• I prefer to reserve the terms 'phylogenetic' and 'phenetic' for description of methods of classification (a separate issue) and to acknowledge that all methods are attempting to infer phylogenies, and succeeding to some extent. (bio.net)
  • GBDP-like methods can be used to reliably infer phylogenies from different kinds of genomic data. (biomedcentral.com)
  • Phylogenies are also important for other forms of evolutionary inference, as it affects how much a species can evolve. (news-medical.net)
  • 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. (illinois.edu)
  • When constructing phylogenies, the similarities of species' characteristics are scored to give an indication of relatedness. (news-medical.net)
  • Phylogeny based on ITS, nLSU and RBP2 regions revealed that Datronia in current sense includes species belonging to three distantly related clades in polypores. (nih.gov)
  • The novel protocols here proposed are critical for the inclusion of rare and poorly known species of Bignonieae into a comprehensive phylogeny of the whole tribe. (bioone.org)
  • A phylogeny illustrates the evolution of species and their relationships to other groups. (coursehero.com)
  • In addition to a taxonomic revision, a molecular phylogeny of the family that includes representatives of all biological species clarifies the evolutionary relationships. (uni-muenchen.de)
  • We collected a 5-gene dataset to estimate phylogeny, and used multilocus genetic networks, analysis of population structure, and a Bayesian coalescent approach to infer species boundaries in this group. (ku.edu)
  • By examining 1107 genomes from Saccharomycotina (332), Pezizomycotina (761), and Taphrinomycotina (14) species, we inferred a robust genome-wide phylogeny that resolves several contentious relationships and estimated that the Ascomycota last common ancestor likely originated in the Ediacaran period. (glbrc.org)
  • Anonymous Reviewer ( 2017 ) Peer Review #1 of 'Mitochondrial genomes of three Tetrigoidea species and phylogeny of Tetrigoidea (v0.2)' . (peerj.com)
  • Most phylogenies are reconstructed from a tiny portion of the genome [ 2 ], but as next-generation sequencing technologies become faster and cheaper, the number of species for which whole genome sequence data are available has increased dramatically. (biomedcentral.com)
  • The Scolodontidae are shown categorically to be the sister group to all other stylommatophoran taxa with robust support and with all phylogeny reconstruction methods. (nottingham.ac.uk)
  • The suitability of these distance formulae for phylogeny reconstruction is directly estimated by computing a recently described measure of "treelikeness", the so-called δ value, from the respective distance matrices. (biomedcentral.com)
  • Here we report the first well-resolved phylogeny of Acer based on DNA sequences of over 500 nuclear loci generated using the anchored hybrid enrichment method and explore the implications of the robust phylogeny for Acer systematics and biogeography. (datadryad.org)
  • Various plant families are treated with focus on phylogeny, diagnostic traits, biogeography and cultural plants. (lu.se)
  • Therefore, constructing a phylogeny from genomic data would be a valuable tool even if genome datasets were not collected with this in mind. (biomedcentral.com)
  • How phylogenies are depicted and used in informal science settings impacts their accessibility and effectiveness in communicating about evolution to visitors. (springer.com)
  • To test competing hypotheses regarding the origins and evolution of social parasitism, we reconstructed the first global phylogeny of Formica ants and representative formicine outgroups. (biorxiv.org)
  • Phylogeny and evolution of Neuropterida: Where have wings of lace taken us? (bugguide.net)
  • Despite its importance, we lack a comprehensive genome-scale phylogeny or understanding of the similarities and differences in the mode of genome evolution within this phylum. (glbrc.org)
  • gene repertoire, phylogeny and evolution. (medlineplus.gov)
  • Andrea Waeschenbach (NERC Postdoctoral Fellow, Zoology), Paul Taylor (Palaeontology) and Tim Littlewood (Zoology) have had accepted for publication the most comprehensive molecular phylogeny of bryozoans to date, using mitochondrial and ribosomal genes. (nhm.ac.uk)
