Computational Analysis of Distance based Phylogenetic Tree for Azotobacter Species

Phylogenetic tree is a pictorial representation of evolutionary relationships between organisms. It is important method to analyze the biological data. Phylogenetic trees are based on two methods : Distance based and Character based. Phylogenetic tree are used comparative analysis of any organism like human Beings, Animals, Bacteria, Viruses and Fungi’s etc. In this paper we compare 12 different nucleotide sequences of Azotobacter species having linear DNA of 999 BP as maximum size using substitution model and phylogenetic model. In this study two different models name P-Distance and Jukes cantor model are used and helped in finding UPGMA or Neighbour joining method efficiency in evaluating the similarity and dissimilarity of bacterial species. This paper gives influence in reconciliation of Azotobacter species to produce phylogram with informative branch lengths. This further leads to analyze and understand various expressive characters of Azotobacter in agriculture field.

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Markov Katana: a Novel Method for Bayesian Resampling of Parameter Space Applied to Phylogenetic Trees

10.1101/250951 ◽

2018 ◽

Author(s):

Stephen T. Pollard ◽

Kenji Fukushima ◽

Zhengyuan O. Wang ◽

Todd A. Castoe ◽

David D. Pollock

Keyword(s):

Phylogenetic Tree ◽

Phylogenetic Trees ◽

Statistical Approach ◽

Evolutionary Model ◽

Complex Model ◽

Tree Topology ◽

Added Value ◽

General Idea ◽

Branch Lengths ◽

Tree Space

ABSTRACTPhylogenetic inference requires a means to search phylogenetic tree space. This is usually achieved using progressive algorithms that propose and test small alterations in the current tree topology and branch lengths. Current programs search tree topology space using branch-swapping algorithms, but proposals do not discriminate well between swaps likely to succeed or fail. When applied to datasets with many taxa, the huge number of possible topologies slows these programs dramatically. To overcome this, we developed a statistical approach for proposal generation in Bayesian analysis, and evaluated its applicability for the problem of searching phylogenetic tree space. The general idea of the approach, which we call ‘Markov katana’, is to make proposals based on a heuristic algorithm using bootstrapped subsets of the data. Such proposals induce an unintended sampling distribution that must be determined and removed to generate posterior estimates, but the cost of this extra step can in principle be small compared to the added value of more efficient parameter exploration in Markov chain Monte Carlo analyses. Our prototype application uses the simple neighbor-joining distance heuristic on data subsets to propose new reasonably likely phylogenetic trees (including topologies and branch lengths). The evolutionary model used to generate distances in our prototype was far simpler than the more complex model used to evaluate the likelihood of phylogenies based on the full dataset. This prototype implementation indicates that the Markov katana approach could be easily incorporated into existing phylogenetic search programs and may prove a useful alternative in conjunction with existing methods. The general features of this statistical approach may also prove useful in disciplines other than phylogenetics. We demonstrate that this method can be used to efficiently estimate a Bayesian posterior.

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Phylogenetic positions of ‘Candidatus Phytoplasma asteris' and Spiroplasma kunkelii as inferred from multiple sets of concatenated core housekeeping proteins

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijs.0.63655-0 ◽

2005 ◽

Vol 55 (5) ◽

pp. 2131-2141 ◽

Cited By ~ 25

Author(s):

Yan Zhao ◽

Robert E. Davis ◽

Ing-Ming Lee

Keyword(s):

