Faster Algorithms for Computing the R* Consensus Tree

2014 ◽  
pp. 414-425 ◽  
Author(s):  
Jesper Jansson ◽  
Wing-Kin Sung ◽  
Hoa Vu ◽  
Siu-Ming Yiu
Keyword(s):  
Consensus Tree

Phylogenetic relationships between the genera Aphidius and Lysaphidus (Hymenoptera: Braconidae: Aphidiinae) with description of Aphidius iranicus sp. nov.

2007 ◽  
Vol 139 (3) ◽  
pp. 297-307 ◽  
Author(s):  
Željko Tomanović ◽  
Ehsan Rakhshani ◽  
Petr Starý ◽  
Nickolas G. Kavallieratos ◽  
Ljubiša Ž. Stanisavljević ◽  
...  
Keyword(s):  
Phylogenetic Relationships ◽  
Morphological Characters ◽  
Taxonomic Position ◽  
Parsimony Analysis ◽  
Parasitoid Species ◽  
Consensus Tree ◽  
Artemisia Absinthium ◽  
Diagnostic Characters ◽  
Line Drawings ◽  
Generic Status

AbstractWe analyzed the phylogenetic relationships between eight Aphidius Nees and six Lysaphidus Smith species on the basis of 12 morphological characters by parsimony analysis. The consensus tree does not support the generic status of Lysaphidus. Aphidius iranicus, sp. nov., associated with Titanosiphon bellicosum Nevsky on Artemisia absinthium L. from Iran, is described. The new parasitoid species is described and illustrated by line drawings, and its diagnostic characters are discussed. The taxonomic position of the subgenus Tremblayia Tizado and Núñez-Pérez is also considered. Tremblayia and Lysaphidus are newly classified as synonyms of Aphidius. The following new or revised combinations are proposed: Aphidius adelocarinus Smith, comb. rev., A. ramythirus Smith, comb. rev., A. rosaphidis Smith, comb. rev., A. viaticus (Sedlag), comb. nov., A. arvensis (Starý), comb. nov., and A. erysimi (Starý), comb. nov.

Genetic diversity and morphological variability in Polygonum aviculare s.l. (Polygonaceae) of Iran

Phytotaxa ◽  
2015 ◽  
Vol 233 (2) ◽  
pp. 166 ◽  
Author(s):  
Samaneh Mosaferi ◽  
Masoud Sheidai ◽  
Maryam Keshavarzi ◽  
Zahra Noormohammdai
Keyword(s):  
Morphological Variability ◽  
Genetic Data ◽  
Mantel Test ◽  
Gene Exchange ◽  
Consensus Tree ◽  
Polygonum Aviculare ◽  
Molecular Investigation ◽  
Variable Species ◽  
Issr Molecular Markers ◽  
Positive Significant Correlation

A molecular investigation was carried out on the variable species Polygonum aviculare using 109 plants from 12 Iranian populations. ISSR molecular markers were used for genetic study. AMOVA and Gst analyses revealed a high genetic variability both within and among populations. Mantel test showed positive significant correlation between genetic and geographical distance of populations. Structure and K-Means clustering revealed stratification ingenetic characteristics of accessions. Networking and reticulation analyses showed some degree of gene exchange among populations. Consensus tree based on morphological and genetic data separated some of these populations from the others suggesting the existence of new taxa within this species.

A cladistic analysis of the Old World species of Lotus L. (Fabaceae: Loteae)

2000 ◽  
Vol 78 (3) ◽  
pp. 351-360 ◽  
Author(s):  
Ana M Arambarri
Keyword(s):  
Cladistic Analysis ◽  
Morphological Characters ◽  
Comparison Method ◽  
Data Matrix ◽  
Consensus Tree ◽  
Strict Consensus Tree ◽  
World Species ◽  
Old World ◽  
Species Phylogeny ◽  
The World

The diagnostic characters of the genus Lotus L. are a claw with a thickened infolded margin, diadelphous stamens, and a style hardened from the base. This genus contains about 100 species that are distributed throughout the world. To investigate the phylogeny of the Old World species of Lotus, subgenus Edentolotus, sections Krokeria, Xantholotus, and Erythrolotus, a cladistic analysis was performed using 31 morphological characters. To test the phylogenetic relationships among species of Lotus-Edentolotus and Dorycnium, Pedrosia, and Tetragonolobus, these taxa were included as part of the ingroup. The polarity of the characters was based on the outgroup comparison method, using Anthyllis as one outgroup and Tripodion as another. The analysis with Anthyllis as outgroup yielded eight equally parsimonious trees (with all characters equally weighted), each with 62 steps, a consistency index of 0.53, and a retention index of 0.75. All trees (including the strict consensus tree from the eight initial trees) showed that genus Lotus, subgenus Edentolotus, and sections Xantholotus and Erythrolotus are polyphyletic, with only section Krokeria appearing as monophyletic. On the other hand, the groups of species Lotus angustissimus, Lotus corniculatus, Lotus creticus, and Lotus peregrinus are monophyletic. Identical results were derived from the data matrix using Tripodion as the outgroup. Results are compared with previous cytogenetic and biochemical evidence.Key words: cladistic analysis, Fabaceae, Loteae, Lotus, Old World species, phylogeny.