  • Here, we extend the recently described Genome BLAST Distance Phylogeny (GBDP) strategy to compute phylogenetic trees from all completely sequenced plastid genomes currently available and from a selection of mitochondrial genomes representing the major eukaryotic lineages. (biomedcentral.com)
  • Our results indicate that, at this taxonomic level, plastid genomes are much more valuable for inferring phylogenies than are mitochondrial genomes, and that distances based on breakpoints are of little use. (biomedcentral.com)
  • To greatly simplify the analysis, we present an Assembly and Alignment-Free (AAF) method ( https://sourceforge.net/projects/aaf-phylogeny ) that constructs phylogenies directly from unassembled genome sequence data, bypassing both genome assembly and alignment. (biomedcentral.com)
  • Currently, the simple step of generating a robust phylogeny for a group of poorly studied organisms can require substantial research investment. (biomedcentral.com)
  • Learn all about phylogenies and clades in just a few minutes! (coursehero.com)
  • This study provides molecular phylogenies for the Stylommatophora and Hygrophila at multiple scales including deep phylogenetic relationships of the major stylommatophoran and hygrophilan clades and family level relationships within the Orthurethra and Lymnaeoidea. (nottingham.ac.uk)
  • Systematics and Phylogeny of Siphanthera (Melastomataceae). (koeltz.com)
  • Introduction to Phylogeny and Systematics of Flowering Plants. (koeltz.com)
  • Phylogenies show how organisms are related to each other by placing them in an ordered map of them and their relatives. (news-medical.net)
  • A phylogeny is a proposal of how organisms are related by their evolutionary history. (kiddle.co)
  • Diversity and Phylogeny of the Moncotyledons: Contributions from Monocots V: The 5th International Conference on Comparative Biology of Monocotyledons. (koeltz.com)
  • to 11.06.2010, the Dagstuhl Seminar 10231 ``Structure Discovery in Biology: Motifs, Networks & Phylogenies '' was held in Schloss Dagstuhl~--~Leibniz Center for Informatics. (dagstuhl.de)
  • Conodont biology and phylogeny - interpreting the fossil record. (lu.se)
  • The BIONJ algorithm results in phylogenies most in accordance with the current NCBI taxonomy, with NJ and FastME performing insignificantly worse, and STC performing as well if applied to high quality distance matrices. (biomedcentral.com)
  • This dataset contains the digitized treatments in Plazi based on the original journal article Tol, Van (2016): Taxonomy and molecular phylogeny of the Platystictidae of Sri Lanka (Insecta: Odonata). (gbif.org)
  • By utilizing algorithms derived from perfect phylogeny data we are able to attempt to reconstruct a phylogenetic tree in spite of these limitations. (wikipedia.org)
  • We incorporate distinguishing features - features that uniquely identify a tree - into a probabilistic model that infers the number of cells to sequence so as to confidently reconstruct the phylogeny of the tumor. (illinois.edu)
  • 2. The imago-worker mandibles of termites provide a conservative morphological character significant for the study of phylogeny. (amnh.org)
  • The evidence for phylogeny comes from palaeontology , comparative anatomy , and DNA sequence analysis . (kiddle.co)
  • Tree of life diagrams are graphic representations of phylogeny-the evolutionary history and relationships of lineages-and as such these graphics have the potential to convey key evolutionary ideas and principles to a variety of audiences. (springer.com)
  • The idea of a "tree of life" represents a core concept of evolutionary science-phylogeny-and is depicted graphically using an almost bewildering array of formats and terminology, in which even a particular geometry used can have multiple names associated with it. (springer.com)
  • A phylogeny is the evolutionary history of groups of organisms. (coursehero.com)
  • These analyses typically go beyond the expertise of researchers who only require a phylogeny to place comparative studies into an evolutionary framework. (biomedcentral.com)
