Phylogenetic Tree Construction Methods Research Articles

Distribution rules of antiviral traditional Chinese medicine based on data driven analysis

Objective: To mine the distribution rules of antiviral traditional Chinese medicine (TCM), in order to provide the basis for the screening of antiviral activity of TCM and candidate for current epidemic prevention and control. Methods: Taking the Research and Application of Antiviral Chinese Herbal Medicine and the literature reports of antiviral TCM in CNKI and Web of science as information sources, the relevant information was standardized, and the distribution rules of medicinal properties, families and genera, active ingredients and activity of antiviral TCM were mined by frequency analysis, co-occurrence analysis and phylogenetic tree construction methods. Results: A total of 511 antiviral TCM were screened, containing 41 of the 48 herbs involved in the medicines and three prescriptions of coronavirus disease 2019 (COVID-19). Mostly with medicinal properties such as cold nature, bitter taste, return to the lung and liver meridian, among which Bailangen (Isatidis Radix), Huangqin (Scutellariae Radix), and Jinyinhua (Lonicerae Japonicae Flos) were the most common. The data of coronaviridae was 135, and the high-frequency TCM were Chaihu (Bupleuri Radix), Gancao (Glycyrrhizae Radix et Rhizoma), and Isatidis Radix. Meanwhile, it was found that Isatidis Radix and Kudouzi (the seed of Sophora alopecuroides) were the most studied TCM during the SARS period in 2003, while in 2020, the research on Sangbaipi (Mori Cortex) was the first when COVID-19 was sudden. The effective ingredients of antiviral TCM were mostly polysaccharides and flavonoids. TCM with antiviral effects involved a total of 564 base source species, which had significant clustering on phylogenetic trees and were mainly distributed in the chrysanthemum and rose branches of the seed plant phylum, with Asteraceae, Labiatae, Leguminosae, and Rosaceae having the most antiviral TCM. Conclusion: These results suggested that the attributes of TCM with antiviral effects are mainly bitter, cold, lung and liver meridian. TCM origin from Asteraceae, Labiatae, and Leguminosae are more likely to have antiviral effects. Their effective components such as astragalus polysaccharide, Isatidis Radix polysaccharide, quercetin, caffeic acid and ursolic acid are polysaccharides or flavonoids, and these rules are basically consistent with the medicines and three prescriptions promoted and used in this fight against the COVID-19 epidemic. This study provides a reference for the screening of antiviral TCM activity, especially for the screening of candidate TCM for the prevention and control of the current COVID-19.

Phylogenetic Tree Construction Using K-Mer Forest- Based Distance Calculation

Phylogenetics is one of the dominant data engineering research disciplines based on biological information. More particularly here, we consider raw DNA sequences and do comparative analysis in order to come up with important conclusions. When representing evolutionary relationships among different organisms in a concise manner, the phylogenetic tree helps significantly. When constructing phylogenetic trees, the elementary step is to calculate the genetic distance among species. Alignment-based sequencing and alignment-free sequencing are the two main distance computation methods that are used to find genetic relatedness of different species. In this paper we propose a novel alignment-free, pairwise, distance calculation method based on k-mers and a state of art machine learning-based phylogenetic tree construction mechanism. With the proposed approach we can convert longer DNA sequences into compendious k-mer forests which gear up the efficiency of comparison. Later we construct the phylogenetic tree based on calculated distances with the help of an algorithm build upon k-medoid clustering, which guaranteed significant efficiency and accuracy compared to traditional phylogenetic tree construction methods.

Applying MSSIM combined chaos game representation to genome sequences analysis

Converting DNA sequence to image by using chaos game representation (CGR) is an effective genome sequence pretreatment technology, which provides the basis for further analysis between the different genes. In this paper, we have constructed 10 mammal species, 48 hepatitis E virus (HEV), and 10 kinds of bacteria genetic CGR images, respectively, to calculate the mean structural similarity (MSSIM) coefficient between every two CGR images. From our analysis, the MSSIM coefficient of gene CGR images can accurately reflect the similarity degrees between different genomes. Hierarchical clustering analysis was used to calculate the class affiliation and construct a dendrogram. Large numbers of experiments showed that this method gives comparable results to the traditional Clustal X phylogenetic tree construction method, and is significantly faster in the clustering analysis process. Meanwhile MSSIM combined CGR method was also able to efficiently clustering of large genome sequences, which the traditional multiple sequence alignment methods (e.g. Clustal X, Clustal Omega, Clustal W, et al.) cannot classify.

