Genome-scale approaches to resolving incongruence in molecular phylogenies View Full Text


Ontology type: schema:ScholarlyArticle     


Article Info

DATE

2003-10

AUTHORS

Antonis Rokas, Barry L. Williams, Nicole King, Sean B. Carroll

ABSTRACT

One of the most pervasive challenges in molecular phylogenetics is the incongruence between phylogenies obtained using different data sets, such as individual genes. To systematically investigate the degree of incongruence, and potential methods for resolving it, we screened the genome sequences of eight yeast species and selected 106 widely distributed orthologous genes for phylogenetic analyses, singly and by concatenation. Our results suggest that data sets consisting of single or a small number of concatenated genes have a significant probability of supporting conflicting topologies. By contrast, analyses of the entire data set of concatenated genes yielded a single, fully resolved species tree with maximum support. Comparable results were obtained with a concatenation of a minimum of 20 genes; substantially more genes than commonly used but a small fraction of any genome. These results have important implications for resolving branches of the tree of life. More... »

PAGES

798

Identifiers

URI

http://scigraph.springernature.com/pub.10.1038/nature02053

DOI

http://dx.doi.org/10.1038/nature02053

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1029791427

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/14574403


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/2008/0604", 
        "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
        "name": "Genetics", 
        "type": "DefinedTerm"
      }, 
      {
        "id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/06", 
        "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
        "name": "Biological Sciences", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Genes, Fungal", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Genome, Fungal", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Genomics", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Phylogeny", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Regression Analysis", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Reproducibility of Results", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Saccharomyces", 
        "type": "DefinedTerm"
      }
    ], 
    "author": [
      {
        "affiliation": {
          "alternateName": "University of Wisconsin\u2013Madison", 
          "id": "https://www.grid.ac/institutes/grid.14003.36", 
          "name": [
            "Howard Hughes Medical Institute, Laboratory of Molecular Biology, R. M. Bock Laboratories, University of Wisconsin-Madison, 1525 Linden Drive, Madison, Wisconsin 53706, USA"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Rokas", 
        "givenName": "Antonis", 
        "id": "sg:person.01313127416.84", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01313127416.84"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "University of Wisconsin\u2013Madison", 
          "id": "https://www.grid.ac/institutes/grid.14003.36", 
          "name": [
            "Howard Hughes Medical Institute, Laboratory of Molecular Biology, R. M. Bock Laboratories, University of Wisconsin-Madison, 1525 Linden Drive, Madison, Wisconsin 53706, USA"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Williams", 
        "givenName": "Barry L.", 
        "id": "sg:person.0772204572.55", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0772204572.55"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "University of Wisconsin\u2013Madison", 
          "id": "https://www.grid.ac/institutes/grid.14003.36", 
          "name": [
            "Howard Hughes Medical Institute, Laboratory of Molecular Biology, R. M. Bock Laboratories, University of Wisconsin-Madison, 1525 Linden Drive, Madison, Wisconsin 53706, USA"
          ], 
          "type": "Organization"
        }, 
        "familyName": "King", 
        "givenName": "Nicole", 
        "id": "sg:person.0763431022.88", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0763431022.88"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "University of Wisconsin\u2013Madison", 
          "id": "https://www.grid.ac/institutes/grid.14003.36", 
          "name": [
            "Howard Hughes Medical Institute, Laboratory of Molecular Biology, R. M. Bock Laboratories, University of Wisconsin-Madison, 1525 Linden Drive, Madison, Wisconsin 53706, USA"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Carroll", 
        "givenName": "Sean B.", 
        "id": "sg:person.01044327353.21", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01044327353.21"
        ], 
        "type": "Person"
      }
    ], 
    "citation": [
      {
        "id": "sg:pub.10.1038/42711", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1000430591", 
          "https://doi.org/10.1038/42711"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/42711", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1000430591", 
          "https://doi.org/10.1038/42711"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1073/pnas.142101099", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1000983381"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1126/science.276.5313.734", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1002629483"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1073/pnas.90.24.11558", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1002714035"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/s1567-1356(03)00012-6", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1003379329"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/0169-5347(96)10006-9", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1004741147"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/35011054", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1009352761", 
          "https://doi.org/10.1038/35011054"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/35011054", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1009352761", 
          "https://doi.org/10.1038/35011054"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/46528", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1010205069", 
          "https://doi.org/10.1038/46528"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/46528", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1010205069", 
          "https://doi.org/10.1038/46528"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nature01419", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1010286142", 
          "https://doi.org/10.1038/nature01419"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nature01419", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1010286142", 
          "https://doi.org/10.1038/nature01419"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nature01644", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1010517605", 
          "https://doi.org/10.1038/nature01644"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nature01644", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1010517605", 
          "https://doi.org/10.1038/nature01644"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1073/pnas.032662799", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1013835406"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/387489a0", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1014476080", 
          "https://doi.org/10.1038/387489a0"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/sysbio/45.4.524", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1017545132"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1006/mpev.2000.0704", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1019541120"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1146/annurev.ecolsys.33.010802.150509", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1025744795"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/35093097", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1026689691", 
          "https://doi.org/10.1038/35093097"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/35093097", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1026689691", 
          "https://doi.org/10.1038/35093097"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/oxfordjournals.molbev.a003973", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1027077241"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/35093090", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1027886586", 
