Distribution and asymptotic behavior of the phylogenetic transfer distance View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2019-04-29

AUTHORS

Miraine Dávila Felipe, Jean-Baka Domelevo Entfellner, Frédéric Lemoine, Jakub Truszkowski, Olivier Gascuel

ABSTRACT

The transfer distance (TD) was introduced in the classification framework and studied in the context of phylogenetic tree matching. Recently, Lemoine et al. (Nature 556(7702):452–456, 2018. 10.1038/s41586-018-0043-0) showed that TD can be a powerful tool to assess the branch support on large phylogenies, thus providing a relevant alternative to Felsenstein’s bootstrap. This distance allows a reference branchβ\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\beta $$\end{document} in a reference tree T\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$${\mathcal {T}}$$\end{document} to be compared to a branch b from another tree T (typically a bootstrap tree), both on the same set of n taxa. The TD between these branches is the number of taxa that must be transferred from one side of b to the other in order to obtain β\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\beta $$\end{document}. By taking the minimum TD from β\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\beta $$\end{document} to all branches in T we define the transfer index, denoted by ϕ(β,T)\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\phi (\beta ,T)$$\end{document}, measuring the degree of agreement of T with β\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\beta $$\end{document}. Let us consider a reference branch β\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\beta $$\end{document} having p tips on its light side and define the transfer support (TS) as 1-ϕ(β,T)/(p-1)\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$1 - \phi (\beta ,T)/(p-1)$$\end{document}. Lemoine et al. (2018) used computer simulations to show that the TS defined in this manner is close to 0 for random “bootstrap” trees. In this paper, we demonstrate that result mathematically: when T is randomly drawn, TS converges in probability to 0 when n tends to ∞\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\infty $$\end{document}. Moreover, we fully characterize the distribution of ϕ(β,T)\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\phi (\beta ,T)$$\end{document} on caterpillar trees, indicating that the convergence is fast, and that even when n is small, moderate levels of branch support cannot appear by chance. More... »

PAGES

485-508

References to SciGraph publications

  • 2006-06. Maximum Transfer Distance Between Partitions in JOURNAL OF CLASSIFICATION
  • 2008-11-08. Transfer distance between partitions in ADVANCES IN DATA ANALYSIS AND CLASSIFICATION
  • 1985-12. Optimal algorithms for comparing trees with labeled leaves in JOURNAL OF CLASSIFICATION
  • 2018-04-18. Renewing Felsenstein’s phylogenetic bootstrap in the era of big data in NATURE
  • Identifiers

    URI

    http://scigraph.springernature.com/pub.10.1007/s00285-019-01365-0

    DOI

    http://dx.doi.org/10.1007/s00285-019-01365-0

    DIMENSIONS

    https://app.dimensions.ai/details/publication/pub.1113808345

    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/31037350


    Indexing Status Check whether this publication has been indexed by Scopus and Web Of Science using the SN Indexing Status Tool
    Incoming Citations Browse incoming citations for this publication using opencitations.net

    JSON-LD is the canonical representation for SciGraph data.

    TIP: You can open this SciGraph record using an external JSON-LD service: JSON-LD Playground Google SDTT

