices of RAPD, ISSR, iPBS and SCoT markers revealed the effectiveness of each marker system in determining the genetic relationship between bamboos. UPGMA (Unweighted Pair Group Arithmetic Mean Method) dendrograms generated from DNA marker analysis demonstrated species-specific clustering of different bamboo genotypes. Except for RAPD, the dendrograms of ISSR, iPBS and SCoT markers also showed a close association of bamboo genotypes based on geographical origin. Principal coordinate analysis (PCoA) revealed the distribution of different bamboo genotypes in accordance with the cluster analysis. The cluster grouping based on phytochemical study not only discriminated the different bamboo species but also illustrated a location-specific grouping of the genotypes. The bamboo clustering pattern derived from phytochemical analysis matched closely with the dendrograms generated by the DNA markers. The present investigation established the possibility of using a combined molecular and phytochemical marker approach to determine the genetic relationship between 5 native bamboos of North-East India with high precision.
UPGMA dendrogram of 5 bamboo species based on RAPD, ISSR, SCoT and iPBS combined data. Bi-plot PCA (Principal Component Analysis) of the 20 genotypes of 5 bamboo species generated from 5 biochemical parameters. Display omitted
•RAPD, ISSR, iPBS and SCoT markers were employed to study the genetic relationship of 50 different genotypes belonging to 5 native bamboos of North-East India.•Comparative study of the marker systems based on PIC, EMR and MI values revealed SCoT markers to be more informative than other markers.•The close correspondence between the genetic matrixes of 4 markers as indicated by high (r) value showed the effectiveness of each marker system.•The UPGMA dendrograms of ISSR, iPBS, and SCoT exhibited a closed association of the bamboo genotypes based on geographical origins.•The bamboo clustering pattern derived from the phytochemical variation study matched closely with the UPGMA dendrograms generated by DNA markers.
In order to accurately monitor the changes in a freshwater ecosystem in response to anthropogenic stressors, microbe–environment correlations and microbe–microbe interactions were combined to ...determine crucial indicator taxa in contaminated sediments. The diversity, composition, and co–occurrence pattern of bacterial communities in 23 sediment samples collected from Lake Taihu were explored using 16S rRNA amplicon sequencing analysis. Fisher's exact test showed that the cluster analyses of samples could show a direct correlation between the relative abundance of bacterial communities and the physicochemical properties of the sediment (P < 0.0001), suggesting that bacterial communities can be used to monitor contamination gradients in freshwater sediments. According to the microbe–environment correlation, 24 orders and 60 families were initially identified via indicator species analysis as indicator taxa of different pollution levels. The co–occurrence network further showed that topological features of bacterial communities were clearly different at different pollution levels, although the diversity and composition of bacterial communities displayed similarities between minimally and moderately polluted sites. Indicator taxa were then screened for keystone species, which co–occurrence relationships showed the high degree and low betweenness centrality values (i.e. degree >5, betweenness centrality <1000) of the network. Nine orders and 13 families were finally extracted as crucial indicator taxa of the different pollution levels in eutrophic Lake Taihu. Obtaining crucial indicator taxa from environmental sequences allows to trace increasing levels of pollution in aquatic ecosystems and provides a novel mean to monitor watersheds sensitive to anthropic influences.
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•Microbe–environment correlations and microbe–microbe interactions were combined to determine crucial indicator.•Bacterial community assembly was mainly driven by pollution level at sampling sites.•Topological features of bacterial co–occurrence network were different at different pollution levels.•Nine orders and 13 families were identified as crucial indicators of the different pollution levels.
Crucial indicators of different pollution levels were identified by combining microbe–environment correlation and microbe–microbe interrelations.
The study of functional diversity (FD) provides ways to understand phenomena as complex as community assembly or the dynamics of biodiversity change under multiple pressures. Different frameworks are ...used to quantify FD, either based on dissimilarity matrices (e.g. Rao entropy, functional dendrograms) or multidimensional spaces (e.g. convex hulls, kernel‐density hypervolumes), each with their own strengths and limits. Frameworks based on dissimilarity matrices either do not enable the measurement of all components of FD (i.e. richness, divergence, and regularity), or result in the distortion of the functional space. Frameworks based on multidimensional spaces do not allow for comparisons with phylogenetic diversity (PD) measures and can be sensitive to outliers.