          "https://doi.org/10.1038/35093090"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/35093090", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1027886586", 
          "https://doi.org/10.1038/35093090"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/bioinformatics/14.9.817", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1029580565"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/sysbio/46.3.523", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1030043307"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1073/pnas.181187698", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1031728402"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/35054550", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1034389621", 
          "https://doi.org/10.1038/35054550"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/35054550", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1034389621", 
          "https://doi.org/10.1038/35054550"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1046/j.1525-142x.2003.03042.x", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1036097161"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/nar/22.22.4673", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1042438223"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/90129", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1042537539", 
          "https://doi.org/10.1038/90129"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/90129", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1042537539", 
          "https://doi.org/10.1038/90129"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nature01743", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1042649770", 
          "https://doi.org/10.1038/nature01743"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nature01743", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1042649770", 
          "https://doi.org/10.1038/nature01743"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1007/978-1-4615-5419-6_10", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1043419348", 
          "https://doi.org/10.1007/978-1-4615-5419-6_10"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1007/978-1-4615-5419-6_10", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1043419348", 
          "https://doi.org/10.1007/978-1-4615-5419-6_10"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1111/j.1438-8677.1996.tb00515.x", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1046180922"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1126/science.284.5423.2129", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1046634615"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1186/1471-2148-2-7", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1047674197", 
          "https://doi.org/10.1186/1471-2148-2-7"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/oxfordjournals.molbev.a025813", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1048211688"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/383130a0", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1053714297", 
          "https://doi.org/10.1038/383130a0"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1080/10635150290069995", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1058369279"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1080/10635150290102410", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1058369293"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1080/106351598260996", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1058369876"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1080/106351598261030", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1058369880"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/sysbio/42.3.384", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1060048112"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/sysbio/44.1.17", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1060048210"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/sysbio/45.3.375", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1060048285"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1099/00207713-50-5-1931", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1060350366"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1126/science.1084337", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1062448096"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1126/science.274.5287.546", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1062554574"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1126/science.287.5456.1283", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1062568434"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1126/science.290.5493.972", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1062571966"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.2307/2413481", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1069921718"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/oxfordjournals.molbev.a040258", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1082376727"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/oxfordjournals.molbev.a040112", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1082684223"
        ], 
        "type": "CreativeWork"
      }
    ], 
    "datePublished": "2003-10", 
    "datePublishedReg": "2003-10-01", 
    "description": "One of the most pervasive challenges in molecular phylogenetics is the incongruence between phylogenies obtained using different data sets, such as individual genes. To systematically investigate the degree of incongruence, and potential methods for resolving it, we screened the genome sequences of eight yeast species and selected 106 widely distributed orthologous genes for phylogenetic analyses, singly and by concatenation. Our results suggest that data sets consisting of single or a small number of concatenated genes have a significant probability of supporting conflicting topologies. By contrast, analyses of the entire data set of concatenated genes yielded a single, fully resolved species tree with maximum support. Comparable results were obtained with a concatenation of a minimum of 20 genes; substantially more genes than commonly used but a small fraction of any genome. These results have important implications for resolving branches of the tree of life.", 
    "genre": "research_article", 
    "id": "sg:pub.10.1038/nature02053", 
    "inLanguage": [
      "en"
    ], 
    "isAccessibleForFree": false, 
    "isPartOf": [
      {
        "id": "sg:journal.1018957", 
        "issn": [
          "0090-0028", 
          "1476-4687"
        ], 
        "name": "Nature", 
        "type": "Periodical"
      }, 
      {
        "issueNumber": "6960", 
        "type": "PublicationIssue"
      }, 
      {
        "type": "PublicationVolume", 
        "volumeNumber": "425"
      }
    ], 
    "name": "Genome-scale approaches to resolving incongruence in molecular phylogenies", 
    "pagination": "798", 
    "productId": [
      {
        "name": "readcube_id", 
        "type": "PropertyValue", 
        "value": [
          "8debd85ccea223a32a039c689df15c5b0ebf61d874a12a978f3bd54a9669f8e7"
        ]
      }, 
      {
        "name": "pubmed_id", 
        "type": "PropertyValue", 
        "value": [
          "14574403"
        ]
      }, 
      {
        "name": "nlm_unique_id", 
        "type": "PropertyValue", 
        "value": [
          "0410462"
        ]
      }, 
      {
        "name": "doi", 
        "type": "PropertyValue", 
        "value": [
          "10.1038/nature02053"
        ]
      }, 
      {
        "name": "dimensions_id", 
        "type": "PropertyValue", 
        "value": [
          "pub.1029791427"
        ]
      }
    ], 
    "sameAs": [
      "https://doi.org/10.1038/nature02053", 
      "https://app.dimensions.ai/details/publication/pub.1029791427"
    ], 
    "sdDataset": "articles", 
    "sdDatePublished": "2019-04-11T12:21", 
    "sdLicense": "https://scigraph.springernature.com/explorer/license/", 
    "sdPublisher": {
      "name": "Springer Nature - SN SciGraph project", 
      "type": "Organization"
    }, 
    "sdSource": "s3://com-uberresearch-data-dimensions-target-20181106-alternative/cleanup/v134/2549eaecd7973599484d7c17b260dba0a4ecb94b/merge/v9/a6c9fde33151104705d4d7ff012ea9563521a3ce/jats-lookup/v90/0000000362_0000000362/records_87078_00000001.jsonl", 
    "type": "ScholarlyArticle", 
    "url": "https://www.nature.com/articles/nature02053"
  }
]
 