    [
      {
        "@context": "https://springernature.github.io/scigraph/jsonld/sgcontext.json", 
        "about": [
          {
            "id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/01", 
            "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
            "name": "Mathematical Sciences", 
            "type": "DefinedTerm"
          }, 
          {
            "id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/0104", 
            "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
            "name": "Statistics", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Algorithms", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Computer Simulation", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Gene Transfer, Horizontal", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Models, Genetic", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Phylogeny", 
            "type": "DefinedTerm"
          }
        ], 
        "author": [
          {
            "affiliation": {
              "alternateName": "Unit\u00e9 Bioinformatique Evolutive, C3BI, USR 3756, Institut Pasteur & CNRS, Paris, France", 
              "id": "http://www.grid.ac/institutes/grid.428999.7", 
              "name": [
                "Unit\u00e9 Bioinformatique Evolutive, C3BI, USR 3756, Institut Pasteur & CNRS, Paris, France"
              ], 
              "type": "Organization"
            }, 
            "familyName": "D\u00e1vila Felipe", 
            "givenName": "Miraine", 
            "id": "sg:person.016454637671.27", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.016454637671.27"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Biosciences eastern and central Africa (BecA-ILRI Hub), International Livestock Research Institute, PO Box 30709, 00100, Nairobi, Kenya", 
              "id": "http://www.grid.ac/institutes/grid.419369.0", 
              "name": [
                "Biosciences eastern and central Africa (BecA-ILRI Hub), International Livestock Research Institute, PO Box 30709, 00100, Nairobi, Kenya"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Domelevo Entfellner", 
            "givenName": "Jean-Baka", 
            "id": "sg:person.012353306017.54", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.012353306017.54"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Hub Bioinformatique et Biostatistique, C3BI, USR 3756, Institut Pasteur & CNRS, Paris, France", 
              "id": "http://www.grid.ac/institutes/grid.428999.7", 
              "name": [
                "Unit\u00e9 Bioinformatique Evolutive, C3BI, USR 3756, Institut Pasteur & CNRS, Paris, France", 
                "Hub Bioinformatique et Biostatistique, C3BI, USR 3756, Institut Pasteur & CNRS, Paris, France"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Lemoine", 
            "givenName": "Fr\u00e9d\u00e9ric", 
            "id": "sg:person.01350441776.80", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01350441776.80"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "M\u00e9thodes et Algorithmes pour la Bioinformatique, IBC - LIRMM, UMR 5506, Universit\u00e9 de Montpellier & CNRS, Montpellier, France", 
              "id": "http://www.grid.ac/institutes/grid.121334.6", 
              "name": [
                "M\u00e9thodes et Algorithmes pour la Bioinformatique, IBC - LIRMM, UMR 5506, Universit\u00e9 de Montpellier & CNRS, Montpellier, France"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Truszkowski", 
            "givenName": "Jakub", 
            "id": "sg:person.01320220640.40", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01320220640.40"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "M\u00e9thodes et Algorithmes pour la Bioinformatique, IBC - LIRMM, UMR 5506, Universit\u00e9 de Montpellier & CNRS, Montpellier, France", 
              "id": "http://www.grid.ac/institutes/grid.121334.6", 
              "name": [
                "Unit\u00e9 Bioinformatique Evolutive, C3BI, USR 3756, Institut Pasteur & CNRS, Paris, France", 
                "M\u00e9thodes et Algorithmes pour la Bioinformatique, IBC - LIRMM, UMR 5506, Universit\u00e9 de Montpellier & CNRS, Montpellier, France"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Gascuel", 
            "givenName": "Olivier", 
            "id": "sg:person.0600225453.04", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0600225453.04"
            ], 
            "type": "Person"
          }
        ], 
        "citation": [
          {
            "id": "sg:pub.10.1007/s00357-006-0006-2", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1034535077", 
              "https://doi.org/10.1007/s00357-006-0006-2"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1007/s11634-008-0029-0", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1020740395", 
              "https://doi.org/10.1007/s11634-008-0029-0"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1007/bf01908061", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1030909210", 
              "https://doi.org/10.1007/bf01908061"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/s41586-018-0043-0", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1103449745", 
              "https://doi.org/10.1038/s41586-018-0043-0"
            ], 
            "type": "CreativeWork"
          }
        ], 
        "datePublished": "2019-04-29", 
        "datePublishedReg": "2019-04-29", 