Phylogenetic Trees ◽

Bacterial Species ◽

Likelihood Methods ◽

Gram Positive Bacteria ◽

Genome Data ◽

Spiroplasma Kunkelii ◽

Branch Lengths ◽

Genes Encoding ◽

Micro Organisms ◽

Phytopathogenic Mollicutes

Phytopathogenic mollicutes, which include spiroplasmas and phytoplasmas, are cell wall-less bacteria that parasitize plant hosts and insect vectors. Knowledge of the evolution of these agents is important in understanding their biology. The availability of the first complete phytoplasma and several partial spiroplasma and phytoplasma genome sequences made possible an investigation of evolutionary relationships between phytopathogenic mollicutes and other micro-organisms, especially Gram-positive bacteria, using a comparative genomics approach. Genome data from a total of 41 bacterial species were used in the analysis. Sixty-one conserved proteins were selected from each species for the construction of a hypothetical phylogenetic tree. The genes encoding these selected proteins are among a core of genetic elements that constitute a hypothetical minimal genome. The proteins were concatenated into five superproteins according to their functional categories, and phylogenetic trees were reconstructed using distance, parsimony and likelihood methods. Phylogenetic trees based on the five sets of concatenated proteins were congruent in both clade topology and relative branching length. Spiroplasma kunkelii and phytoplasmas clustered together with other mollicutes, forming a monophyletic group. Phytoplasmas diverged from spiroplasmas and mycoplasmas at early stages in the evolution of mollicutes. Branch lengths on the phylogenetic trees were noticeably longer in the Mollicutes clade, suggesting that the genes encoding the five sets of proteins evolved at a greater rate in this clade than in other clades. This observation reinforces the concept that mollicutes have rapidly evolving genomes.

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PhyD3: a phylogenetic tree viewer with extended phyloXML support for functional genomics data visualization

10.1101/107276 ◽

2017 ◽

Author(s):

Łukasz Kreft ◽

Alexander Botzki ◽

Frederik Coppens ◽

Klaas Vandepoele ◽

Michiel Van Bel

Keyword(s):

Phylogenetic Tree ◽

Functional Genomics ◽

Open Source ◽

Web Sites ◽

Phylogenetic Trees ◽

Biological Data ◽

Web Technologies ◽

Link Type ◽

Current Implementation ◽

Tree Viewer

AbstractMotivation:Comparative and evolutionary studies utilise phylogenetic trees to analyse and visualise biological data. Recently, several web-based tools for the display, manipulation, and annotation of phylogenetic trees, such as iTOL and Evolview, have released updates to be compatible with the latest web technologies. While those web tools operate an open server access model with a multitude of registered users, a feature-rich open source solution using current web technologies is not available.Results:Here, we present an extension of the widely used PhyloXML standard with several new options to accommodate functional genomics or annotation datasets for advanced visualization. Furthermore, PhyD3 has been developed as a lightweight tool using the JavaScript library D3.js to achieve a state-of-the-art phylogenetic tree visualisation in the web browser, with support for advanced annotations. The current implementation is open source, easily adaptable and easy to implement in third parties’ web sites.Availability:More information about PhyD3 itself, installation procedures, and implementation links are available at http://phyd3.bits.vib.be and at http://github.com/vibbits/phyd3/.Contact:[email protected]

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Computing nearest neighbour interchange distances between ranked phylogenetic trees

Journal of Mathematical Biology ◽

10.1007/s00285-021-01567-5 ◽

2021 ◽

Vol 82 (1-2) ◽

Author(s):

Lena Collienne ◽

Alex Gavryushkin

Keyword(s):