We propose the use of neighbor‐joining trees (NJ) to represent and quantify FD in a way that combines the strengths of current frameworks without many of their weaknesses. Importantly, our approach is uniquely suited for studies that compare FD with PD, as both share the use of trees (NJ or others) and the same mathematical principles.
We test the ability of this novel framework to represent the initial functional distances between species with minimal functional space distortion and sensitivity to outliers. The results using NJ are compared with conventional functional dendrograms, convex hulls, and kernel‐density hypervolumes using both simulated and empirical datasets.
Using NJ, we demonstrate that it is possible to combine much of the flexibility provided by multidimensional spaces with the simplicity of tree‐based representations. Moreover, the method is directly comparable with taxonomic diversity (TD) and PD measures, and enables quantification of the richness, divergence and regularity of the functional space.
The electrical power grid is a critical infrastructure, with disruptions in transmission having severe repercussions on daily activities, across multiple sectors. To identify, prevent, and mitigate ...such events, power grids are being refurbished as 'smart' systems that include the widespread deployment of GPS-enabled phasor measurement units (PMUs). PMUs provide fast, precise, and time-synchronized measurements of voltage and current, enabling real-time wide-area monitoring and control. However, the potential benefits of PMUs, for analyzing grid events like abnormal power oscillations and load fluctuations, are hindered by the fact that these sensors produce large, concurrent volumes of noisy data. In this paper, we describe working with power grid engineers to investigate how this problem can be addressed from a visual analytics perspective. As a result, we have developed PMU Tracker, an event localization tool that supports power grid operators in visually analyzing and identifying power grid events and tracking their propagation through the power grid's network. As a part of the PMU Tracker interface, we develop a novel visualization technique which we term an epicentric cluster dendrogram , which allows operators to analyze the effects of an event as it propagates outwards from a source location. We robustly validate PMU Tracker with: (1) a usage scenario demonstrating how PMU Tracker can be used to analyze anomalous grid events, and (2) case studies with power grid operators using a real-world interconnection dataset. Our results indicate that PMU Tracker effectively supports the analysis of power grid events; we also demonstrate and discuss how PMU Tracker's visual analytics approach can be generalized to other domains composed of time-varying networks with epicentric event characteristics.
In amniotes, the predominant developmental strategy underlying body size evolution is thought to be adjustments to the rate of growth rather than its duration. However, most theoretical and ...experimental studies supporting this axiom focus on pairwise comparisons and/or lack an explicit phylogenetic framework. We present the first large-scale phylogenetic comparative analysis examining developmental strategies underlying the evolution of body size, focusing on non-avialan theropod dinosaurs. We reconstruct ancestral states of growth rate and body mass in a taxonomically rich dataset, finding that contrary to expectations, changes in the rate and duration of growth played nearly equal roles in the evolution of the vast body size disparity present in non-avialan theropods-and perhaps that of amniotes in general.
Sets of multiple scalar fields can be used to model many types of variation in data, such as uncertainty in measurements and simulations or time‐dependent behavior of scalar quantities. Many ...structural properties of such fields can be explained by dependencies between different points in the scalar field. Although these dependencies can be of arbitrary complexity, correlation, i.e., the linear dependency, already provides significant structural information. Existing methods for correlation analysis are usually limited to positive correlation, handle only local dependencies, or use combinatorial approximations to this continuous problem. We present a new approach for computing and visualizing correlated regions in sets of 2‐dimensional scalar fields. This paper describes the following three main contributions: (i) An algorithm for hierarchical correlation clustering resulting in a dendrogram, (ii) a generalization of topological landscapes for dendrogram visualization, and (iii) a new method for incorporating negative correlation values in the clustering and visualization. All steps are designed to preserve the special properties of correlation coefficients. The results are visualized in two linked views, one showing the cluster hierarchy as 2D landscape and the other providing a spatial context in the scalar field's domain. Different coloring and texturing schemes coupled with interactive selection support an exploratory data analysis.