Phylogenetic relationships among families of the order Anomopoda (Crustacea, Branchiopoda, Cladocera)

Zootaxa ◽  
2004 ◽  
Vol 760 (1) ◽  
pp. 1 ◽  
Author(s):  
LOURDES M.A. ELMOOR-LOUREIRO
Keyword(s):  
Phylogenetic Relationships ◽  
Cladistic Analysis ◽  
Consensus Tree ◽  
Strict Consensus Tree ◽  
Trunk Limbs ◽  
Trunk Limb

The phylogenetic relationships among families of the Order Anomopoda (Crustacea, Branchiopoda, Cladocera) were investigated through a cladistic analysis including 93 characters and 37 terminal taxa (2 as outgroups). The strict consensus tree supported the monophyly of the Anomopoda and its families, and indicated the existence of two main clades: (Moinidae+Daphniidae) and (Dumontidae (Ilyocryptidae+Bosminidae+Radopoda)). The later clade was supported by trunk limb characters, probably related to life associated with the bottom or with macrophytes (lifestyle lost in Bosminidae, but still visible in some of its trunk limbs). Within the Radopoda, the Eurycercoidea was monophyletic, but the monophyly of the Macrothricoidea was not supported.

An overview of glossiphoniid leech development

2001 ◽  
Vol 79 (2) ◽  
pp. 218-232 ◽  
Author(s):  
David A Weisblat ◽  
Françoise Z Huang
Keyword(s):  
Model Systems ◽  
Model Organisms ◽  
Consensus Tree ◽  
Comparative Development ◽  
Experimental Embryology ◽  
Molecular Studies ◽  
Research Questions ◽  
Per Se ◽  
Molecular Phylogenies ◽  
Development And Evolution

Dramatic advances in understanding the development of selected "model" organisms, coupled with the realization that genes which regulate development are often conserved between diverse taxa, have renewed interest in comparative development and evolution. Recent molecular phylogenies seem to be converging on a new consensus "tree," according to which higher bilaterians fall into three major groups, Deuterostoma, Ecdysozoa, and Lophotrochozoa. Commonly studied model systems for development fall almost exclusively within the first two of these groups. Glossiphoniid leeches (phylum Annelida) offer certain advantages for descriptive and experimental embryology per se, and can also serve to represent the lophotrochozoan clade. We present an overview of the development of glossiphoniid leeches, highlighting some current research questions and the potential for comparative cellular and molecular studies.

scholarly journals Summarizing the solution space in tumor phylogeny inference by multiple consensus trees

2019 ◽  
Vol 35 (14) ◽  
pp. i408-i416 ◽  
Author(s):  
Nuraini Aguse ◽  
Yuanyuan Qi ◽  
Mohammed El-Kebir
Keyword(s):  
Solution Space ◽  
Simulated Data ◽  
Exact Algorithm ◽  
Real Data ◽  
Supplementary Information ◽  
Mixed Integer ◽  
Consensus Tree ◽  
Large Solution ◽  
Consensus Trees ◽  
Topological Features

Abstract Motivation Cancer phylogenies are key to studying tumorigenesis and have clinical implications. Due to the heterogeneous nature of cancer and limitations in current sequencing technology, current cancer phylogeny inference methods identify a large solution space of plausible phylogenies. To facilitate further downstream analyses, methods that accurately summarize such a set T of cancer phylogenies are imperative. However, current summary methods are limited to a single consensus tree or graph and may miss important topological features that are present in different subsets of candidate trees. Results We introduce the Multiple Consensus Tree (MCT) problem to simultaneously cluster T and infer a consensus tree for each cluster. We show that MCT is NP-hard, and present an exact algorithm based on mixed integer linear programming (MILP). In addition, we introduce a heuristic algorithm that efficiently identifies high-quality consensus trees, recovering all optimal solutions identified by the MILP in simulated data at a fraction of the time. We demonstrate the applicability of our methods on both simulated and real data, showing that our approach selects the number of clusters depending on the complexity of the solution space T. Availability and implementation https://github.com/elkebir-group/MCT. Supplementary information Supplementary data are available at Bioinformatics online.

Linguistic homoplasy and phylogeny reconstruction. The cases of Lezgian and Tsezic languages (North Caucasus)

2017 ◽  
Vol 51 (s38) ◽  
Author(s):  
Alexei S. Kassian
Keyword(s):  
Phylogeny Reconstruction ◽  
Neighbor Joining ◽  
North Caucasus ◽  
Input Matrix ◽  
Consensus Tree ◽  
Strict Consensus Tree ◽  
Bayesian Mcmc ◽  
Phylogenetic Methods ◽  
Network Method ◽  
Ancestral Character States

AbstractThis paper deals with the problem of linguistic homoplasy (parallel or backward development), how it can be detected, what kinds of linguistic homoplasy can be distinguished and which varieties of the phenomenon are the most deleterious for the reconstruction of language phylogeny. It is proposed that language phylogeny reconstruction should consist of two main stages. Firstly, a strict consensus tree should be built on the basis of high-quality input data elaborated with the help of the main phylogenetic methods (such as Neighbor-joining, Bayesian MCMC, and Maximum parsimony), and ancestral character states, allowing us to reveal a certain number of homoplastic characters. Secondly, after the detected instances of homoplasy are eliminated from the input matrix, the consensus tree is to be compiled again. It is expected that after homoplastic optimization it will be possible to better resolve individual “problem clades”, and generally the homoplasy-optimized phylogeny should be more robust than the tree constructed initially. The proposed procedure is tested on the 110-item Swadesh wordlists of the Lezgian and Tsezic groups. The Lezgian and Tsezic results generally support theoretical expectations. The MLN (minimal lateral network) method, currently implemented in the LingPy software, is a helpful tool for the detection of linguistic homoplasy.

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