        "description": "The transfer distance (TD) was introduced in the classification framework and studied in the context of phylogenetic tree matching. Recently, Lemoine et al. (Nature 556(7702):452\u2013456, 2018. 10.1038/s41586-018-0043-0) showed that TD can be a powerful tool to assess the branch support on large phylogenies, thus providing a relevant alternative to Felsenstein\u2019s bootstrap. This distance allows a reference branch\u03b2\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym}\n\t\t\t\t\\usepackage{amsfonts}\n\t\t\t\t\\usepackage{amssymb}\n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\beta $$\\end{document} in a reference tree T\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym}\n\t\t\t\t\\usepackage{amsfonts}\n\t\t\t\t\\usepackage{amssymb}\n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$${\\mathcal {T}}$$\\end{document} to be compared to a branch b from another tree T (typically a bootstrap tree), both on the same set of n taxa. The TD between these branches is the number of taxa that must be transferred from one side of b to the other in order to obtain \u03b2\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym}\n\t\t\t\t\\usepackage{amsfonts}\n\t\t\t\t\\usepackage{amssymb}\n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\beta $$\\end{document}. By taking the minimum TD from \u03b2\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym}\n\t\t\t\t\\usepackage{amsfonts}\n\t\t\t\t\\usepackage{amssymb}\n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\beta $$\\end{document} to all branches in T we define the transfer index, denoted by \u03d5(\u03b2,T)\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym}\n\t\t\t\t\\usepackage{amsfonts}\n\t\t\t\t\\usepackage{amssymb}\n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\phi (\\beta ,T)$$\\end{document}, measuring the degree of agreement of T with \u03b2\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym}\n\t\t\t\t\\usepackage{amsfonts}\n\t\t\t\t\\usepackage{amssymb}\n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\beta $$\\end{document}. Let us consider a reference branch \u03b2\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym}\n\t\t\t\t\\usepackage{amsfonts}\n\t\t\t\t\\usepackage{amssymb}\n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\beta $$\\end{document} having p tips on its light side and define the transfer support (TS) as 1-\u03d5(\u03b2,T)/(p-1)\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym}\n\t\t\t\t\\usepackage{amsfonts}\n\t\t\t\t\\usepackage{amssymb}\n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$1 - \\phi (\\beta ,T)/(p-1)$$\\end{document}. Lemoine et\u00a0al. (2018) used computer simulations to show that the TS defined in this manner is close to 0 for random \u201cbootstrap\u201d trees. In this paper, we demonstrate that result mathematically: when T is randomly drawn, TS converges in probability to 0 when n tends to \u221e\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym}\n\t\t\t\t\\usepackage{amsfonts}\n\t\t\t\t\\usepackage{amssymb}\n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\infty $$\\end{document}. Moreover, we fully characterize the distribution of \u03d5(\u03b2,T)\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym}\n\t\t\t\t\\usepackage{amsfonts}\n\t\t\t\t\\usepackage{amssymb}\n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\phi (\\beta ,T)$$\\end{document} on caterpillar trees, indicating that the convergence is fast, and that even when n is small, moderate levels of branch support cannot appear by chance.", 
        "genre": "article", 
        "id": "sg:pub.10.1007/s00285-019-01365-0", 
        "isAccessibleForFree": true, 
        "isFundedItemOf": [
          {
            "id": "sg:grant.3938159", 
            "type": "MonetaryGrant"
          }
        ], 
        "isPartOf": [
          {
            "id": "sg:journal.1081642", 
            "issn": [
              "0303-6812", 
              "1432-1416"
            ], 
            "name": "Journal of Mathematical Biology", 
            "publisher": "Springer Nature", 
            "type": "Periodical"
          }, 
          {
            "issueNumber": "2", 
            "type": "PublicationIssue"
          }, 
          {
            "type": "PublicationVolume", 
            "volumeNumber": "79"
          }
        ], 
        "keywords": [
          "Felsenstein\u2019s bootstrap", 
          "T converges", 
          "asymptotic behavior", 
          "caterpillar trees", 
          "computer simulations", 
          "large phylogenies", 
          "bootstrap", 
          "branch B", 
          "tree T", 
          "reference branch", 
          "p-tip", 
          "powerful tool", 
          "converges", 
          "et al", 
          "same set", 
          "convergence", 
          "distance", 
          "branches", 
          "simulations", 
          "probability", 
          "distribution", 
          "set", 
          "number of taxa", 
          "transfer distance", 
          "framework", 
          "tree matching", 
          "al", 
          "reference trees", 
          "transfer index", 
          "agreement", 
          "matching", 
          "trees", 
          "number", 
          "order", 
          "transfer support", 
          "et", 
          "classification framework", 
          "tool", 
          "degree of agreement", 
          "results", 
          "behavior", 
          "branch support", 
          "reference", 
          "side", 
          "degree", 
          "relevant alternative", 
          "alternative", 
          "light side", 
          "manner", 
          "context", 
          "index", 
          "tip", 
          "support", 
          "chance", 
          "levels", 
          "phylogeny", 
          "moderate levels", 
          "Lemoine et al", 
          "taxa", 
          "paper"
        ], 
        "name": "Distribution and asymptotic behavior of the phylogenetic transfer distance", 
        "pagination": "485-508", 
        "productId": [
          {
            "name": "dimensions_id", 
            "type": "PropertyValue", 
            "value": [
              "pub.1113808345"
            ]
          }, 
          {
            "name": "doi", 
            "type": "PropertyValue", 
            "value": [
              "10.1007/s00285-019-01365-0"
            ]
          }, 
          {
            "name": "pubmed_id", 
            "type": "PropertyValue", 
            "value": [
              "31037350"
            ]
          }
        ], 
        "sameAs": [
          "https://doi.org/10.1007/s00285-019-01365-0", 
          "https://app.dimensions.ai/details/publication/pub.1113808345"
        ], 
        "sdDataset": "articles", 
        "sdDatePublished": "2022-12-01T06:40", 
        "sdLicense": "https://scigraph.springernature.com/explorer/license/", 
        "sdPublisher": {
          "name": "Springer Nature - SN SciGraph project", 
          "type": "Organization"
        }, 
        "sdSource": "s3://com-springernature-scigraph/baseset/20221201/entities/gbq_results/article/article_812.jsonl", 
        "type": "ScholarlyArticle", 
        "url": "https://doi.org/10.1007/s00285-019-01365-0"
      }
    ]
     

