Supertree Research Articles

EasyCGTree: a pipeline for prokaryotic phylogenomic analysis based on core gene sets

BackgroundGenome-scale phylogenetic analysis based on core gene sets is routinely used in microbiological research. However, the techniques are still not approachable for individuals with little bioinformatics experience. Here, we present EasyCGTree, a user-friendly and cross-platform pipeline to reconstruct genome-scale maximum-likehood (ML) phylogenetic tree using supermatrix (SM) and supertree (ST) approaches.ResultsEasyCGTree was implemented in Perl programming languages and was built using a collection of published reputable programs. All the programs were precompiled as standalone executable files and contained in the EasyCGTree package. It can run after installing Perl language environment. Several profile hidden Markov models (HMMs) of core gene sets were prepared in advance to construct a profile HMM database (PHD) that was enclosed in the package and available for homolog searching. Customized gene sets can also be used to build profile HMM and added to the PHD via EasyCGTree. Taking 43 genomes of the genus Paracoccus as the testing data set, consensus (a variant of the typical SM), SM, and ST trees were inferred via EasyCGTree successfully, and the SM trees were compared with those inferred via the pipelines UBCG and bcgTree, using the metrics of cophenetic correlation coefficients (CCC) and Robinson–Foulds distance (topological distance). The results suggested that EasyCGTree can infer SM trees with nearly identical topology (distance < 0.1) and accuracy (CCC > 0.99) to those of trees inferred with the two pipelines.ConclusionsEasyCGTree is an all-in-one automatic pipeline from input data to phylogenomic tree with guaranteed accuracy, and is much easier to install and use than the reference pipelines. In addition, ST is implemented in EasyCGTree conveniently and can be used to explore prokaryotic evolutionary signals from a different perspective. The EasyCGTree version 4 is freely available for Linux and Windows users at Github (https://github.com/zdf1987/EasyCGTree4).

Chocolate coverage based on two Ecuadorian varieties CCN51 and Super Tree in the province of Pastaza, Ecuador

Objective: Its objective is to produce a bitter-type chocolate coating from the combination of cocoa of the CCN51 and Super Tree variety. Methodology: the product was elaborated through an experimental, quantitative, and qualitative method. Results: 18 experimental units were generated in the design, where 2 formulations with 2 replications were obtained, which allowed us to determine the best treatment through sensory analysis with a structured hedonic scale of acceptability (assessment from 1 to 5). The sensory evaluation was carried out with 30 untrained panelists, where they determined that T1 with 70% cocoa liquor is the most accepted, while for the trained judges there was no significant difference. The samples were subjected to bromatological analysis, obtaining as a result a moisture content of 1.59%, fat 37.86%, protein 9.26%, ash 2.04%, dry extract of defatted cocoa 99.38%, dry extract of total cocoa 98.41%, microbiological less than 100 cfu. ml-1 in total mesophiles, yeasts, and total coliforms. Limitations: have pilot equipment for processing. Conclusions: The parameters of the best treatment T1 are framed in the NTE INEN 621: 2010 in force in Ecuador for the manufacture of chocolates.

Chocolate couvertures development from combination of CCN51 and Super Tree cocoa varieties, in the Pastaza Province

Dark chocolate coatings contain a high percentage of cocoa, which is pleasing to the consumer’s taste. The aim of the research was to develop a bitter-type chocolate coating from the combination of CCN51 and super tree cocoa. In this study, an experimental method, with 18 treatments was applied. In the sensory analysis a hedonic scale test with 30 untrained judges and 15 trained ones was carried out, applying a completely random unifactorial design. The judges determined that T1 treatment with a content of 70% cocoa liquor, had a mean value of 3.8, while the value for the untrained judges was not significance. A bromatological analysis of the best treatment was made based on the NTE INEN 621:2010, resulting in moisture content of 37.86%, fat 9.26%, protein 2.04% and ash 99.38%, defatted cocoa dry extract 98.41%, dry extract of total cocoa and microbiological results less than 100 ufc.ml-1 in total mesophiles, yeasts and total coliforms, parameters that are within the permissible limit.

Native Super Trees Could Provide Climate Solutions to Houston

A Houston nonprofit identified 14 native “super tree” species that are particularly promising for mitigating climate change and public health concerns.