Evaluation of the taxonomic status of water dropwort (Oenanthe, Apiaceae) accessions from East Asia based on nuclear rDNA internal transcribed spacer sequences.

Oenanthe L. is a taxonomically complex genus, several species of which have long been used as vegetables and traditional medicines in East Asia. In order to clarify the taxonomic status of Oenanthe accessions and provide baseline data for the sustainable use of its genetic resources, we examined sequence variations in the internal transcribed spacer (ITS) region of Oenanthe accessions collected from a wide geographical area in China and its neighboring countries. For comparison, ITS sequences in GenBank for almost all currently reported species of Oenanthe were also included in our analyses. Both phylogenetic tree construction methods (Bayesian inference and maximum likelihood) revealed that the accessions tended to cluster into two groups, which were closely related to O. mildbraedii and O. sarmentosa. However, these two species have never been recorded in China or its neighboring countries. Therefore, it seems probable that in our sampled locations, Oenanthe accessions have been given an incorrect name, such as O. javanica. Future studies should carefully check the morphological characteristics of other Oenanthe species and sequence their ITS regions in order to clarify the taxonomic status of the genus.

Phylogenetic tree construction using sequential stochastic approximation Monte Carlo

Monte Carlo methods have received much attention recently in the literature of phylogenetic tree construction. However, they often suffer from two difficulties, the curse of dimensionality and the local-trap problem. The former one is due to that the number of possible phylogenetic trees increases at a super-exponential rate as the number of taxa increases. The latter one is due to that the phylogenetic tree has often a rugged energy landscape. In this paper, we propose a new phylogenetic tree construction method, which attempts to alleviate these two difficulties simultaneously by making use of the sequential structure of phylogenetic trees in conjunction with stochastic approximation Monte Carlo (SAMC) simulations. The use of the sequential structure of the problem provides substantial help to reduce the curse of dimensionality in simulations, and SAMC effectively prevents the system from getting trapped in local energy minima. The new method is compared with a variety of existing Bayesian and non-Bayesian methods on simulated and real datasets. Numerical results are in favor of the new method in terms of quality of the resulting phylogenetic trees.

A novel approach to phylogenetic tree construction using stochastic optimization and clustering

BackgroundThe problem of inferring the evolutionary history and constructing the phylogenetic tree with high performance has become one of the major problems in computational biology.ResultsA new phylogenetic tree construction method from a given set of objects (proteins, species, etc.) is presented. As an extension of ant colony optimization, this method proposes an adaptive phylogenetic clustering algorithm based on a digraph to find a tree structure that defines the ancestral relationships among the given objects.ConclusionOur phylogenetic tree construction method is tested to compare its results with that of the genetic algorithm (GA). Experimental results show that our algorithm converges much faster and also achieves higher quality than GA.

Relaxed Neighbor Joining: A Fast Distance-Based Phylogenetic Tree Construction Method

Our ability to construct very large phylogenetic trees is becoming more important as vast amounts of sequence data are becoming readily available. Neighbor joining (NJ) is a widely used distance-based phylogenetic tree construction method that has historically been considered fast, but it is prohibitively slow for building trees from increasingly large datasets. We developed a fast variant of NJ called relaxed neighbor joining (RNJ) and performed experiments to measure the speed improvement over NJ. Since repeated runs of the RNJ algorithm generate a superset of the trees that repeated NJ runs generate, we also assessed tree quality. RNJ is dramatically faster than NJ, and the quality of resulting trees is very similar for the two algorithms. The results indicate that RNJ is a reasonable alternative to NJ and that it is especially well suited for uses that involve large numbers of taxa or highly repetitive procedures such as bootstrapping.

Molecular phylogeny applied to species and related ascomycetous yeasts

Molecular phylogeny applied to Candida species and related ascomycetous yeasts , Heide-Marie Daniel. ISBN 3-89700-375-9Berlin, Germany, Verlag fur Wissenschaft und Forschung, 2003. This book, based on a Ph.D. thesis, provides a comprehensive description of molecular approaches to study species and gene phylogenies of ascomycetous yeasts, in particular of the artificial genus Candida . It is a considerable contribution towards a natural classification of ascomycetous yeasts by establishing phylogenetic relationships between the major lineages. The introduction is of particular value for non-experts in the field of phylogenetic analysis. It outlines the necessity of a phylogenetically based taxonomic system and introduces the methods of phylogenetic tree construction, interpretation of molecular data for phylogenetic purposes, and the current classification of ascomycetous yeasts. Background information is given for the three … E-mail address : boekhout{at}cbs.knaw.nl