Cancer Research ◽

Computational Complexity ◽

Phylogenetic Tree ◽

Shortest Path ◽

Phylogenetic Trees ◽

Shortest Paths ◽

Nearest Neighbour ◽

Tree Inference ◽

Subtree Prune And Regraft ◽

Comparison Algorithms

AbstractMany popular algorithms for searching the space of leaf-labelled (phylogenetic) trees are based on tree rearrangement operations. Under any such operation, the problem is reduced to searching a graph where vertices are trees and (undirected) edges are given by pairs of trees connected by one rearrangement operation (sometimes called a move). Most popular are the classical nearest neighbour interchange, subtree prune and regraft, and tree bisection and reconnection moves. The problem of computing distances, however, is $${\mathbf {N}}{\mathbf {P}}$$ N P -hard in each of these graphs, making tree inference and comparison algorithms challenging to design in practice. Although anked phylogenetic trees are one of the central objects of interest in applications such as cancer research, immunology, and epidemiology, the computational complexity of the shortest path problem for these trees remained unsolved for decades. In this paper, we settle this problem for the ranked nearest neighbour interchange operation by establishing that the complexity depends on the weight difference between the two types of tree rearrangements (rank moves and edge moves), and varies from quadratic, which is the lowest possible complexity for this problem, to $${\mathbf {N}}{\mathbf {P}}$$ N P -hard, which is the highest. In particular, our result provides the first example of a phylogenetic tree rearrangement operation for which shortest paths, and hence the distance, can be computed efficiently. Specifically, our algorithm scales to trees with tens of thousands of leaves (and likely hundreds of thousands if implemented efficiently).

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Predicting the Impact of Describing New Species on Phylogenetic Patterns

Integrative Organismal Biology ◽

10.1093/iob/obz028 ◽

2019 ◽

Vol 1 (1) ◽

Cited By ~ 1

Author(s):

D C Blackburn ◽

G Giribet ◽

D E Soltis ◽

E L Stanley

Keyword(s):

New Species ◽

Phylogenetic Trees ◽

Branch Length ◽

Length Variation ◽

Tree Shape ◽

Branch Lengths ◽

Taxonomic History ◽

Ecological Patterns ◽

The Impact ◽

Incomplete Sampling

Abstract Although our inventory of Earth’s biodiversity remains incomplete, we still require analyses using the Tree of Life to understand evolutionary and ecological patterns. Because incomplete sampling may bias our inferences, we must evaluate how future additions of newly discovered species might impact analyses performed today. We describe an approach that uses taxonomic history and phylogenetic trees to characterize the impact of past species discoveries on phylogenetic knowledge using patterns of branch-length variation, tree shape, and phylogenetic diversity. This provides a framework for assessing the relative completeness of taxonomic knowledge of lineages within a phylogeny. To demonstrate this approach, we use recent large phylogenies for amphibians, reptiles, flowering plants, and invertebrates. Well-known clades exhibit a decline in the mean and range of branch lengths that are added each year as new species are described. With increased taxonomic knowledge over time, deep lineages of well-known clades become known such that most recently described new species are added close to the tips of the tree, reflecting changing tree shape over the course of taxonomic history. The same analyses reveal other clades to be candidates for future discoveries that could dramatically impact our phylogenetic knowledge. Our work reveals that species are often added non-randomly to the phylogeny over multiyear time-scales in a predictable pattern of taxonomic maturation. Our results suggest that we can make informed predictions about how new species will be added across the phylogeny of a given clade, thus providing a framework for accommodating unsampled undescribed species in evolutionary analyses.

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A Study of Correlation between Morphology and Evolution of Euphorbiaceae s.l. using Taxonomic Congruence and Total Evidence

Science & Technology Journal ◽

10.22232/stj.2021.09.01.09 ◽

2021 ◽

Vol 9 (1) ◽

pp. 49-55

Author(s):

Vanlal hruaia ◽

◽

Lal rinmuana ◽

J Lalbiaknunga ◽

Laldinfeli Ralte

Keyword(s):

Phylogenetic Tree ◽

Evolutionary Relationship ◽

Cladistic Analysis ◽

Morphological Characters ◽

Flowering Plants ◽

Morphological Features ◽

Total Evidence ◽

Pictorial Representation ◽

Phenetic Analysis ◽

Morphological Relationship

Euphorbiaceae is one of the largest family of flowering plants, in our study different species were collected from different localities of Mizoram, the collected specimens were studied and their morphological features noted. 34 genera of Euphorbiaceae s.l were used in the study. Cladistic analysis was performed in Mesquite software and Phenetic analysis was done in NTsys software. Both analyses produce a pictorial representation in a form of a tree; cladistic analysis produce phylogenetic tree (evolutionary relationship) while phenetic analysis produce phenogram (morphological relationship). The results of the aforementioned analyses were further analysed by total evidence technique and taxonomic congruence, a phylogenetic software PAUP is used for this purpose. The resultant trees were very different and comparison was done to find correlation between evolution and morphological characters. The research finds various correlation among characters like the number of locule in ovule, phyllanthoid branching and support the inclusion of genus like Breynia, Sauropus into Phyllanthus.