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.10.1038/nature02053'

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

curl -H 'Accept: application/n-triples' 'https://scigraph.springernature.com/pub.10.1038/nature02053'

Turtle is a human-readable linked data format.

curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1038/nature02053'

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

curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1038/nature02053'


 

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

273 TRIPLES      21 PREDICATES      83 URIs      28 LITERALS      16 BLANK NODES

Subject Predicate Object
1 sg:pub.10.1038/nature02053 schema:about N142ba4c8f89642c4bb45c762b10fb1bf
2 N3d681212737f481595d4049fa94e1247
3 N54555db047bf429a8f8d0261bbeda201
4 N79f4e3cc382e471d8e125a6617406e89
5 Na21130b20c8e48e8a6dbd351f3f9bf6d
6 Nb012320acf774f66afd5b26398b376f8
7 Nc9e3f7e3bbd24481b8adc0ad6b852a61
8 anzsrc-for:06
9 anzsrc-for:0604
10 schema:author N189db1a4fc8346e3bd787ee0ff461dca
11 schema:citation sg:pub.10.1007/978-1-4615-5419-6_10
12 sg:pub.10.1038/35011054
13 sg:pub.10.1038/35054550
14 sg:pub.10.1038/35093090
15 sg:pub.10.1038/35093097
16 sg:pub.10.1038/383130a0
17 sg:pub.10.1038/387489a0
18 sg:pub.10.1038/42711
19 sg:pub.10.1038/46528
20 sg:pub.10.1038/90129
21 sg:pub.10.1038/nature01419
22 sg:pub.10.1038/nature01644
23 sg:pub.10.1038/nature01743
24 sg:pub.10.1186/1471-2148-2-7
25 https://doi.org/10.1006/mpev.2000.0704
26 https://doi.org/10.1016/0169-5347(96)10006-9
27 https://doi.org/10.1016/s1567-1356(03)00012-6
28 https://doi.org/10.1046/j.1525-142x.2003.03042.x
29 https://doi.org/10.1073/pnas.032662799
30 https://doi.org/10.1073/pnas.142101099
31 https://doi.org/10.1073/pnas.181187698
32 https://doi.org/10.1073/pnas.90.24.11558
33 https://doi.org/10.1080/10635150290069995
34 https://doi.org/10.1080/10635150290102410
35 https://doi.org/10.1080/106351598260996
36 https://doi.org/10.1080/106351598261030
37 https://doi.org/10.1093/bioinformatics/14.9.817
38 https://doi.org/10.1093/nar/22.22.4673
39 https://doi.org/10.1093/oxfordjournals.molbev.a003973
40 https://doi.org/10.1093/oxfordjournals.molbev.a025813
41 https://doi.org/10.1093/oxfordjournals.molbev.a040112
42 https://doi.org/10.1093/oxfordjournals.molbev.a040258
43 https://doi.org/10.1093/sysbio/42.3.384
44 https://doi.org/10.1093/sysbio/44.1.17
45 https://doi.org/10.1093/sysbio/45.3.375
46 https://doi.org/10.1093/sysbio/45.4.524
47 https://doi.org/10.1093/sysbio/46.3.523
48 https://doi.org/10.1099/00207713-50-5-1931
49 https://doi.org/10.1111/j.1438-8677.1996.tb00515.x
50 https://doi.org/10.1126/science.1084337
51 https://doi.org/10.1126/science.274.5287.546
52 https://doi.org/10.1126/science.276.5313.734
53 https://doi.org/10.1126/science.284.5423.2129
54 https://doi.org/10.1126/science.287.5456.1283
55 https://doi.org/10.1126/science.290.5493.972
56 https://doi.org/10.1146/annurev.ecolsys.33.010802.150509
57 https://doi.org/10.2307/2413481
58 schema:datePublished 2003-10
59 schema:datePublishedReg 2003-10-01
