A review of metrics measuring dissimilarity for rooted phylogenetic networks

2018 ◽  
Vol 20 (6) ◽  
pp. 1972-1980 ◽  
Author(s):  
Juan Wang ◽  
Maozu Guo
Keyword(s):  
Polynomial Time ◽  
Phylogenetic Network ◽  
Phylogenetic Networks ◽  
Evolutionary Relationships ◽  
Comprehensive Review ◽  
Phylogenic Analysis ◽  
The Past ◽  
Important Structure

Abstract A rooted phylogenetic network is an important structure in the description of evolutionary relationships. Computing the distance (topological dissimilarity) between two rooted phylogenetic networks is a fundamental in phylogenic analysis. During the past few decades, several polynomial-time computable metrics have been described. Here, we give a comprehensive review and analysis on those metrics, including the correlation among metrics and the distribution of distance values computed by each metric. Moreover, we describe the software and website, CDRPN (Computing Distance for Rooted Phylogenetic Networks), for measuring the topological dissimilarity between rooted phylogenetic networks. Availability http://bioinformatics.imu.edu.cn/distance/ Contact [email protected]

scholarly journals On the Subnet Prune and Regraft Distance

10.37236/7860 ◽  
2019 ◽  
Vol 26 (2) ◽  
Author(s):  
Jonathan Klawitter ◽  
Simone Linz
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Phylogenetic Tree ◽  
Phylogenetic Network ◽  
Directed Acyclic Graphs ◽  
Phylogenetic Networks ◽  
Evolutionary Relationships ◽  
Acyclic Graphs ◽  
Subtree Prune And Regraft

Phylogenetic networks are rooted directed acyclic graphs that represent evolutionary relationships between species whose past includes reticulation events such as hybridisation and horizontal gene transfer. To search the space of phylogenetic networks, the popular tree rearrangement operation rooted subtree prune and regraft (rSPR) was recently generalised to phylogenetic networks. This new operation – called subnet prune and regraft (SNPR) – induces a metric on the space of all phylogenetic networks as well as on several widely-used network classes. In this paper, we investigate several problems that arise in the context of computing the SNPR-distance. For a phylogenetic tree $T$ and a phylogenetic network $N$, we show how this distance can be computed by considering the set of trees that are embedded in $N$ and then use this result to characterise the SNPR-distance between $T$ and $N$ in terms of agreement forests. Furthermore, we analyse properties of shortest SNPR-sequences between two phylogenetic networks $N$ and $N'$, and answer the question whether or not any of the classes of tree-child, reticulation-visible, or tree-based networks isometrically embeds into the class of all phylogenetic networks under SNPR.

OPTIMAL, EFFICIENT RECONSTRUCTION OF PHYLOGENETIC NETWORKS WITH CONSTRAINED RECOMBINATION

2004 ◽  
Vol 02 (01) ◽  
pp. 173-213 ◽  
Author(s):  
DAN GUSFIELD ◽  
SATISH EDDHU ◽  
CHARLES LANGLEY
Keyword(s):  
Phylogenetic Tree ◽  
Polynomial Time ◽  
Phylogenetic Network ◽  
Polynomial Time Algorithm ◽  
Time Algorithm ◽  
Phylogenetic Networks ◽  
Seminal Paper ◽  
Back Mutation ◽  
True Tree ◽  
The One

A phylogenetic network is a generalization of a phylogenetic tree, allowing structural properties that are not tree-like. In a seminal paper, Wang et al.1 studied the problem of constructing a phylogenetic network, allowing recombination between sequences, with the constraint that the resulting cycles must be disjoint. We call such a phylogenetic network a "galled-tree". They gave a polynomial-time algorithm that was intended to determine whether or not a set of sequences could be generated on galled-tree. Unfortunately, the algorithm by Wang et al.1 is incomplete and does not constitute a necessary test for the existence of a galled-tree for the data. In this paper, we completely solve the problem. Moreover, we prove that if there is a galled-tree, then the one produced by our algorithm minimizes the number of recombinations over all phylogenetic networks for the data, even allowing multiple-crossover recombinations. We also prove that when there is a galled-tree for the data, the galled-tree minimizing the number of recombinations is "essentially unique". We also note two additional results: first, any set of sequences that can be derived on a galled tree can be derived on a true tree (without recombination cycles), where at most one back mutation per site is allowed; second, the site compatibility problem (which is NP-hard in general) can be solved in polynomial time for any set of sequences that can be derived on a galled tree. Perhaps more important than the specific results about galled-trees, we introduce an approach that can be used to study recombination in general phylogenetic networks. This paper greatly extends the conference version that appears in an earlier work.8 PowerPoint slides of the conference talk can be found at our website.7

