A DNA sequence distance measure approach for phylogenetic tree construction

Phylogenetic tree reconstruction via graph cut presented using a quantum-inspired computer

Artemisia vulgaris L. belongs to Asteraceae, is a herbal plant that has various benefits in the medical field, so that its use in the medical field can be explored optimally, the plant must be thoroughly identified. This study aims to identify A. vulgaris both in terms of descriptive morpho-anatomy and DNA barcoding using BLAST and phylogenetic tree reconstruction. The morpho-anatomical character was observed on root, stem, and leaf. DNA barcoding analysis was carried out through amplification and alignment of the rbcL and matK genes. All studies were conducted on three samples from Taman Husada (Medicinal Plant Garden) Graha Famili Surabaya, Indonesia. The anatomical slide was prepared by the paraffin method. Morphological studies revealed that the leaves of A. vulgaris both on the lower-middle part and on the upper part of the stem have differences, especially in the character of the stipules, petioles, and incisions they have. Meanwhile, from the study of anatomy, A. vulgaris has an anomocytic type of stomata and its distribution is mostly on the ventral part of the leaves. Through the BLAST process and phylogenetic tree reconstruction, the plant sequences being studied are closely related to several species of the genus Artemisia as indicated by a percentage identity above 98% and branch proximity between taxa in the reconstructed phylogenetic tree.

Researchers have developed a wide variety of methods for string data, that can be applied with success in different fields such as computational biology, natural language processing and so on. Such methods range from clustering techniques used to analyze the phylogenetic trees of different organisms, to kernel methods used to identify authorship or native language from text. Results of such methods are not perfect and can always be improved. Some of these methods are based on a distance or similarity measure for strings, such as Hamming, Levenshtein, Kendall-tau, rank distance, or string kernel. This paper aims to introduce a new distance measure, termed Local Rank Distance (LRD), inspired from the recently introduced Local Patch Dissimilarity for images. Designed to conform to more general principles and adapted to DNA strings, LRD comes to improve over state of the art methods for phylogenetic analysis. This paper shows two applications of LRD. The first application is the phylogenetic analysis of mammals. Experiments show that phylogenetic trees produced by LRD are better or at least similar to those reported in the literature. The second application is to identify native language of English learners. By working at character level, the proposed method is completely language independent and theory neutral. In conclusion, LRD can be used as a general approach to measure string similarity, despite being designed for DNA.

Based on molecular clock hypothesis, and neutral theory of molecular evolution, molecular phylogenies have been widely used for inferring evolutionary history of organisms and individual genes. Traditionally, alignments and phylogeny trees of proteins and their coding DNA sequences are constructed separately, thus often different conclusions were drawn. Here we present a new strategy for sequence alignment and phylogenetic tree reconstruction, codon and amino acid unified sequence alignment (CAUSA), which aligns DNA and protein sequences and draw phylogenetic trees in a unified manner. We demonstrated that CAUSA improves both the accuracy of multiple sequence alignments and phylogenetic trees by solving a variety of molecular evolutionary problems in virus, bacteria and mammals. Our results support the hypothesis that the molecular clock for proteins has two pointers existing separately in DNA and protein sequences. It is more accurate to read the molecular clock by combination (additive) of these two pointers, since the ticking rates of them are sometimes consistent, sometimes different. CAUSA software were released as Open Source under GNU/GPL license, and are downloadable free of charge from the website www.dnapluspro.com.

Evolutionary and systems biology increasingly rely on the construction of large phylogenetic trees which represent the relationships between species of interest. As the number and size of such trees increases, so does the need for efficient data storage and query capabilities. Although much attention has been focused on XML as a tree data model, phylogenetic trees differ from document-oriented applications in their size and depth, and their need for structure-based queries rather than path-based queries.This paper focuses on Crimson, a tree storage system for phylogenetic trees used to evaluate phylogenetic tree reconstruction algorithms within the context of the NSF CIPRes project. A goal of the modeling component of the CIPRes project is to construct a huge simulation tree representing a gold standard of evolutionary history against which phylogenetic tree reconstruction algorithms can be tested.In this demonstration, we highlight our storage and indexing strategies and show how Crimson is used for benchmarking phylogenetic tree reconstruction algorithms. We also show how our design can be used to support more general queries over phylogenetic trees.