60 schema:description One of the most pervasive challenges in molecular phylogenetics is the incongruence between phylogenies obtained using different data sets, such as individual genes. To systematically investigate the degree of incongruence, and potential methods for resolving it, we screened the genome sequences of eight yeast species and selected 106 widely distributed orthologous genes for phylogenetic analyses, singly and by concatenation. Our results suggest that data sets consisting of single or a small number of concatenated genes have a significant probability of supporting conflicting topologies. By contrast, analyses of the entire data set of concatenated genes yielded a single, fully resolved species tree with maximum support. Comparable results were obtained with a concatenation of a minimum of 20 genes; substantially more genes than commonly used but a small fraction of any genome. These results have important implications for resolving branches of the tree of life.
61 schema:genre research_article
62 schema:inLanguage en
63 schema:isAccessibleForFree false
64 schema:isPartOf N12548565a6904dbd81078a62ff590600
65 N64117cb0268d417e8b0df4eeb03ab2a1
66 sg:journal.1018957
67 schema:name Genome-scale approaches to resolving incongruence in molecular phylogenies
68 schema:pagination 798
69 schema:productId N3820ef275a454bc8a5925c2abb6d72ce
70 N3c3c3dcd55cc49739101d5d774e1266e
71 N9c8f00fb0700487f8c35d757232a57ec
72 N9f5a7aeb04c84ebdad7a3e52f4d4200c
73 Ne0281098f4734f5794e5008986489fab
74 schema:sameAs https://app.dimensions.ai/details/publication/pub.1029791427
75 https://doi.org/10.1038/nature02053
76 schema:sdDatePublished 2019-04-11T12:21
77 schema:sdLicense https://scigraph.springernature.com/explorer/license/
78 schema:sdPublisher Nf3f7c84660794bec86fa67a326d9364f
79 schema:url https://www.nature.com/articles/nature02053
80 sgo:license sg:explorer/license/
81 sgo:sdDataset articles
82 rdf:type schema:ScholarlyArticle
83 N12548565a6904dbd81078a62ff590600 schema:volumeNumber 425
84 rdf:type schema:PublicationVolume
85 N142ba4c8f89642c4bb45c762b10fb1bf schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
86 schema:name Phylogeny
87 rdf:type schema:DefinedTerm
88 N189db1a4fc8346e3bd787ee0ff461dca rdf:first sg:person.01313127416.84
89 rdf:rest N8fe24adb0e7e4efbb5f59bc85b11184c
90 N3820ef275a454bc8a5925c2abb6d72ce schema:name pubmed_id
91 schema:value 14574403
92 rdf:type schema:PropertyValue
93 N3c3c3dcd55cc49739101d5d774e1266e schema:name readcube_id
94 schema:value 8debd85ccea223a32a039c689df15c5b0ebf61d874a12a978f3bd54a9669f8e7
95 rdf:type schema:PropertyValue
96 N3d681212737f481595d4049fa94e1247 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
97 schema:name Saccharomyces
98 rdf:type schema:DefinedTerm
99 N480c5fb27b964fd69e7a84086741b49c rdf:first sg:person.01044327353.21
100 rdf:rest rdf:nil
101 N54555db047bf429a8f8d0261bbeda201 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
102 schema:name Genes, Fungal
103 rdf:type schema:DefinedTerm
104 N64117cb0268d417e8b0df4eeb03ab2a1 schema:issueNumber 6960
105 rdf:type schema:PublicationIssue
106 N6f353df198e6405ca02ae1edc69ef988 rdf:first sg:person.0763431022.88
107 rdf:rest N480c5fb27b964fd69e7a84086741b49c
108 N79f4e3cc382e471d8e125a6617406e89 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
109 schema:name Reproducibility of Results
110 rdf:type schema:DefinedTerm
111 N8fe24adb0e7e4efbb5f59bc85b11184c rdf:first sg:person.0772204572.55
112 rdf:rest N6f353df198e6405ca02ae1edc69ef988
113 N9c8f00fb0700487f8c35d757232a57ec schema:name doi
114 schema:value 10.1038/nature02053
115 rdf:type schema:PropertyValue
116 N9f5a7aeb04c84ebdad7a3e52f4d4200c schema:name dimensions_id
