A Survey of Metrics Measuring Difference for Rooted Phylogenetic Trees

2020 ◽  
Vol 15 (7) ◽  
pp. 697-702
Author(s):  
Juan Wang ◽  
Xinyue Qi ◽  
Bo Cui ◽  
Maozu Guo
Keyword(s):  
Phylogenetic Trees ◽  
Evolutionary History ◽  
Web Server ◽  
Home Page ◽  
Gaussian Fitting ◽  
History Of ◽  
On Line ◽  
The Difference ◽  
Better Than

Background: The evolutionary history of organisms can be described by phylogenetic trees. We need to compare the topologies of rooted phylogenetic trees when researching the evolution of a given set of species. Objective: Up to now, there are several metrics measuring the dissimilarity between rooted phylogenetic trees, and those metrics are defined by different ways. Methods: This paper analyzes those metrics from their definitions and the distance values computed by those metrics by terms of experiments. Results: The results of experiments show that the distances calculated by the cluster metric, the partition metric, and the equivalent metric have a good Gaussian fitting, and the equivalent metric can describe the difference between trees better than the others. Conclusion: Moreover, it presents a tool called as CDRPT (Computing Distance for Rooted Phylogenetic Trees). CDRPT is a web server to calculate the distance for trees by an on-line way. CDRPT can also be off-line used by means of installing application packages for the Windows system. It greatly facilitates the use of researchers. The home page of CDRPT is http://bioinformatics.imu.edu.cn/tree/.

INFERRING PHYLOGENETIC RELATIONSHIPS AVOIDING FORBIDDEN ROOTED TRIPLETS

2006 ◽  
Vol 04 (01) ◽  
pp. 59-74 ◽  
Author(s):  
YING-JUN HE ◽  
TRINH N. D. HUYNH ◽  
JESPER JANSSON ◽  
WING-KIN SUNG
Keyword(s):  
Approximation Algorithms ◽  
Phylogenetic Tree ◽  
Phylogenetic Trees ◽  
Evolutionary History ◽  
Phylogenetic Network ◽  
Evolutionary Relationships ◽  
Large Set ◽  
Tree Network ◽  
History Of ◽  
Overlapping Sets

To construct a phylogenetic tree or phylogenetic network for describing the evolutionary history of a set of species is a well-studied problem in computational biology. One previously proposed method to infer a phylogenetic tree/network for a large set of species is by merging a collection of known smaller phylogenetic trees on overlapping sets of species so that no (or as little as possible) branching information is lost. However, little work has been done so far on inferring a phylogenetic tree/network from a specified set of trees when in addition, certain evolutionary relationships among the species are known to be highly unlikely. In this paper, we consider the problem of constructing a phylogenetic tree/network which is consistent with all of the rooted triplets in a given set [Formula: see text] and none of the rooted triplets in another given set [Formula: see text]. Although NP-hard in the general case, we provide some efficient exact and approximation algorithms for a number of biologically meaningful variants of the problem.

scholarly journals A New Borrelia Species Defined by Multilocus Sequence Analysis of Housekeeping Genes

2009 ◽  
Vol 75 (16) ◽  
pp. 5410-5416 ◽  
Author(s):  
Gabriele Margos ◽  
Stephanie A. Vollmer ◽  
Muriel Cornet ◽  
Martine Garnier ◽  
Volker Fingerle ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
Lyme Borreliosis ◽  
Phylogenetic Trees ◽  
Evolutionary History ◽  
Housekeeping Genes ◽  
Multilocus Sequence Analysis ◽  
Species Status ◽  
Borrelia Garinii ◽  
Analysis Scheme ◽  
History Of

ABSTRACT Analysis of Lyme borreliosis (LB) spirochetes, using a novel multilocus sequence analysis scheme, revealed that OspA serotype 4 strains (a rodent-associated ecotype) of Borrelia garinii were sufficiently genetically distinct from bird-associated B. garinii strains to deserve species status. We suggest that OspA serotype 4 strains be raised to species status and named Borrelia bavariensis sp. nov. The rooted phylogenetic trees provide novel insights into the evolutionary history of LB spirochetes.