The super tree property at the successor of a singular

For an inaccessible cardinal κ, the super tree property (ITP) at κ holds if and only if κ is supercomact. However, just like the tree property, it can hold at successor cardinals. We show that ITP holds at the successor of the limit of ω many supercompact cardinals. Then we show that it can consistently hold at ℵω+1. We also consider a stronger principle, ISP and certain weaker variations of it. We determine which level of ISP can hold at a successor of a singular. These results fit in the broad program of testing how much compactness can exist in the universe, and obtaining large cardinal-type properties at smaller cardinals.

'Multi-SpaM': a maximum-likelihood approach to phylogeny reconstruction using multiple spaced-word matches and quartet trees.

Word-based or ‘alignment-free’ methods for phylogeny inference have become popular in recent years. These methods are much faster than traditional, alignment-based approaches, but they are generally less accurate. Most alignment-free methods calculate ‘pairwise’ distances between nucleic-acid or protein sequences; these distance values can then be used as input for tree-reconstruction programs such as neighbor-joining. In this paper, we propose the first word-based phylogeny approach that is based on ‘multiple’ sequence comparison and ‘maximum likelihood’. Our algorithm first samples small, gap-free alignments involving four taxa each. For each of these alignments, it then calculates a quartet tree and, finally, the program ‘Quartet MaxCut’ is used to infer a super tree for the full set of input taxa from the calculated quartet trees. Experimental results show that trees produced with our approach are of high quality.

Evolutionary divergence of the nuclear pore complex from fungi to metazoans.

Nuclear pore complex (NPC) is the largest multimeric protein assembly of the eukaryotic cell, which mediates the nucleocytoplasmic transport. The constituent proteins of this assembly (nucleoporins) are present in varying copy numbers to give a size from ~ 60 MDa (yeast) to 112 MDa (human) and share common ancestry with other membrane‐associated complexes such as COPI/COPII and thus share the same structural folds. However, the nucleoporins across species exhibit very low percentage sequence similarity and this reflects in their distinct secondary structure and domain organization. We employed thorough sequence and phylogenetic analysis guided from structure‐based alignments of all the nucleoporins from fungi to metazoans to understand the evolution of NPC. Through evolutionary pressure analysis on various nucleoporins, we deduced that these proteins are under differential selection pressure and hence the homologous interacting partners do not complement each other in the in vitro pull‐down assay. The super tree analysis of all nucleoporins taken together illustrates divergent evolution of nucleoporins and notably, the degree of divergence is more apparent in higher order organisms as compared to lower species. Overall, our results support the hypothesis that the protein–protein interactions in such large multimeric assemblies are species specific in nature and hence their structure and function should also be studied in an organism‐specific manner.

On statistical models on super trees

We consider a particular example of interplay between statistical models related to CFT on one hand, and to the spectral properties of ODE, known as ODE/IS correspondence, on the other hand. We focus at the representation of wave functions of Schrödinger operators in terms of spectral properties of associated transfer matrices on “super trees” (the trees whose vertex degree changes with the distance from the root point). Such trees with varying branchings encode the structure of the Fock space of the model. We discuss basic spectral properties of “averaged random matrix ensembles” in terms of Hermite polynomials for the transfer matrix of super trees. At small “branching velocities” we have related the problem of paths counting on super trees to the statistics of area-weighted one-dimensional Dyck paths. We also discuss the connection of the spectral statistics of random walks on super trees with the Kardar-Parisi-Zhang scaling.

Taxonomic variation among &lt;i&gt;Schinus molle&lt;/i&gt; L. plants associated with a slight change in elevation