117 schema:value pub.1029791427
118 rdf:type schema:PropertyValue
119 Na21130b20c8e48e8a6dbd351f3f9bf6d schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
120 schema:name Regression Analysis
121 rdf:type schema:DefinedTerm
122 Nb012320acf774f66afd5b26398b376f8 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
123 schema:name Genomics
124 rdf:type schema:DefinedTerm
125 Nc9e3f7e3bbd24481b8adc0ad6b852a61 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
126 schema:name Genome, Fungal
127 rdf:type schema:DefinedTerm
128 Ne0281098f4734f5794e5008986489fab schema:name nlm_unique_id
129 schema:value 0410462
130 rdf:type schema:PropertyValue
131 Nf3f7c84660794bec86fa67a326d9364f schema:name Springer Nature - SN SciGraph project
132 rdf:type schema:Organization
133 anzsrc-for:06 schema:inDefinedTermSet anzsrc-for:
134 schema:name Biological Sciences
135 rdf:type schema:DefinedTerm
136 anzsrc-for:0604 schema:inDefinedTermSet anzsrc-for:
137 schema:name Genetics
138 rdf:type schema:DefinedTerm
139 sg:journal.1018957 schema:issn 0090-0028
140 1476-4687
141 schema:name Nature
142 rdf:type schema:Periodical
143 sg:person.01044327353.21 schema:affiliation https://www.grid.ac/institutes/grid.14003.36
144 schema:familyName Carroll
145 schema:givenName Sean B.
146 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01044327353.21
147 rdf:type schema:Person
148 sg:person.01313127416.84 schema:affiliation https://www.grid.ac/institutes/grid.14003.36
149 schema:familyName Rokas
150 schema:givenName Antonis
151 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01313127416.84
152 rdf:type schema:Person
153 sg:person.0763431022.88 schema:affiliation https://www.grid.ac/institutes/grid.14003.36
154 schema:familyName King
155 schema:givenName Nicole
156 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0763431022.88
157 rdf:type schema:Person
158 sg:person.0772204572.55 schema:affiliation https://www.grid.ac/institutes/grid.14003.36
159 schema:familyName Williams
160 schema:givenName Barry L.
161 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0772204572.55
162 rdf:type schema:Person
163 sg:pub.10.1007/978-1-4615-5419-6_10 schema:sameAs https://app.dimensions.ai/details/publication/pub.1043419348
164 https://doi.org/10.1007/978-1-4615-5419-6_10
165 rdf:type schema:CreativeWork
166 sg:pub.10.1038/35011054 schema:sameAs https://app.dimensions.ai/details/publication/pub.1009352761
167 https://doi.org/10.1038/35011054
168 rdf:type schema:CreativeWork
169 sg:pub.10.1038/35054550 schema:sameAs https://app.dimensions.ai/details/publication/pub.1034389621
170 https://doi.org/10.1038/35054550
171 rdf:type schema:CreativeWork
172 sg:pub.10.1038/35093090 schema:sameAs https://app.dimensions.ai/details/publication/pub.1027886586
173 https://doi.org/10.1038/35093090
174 rdf:type schema:CreativeWork
175 sg:pub.10.1038/35093097 schema:sameAs https://app.dimensions.ai/details/publication/pub.1026689691
176 https://doi.org/10.1038/35093097
177 rdf:type schema:CreativeWork
178 sg:pub.10.1038/383130a0 schema:sameAs https://app.dimensions.ai/details/publication/pub.1053714297
179 https://doi.org/10.1038/383130a0
180 rdf:type schema:CreativeWork
181 sg:pub.10.1038/387489a0 schema:sameAs https://app.dimensions.ai/details/publication/pub.1014476080
182 https://doi.org/10.1038/387489a0
183 rdf:type schema:CreativeWork