Phylogenetic tree reconstruction is a fundamental biological problem. Quartet trees, trees over four species, are the minimal informational unit for phylogenetic classification. While every phylogenetic tree over $n$ species defines ${n \choose 4}$ quartets, not every set of quartets is compatible with some phylogenetic tree. Here we focus on the compatibility of quartet sets. We provide several results addressing the question of what can be inferred about the compatibility of a set from its subsets. Most of our results use probabilistic arguments to prove the sought characteristics. In particular we show that there are quartet sets $Q$ of size $m=c n \log n$ in which every subset of cardinality $c' n/ \log n$ is compatible, and yet no fraction of more than $1/3+\epsilon$ of $Q$ is compatible. On the other hand, in contrast to the classical result stating when $Q$ is the densest, i.e., $m={n \choose 4}$ and the compatibility of any set of three quartets implies full compatibility, we show that even for $m=\Theta\big({n \choose 4}\big)$ there are (very) incompatible sets for which every subset of large constant cardinality is compatible. Our final result relates to the conjecture of Bandelt and Dress regarding the maximum quartet distance between trees. We provide asymptotic upper and lower bounds for this value.

With the increasing emphasis in biology on reconstruction of phylogenetic trees, questions have arisen as to how confident one should be in a given phylogenetic tree and how support for phylogenetic trees should be measured. Felsenstein suggested that bootstrapping be applied across characters of a taxon-by-character data matrix to produce replicate "bootstrap data sets," each of which is then analyzed phylogenetically, with a consensus tree constructed to summarize the results of all replicates. The proportion of trees/replicates in which a grouping is recovered is presented as a measure of support for that group. Bootstrapping has become a common feature of phylogenetic analysis. However, the interpretation of bootstrap values remains open to discussion, and phylogeneticists have used these values in multiple ways. The usefulness of phylogenetic bootstrapping is potentially limited by a number of features, such as the size of the data matrix and the underlying assu! mptions of the phylogeny reconstruction program. Recent studies have explored the application of bootstrapping to large data sets and the relative performance of bootstrapping and jackknifing.

With the development of new sequencing techniques, whole genomes of many species have become available. This huge amount of data gives rise to new opportunities and challenges. These new sequences provide valuable information on relationships among species, e.g. genome recombination and conservation. One of the principal ways to investigate such information is multiple sequence alignment (MSA). Currently, there is large amount of MSA data on the internet, such as the UCSC genome database, but how to effectively use this information to solve classical and new problems is still an area lacking of exploration. In this thesis, we explored how to use this information in four problems, i.e. sequence orthology search problem, multiple alignment improvement problem, short read mapping problem, and genome rearrangement inference problem. For the first problem, we developed a EM algorithm to iteratively align a query with a multiple alignment database with the information from a phylogeny relating the query species and the species in the multiple alignment. We also infer the query's location in the phylogeny. We showed that by doing alignment and phylogeny inference together, we can improve the accuracies for both problems. For the second problem, we developed an optimization algorithm to iteratively refine the multiple alignment quality. Experiment results showed our algorithm is very stable in term of resulting alignments. The results showed that our method is more accurate than existing methods, i.e. Mafft, Clustal-O, and Mavid, on test data from three sets of species from the UCSC genome database. For the third problem, we developed a model, PhyMap, to align a read to a multiple alignment allowing mismatches and indels. PhyMap computes local alignments of a query sequence against a fixed multiple-genome alignment of closely related species. PhyMap uses a known phylogenetic tree on the species in the multiple alignment to improve the quality of its computed alignments while also estimating the placement of the query on this tree. Both theoretical computation and experiment results show that our model can differentiate between orthologous and paralogous alignments better than other popular short read mapping tools (BWA, BOWTIE and BLAST). For the fourth problem, we gave a simple genome recombination model which can express insertions, deletions, inversions, translocations and inverted translocations on aligned genome segments. We also developed an MCMC algorithm to infer the order of the query segments. We proved that using any Euclidian metrics to measure distance between two sequence orders in the tree optimization goal function will lead to a degenerated solution where the inferred order will be the order of one of the leaf nodes. We also gave a graph-based formulation of the problem which can represent the probability distribution of the order of the query sequences.