Synthesis of Drugs and Biorelevant N-heterocycles Employing Recent Advances in C-N Bond Formation

2020 ◽  
Vol 24 (20) ◽  
pp. 2293-2340
Author(s):  
Firdoos Ahmad Sofi ◽  
Prasad V. Bharatam
Keyword(s):  
Kinase Inhibitors ◽  
Bond Formation ◽  
Comprehensive Review ◽  
Biologically Relevant ◽  
Lead Compounds ◽  
Heterocyclic Molecules ◽  
The Past ◽  
Anti Cancer ◽  
Modern Methods ◽  
Bond Formation Reactions

C-N bond formation is a particularly important step in the generation of many biologically relevant heterocyclic molecules. Several methods have been reported for this purpose over the past few decades. Well-known named reactions like Ullmann-Goldberg coupling, Buchwald-Hartwig coupling and Chan-Lam coupling are associated with the C-N bond formation reactions. Several reviews covering this topic have already been published. However, no comprehensive review covering the synthesis of drugs/ lead compounds using the C-N bond formation reactions was reported. In this review, we cover many modern methods of the C-N bond formation reactions, with special emphasis on metal-free and green chemistry methods. We also report specific strategies adopted for the synthesis of drugs, which involve the C-N bond formation reactions. Examples include anti-cancer, antidepressant, anti-inflammatory, anti-atherosclerotic, anti-histaminic, antibiotics, antibacterial, anti-rheumatic, antiepileptic and anti-diabetic agents. Many recently developed lead compounds generated using the C-N bond formation reactions are also covered in this review. Examples include MAP kinase inhibitors, TRKs inhibitors, Polo-like Kinase inhibitors and MPS1 inhibitors.

Phytochemical and Pharmacological Review on Two Herbs of Baijiangcao: Patrinia scabiosaefolia Fisch. ex Trev. and Patrinia villosa (Thunb.) Juss

2020 ◽  
Vol 17 (5) ◽  
pp. 496-517
Author(s):  
Yangcheng Liu ◽  
Wei Liu ◽  
Jiaqi Wang ◽  
Yang Liu ◽  
Changlan Chen ◽  
...  
Keyword(s):  
Chemical Constituents ◽  
Volatile Components ◽  
Research Papers ◽  
Pharmacological Activities ◽  
Comprehensive Review ◽  
Scientific Databases ◽  
The Past ◽  
Current State ◽  
Patrinia Scabiosaefolia ◽  
Antiviral Activities

Patrinia scabiosaefolia Fisch. Trev. and Patrinia villosa (Thunb.) Juss, are two species of Patrinia recorded in the Chinese Pharmacopoeia with the same Chinese name “Baijiangcao” and similar therapeutic effect in traditional Chinese medicine. The present article is the first comprehensive review on the chemical composition and pharmacological activities of these herbs. In this review, data on chemical constituents and pharmacological profile of the two herbs are provided. This review discusses all the classes of the 223 compounds (phenylpropanoids, flavonoids, terpenes, saponins and volatile components, etc.) detected in the two herbs providing information on the current state of knowledge of the phytochemicals present in them. In the past three years, our research group has isolated and identified about more than 100 ingredients from the two herbs. Therefore, we published a systematic review of our research papers and studies on the two herbs were carried out using resources such as classic books about Chinese herbal medicine and scientific databases including Pubmed, Web of Science, SciFinder, CNKI. etc. The present review discusses the most thoroughly studied pharmacological activities (antioxidant, anti-inflammatory, immunomodulatory, antimicrobial, antitumor and antiviral activities) of the two herbs. This comprehensive review will be informative for scientists searching for new properties of these herbs and will be important and significant for the discovery of bioactive compounds from the two herbs and in complete utilization of Patrinia scabiosaefolia Fisch. ex Trev. and Patrinia villosa (Thunb.) Juss.