Ramadiana S, Hapsoro D, Evizal R, Setiawan K, Karyanto A, Yusnita. 2021. Genetic diversity among 24 clones of robusta coffee in Lampung based on RAPD markers. Biodiversitas 22: 3122-3129. This study ...aimed to estimate the genetic diversity among 24 clones of Robusta coffee from Lampung, Indonesia, by use of RAPD markers. The clones consisted of 18 local and 6 BP clones. These BP clones were developed from a breeding program of The Indonesian Coffee and Cocoa Research Institute. Genomic DNAs extracted from these clones were subjected to polymerase chain reaction and the amplified products were run using gel electrophoresis. Eleven random primers produced clear, reproducible, scorable bands. Fifty-four of 86 bands showed polymorphism and were used to construct a dendrogram based on UPGMA Jaccard's Similarity Coefficients. The genetic base of the population was narrow (average genetic similarity 68.4%), ranging from 26-93%. The genetic similarity of the local clones was higher than that of BP clones. The clones were clustered into five groups. Group 1 contained one clone (BP 534), while each of Group II-V contained more than one clone. The average genetic similarity of BP 534 to each clone of Group II-V was 41%. The genetic similarity of clones in Group II, III, IV, and V were 55.5%, 43.0%, 81.1%, and 80.1%, respectively. This research should be very useful for selecting parents in a breeding program to produce better clones of Robusta coffee.
The Middle Stone Age (MSA) of eastern Africa has a long history of research and is accompanied by a rich fossil record, which, combined with its geographic location, have led it to play an important ...role in investigating the origins and expansions of Homo sapiens. Recent evidence has suggested an earlier appearance of our species, indicating a more mosaic origin of modern humans, highlighting the importance of regional and inter-regional patterning and bringing into question the role that eastern Africa has played. Previous evaluations of the eastern African MSA have identified substantial variability, only a small proportion of which is explained by chronology and geography. Here, we examine the structure of behavioural, temporal, geographic and environmental variability within and between sites across eastern Africa using a quantitative approach. The application of hierarchical clustering identifies enduring patterns of tool use and site location through the MSA as well as phases of significant behavioural diversification and colonisation of new landscapes, particularly notable during Marine Isotope Stage 5. As the quantity and detail of technological studies from individual sites in eastern Africa gathers pace, the structure of the MSA record highlighted here offers a roadmap for comparative studies.
•Quantitative analyses of Middle Stone Age stone tool typology from eastern Africa.•A core set of stone tool types consistently found in MSA assemblages is identified.•Longstanding occupation of key geographic and environmental contexts identified.•Expansions into new landscape types in MIS 5.•Core tool set augmented by additional forms during interglacial phases.
Sabah (Malaysia) on the Island of Borneo has a high plant diversity (>8000 species) occurring on a wide range of soils, including ultramafic soils which are known to host hyperaccumulator plants. In ...this study a new approach (“Herbarium X-ray Fluorescence Ionomics”) was used to obtain elemental data from herbarium specimens using non-destructive X-ray Fluorescence spectroscopy analysis. In total ~7300 specimens were thus analysed for nickel, cobalt, and manganese concentrations at the Herbarium of the Forest Research Centre (FRC) in Sepilok, Sabah. The measurements led to recording a total of 759 specimens (originating from 17 families in 30 genera and 74 species) as trace element hyperaccumulators, including 28 nickel hyperaccumulator species (in 10 families, 17 genera), 12 cobalt hyperaccumulator species (in 3 families, 7 genera), and 51 manganese hyperaccumulator species (in 12 families, 24 genera). The outcomes of this research demonstrate that X-ray Fluorescence scanning is highly useful approach for hyperaccumulator plant discovery in herbarium collections that has the potential to add vast numbers of hyperaccumulating taxa to the global inventory.
•Handheld X-Ray Fluorescence analysis can be used to obtain elemental data from vast numbers of herbarium specimens.•In total, ~7300 herbarium specimens were analysed for nickel, cobalt, and manganese concentrations at the Herbarium of the Forest Research Centre (FRC) in Sepilok, Sabah, Malaysia.•This led to the discovery of 28 nickel hyperaccumulator species (in 10 families, 17 genera), 12 cobalt hyperaccumulator species (in 3 families, 7 genera), and 51 manganese hyperaccumulator species (in 12 families, 24 genera).
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