    Download the RDF metadata as:  json-ld nt turtle xml License info

    HOW TO GET THIS DATA PROGRAMMATICALLY:

    JSON-LD is a popular format for linked data which is fully compatible with JSON.

    curl -H 'Accept: application/ld+json' 'https://scigraph.springernature.com/pub.10.1007/s00285-019-01365-0'

    N-Triples is a line-based linked data format ideal for batch operations.

    curl -H 'Accept: application/n-triples' 'https://scigraph.springernature.com/pub.10.1007/s00285-019-01365-0'

    Turtle is a human-readable linked data format.

    curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1007/s00285-019-01365-0'

    RDF/XML is a standard XML format for linked data.

    curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1007/s00285-019-01365-0'


     

    This table displays all metadata directly associated to this object as RDF triples.

    196 TRIPLES      21 PREDICATES      94 URIs      82 LITERALS      12 BLANK NODES

    Subject Predicate Object
    1 sg:pub.10.1007/s00285-019-01365-0 schema:about N18ab7aa850f342d2a8b160a8a5374ab0
    2 N4eb68cd482424a20b4b3f1f661f2d476
    3 N726cb68b447d412b8baa23872287c1bb
    4 N8759a357068d4e2bbb5258629b2f938d
    5 N8acf24a3940b4b55b74fb8c0aedd784d
    6 anzsrc-for:01
    7 anzsrc-for:0104
    8 schema:author Naa97987cd1654566bac3b1009cb0893d
    9 schema:citation sg:pub.10.1007/bf01908061
    10 sg:pub.10.1007/s00357-006-0006-2
    11 sg:pub.10.1007/s11634-008-0029-0
    12 sg:pub.10.1038/s41586-018-0043-0
    13 schema:datePublished 2019-04-29
    14 schema:datePublishedReg 2019-04-29
    15 schema:description The transfer distance (TD) was introduced in the classification framework and studied in the context of phylogenetic tree matching. Recently, Lemoine et al. (Nature 556(7702):452–456, 2018. 10.1038/s41586-018-0043-0) showed that TD can be a powerful tool to assess the branch support on large phylogenies, thus providing a relevant alternative to Felsenstein’s bootstrap. This distance allows a reference branchβ\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\beta $$\end{document} in a reference tree T\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$${\mathcal {T}}$$\end{document} to be compared to a branch b from another tree T (typically a bootstrap tree), both on the same set of n taxa. The TD between these branches is the number of taxa that must be transferred from one side of b to the other in order to obtain β\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\beta $$\end{document}. By taking the minimum TD from β\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\beta $$\end{document} to all branches in T we define the transfer index, denoted by ϕ(β,T)\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\phi (\beta ,T)$$\end{document}, measuring the degree of agreement of T with β\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\beta $$\end{document}. Let us consider a reference branch β\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\beta $$\end{document} having p tips on its light side and define the transfer support (TS) as 1-ϕ(β,T)/(p-1)\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$1 - \phi (\beta ,T)/(p-1)$$\end{document}. Lemoine et al. (2018) used computer simulations to show that the TS defined in this manner is close to 0 for random “bootstrap” trees. In this paper, we demonstrate that result mathematically: when T is randomly drawn, TS converges in probability to 0 when n tends to ∞\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\infty $$\end{document}. Moreover, we fully characterize the distribution of ϕ(β,T)\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\phi (\beta ,T)$$\end{document} on caterpillar trees, indicating that the convergence is fast, and that even when n is small, moderate levels of branch support cannot appear by chance.
    16 schema:genre article
    17 schema:isAccessibleForFree true
    18 schema:isPartOf N741b08e952f3431e89172b99b2d9fba4
    19 Ne6235308c9124634a4a9af7426cc13ec
    20 sg:journal.1081642
    21 schema:keywords Felsenstein’s bootstrap