Lactate dehydrogenase genes of caiman and Chinese soft-shelled turtle, with emphasis on the molecular phylogenetics and evolution of reptiles

L-Lactate dehydrogenase (LDH) cDNAs encoding for LDH-A4 (muscle) and LDH-B4 (heart) isozymes from caiman (Caiman crocodilus apaporiensis) belonging to the order Crocodilia and Chinese soft-shelled turtle (Pelodiscus sinensis) belonging to the order Chelonia were sequenced. The phylogenetic relationships of the newly determined cDNA and their deduced protein sequences, as well as the previously published sequences of vertebrate LDH isozymes, were analyzed by various phylogenetic tree construction methods. These results indicated that Chelonia is indeed more closely related to Crocodilia. The divergent times between caiman and alligator, turtle and soft-shelled turtle, and Chelonia and Crocodilia were estimated to be approximately 36, 100 and 177 million years, respectively.

Guinea pig D-amino-acid oxidase cDNA and phylogenetic position.

The nucleotide sequence of cDNA that encodes guinea pig D-amino-acid oxidase (DAO) was determined. The cDNA consisted of 1,399 nucleotides and a poly(A) tail. The cDNA encodes 347 amino acid residues. In contrast to the hamster, rat, and mouse DAOs, guinea pig DAO had the 25th amino acid residue. The homology in amino acid sequences between the guinea pig DAO and the rodent DAOs was not high in comparison to the homology in amino acid sequences between the guinea pig DAO and DAOs of humans, pigs and rabbits. The phylogenetic position of the guinea pig varied depending on the source of sequences (amino acids or nucleotides) and the methods of phylogenetic tree construction. These results suggest that the guinea pig is not a simple rodent.

Use of mtDNA Direct Polymerase Chain Reaction (PCR) Sequencing and PCR−Restriction Fragment Length Polymorphism Methodologies in Species Identification of Canned Tuna

Identification of six canned tuna species using DNA-based methodology was studied. DNA was degraded during the canning process of fish muscle: DNA fragment sizes that ranged from <100 up to 200 bp were obtained from canned tuna muscle, whereas DNA sizes for frozen tuna muscle ranged from <100 up to 20 000 bp. Amplification of DNA from canned tuna muscle was carried out using primers flanking a region of cytochrome b gene of 126 bp. Sequences from PCR-amplified DNA of six tuna species were studied for polymorphic sites; seven diagnostic positions were identified in this fragment for the species studied. The suitability of a genetic distance measurement with phylogenetic tree construction method for the identification of canned tuna species using two cytochrome b sequences (299 and 126 bp) was studied. PCR-amplified DNA from canned tuna was also analyzed by using three restriction endonucleases, BsiYI, MboI, and MnlI. The restriction fragments allowed for the identification of the six tuna species studied. Keywords: Canned tuna; species identification; cytochrome b; genetic distance; RFLP−PCR

Phylogeny and evolution of the piroplasms.

Small subunit ribosomal RNA (srRNA) genes of three Theileria species, one Cytauxzoon and four Babesia species were amplified using the polymerase chain reaction (PCR), cloned and sequenced. Our sequences were aligned with srRNA sequences previously published for eight species of Apicomplexa, one ciliate and one dinoflagellate, the last two being included as free-living outgroup species. Phylogenetic relationships between the organisms were inferred by four independent methods of phylogenetic tree construction using the ciliate Oxytricha nova to root the trees. Our trees fail to show a consensus branching order. They do, however, clearly indicate that the theilerias form a monophyletic taxon derived from a paraphyletic group which includes the species B. equi, C. felis and B. rodhaini. The distance trees indicate that the babesias sensu stricto (B. canis, B. caballi, B. bigemina and B. bovis) form another monophyletic taxon which diverged before the theilerias separated from the above-mentioned paraphyletic group. The parsimony and maximum likelihood trees suggest that the babesias and theilerias are sister taxa, both of which were derived from the paraphyletic group.