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Techniques for the verification of minimal phylogenetic trees illustrated with ten mammalian haemoglobin sequences

Biochemical Journal ◽

10.1042/bj1870065 ◽

1980 ◽

Vol 187 (1) ◽

pp. 65-74 ◽

Cited By ~ 12

Author(s):

D Penny ◽

M D Hendy ◽

L R Foulds

Keyword(s):

Amino Acid ◽

Phylogenetic Tree ◽

Protein Sequence ◽

Phylogenetic Trees ◽

Sequence Data ◽

Protein Sequences ◽

Nucleotide Sequences ◽

Amino Acid Sequences ◽

Minimal Tree ◽

Protein Sequence Data

We have recently reported a method to identify the shortest possible phylogenetic tree for a set of protein sequences [Foulds Hendy & Penny (1979) J. Mol. Evol. 13. 127–150; Foulds, Penny & Hendy (1979) J. Mol. Evol. 13, 151–166]. The present paper discusses issues that arise during the construction of minimal phylogenetic trees from protein-sequence data. The conversion of the data from amino acid sequences into nucleotide sequences is shown to be advantageous. A new variation of a method for constructing a minimal tree is presented. Our previous methods have involved first constructing a tree and then either proving that it is minimal or transforming it into a minimal tree. The approach presented in the present paper progressively builds up a tree, taxon by taxon. We illustrate this approach by using it to construct a minimal tree for ten mammalian haemoglobin alpha-chain sequences. Finally we define a measure of the complexity of the data and illustrate a method to derive a directed phylogenetic tree from the minimal tree.

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Comparative Genomics ofH. pyloriand Non-PyloriHelicobacterSpecies to Identify New Regions Associated with Its Pathogenicity and Adaptability

BioMed Research International ◽

10.1155/2016/6106029 ◽

2016 ◽

Vol 2016 ◽

pp. 1-15 ◽

Cited By ~ 8

Author(s):

De-Min Cao ◽

Qun-Feng Lu ◽

Song-Bo Li ◽

Ju-Ping Wang ◽

Yu-Li Chen ◽

...

Keyword(s):

Gastric Cancer ◽

Functional Annotation ◽

Human Population ◽

Large Scale ◽

Bacterial Species ◽

Human Beings ◽

Gram Negative ◽

Protein Protein Interaction ◽

H Pylori ◽

Cooperation Relationship

The genusHelicobacteris a group of Gram-negative, helical-shaped pathogens consisting of at least 36 bacterial species.Helicobacter pylori(H. pylori), infecting more than 50% of the human population, is considered as the major cause of gastritis, peptic ulcer, and gastric cancer. However, the genetic underpinnings ofH. pylorithat are responsible for its large scale epidemic and gastrointestinal environment adaption within human beings remain unclear. Core-pan genome analysis was performed among 75 representativeH. pyloriand 24 non-pylori Helicobactergenomes. There were 1173 conserved protein families ofH. pyloriand 673 of all 99Helicobactergenus strains. We found 79 genome unique regions, a total of 202,359bp, shared by at least 80% of theH. pyloribut lacked in non-pylori Helicobacterspecies. The operons, genes, and sRNAs within theH. pyloriunique regions were considered as potential ones associated with its pathogenicity and adaptability, and the relativity among them has been partially confirmed by functional annotation analysis. However, functions of at least 54 genes and 10 sRNAs were still unclear. Our analysis of protein-protein interaction showed that 30 genes within them may have the cooperation relationship.