    22 Lemoine et al
    23 T converges
    24 agreement
    25 al
    26 alternative
    27 asymptotic behavior
    28 behavior
    29 bootstrap
    30 branch B
    31 branch support
    32 branches
    33 caterpillar trees
    34 chance
    35 classification framework
    36 computer simulations
    37 context
    38 convergence
    39 converges
    40 degree
    41 degree of agreement
    42 distance
    43 distribution
    44 et
    45 et al
    46 framework
    47 index
    48 large phylogenies
    49 levels
    50 light side
    51 manner
    52 matching
    53 moderate levels
    54 number
    55 number of taxa
    56 order
    57 p-tip
    58 paper
    59 phylogeny
    60 powerful tool
    61 probability
    62 reference
    63 reference branch
    64 reference trees
    65 relevant alternative
    66 results
    67 same set
    68 set
    69 side
    70 simulations
    71 support
    72 taxa
    73 tip
    74 tool
    75 transfer distance
    76 transfer index
    77 transfer support
    78 tree T
    79 tree matching
    80 trees
    81 schema:name Distribution and asymptotic behavior of the phylogenetic transfer distance
    82 schema:pagination 485-508
    83 schema:productId N3bc2848a8d7e43d1a041fd655622dec2
    84 N525facb14ea047b7a382c34e7b9fb34f
    85 Nc84701719ae2414398474a374ca6c316
    86 schema:sameAs https://app.dimensions.ai/details/publication/pub.1113808345
    87 https://doi.org/10.1007/s00285-019-01365-0
    88 schema:sdDatePublished 2022-12-01T06:40
    89 schema:sdLicense https://scigraph.springernature.com/explorer/license/
    90 schema:sdPublisher N26aa191e30d04d4c9984c9d026c1c9ff
    91 schema:url https://doi.org/10.1007/s00285-019-01365-0
    92 sgo:license sg:explorer/license/
    93 sgo:sdDataset articles
    94 rdf:type schema:ScholarlyArticle
    95 N086c1e08321e41b0af9926b4a7b09696 rdf:first sg:person.0600225453.04
    96 rdf:rest rdf:nil
    97 N18ab7aa850f342d2a8b160a8a5374ab0 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    98 schema:name Models, Genetic
    99 rdf:type schema:DefinedTerm
    100 N26aa191e30d04d4c9984c9d026c1c9ff schema:name Springer Nature - SN SciGraph project
    101 rdf:type schema:Organization
    102 N3bc2848a8d7e43d1a041fd655622dec2 schema:name dimensions_id
    103 schema:value pub.1113808345
    104 rdf:type schema:PropertyValue
    105 N4eb68cd482424a20b4b3f1f661f2d476 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    106 schema:name Algorithms
    107 rdf:type schema:DefinedTerm
    108 N525facb14ea047b7a382c34e7b9fb34f schema:name pubmed_id
    109 schema:value 31037350
    110 rdf:type schema:PropertyValue
    111 N726cb68b447d412b8baa23872287c1bb schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    112 schema:name Phylogeny
    113 rdf:type schema:DefinedTerm
    114 N741b08e952f3431e89172b99b2d9fba4 schema:issueNumber 2
    115 rdf:type schema:PublicationIssue
    116 N8759a357068d4e2bbb5258629b2f938d schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    117 schema:name Computer Simulation
    118 rdf:type schema:DefinedTerm
    119 N8acf24a3940b4b55b74fb8c0aedd784d schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    120 schema:name Gene Transfer, Horizontal
    121 rdf:type schema:DefinedTerm
    122 Naa97987cd1654566bac3b1009cb0893d rdf:first sg:person.016454637671.27
    123 rdf:rest Nd9bd5d2bfb6344bf8b77b5e37ba0b769
    124 Nc84701719ae2414398474a374ca6c316 schema:name doi
    125 schema:value 10.1007/s00285-019-01365-0
    126 rdf:type schema:PropertyValue
    127 Nd9bd5d2bfb6344bf8b77b5e37ba0b769 rdf:first sg:person.012353306017.54
    128 rdf:rest Nf507de4131f94851a9ea66e46cb64d04
    129 Ne6235308c9124634a4a9af7426cc13ec schema:volumeNumber 79
    130 rdf:type schema:PublicationVolume
    131 Nf507de4131f94851a9ea66e46cb64d04 rdf:first sg:person.01350441776.80
    132 rdf:rest Nfba0f3978fb1482c859d48e741678829
    133 Nfba0f3978fb1482c859d48e741678829 rdf:first sg:person.01320220640.40
    134 rdf:rest N086c1e08321e41b0af9926b4a7b09696
    135 anzsrc-for:01 schema:inDefinedTermSet anzsrc-for:
    136 schema:name Mathematical Sciences
    137 rdf:type schema:DefinedTerm
    138 anzsrc-for:0104 schema:inDefinedTermSet anzsrc-for:
    139 schema:name Statistics
    140 rdf:type schema:DefinedTerm
    141 sg:grant.3938159 http://pending.schema.org/fundedItem sg:pub.10.1007/s00285-019-01365-0
    142 rdf:type schema:MonetaryGrant
    143 sg:journal.1081642 schema:issn 0303-6812
    144 1432-1416
    145 schema:name Journal of Mathematical Biology
    146 schema:publisher Springer Nature
    147 rdf:type schema:Periodical
    148 sg:person.012353306017.54 schema:affiliation grid-institutes:grid.419369.0
    149 schema:familyName Domelevo Entfellner
    150 schema:givenName Jean-Baka
    151 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.012353306017.54
    152 rdf:type schema:Person
    153 sg:person.01320220640.40 schema:affiliation grid-institutes:grid.121334.6
    154 schema:familyName Truszkowski
    155 schema:givenName Jakub
    156 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01320220640.40
    157 rdf:type schema:Person
    158 sg:person.01350441776.80 schema:affiliation grid-institutes:grid.428999.7
    159 schema:familyName Lemoine
    160 schema:givenName Frédéric
    161 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01350441776.80
    162 rdf:type schema:Person
    163 sg:person.016454637671.27 schema:affiliation grid-institutes:grid.428999.7
    164 schema:familyName Dávila Felipe
    165 schema:givenName Miraine
    166 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.016454637671.27
    167 rdf:type schema:Person
    168 sg:person.0600225453.04 schema:affiliation grid-institutes:grid.121334.6
    169 schema:familyName Gascuel
    170 schema:givenName Olivier
    171 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0600225453.04
    172 rdf:type schema:Person
    173 sg:pub.10.1007/bf01908061 schema:sameAs https://app.dimensions.ai/details/publication/pub.1030909210
    174 https://doi.org/10.1007/bf01908061
    175 rdf:type schema:CreativeWork
    176 sg:pub.10.1007/s00357-006-0006-2 schema:sameAs https://app.dimensions.ai/details/publication/pub.1034535077
    177 https://doi.org/10.1007/s00357-006-0006-2
    178 rdf:type schema:CreativeWork
    179 sg:pub.10.1007/s11634-008-0029-0 schema:sameAs https://app.dimensions.ai/details/publication/pub.1020740395
    180 https://doi.org/10.1007/s11634-008-0029-0
    181 rdf:type schema:CreativeWork
    182 sg:pub.10.1038/s41586-018-0043-0 schema:sameAs https://app.dimensions.ai/details/publication/pub.1103449745
    183 https://doi.org/10.1038/s41586-018-0043-0
    184 rdf:type schema:CreativeWork
    185 grid-institutes:grid.121334.6 schema:alternateName Méthodes et Algorithmes pour la Bioinformatique, IBC - LIRMM, UMR 5506, Université de Montpellier & CNRS, Montpellier, France
    186 schema:name Méthodes et Algorithmes pour la Bioinformatique, IBC - LIRMM, UMR 5506, Université de Montpellier & CNRS, Montpellier, France
    187 Unité Bioinformatique Evolutive, C3BI, USR 3756, Institut Pasteur & CNRS, Paris, France
    188 rdf:type schema:Organization
    189 grid-institutes:grid.419369.0 schema:alternateName Biosciences eastern and central Africa (BecA-ILRI Hub), International Livestock Research Institute, PO Box 30709, 00100, Nairobi, Kenya
    190 schema:name Biosciences eastern and central Africa (BecA-ILRI Hub), International Livestock Research Institute, PO Box 30709, 00100, Nairobi, Kenya
    191 rdf:type schema:Organization
    192 grid-institutes:grid.428999.7 schema:alternateName Hub Bioinformatique et Biostatistique, C3BI, USR 3756, Institut Pasteur & CNRS, Paris, France
    193 Unité Bioinformatique Evolutive, C3BI, USR 3756, Institut Pasteur & CNRS, Paris, France
    194 schema:name Hub Bioinformatique et Biostatistique, C3BI, USR 3756, Institut Pasteur & CNRS, Paris, France
    195 Unité Bioinformatique Evolutive, C3BI, USR 3756, Institut Pasteur & CNRS, Paris, France
    196 rdf:type schema:Organization
     




    Preview window. Press ESC to close (or click here)


    ...