  • In this study we compare birds over the entire passerine phylogeny, so that we can compensate for evolutionary kinship. (lu.se)
  • Tol, Van (2016): Taxonomy and molecular phylogeny of the Platystictidae of Sri Lanka (Insecta: Odonata). (gbif.org)
  • The YFV Uganda 2016 strain envelope sequence was aligned with reference YFV genomes by using MAFFT through the EMBL-EBI server ( http://www.ebi.ac.uk ), and phylogenies were generated with BEAST 1.8.4 ( 9 ), as previously described ( 7 ). (cdc.gov)
  • Nowadays, an increasing number of completely sequenced genomes are available and a growing field of phylogenetic research deals with the question of how to infer reliable phylogenies from this large amount of data to overcome the limitations of single-gene phylogenies. (biomedcentral.com)
  • Phylogeny-Aware Analysis of Metagenome Community Ecology Based on Matched Reference Genomes while Bypassing Taxonomy. (bvsalud.org)
  • These findings are described in the article entitled Selective intra-dinucleotide interactions and periodicities of bases separated by K sites: a new vision and tool for phylogeny analyses , published in the journal Biological Research . (databasefootball.com)
  • Molecular phylogenies of many taxonomic groups are based on analyses of single loci. (biomedcentral.com)
  • For pathogenic microorganisms, several specific traits are of interest when it comes to constructing phylogenies. (news-medical.net)
  • Phylogenies can show how strains of bacteria acquire these traits that can turn a microorganism into a pathogenic microorganism. (news-medical.net)
  • It is rare that actual data adheres to the concept of perfect phylogeny. (wikipedia.org)
  • By utilizing the concepts and algorithms described in perfect phylogeny one can determine information regarding missing and unavailable haplotype data. (wikipedia.org)
  • By assuming that the set of haplotypes that result from genotype mapping corresponds and adheres to the concept of perfect phylogeny (as well as other assumptions such as perfect Mendelian inheritance and the fact that there is only one mutation per SNP), one is able to infer missing haplotype data. (wikipedia.org)
  • Inferring a phylogeny from noisy VAF data under the PPM is a hard problem. (wikipedia.org)
  • Molecular phylogeny of tribe Dipterocarpeae (family Dipterocarpaceae) based on sequence data of chloroplast and nuclear DNA. (uni-goettingen.de)
  • To facilitate further downstream analysis, one can either summarize the set of cancer phylogenies or use additional data to eliminate trees and further reduce the solution space. (illinois.edu)
  • As a test case with real data, we successfully reconstructed the phylogeny of 12 mammals using raw sequencing reads. (biomedcentral.com)
  • Character state matrices An example of a character matrix that can be depicted as a perfect phylogeny Perfect phylogeny is a theoretical framework that can also be used in more practical methods. (wikipedia.org)
  • Cancer phylogenies are key to studying tumorigenesis and have clinical implications. (illinois.edu)
  • We apply the method to propose a comprehensive phylogeny of the strepsirrhines, a major group of the primates. (cnrs.fr)
  • Usually distance matrices are calculated directly from the distribution of k -mers, and phylogenies are built from these distances [ 16 ]. (biomedcentral.com)
  • The use of phylogenies for understanding pathogenic microorganisms can have distinct advantages over other methods. (news-medical.net)
  • The issue most people are interested in is whether these methods can legitimately be used to infer a phylogeny. (bio.net)
  • Phylogeny of major intrinsic proteins. (lu.se)
  • 1. Phylogeny and major taxonomic groups. (lu.se)
  • As visual representations of the history of lineages or phylogeny, trees reflect the core concept of common ancestry. (springer.com)
  • When done on microorganisms, phylogenies can provide valuable insight into how diseases evolve, spread, and adapt to their hosts. (news-medical.net)
  • The statistical components of a perfect phylogenetic tree can best be described as follows: A perfect phylogeny for an n x m character state matrix M is a rooted tree T with n leaves satisfying: i. (wikipedia.org)