This study examined the degree of variations in DNA fingerprints associated with slight altitudinal change of Schinus molle grown in Abha region, Saudi Arabia. Seven populations from Schinus molle plants located at 2193.0, 2246.0, 2197.7, 2441.0, 2372.0, 2250.6 and 2175.0 meters had been investigated. The degree of genetic variability was evaluated using random amplified polymorphic DNA (RAPD), mixed RAPD and intersimple sequence repeat markers (ISSR). The genetic similarity coefficients from RAPD analysis revealed the maximum similarity value (89.9%) was between population at 2250.6 m and population at 2175.0 m. The genetic similarity coefficients from mixed RAPD primers displayed the highest similarity value (87.6%) between population at 2246.0 m and population at 2197.7 m. Similarity coefficients from ISSR analysis revealed the highest similarity value (86.2%) among populations at 2193.0 m, 2246.0 m, 2441.0 m and at 2250.6 m. Super tree analysis (RAPD + mixed RAPD + ISSR) showed the highest similarity value (85.5%) between population at 2441.0 m and population at 2250.6 m. In conclusion, marker systems including RAPD, mixed RAPD and ISSR, alone or combined can be effectively used in determining the genetic relationship among Schinus molle plants even at very close populations.Bangladesh J. Plant Taxon. 24(2): 205–214.

The strong tree property and weak square

We show that it is consistent, relative to ω many supercompact cardinals, that the super tree property holds at for all but there are weak square and a very good scale at .

Reconstructing a SuperGeneTree minimizing reconciliation.

Combining a set of trees on partial datasets into a single tree is a classical method for inferring large phylogenetic trees. Ideally, the combined tree should display each input partial tree, which is only possible if input trees do not contain contradictory phylogenetic information. The simplest version of the supertree problem is thus to state whether a set of trees is compatible, and if so, construct a tree displaying them all. Classically, supertree methods have been applied to the reconstruction of species trees. Here we rather consider reconstructing a super gene tree in light of a known species tree S. We define the supergenetree problem as finding, among all supertrees displaying a set of input gene trees, one supertree minimizing a reconciliation distance with S. We first show how classical exact methods to the supertree problem can be extended to the supergenetree problem. As all these methods are highly exponential, we also exhibit a natural greedy heuristic for the duplication cost, based on minimizing the set of duplications preceding the first speciation event. We then show that both the supergenetree problem and its restriction to minimizing duplications preceding the first speciation are NP-hard to approximate within a n1-ϵ factor, for any 0 < ϵ < 1. Finally, we show that a restriction of this problem to uniquely labeled speciation gene trees, which is relevant to many biological applications, is also NP-hard. Therefore, we introduce new avenues in the field of supertrees, and set the theoretical basis for the exploration of various algorithmic aspects of the problems.

InTB - a data integration platform for molecular and clinical epidemiological analysis of tuberculosis

BackgroundTuberculosis is currently the second highest cause of death from infectious diseases worldwide. The emergence of multi and extensive drug resistance is threatening to make tuberculosis incurable. There is growing evidence that the genetic diversity of Mycobacterium tuberculosis may have important clinical consequences. Therefore, combining genetic, clinical and socio-demographic data is critical to understand the epidemiology of this infectious disease, and how virulence and other phenotypic traits evolve over time. This requires dedicated bioinformatics platforms, capable of integrating and enabling analyses of this heterogeneous data.ResultsWe developed inTB, a web-based system for integrated warehousing and analysis of clinical, socio-demographic and molecular data for Mycobacterium sp. isolates. As a database it can organize and display data from any of the standard genotyping methods (SNP, MIRU-VNTR, RFLP and spoligotype), as well as an extensive array of clinical and socio-demographic variables that are used in multiple countries to characterize the disease. Through the inTB interface it is possible to insert and download data, browse the database and search specific parameters. New isolates are automatically classified into strains according to an internal reference, and data uploaded or typed in is checked for internal consistency. As an analysis framework, the system provides simple, point and click analysis tools that allow multiple types of data plotting, as well as simple ways to download data for external analysis. Individual trees for each genotyping method are available, as well as a super tree combining all of them. The integrative nature of inTB grants the user the ability to generate trees for filtered subsets of data crossing molecular and clinical/socio-demografic information. inTB is built on open source software, can be easily installed locally and easily adapted to other diseases. Its design allows for use by research laboratories, hospitals or public health authorities. The full source code as well as ready to use packages is available at http://www.evocell.org/inTB.ConclusionsTo the best of our knowledge, this is the only system capable of integrating different types of molecular data with clinical and socio-demographic data, empowering researchers and clinicians with easy to use analysis tools that were not possible before.