Phylogenetic tree reconstruction is a fundamental biological problem. Quartet amalgamation---combining a set of trees over four taxa into a tree over the full set of taxa---stands at the core of many phylogenetic reconstruction methods. This task has attracted many theoretical as well as practical works. However, even reconstruction from a consistent set of quartet trees is NP-hard, and the best approximation ratio known is 1/3. Despite its importance, the only rigorous results for approximating quartets are the naive 1/3 approximation that applies to the general case and a polynomial time approximation scheme (PTAS) when the input is the complete set of all ${n \choose 4}$ possible quartets. Even when it is possible to determine the correct quartet induced by every four taxa, the time needed to generate the complete set of all quartets may be impractical. A faster approach is to sample at random just $m \ll {n \choose 4}$ quartets and provide this sample as an input. In this work we present the first polynomial time approximation algorithm whose expected guaranteed approximation is strictly better than 1/3 when the input is any random sample of $m$ consistent quartets. The approximation ratio of the algorithm is greater than 0.425. An important ingredient in our algorithm involves solving a weighted maximum cut problem in a certain weighted graph that corresponds to the set of input quartets. Our second main result generalizes the aforementioned PTAS algorithm to handle dense, rather than complete, inputs.

PAML, currently in version 1.2, is a package of programs for phylogenetic analyses of DNA and protein sequences using the method of maximum likelihood (ML). The programs can be used for (i) maximum likelihood estimation of evolutionary parameters such as branch lengths in a phylogenetic tree, the transition/transversion rate ratio, the shape parameter of the gamma distribution for variable evolutionary rates at sites, and rate parameters for different genes; (ii) likelihood ratio test of hypotheses concerning sequence evolution, such as rate constancy and independence among sites and rate constancy among lineages (the molecular clock); (iii) calculation of substitution rates at sites and reconstruction of ancestral nucleotide or amino acid sequences; and (iv) phylogenetic tree reconstruction by maximum likelihood and Bayesian methods. The strength of PAML, in comparison with other phylogenetic packages currently available, is its implementation of a variety of evolutionary models. These include several models of variable evolutionary rates among sites, models for combined analyses of multiple gene sequence data and models for amino acid sequences. Multifurcating trees are supported, as well as trees in which some sequences are ancestral to some others. A heuristic tree search algorithm (star decomposition) is used in the package, but tree making is not a strong point of the current version, although work is under way to implement efficient search algorithms. Major programs in the package, as well as the types of analyses they perform, are listed in Table 1. More details are available in the documentation included in the package, written using Microsoft Word. PAML is distributed free of charge for academic use only. The package, including ANSI C source codes, documentation, example data sets, and control files, can be obtained by anonymous ftp at mw511.biol.berkeley.edu/pub, or from the Indiana molecular biology ftp site at ftp.bio.indiana.edu under the directory Incoming or molbio/evolve . MAC and PowerMac executables are also available, although DOS executables are not prepared yet. Further information about the package is available from the World Wide Web at

Microsatellite DNA loci or short tandem repeats (STRs) are abundant in eukaryotic genomes and are often used for constructing phylogenetic trees of closely related populations or species. These phylogenetic trees are usually constructed by using some genetic distance measure based on allele frequency data, and there are many distance measures that have been proposed for this purpose. In the past the efficiencies of these distance measures in constructing phylogenetic trees have been studied mathematically or by computer simulations. Recently, however, allele frequencies of 783 STR loci have been compiled from various human populations. We have therefore used these empirical data to investigate the relative efficiencies of different distance measures in constructing phylogenetic trees. The results showed that (1) the probability of obtaining the correct branching pattern of a tree (PC) is generally highest for DA distance; (2) FST*, standard genetic distance (DS), and FST/(1-FST) give similar PC-values, FST* being slightly better than the other two; and (3) (deltamu)2 shows PC-values much lower than the other distance measures. To have reasonably high PC-values for trees similar to ours, at least 30 loci with a minimum of 15 individuals are required when DA distance is used.

Bioinformatics is a rapidly growing field that has emerged from the synergy of computer science, statistics and biology. Given the interdisciplinary nature of bioinformatics, many students from diverse fields struggle with grasping bioinformatic concepts only from classroom lectures. Interactive tools for helping students reinforce their learning would be thus desirable. Here, we present an interactive online educational tool called TeachEnG (acronym for Teaching Engine for Genomics) for reinforcing key concepts in sequence alignment and phylogenetic tree reconstruction. Our instructional games allow students to align sequences by hand, fill out the dynamic programming matrix in the Needleman-Wunsch global sequence alignment algorithm, and reconstruct phylogenetic trees via the maximum parsimony, Unweighted Pair Group Method with Arithmetic mean (UPGMA) and Neighbor-Joining algorithms. With an easily accessible interface and instant visual feedback, TeachEnG will help promote active learning in bioinformatics. TeachEnG is freely available at http://teacheng.illinois.edu. The source code is available from https://github.com/KnowEnG/TeachEnG under the Artistic License 2.0. It is written in JavaScript and compatible with Firefox, Safari, Chrome and Microsoft Edge. songj@illinois.edu.