Corrigendum to: Lamprothamnium in Australia (Characeae, Charophyceae)

2013 ◽  
Vol 26 (6) ◽  
pp. 475
Author(s):  
Michelle T. Casanova
Keyword(s):  
New Species ◽  
Species Level ◽  
Type Material ◽  
Review Of The Literature ◽  
Comprehensive Review ◽  
The Past

Charophytes in the genus Lamprothamnium exhibit a large amount of diversity, particularly in the examples from Australia, although little of that variation has been recognised at species level in the past. The Australian members of the genus are revised here on the basis of extensive new collections, examination of specimens in herbaria and comprehensive review of the literature and available type material. The existing species Lamprothamnium macropogon (A.Braun) Ophel, L. inflatum (Fil. & G.O.Allen ex Fil.) A.García & Karol and L. heraldii A.García & Casanova are retained, eight new species are described (L. australicum Casanova, L. beilbyae Casanova, L. capitatum Casanova, L. compactum Casanova, L. coorongense Casanova, L. diminutum Casanova, L. macroanthum Casanova and L. stipitatum Casanova) and two taxa variously treated at infraspecific rank in Lychnothamnus are transferred to Lamprothamnium at species rank (L. cockajemmyense Casanova, L. tasmanicum (A.Braun) Casanova). Neither L. papulosum (Wallr.) J.Groves nor L. succinctum (A.Braun) R.D.Wood are confirmed for Australia after examination of the type material of these species. Species are distinguished by the arrangement of the gametangia, morphology of the fertile whorls and characteristics of the oospores. Four of these species are dioecious and nine are monoecious, which supports published conjectures concerning the biogeography of charophyte species (Proctor (1980): J. Phycol. 16, 218–233, doi:10.1111/j.1529-8817.1980.tb03023.x).

scholarly journals Men who have sex with men in China have relatively low numbers of sexual partners

2011 ◽  
Vol 3 (1) ◽  
pp. 10 ◽  
Author(s):  
Lei Zhang ◽  
Eric Pui Fung Chow ◽  
David P. Wilson
Keyword(s):  
Median Number ◽  
Sexual Partners ◽  
Hiv Prevalence ◽  
Comprehensive Review ◽  
The Past ◽  
Male Sexual Partners ◽  
Sex With Men ◽  
Over Time

HIV prevalence is increasing rapidly among men who have sex with men (MSM) in China and potentially associated with the number of male sexual partners that each man has on average. This study estimates the distribution of the number of male sexual partners among Chinese MSM through a comprehensive review of English and Chinese published literature. The overall median number of male sexual partners of Chinese MSM in the past 6 months China was estimated to be 1.5 (95% CI, 1.1-1.9) and 3.8 (95% CI 1.5-6.9) sexual partners in the past 6-month and 12-month periods respectively. An estimated 31% of sexual partners of MSM in China are regular partners, 54% are casual partners, and 16% are commercial partners. The reported numbers of sexual partners has not changed over time during the past decade. The numbers of male sexual partners reported by Chinese MSM is consistently lower than other settings and may not be sufficient to explain the recent rapid increase in HIV prevalence.

scholarly journals Digestive involvement in COVID-19: what we have learned in the past 12 months

2021 ◽  
Author(s):  
Vladimir Posmag ◽  
Liliana David ◽  
Dan L. Dumitrascu
Keyword(s):  
Observational Studies ◽  
Digestive System ◽  
Literature Search ◽  
Gastrointestinal Symptoms ◽  
Clinical Findings ◽  
Treatment Schedule ◽  
Gastrointestinal Involvement ◽  
Comprehensive Review ◽  
The Past ◽  
The Relationship

Background and aim. The year 2020 will remain in the medical history as the year of COVID-19 pandemic. Although COVID-19 is considered mainly a respiratory disease, it is well known now that SARS-CoV-2 can affect major organs including the digestive system. This is a comprehensive review on gastrointestinal involvement in the SARS-CoV-2 infection, also the digestive damage due to COVID-19. Methods. A literature search was undertaken in main databases of medical publications following the search items digestive or gastrointestinal or gastric or enteral and SARS-CoV-2 or COVID-19.  Data on gastrointestinal symptoms and alterations in this viral condition were collected and presented. Only observational studies were included. Results. In this review we discuss the recent information on the relationship between COVID-19 and the digestive system. The putative underlying pathogenic mechanisms of COVID-19 as well as the clinical findings in relation to gastrointestinal changes are presented. Conclusions. SARS-CoV-2 virus can affect any part of the digestive system. Patients with chronic diseases are at greatest risk of adverse out-comes. There is a considerable risk for drug-drug interactions in patients who require a large treatment schedule.

scholarly journals Ranking top-k trees in tree-based phylogenetic networks

2019 ◽  
Author(s):  
Momoko Hayamizu ◽  
Kazuhisa Makino
Keyword(s):  
Optimal Algorithm ◽  
Linear Time ◽  
Fundamental Problem ◽  
Phylogenetic Network ◽  
Reticulate Evolution ◽  
Interesting Property ◽  
Biological Data ◽  
Phylogenetic Networks ◽  
Linear Delay ◽  
Algorithmic Problems