Revealing the history of infectious disease epidemics through phylogenetic trees

1995 ◽  
Vol 349 (1327) ◽  
pp. 33-40 ◽  
Keyword(s):  
Phylogenetic Trees ◽  
Viral Transmission ◽  
Human Populations ◽  
Viral Sequence ◽  
Immunodeficiency Virus ◽  
History Of ◽  
The Difference ◽  
Disease Epidemics ◽  
Hiv 1

Phylogenetic trees play an increasing role in molecular epidemiology, where they have been used to understand the forces that shape patterns of viral sequence diversity. Phylogenetic trees can also be used to trace the dynamics of viral transmission within populations. Case studies document the worldwide spread of Human Immunodeficiency Virus type 1 (HIV -1) and hepatitis C virus (HCV). Despite similarities between these viruses, especially in their transmission routes, they are shown to have very different epidemiological histories. A possible reason for the difference is that HCV has coexisted longer with human populations.

scholarly journals The Social Representation of Feminism within the On-line Movement “Women Against Feminism”

2017 ◽  
Vol 19 (1) ◽  
pp. 5
Author(s):  
Oana Crusmac
Keyword(s):  
Social Representations ◽  
Social Representation ◽  
Third Wave ◽  
The Past ◽  
Lack Of Information ◽  
The Social ◽  
History Of ◽  
On Line ◽  
The Difference ◽  
Line Movement

The present paper aims to analyse the social representation of feminism within the “Women Against Feminism” (WAF) on-line movement that is based on a shared blog which gained significant coverage in the U.S. and U.K. media since the summer of 2014. Using the method of quantitative content analysis and the insights provided by social representations theory, the paper will disclose what lies behind the concept of ‘feminism’ for the group embracing the WAF movement and also aims to find whether the members of this on-line community can be described as postfeminists. The article will conclude that the social representation of feminism within the WAF on-line movement is not based on a lack of information, but rather on a stereotypical understanding of the concept and on a non-nuanced perspective upon the history of feminism and its current developments (in particular the difference between post-feminism and third wave feminism). Moreover, similar arguments raised against feminism have been also drawn in the past, WAF sharing similar arguments with the ‘80s media backlash against feminsim.

scholarly journals Interspecies variation of larval locomotion kinematics in the genus Drosophila and its relation to habitat temperature

2020 ◽  
Author(s):  
Yuji Matsuo ◽  
Akinao Nose ◽  
Hiroshi Kohsaka
Keyword(s):  
Bayesian Inference ◽  
Phylogenetic Trees ◽  
Evolutionary History ◽  
Evolutionary Rate ◽  
Phylogenetic Analyses ◽  
The Body ◽  
Quantitative Relation ◽  
Individual Species ◽  
Habitat Temperature ◽  
History Of

AbstractSpeed and trajectory of locomotion are characteristic traits of individual species. During evolution, locomotion kinematics is likely to have been tuned for survival in the habitats of each species. Although kinematics of locomotion is thought to be influenced by habitats, the quantitative relation between the kinematics and environmental factors has not been fully revealed. Here, we performed comparative analyses of larval locomotion in 11 Drosophila species. We found that larval locomotion kinematics are divergent among the species. The diversity is not correlated to the body length but is correlated instead to the minimum habitat temperature of the species. Phylogenetic analyses using Bayesian inference suggest that the evolutionary rate of the kinematics is diverse among phylogenetic trees. The results of this study imply that the kinematics of larval locomotion has diverged in the evolutionary history of the genus Drosophila and evolved under the effects of the minimum ambient temperature of habitats.

scholarly journals Gastrointestinal Tolerability of Ibuprofen Compared with Paracetamol and Aspirin at Over-the-Counter Doses

2002 ◽  
Vol 30 (3) ◽  
pp. 301-308 ◽  
Author(s):  
P Rampal ◽  
N Moore ◽  
E Van Ganse ◽  
J-M Le Parc ◽  
R Wall ◽  
...  
Keyword(s):  
Abdominal Pain ◽  
Adverse Events ◽  
Over The Counter ◽  
Parallel Group Study ◽  
Parallel Group ◽  
Gastrointestinal Tolerability ◽  
History Of ◽  
The Difference ◽  
Better Than

This multicentre, randomized, investigator-blinded, parallel-group study compared the gastrointestinal (GI) tolerability of ibuprofen, paracetamol and aspirin at over-the-counter doses for common pain indications. Patients (of whom 8633 were evaluable) took either ibuprofen up to 1200 mg daily, or paracetamol or aspirin, each up to 3000 mg daily, for 1–7 days. The main outcome was the proportion of patients with GI adverse events. There were significantly more patients who suffered GI adverse events, principally abdominal pain, dyspepsia, nausea and diarrhoea, with aspirin (18.5%) than with ibuprofen (11.5%), but the difference between ibuprofen and paracetamol (13.1%) was not significant. Significantly more of those patients with a history of non-ulcer GI disease ( n = 371) developed GI adverse events than did those with no such history; the incidence of GI adverse events in both groups was lowest with ibuprofen. More women than men experienced GI adverse events (15.5% versus 12.8%). The higher incidence of GI adverse events with aspirin was evident from the first day of treatment. In conclusion, the GI tolerability of ibuprofen, at over-the-counter doses of up to 1200 mg daily for up to 7 days, was at least as good as that of paracetamol and significantly better than that of aspirin.