184 sg:pub.10.1038/42711 schema:sameAs https://app.dimensions.ai/details/publication/pub.1000430591
185 https://doi.org/10.1038/42711
186 rdf:type schema:CreativeWork
187 sg:pub.10.1038/46528 schema:sameAs https://app.dimensions.ai/details/publication/pub.1010205069
188 https://doi.org/10.1038/46528
189 rdf:type schema:CreativeWork
190 sg:pub.10.1038/90129 schema:sameAs https://app.dimensions.ai/details/publication/pub.1042537539
191 https://doi.org/10.1038/90129
192 rdf:type schema:CreativeWork
193 sg:pub.10.1038/nature01419 schema:sameAs https://app.dimensions.ai/details/publication/pub.1010286142
194 https://doi.org/10.1038/nature01419
195 rdf:type schema:CreativeWork
196 sg:pub.10.1038/nature01644 schema:sameAs https://app.dimensions.ai/details/publication/pub.1010517605
197 https://doi.org/10.1038/nature01644
198 rdf:type schema:CreativeWork
199 sg:pub.10.1038/nature01743 schema:sameAs https://app.dimensions.ai/details/publication/pub.1042649770
200 https://doi.org/10.1038/nature01743
201 rdf:type schema:CreativeWork
202 sg:pub.10.1186/1471-2148-2-7 schema:sameAs https://app.dimensions.ai/details/publication/pub.1047674197
203 https://doi.org/10.1186/1471-2148-2-7
204 rdf:type schema:CreativeWork
205 https://doi.org/10.1006/mpev.2000.0704 schema:sameAs https://app.dimensions.ai/details/publication/pub.1019541120
206 rdf:type schema:CreativeWork
207 https://doi.org/10.1016/0169-5347(96)10006-9 schema:sameAs https://app.dimensions.ai/details/publication/pub.1004741147
208 rdf:type schema:CreativeWork
209 https://doi.org/10.1016/s1567-1356(03)00012-6 schema:sameAs https://app.dimensions.ai/details/publication/pub.1003379329
210 rdf:type schema:CreativeWork
211 https://doi.org/10.1046/j.1525-142x.2003.03042.x schema:sameAs https://app.dimensions.ai/details/publication/pub.1036097161
212 rdf:type schema:CreativeWork
213 https://doi.org/10.1073/pnas.032662799 schema:sameAs https://app.dimensions.ai/details/publication/pub.1013835406
214 rdf:type schema:CreativeWork
215 https://doi.org/10.1073/pnas.142101099 schema:sameAs https://app.dimensions.ai/details/publication/pub.1000983381
216 rdf:type schema:CreativeWork
217 https://doi.org/10.1073/pnas.181187698 schema:sameAs https://app.dimensions.ai/details/publication/pub.1031728402
218 rdf:type schema:CreativeWork
219 https://doi.org/10.1073/pnas.90.24.11558 schema:sameAs https://app.dimensions.ai/details/publication/pub.1002714035
220 rdf:type schema:CreativeWork
221 https://doi.org/10.1080/10635150290069995 schema:sameAs https://app.dimensions.ai/details/publication/pub.1058369279
222 rdf:type schema:CreativeWork
223 https://doi.org/10.1080/10635150290102410 schema:sameAs https://app.dimensions.ai/details/publication/pub.1058369293
224 rdf:type schema:CreativeWork
225 https://doi.org/10.1080/106351598260996 schema:sameAs https://app.dimensions.ai/details/publication/pub.1058369876
226 rdf:type schema:CreativeWork
227 https://doi.org/10.1080/106351598261030 schema:sameAs https://app.dimensions.ai/details/publication/pub.1058369880
228 rdf:type schema:CreativeWork
229 https://doi.org/10.1093/bioinformatics/14.9.817 schema:sameAs https://app.dimensions.ai/details/publication/pub.1029580565
230 rdf:type schema:CreativeWork
231 https://doi.org/10.1093/nar/22.22.4673 schema:sameAs https://app.dimensions.ai/details/publication/pub.1042438223
232 rdf:type schema:CreativeWork