Ciliates of the genus Frontonia have been extensively studied to resolve their phylogenetic and evolutionary history, but challenges remain. This study used molecular analyses of SSU rRNA genes, phylogenetic tree reconstruction, molecular dating, and diversification analysis, together with ancestral state reconstruction of morphological traits and habitat preferences. Data included newly sequenced Korean species, GenBank records and published morphological information. Phylogenetic trees revealed paraphyly within Frontonia, identifying four groups that emerged in the Mesozoic era: Group I (~172 mya), Group II (~83 mya), Group III (~115 mya), and Group IV (~190 mya), with a common ancestor dating to ~420 mya in the Palaeozoic era. Diversification analysis revealed higher extinction rates (0.826 and 0.613 species/year) than speciation rates (0.011 and 0.016 species/year). Morphological evolution showed habitat adaptation and plasticity, with habitat transitions unrelated to contractile vacuolar traits. The SSU rRNA gene polymorphism likely contributed to the paraphyletic state of Frontonia. These results highlight the complex evolutionary patterns of the genus, shaped by genetic diversity, morphology, and environmental constraints.

Neighbor joining phylogenetic reconstructions of gene relationships in jawed vertebrates. BMP, Fgf and Msx protein sequences from various species were extracted from the NCBI database (NCBI accession numbers are indicated on each leaf of the tree) and were aligned with the translated sequences of the catshark Scyliorhinus canicula cDNA sequences to be identified, using ClustalX [64] with manual optimization using MUST software [65]. Regions of ambiguous homology were removed. Evolutionary distances (using JTT + gamma = 0.6 model) were computed and a neighbor-joining tree was obtained using MEGA6 [66]. The robustness of the tree nodes was estimated by a bootstrap test (200 replicates). A: phylogenetic tree (total 361 sites) including the Bmp2 and Bmp4 paralogy groups, identification of the catshark ScBmp4 sequence; B: phylogenetic tree (total 144 sites) including the Fgf8, Fgf17 and Fgf18 paralogy groups, identification of the catshark ScFgf8 sequence; C: phylogenetic tree (total 135 sites) including the Msx1, Msx2 and Msx3 paralogy groups, identification of the ScMsx1, ScMsx2 and ScMsx3 sequences; D: phylogenetic tree (total 200 sites) including the Pitx1, Pitx2 and Pitx3 paralogy groups, identification of the ScPitx1, ScPitx2 and ScPitx3 sequences. (PDF 104 kb)

BackgroundIn recent years, several new hypotheses on phylogenetic relations among arthropods have been proposed on the basis of DNA sequences. One of the challenged hypotheses is the monophyly of hexapods. This discussion originated from analyses based on mitochondrial DNA datasets that, due to an unusual positioning of Collembola, suggested that the hexapod body plan evolved at least twice. Here, we re-evaluate the position of Collembola using ribosomal protein gene sequences.ResultsIn total 48 ribosomal proteins were obtained for the collembolan Folsomia candida. These 48 sequences were aligned with sequence data on 35 other ecdysozoans. Each ribosomal protein gene was available for 25% to 86% of the taxa. However, the total sequence information was unequally distributed over the taxa and ranged between 4% and 100%. A concatenated dataset was constructed (5034 inferred amino acids in length), of which ~66% of the positions were filled. Phylogenetic tree reconstructions, using Maximum Likelihood, Maximum Parsimony, and Bayesian methods, resulted in a topology that supports monophyly of Hexapoda.ConclusionAlthough ribosomal proteins in general may not evolve independently, they once more appear highly valuable for phylogenetic reconstruction. Our analyses clearly suggest that Hexapoda is monophyletic. This underpins the inconsistency between nuclear and mitochondrial datasets when analyzing pancrustacean relationships. Caution is needed when applying mitochondrial markers in deep phylogeny.