scholarly journals A Linear-Time Algorithm for the Isometric Reconciliation of Unrooted Trees

Algorithms ◽  
2020 ◽  
Vol 13 (9) ◽  
pp. 225
Author(s):  
Broňa Brejová ◽  
Rastislav Královič
Keyword(s):  
Family History ◽  
Gene Family ◽  
Phylogenetic Trees ◽  
Evolutionary History ◽  
Linear Time ◽  
Gene Tree ◽  
Time Algorithm ◽  
Species Tree ◽  
Linear Time Algorithm ◽  
History Of

In the reconciliation problem, we are given two phylogenetic trees. A species tree represents the evolutionary history of a group of species, and a gene tree represents the history of a family of related genes within these species. A reconciliation maps nodes of the gene tree to the corresponding points of the species tree, and thus helps to interpret the gene family history. In this paper, we study the case when both trees are unrooted and their edge lengths are known exactly. The goal is to root them and to find a reconciliation that agrees with the edge lengths. We show a linear-time algorithm for finding the set of all possible root locations, which is a significant improvement compared to the previous O(N3logN) algorithm.

scholarly journals Conserving the functional and phylogenetic trees of life of European tetrapods

2015 ◽  
Vol 370 (1662) ◽  
pp. 20140005 ◽  
Author(s):  
Wilfried Thuiller ◽  
Luigi Maiorano ◽  
Florent Mazel ◽  
François Guilhaumon ◽  
Gentile Francesco Ficetola ◽  
...  
Keyword(s):  
Phylogenetic Trees ◽  
Evolutionary History ◽  
Current System ◽  
Natura 2000 ◽  
Taxonomic Diversity ◽  
Distinct Species ◽  
Protection System ◽  
Distribution Data ◽  
History Of

Protected areas (PAs) are pivotal tools for biodiversity conservation on the Earth. Europe has had an extensive protection system since Natura 2000 areas were created in parallel with traditional parks and reserves. However, the extent to which this system covers not only taxonomic diversity but also other biodiversity facets, such as evolutionary history and functional diversity, has never been evaluated. Using high-resolution distribution data of all European tetrapods together with dated molecular phylogenies and detailed trait information, we first tested whether the existing European protection system effectively covers all species and in particular, those with the highest evolutionary or functional distinctiveness. We then tested the ability of PAs to protect the entire tetrapod phylogenetic and functional trees of life by mapping species' target achievements along the internal branches of these two trees. We found that the current system is adequately representative in terms of the evolutionary history of amphibians while it fails for the rest. However, the most functionally distinct species were better represented than they would be under random conservation efforts. These results imply better protection of the tetrapod functional tree of life, which could help to ensure long-term functioning of the ecosystem, potentially at the expense of conserving evolutionary history.

scholarly journals GEMME: A Simple and Fast Global Epistatic Model Predicting Mutational Effects

2019 ◽  
Vol 36 (11) ◽  
pp. 2604-2619 ◽  
Author(s):  
Elodie Laine ◽  
Yasaman Karami ◽  
Alessandra Carbone
Keyword(s):  
Evolutionary History ◽  
Recent Progress ◽  
State Of The Art ◽  
Fast Method ◽  
Biological Sequences ◽  
Epistatic Model ◽  
Input Alignment ◽  
Wide Range ◽  
History Of ◽  
Better Than

Abstract The systematic and accurate description of protein mutational landscapes is a question of utmost importance in biology, bioengineering, and medicine. Recent progress has been achieved by leveraging on the increasing wealth of genomic data and by modeling intersite dependencies within biological sequences. However, state-of-the-art methods remain time consuming. Here, we present Global Epistatic Model for predicting Mutational Effects (GEMME) (www.lcqb.upmc.fr/GEMME), an original and fast method that predicts mutational outcomes by explicitly modeling the evolutionary history of natural sequences. This allows accounting for all positions in a sequence when estimating the effect of a given mutation. GEMME uses only a few biologically meaningful and interpretable parameters. Assessed against 50 high- and low-throughput mutational experiments, it overall performs similarly or better than existing methods. It accurately predicts the mutational landscapes of a wide range of protein families, including viral ones and, more generally, of much conserved families. Given an input alignment, it generates the full mutational landscape of a protein in a matter of minutes. It is freely available as a package and a webserver at www.lcqb.upmc.fr/GEMME/.

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