Abstract 'Tree-based' phylogenetic networks provide a mathematically-tractable model for representing reticulate evolution in biology. Such networks consist of an underlying 'support tree' together with arcs between the edges of this tree. However, a tree-based network can have several such support trees, and this leads to a variety of algorithmic problems that are relevant to the analysis of biological data. Recently, Hayamizu (arXiv:1811.05849 [math.CO]) proved a structure theorem for tree-based phylogenetic networks and obtained linear-time and linear-delay algorithms for many basic problems on support trees, such as counting, optimisation, and enumeration. In the present paper, we consider the following fundamental problem in statistical data analysis: given a tree-based phylogenetic network $N$ whose arcs are associated with probability, create the top-$k$ support tree ranking for $N$ by their likelihood values. We provide a linear-delay (and hence optimal) algorithm for the problem and thus reveal the interesting property of tree-based phylogenetic networks that ranking top-$k$ support trees is as computationally easy as picking $k$ arbitrary support trees.

scholarly journals Implementing Large Genomic Single Nucleotide Polymorphism Data Sets in Phylogenetic Network Reconstructions: A Case Study of Particularly Rapid Radiations of Cichlid Fish

2020 ◽  
Vol 69 (5) ◽  
pp. 848-862 ◽  
Author(s):  
Melisa Olave ◽  
Axel Meyer
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Gene Flow ◽  
Genetic Material ◽  
Cichlid Fish ◽  
Phylogenetic Network ◽  
Phylogenetic Networks ◽  
Nucleotide Polymorphism ◽  
Rapid Radiation ◽  
Data Set ◽  
Single Nucleotide

Abstract The Midas cichlids of the Amphilophus citrinellus spp. species complex from Nicaragua (13 species) are an extraordinary example of adaptive and rapid radiation ($<$24,000 years old). These cichlids are a very challenging group to infer its evolutionary history in phylogenetic analyses, due to the apparent prevalence of incomplete lineage sorting (ILS), as well as past and current gene flow. Assuming solely a vertical transfer of genetic material from an ancestral lineage to new lineages is not appropriate in many cases of genes transferred horizontally in nature. Recently developed methods to infer phylogenetic networks under such circumstances might be able to circumvent these problems. These models accommodate not just ILS, but also gene flow, under the multispecies network coalescent (MSNC) model, processes that are at work in young, hybridizing, and/or rapidly diversifying lineages. There are currently only a few programs available that implement MSNC for estimating phylogenetic networks. Here, we present a novel way to incorporate single nucleotide polymorphism (SNP) data into the currently available PhyloNetworks program. Based on simulations, we demonstrate that SNPs can provide enough power to recover the true phylogenetic network. We also show that it can accurately infer the true network more often than other similar SNP-based programs (PhyloNet and HyDe). Moreover, our approach results in a faster algorithm compared to the original pipeline in PhyloNetworks, without losing power. We also applied our new approach to infer the phylogenetic network of Midas cichlid radiation. We implemented the most comprehensive genomic data set to date (RADseq data set of 679 individuals and $>$37K SNPs from 19 ingroup lineages) and present estimated phylogenetic networks for this extremely young and fast-evolving radiation of cichlid fish. We demonstrate that the MSNC is more appropriate than the multispecies coalescent alone for the analysis of this rapid radiation. [Genomics; multispecies network coalescent; phylogenetic networks; phylogenomics; RADseq; SNPs.]

scholarly journals Maxillary Sinus Pneumocele Presenting as Aesthetic Deformity: A Case Report With Literature Review

2019 ◽  
Vol 99 (6) ◽  
pp. 397-401
Author(s):  
Hyun Sang Cho ◽  
Seok Jung Hong ◽  
Hyun Kyu Chae ◽  
Kyung Soo Kim
Keyword(s):  
Case Report ◽  
Maxillary Sinus ◽  
Surgical Approach ◽  
Clinical Symptoms ◽  
Interesting Case ◽  
Operation Technique ◽  
Comprehensive Review ◽  
The Past ◽  
Standard Operation ◽  
Eye Symptoms

We report an interesting case of maxillary sinus pneumocele that presented with aesthetic deformity and completely treated with Caldwell-Luc approach and thoroughly review all of the past literature focusing on clinical symptoms and surgical approach. Based on our comprehensive review of maxillary sinus pneumocele, we found 2 important characteristics. First, maxillary sinus pneumocele may be asymptomatic but cause various symptoms owing to the displacement of neighboring structures, such as facial symptoms, eye symptoms, and nasal obstruction. Second, there is no standard operation technique for maxillary sinus pneumocele, but surgical approach should be individualized depending on patient’s symptoms and needs. Therefore, more case studies are needed to confirm this.

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