Conventional Simulation of Biological Sequences Leads to a Biased Assessment of Multi-Loci Phylogenetic Analysis

Phylogenetic analysis based on multi-loci data sets is performed by means of supermatrix (SM) or supertree (ST) approaches. Recently, methods that rely on species tree (SppT) inference by the multi-species coalescence have also been implemented to tackle this problem. Generally, the relative performance of these three major strategies has been calculated using simulation of biological sequences. However, sequence simulation may not entirely replicate the complexity of the evolutionary process. Thus, issues regarding the usefulness of in silico sequences in studying the performance of phylogenetic methods have been raised. Here, we used both classical simulation and empirical data to investigate the relative performance of ST, SM, and the SppT methods. SM analyses performed better than the ST and SppTs in simulations, but not in empirical analyses where some ST methods significantly outperformed the others. Additionally, SM was the only method that was robust under evolutionary model violations in simulations. These results show that conventional biological sequence simulation cannot adequately resolve which method is most efficient to recover the SppT. In such simulations, the SM approach recovers the established phylogeny in most instances, whereas the performance of the ST and SppT methods is downgraded in simpler cases. When compared, the analyses based on empirical and simulated sequences yielded largely inconsistent results, with the latter showing a bias towards a seemingly superiority of SM approaches.

Invariant based quartet puzzling

BackgroundFirst proposed by Cavender and Felsenstein, and Lake, invariant based algorithms for phylogenetic reconstruction were widely dismissed by practicing biologists because invariants were perceived to have limited accuracy in constructing trees based on DNA sequences of reasonable length. Recent developments by algebraic geometers have led to the construction of lists of invariants which have been demonstrated to be more accurate on small sequences, but were limited in that they could only be used for trees with small numbers of taxa. We have developed and tested an invariant based quartet puzzling algorithm which is accurate and efficient for biologically reasonable data sets.ResultsWe found that our algorithm outperforms Maximum Likelihood based quartet puzzling on data sets simulated with low to medium evolutionary rates. For faster rates of evolution, invariant based quartet puzzling is reasonable but less effective than maximum likelihood based puzzling.ConclusionsThis is a proof of concept algorithm which is not intended to replace existing reconstruction algorithms. Rather, the conclusion is that when seeking solutions to a new wave of phylogenetic problems (super tree algorithms, gene vs. species tree, mixture models), invariant based methods should be considered. This article demonstrates that invariants are a practical, reasonable and flexible source for reconstruction techniques.

Robust Image Watermarking Using Adaptive Structure Based Wavelet Tree Quantization

This work presents a novel robust wavelet-tree-based watermarking method based on structure-based quantization. Wavelet-trees are arranged into super-trees. The watermark bits are then embedded into the super-trees by using the proposed structure-based quantization method. Next, the super-trees are quantized into a significant structure according to these bits. The quantized super-tree has a stronger statistical characteristic than the unquantized super-tree. Based on this characteristic, the watermark bits could be extracted robustly after an image distortion attack. Finally, an adaptive method is developed to raise the PSNR value. Compared with Wang et al. [17] method, the proposed adaptive method increases PSNR about 5.83 dB. The proposed method also has a higher maximum number of watermark bits than other methods, thus increasing the capacity for embedding. Besides, its computation load is low. Experimental results demonstrate that the proposed watermarking method using adaptive structure-based wavelet-tree quantization performs well in JPEG compression, filtering (Gaussian filter, median filter and sharpen) and geometric attacks (pixel shifting and rotation). In addition, it is very robust against multiple watermark attacks.

A Robust Blind Image Watermarking Method Using Local Maximum Amplitude Wavelet Coefficient Quantization

In this paper, an innovative blind watermarking algorithm has been proposed for imagery applications. This algorithm has used the coefficients of the discrete wavelet transform of the host image in the form of super trees to embed the predefined binary watermark in the host image. In this scheme, a pseudo random sequence is generated to determine the exact wavelet super trees used for embedding procedure. In the next step, after choosing the maximum and second maximum amplitude coefficients of each super tree, the distance vector between two coefficients is computed. For embedding bit zero of the specified watermark, the values of the distance vector elements are decreased, while for embedding bit 1, those values will be increased based on the proposed formulas. The experimental results show that the proposed algorithm has significant robustness against image processing attacks, especially JPEG compression and also the PSNR value for the watermarked images generated by the proposed method is more than 42 dB. The watermark bits may be inserted into the host image either in spatial or in the transform domain. It is shown that hiding information in the transform domain will lead to a more robust watermarking system against most of the attacks (6). Among these methods, methods based on discrete wavelet transform (DWT) are of great renown. This is due to specific features of space-frequency localization, multi-resolution display, linear computational complexity and the excellent modeling related to Human Vision System