233 https://doi.org/10.1093/oxfordjournals.molbev.a003973 schema:sameAs https://app.dimensions.ai/details/publication/pub.1027077241
234 rdf:type schema:CreativeWork
235 https://doi.org/10.1093/oxfordjournals.molbev.a025813 schema:sameAs https://app.dimensions.ai/details/publication/pub.1048211688
236 rdf:type schema:CreativeWork
237 https://doi.org/10.1093/oxfordjournals.molbev.a040112 schema:sameAs https://app.dimensions.ai/details/publication/pub.1082684223
238 rdf:type schema:CreativeWork
239 https://doi.org/10.1093/oxfordjournals.molbev.a040258 schema:sameAs https://app.dimensions.ai/details/publication/pub.1082376727
240 rdf:type schema:CreativeWork
241 https://doi.org/10.1093/sysbio/42.3.384 schema:sameAs https://app.dimensions.ai/details/publication/pub.1060048112
242 rdf:type schema:CreativeWork
243 https://doi.org/10.1093/sysbio/44.1.17 schema:sameAs https://app.dimensions.ai/details/publication/pub.1060048210
244 rdf:type schema:CreativeWork
245 https://doi.org/10.1093/sysbio/45.3.375 schema:sameAs https://app.dimensions.ai/details/publication/pub.1060048285
246 rdf:type schema:CreativeWork
247 https://doi.org/10.1093/sysbio/45.4.524 schema:sameAs https://app.dimensions.ai/details/publication/pub.1017545132
248 rdf:type schema:CreativeWork
249 https://doi.org/10.1093/sysbio/46.3.523 schema:sameAs https://app.dimensions.ai/details/publication/pub.1030043307
250 rdf:type schema:CreativeWork
251 https://doi.org/10.1099/00207713-50-5-1931 schema:sameAs https://app.dimensions.ai/details/publication/pub.1060350366
252 rdf:type schema:CreativeWork
253 https://doi.org/10.1111/j.1438-8677.1996.tb00515.x schema:sameAs https://app.dimensions.ai/details/publication/pub.1046180922
254 rdf:type schema:CreativeWork
255 https://doi.org/10.1126/science.1084337 schema:sameAs https://app.dimensions.ai/details/publication/pub.1062448096
256 rdf:type schema:CreativeWork
257 https://doi.org/10.1126/science.274.5287.546 schema:sameAs https://app.dimensions.ai/details/publication/pub.1062554574
258 rdf:type schema:CreativeWork
259 https://doi.org/10.1126/science.276.5313.734 schema:sameAs https://app.dimensions.ai/details/publication/pub.1002629483
260 rdf:type schema:CreativeWork
261 https://doi.org/10.1126/science.284.5423.2129 schema:sameAs https://app.dimensions.ai/details/publication/pub.1046634615
262 rdf:type schema:CreativeWork
263 https://doi.org/10.1126/science.287.5456.1283 schema:sameAs https://app.dimensions.ai/details/publication/pub.1062568434
264 rdf:type schema:CreativeWork
265 https://doi.org/10.1126/science.290.5493.972 schema:sameAs https://app.dimensions.ai/details/publication/pub.1062571966
266 rdf:type schema:CreativeWork
267 https://doi.org/10.1146/annurev.ecolsys.33.010802.150509 schema:sameAs https://app.dimensions.ai/details/publication/pub.1025744795
268 rdf:type schema:CreativeWork
269 https://doi.org/10.2307/2413481 schema:sameAs https://app.dimensions.ai/details/publication/pub.1069921718
270 rdf:type schema:CreativeWork
271 https://www.grid.ac/institutes/grid.14003.36 schema:alternateName University of Wisconsin–Madison
272 schema:name Howard Hughes Medical Institute, Laboratory of Molecular Biology, R. M. Bock Laboratories, University of Wisconsin-Madison, 1525 Linden Drive, Madison, Wisconsin 53706, USA
273 rdf:type schema:Organization
 




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


...