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Genetic diversity analysis and phylogenetic reconstruction of groupers Epinephelus spp. from Madura Island, Indonesia based on partial sequence of CO1 gene

Biodiversitas Journal of Biological Diversity ◽

10.13057/biodiv/d221020 ◽

2021 ◽

Vol 22 (10) ◽

Author(s):

ABDUL BASITH ◽

Abinawanto Abinawanto ◽

ENI KUSRINI ◽

YASMAN YASMAN

Keyword(s):

Genetic Diversity ◽

Phylogenetic Tree ◽

Nucleotide Diversity ◽

Haplotype Diversity ◽

Phylogenetic Reconstruction ◽

Partial Sequence ◽

Diversity Analysis ◽

Epinephelus Coioides ◽

Substitution Model ◽

Genetic Diversity Analysis

Abstract. Basith A, Abinawanto, Kusrini E, Yasman. 2021. Genetic diversity analysis and phylogenetic reconstruction of groupers Epinephelus spp. from Madura Island, Indonesia based on partial sequence of CO1 gene. Biodiversitas 22: 4282-4290. Groupers populations in Indonesia, particularly from Madura Island, East Java are indicated to be over-fished, thereby requiring data collection of more accurate genetic resources as an important step for grouper conservation. A total of 14 samples of the Epinepheplus groupers were obtained from the fish landing port on Madura Island. The 617 bp CO1 gene sequence was utilized for genetic diversity analysis and phylogenetic tree reconstruction. Genetic diversity is based on the value of haplotype diversity (Hd) and nucleotide diversity (?). Reconstruction of the phylogenetic tree includes neighbor-joining (NJ) implementing K2P substitution model, while maximum likelihood (ML) is conducted by implementing HKY+G+I substitution model, both of which were evaluated by employing a bootstrap of 1000 replications. Analysis of genetic distance between species indicated that the farthest distance between E. heniochus and E. fasciatus was 0.189, while the closest distance between E. erythrurus and E. ongus was 0.099. Intrapopulation genetic diversity indicated a high value with details of Hd=0.978 and ?=0.12107. Furthermore, NJ and ML phylogenetic tree demonstrated similar topology in the observed Epinephelus spp. obtained from Madura Island grouped into 7 clades, that is Epinephelus coioides, E. bleekeri, E. areolatus, E. erythrurus, E. heniochus, E. fasciatus, and E. ongus.

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An Insight into the Role of Benefical Bacteria in Periodontal Pocket Recolonization: A Literature Review

Journal of Oral Health and Community Dentistry ◽

10.5005/johcd-8-1-47 ◽

2014 ◽

Vol 8 (1) ◽

pp. 47-50

Author(s):

SM Apoorva ◽

A Suchetha ◽

DB Mundinamane ◽

DP Bhopale ◽

A Bharwani ◽

...

Keyword(s):

Bacterial Species ◽

Periodontal Pocket ◽

Human Beings ◽

Beneficial Bacteria ◽

Initial Attachment ◽

Bacterial Interactions ◽

Tooth Surfaces ◽

Free People ◽

Insight Into

ABSTRACT Microflora can be found in both caries-free and periodontitis-free people and caries-affected and periodontitis-affected people, and many clinical studies reveal that the portion of certain bacterial species such as Streptococcus mutans or Porphyromonas gingivalis, respectively, is increased in patients with caries or periodontitis. Therefore, it seems that the competition that results between beneficial bacteria and virulent bacteria leads to either a healthy or sick status of human beings. Competition between members of the dental microflora and there role in pocket recolonization is very complex and many antagonistic characteristics can be observed from competition for initial attachment on tooth surfaces or for later attachment to pioneer bacteria, competition from bacteriocins or hydrogen peroxide secreted and from facilitating the growth of some species which inhibit other species. To date only some of the details of these mechanisms are known. The present review will provide an overview on the prevalence of beneficial bacteria and the major mechanisms of oral bacterial interactions. Due to the large number of oral bacterial species, only the best characterized species are included in this review.

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