Differential Energy Based Watermarking Algorithm Using Wavelet Tree Group Modulation (WTGM) and Human Visual System

Wavelet tree based watermarking algorithms are using the wavelet coefficient energy difference for copyright protection and ownership verification. WTQ (Wavelet Tree Quantization) algorithm is the representative technique using energy difference for watermarking. According to the cryptanalysis on WTQ, the watermark embedded in the protected image can be removed successfully. In this paper, we present a novel differential energy watermarking algorithm based on the wavelet tree group modulation structure, i.e. WTGM (Wavelet Tree Group Modulation). The wavelet coefficients of host image are divided into disjoint super trees (each super tree containing two sub-super trees). The watermark is embedded in the relatively high-frequency components using the group strategy such that energies of sub-super trees are close. The employment of wavelet tree structure, sum-of-subsets and positive/negative modulation effectively improve the drawbacks of the WTQ scheme for its insecurity. The integration of the HVS (Human Visual System) for WTGM provides a better visual effect of the watermarked image. The experimental results demonstrate the effectiveness of our algorithm in terms of robustness and imperceptibility.

Fifty years of character compatibility concepts at work

In the mid 19th century, systematic biologists realized that observable similarities and differences among a group of related species could be the basis for hypotheses about the evolutionary relationships among the species and their ancestors. Such hypotheses can be expressed as characters. A character is comprised of two or more character states of species considered to be similar with respect to a basis for comparison. The states of a character may also be arranged into a character state tree to hypothesize speciation events associated with changes from one character state to another. In the mid 20th century, some systematists realized that sometimes pairs of characters (or character state trees) could be incompatible as hypotheses, i.e., they could not both be true. Through the 1950s, '60s and '70s, tests for, and ways to resolve, incompatibilities were used to estimate an ancestor rela- tion based on mutually compatible characters. An estimate was often shown as a diagram connecting ancestors to their immediate descendants (not quite correctly) called a phylogenetic tree. More recently, other applications of compatibility concepts have been developed, including: identify characters that appear to be random in the context of their data set; combine estimates of ancestor relations for subsets of taxa in a larger collection into a single estimate (a so-called supertree) for the whole collection; and interpret geographic patterns in an evolutionary context.

On super vertex-magic labeling

For a graph G(V, E) an injective mapping f from V ⋃ E to the set {1, 2, 3, …, v + ε} is a vertex-magic total labeling if there is a constant h so that for every vertex v ∈ V, f (v) + Σ f (uv) = h where the sum runs over all vertices u adjacent to v. A vertex-magic labeling f is called super vertex-magic labeling if f (E) = {1, 2, 3, …, ε} and f (V) = {ε + 1, ε + 2, …, ε + v}. A graph G is called a super vertex-magic if there exists a super vertex-magic labeling of G. In this paper, we established some properties of super vertex magic trees and exhibit super vertex-magic labeling of a kite graph.

Formation of a Tree having a Low Lignin Content

It is important in the 21st century that resources and energy production are increased and solutions to environmental problems are found. One way to do this is to meet some of our food, resource and energy demands with biomass. The major chemical components of biomass are lignin, hemicellulose and cellulose. To utilize them effectively a super tree with an increased polysaccharide and decreased lignin content is needed. Eleven lines of transformants in which the expression of a peroxidase gene has been suppressed were analyzed chemically, biologically and histochemically. The results showed that the lignin content of the transformants was lower than that of the control. It became clear that the lignin content could be suppressed by an antisense RNA method using the peroxidase gene. From the chemical analysis, the liinin of the transformants was found to have more syringyl and uncondensed units than the control. This chemical change faciliited the conversion of biomass and pulping, as shown in a pulping test. It is therefore possible to make a super tree low in lignin and high in polysaccharide.