Phylogeny of primate major histocompatibility complex DRB alleles

ABBREVIATIONS ARS antigen recognition site In contrast to alleles at most other loci, alleles at the major histocompatibility complex (MHC) loci often dif- fer by more than one nucleotide substitution. It is there- fore legitimate to look into the lines of descent of the individual MHC alleles and to construct their phyloge- nies. One of the largest collections of MHC alleles thus far assembled is that of the class II DRB loci in pri- mates, specifically in the great apes. Marsh and Bodmer [1] recently compiled sequences of 42 human (HLA- DRB) alleles; we have obtained the sequences of four gorilla (l~lhcGogo-DRB, M. Kasahara and J. Klein, un- published data), three chimpanzee (MhcPatr.DRB, ref. 2), and two orangutan (MhcPopy-DRB, Ch. Sch6nbach, Z.-F. Zhu, and J. Klein, unpublished data.) ~ To deter- mine the relationships among these 51 sequences, we analyzed them using two methods of phylogenetic tree construction: the neighbor-joining method of Saitou and Nei [4] and the maximal parsimony method of Felsenstein [5]. Since the former produced more realis- tic trees than the latter, we shall limit our discussion to the tree obtained by the application of this method to the exon 2 (first domain) DRB sequences, using the l The designations of nonhuman primate MHCs accord with the recent nomenclatorial agreement; see ref. 3. Prom the Dopartment of Microbiology~ and Immunology, University of Miami School of Medicine, Miami, Florida (J.K.; M.K.), and the Max- Planck-lnstitut f~r Bidogie, Abteilung lmmungenetik, Tabingen, Ger- many (J.K.; J.G.; C.$.). Add~ss reprint requests to Professor Jan Klein, Max-Planck-lnstitut f~r Biologie, Abteilung lmmungenetik, D-7400 T~'bingen, Germany. Accepted November 16,1990. 28 0198-8859/91/$3.50 MHC major hismcompatibility complex mouse H-2Eb b sequence as a root (Fig. 1). The restric- tion to exon 2 sequences was dictated by two consider- ations: first, it is the only exon for which sequences of all the 51 alleles are available; and second, when comparing alleles, exons are better evolutionary units than whole genes because recombination may produce hybrid genes that could complicate the interpretation of allelic phylogenies. A remarkable feature of the tree in Fig. 1 is the inter- mingling of sequences from the four primate species, Homo sapiens, Pan troglodytes, Gorilla gorilla, and Pongo pygmeus. This intermingling provides further support for the notion that was first put forward as a hypotheti- cal possibility [6] but has since been supported by a growing body of observations [2,7-11], namely, that the history of many of the bIHC alleles extends beyond the species' boundaries. It can safely be concluded from the tree that all its main branches were established be- fore the divergence of chimpanzee, gorilla, and human lineages from a common ancestral lineage more than 5 million years (my) ago and that at least some of them existed as separate lineages before the split of orangutan ancestors from the gorilla-chimpanzee-human ancestors more than 10 my ago. If we accept that Homo sapiens emerged between 300,000 and 500,000 years ago [12], we must conclude that all alleles differing by more thau one substitution outside the antigen recognition site (ARS) were most likely established before this event [13]. All these alleles, therefore, predate speciation. A phylogenetic tree of the sort shown in Fig. 1 is constructed to reflect the succession of substitutions at Human Immunology 31, 28-35 (1991) © American $ociet,/for Histocompatibillty and lmmunogenetics, 1991

Relative Efficiencies of the Fitch-Margoliash, Maximum-Parsimony, Maximum-Likelihood, Minimum-Evolution, and Neighbor-joining Methods of Phylogenetic Tree Construction in Obtaining the Correct Tree

The relative efficiencies of several tree-making methods for obtaining the correct phylogenetic tree were studied by using computer simulation. The methods examined were the Fitch-Margoliash (FM), maximum-parsimony (MP), maximumlikelihood (ML), minimum-evolution (ME), and neighbor-joining (NJ) methods. We simulated the evolutionary changes of six DNA sequences each with a length of either 300 or 600 nucleotides. Both constant and varying rates of nucleotide substitution were considered. The DNA sequences generated were used to reconstruct phylogenetic trees by applying the five tree-making methods, and the trees obtained were compared with the model (correct) tree. This process was repeated 50 times for each case, and the following results were obtained: ( 1) The efficiency of obtaining the correct tree for the FM method was considerably lower than those for the other methods. (2) The NJ and ME methods showed a high performance in obtaining the correct tree, and their relative efficiencies were similar to each other. ( 3) For distance methods (NJ, FM, and ME), the results obtained by using corrected nucleotide substitutions were much better than those obtained by using nucleotide differences when the rate of substitution varied greatly among different branches. (4) The ML method was slightly inferior to the NJ and ME methods when a constant rate of nucleotide substitution was assumed, but it was slightly better than the latter two methods when the evolutionary rate varied drastically among branches. If one considers the computational time involved, the NJ method seems to be a method of choice.