Long branch effects distort maximum likelihood phylogenies in simulations despite selection of the correct model
The aim of our study was to test the robustness and efficiency of maximum likelihood with respect to different long branch effects on multiple-taxon trees. We simulated data of different alignment lengths under two different 11-taxon trees and a broad range of different branch length conditions. The...
Gespeichert in:
| Veröffentlicht in: | PloS one 2012-05, Vol.7 (5), p.e36593-e36593 |
|---|---|
| Hauptverfasser: | , , , |
| Format: | Artikel |
| Sprache: | eng |
| Schlagworte: | |
| Online-Zugang: | Volltext |
| Tags: |
Tag hinzufügen
Keine Tags, Fügen Sie den ersten Tag hinzu!
|
| container_end_page | e36593 |
|---|---|
| container_issue | 5 |
| container_start_page | e36593 |
| container_title | PloS one |
| container_volume | 7 |
| creator | Kück, Patrick Mayer, Christoph Wägele, Johann-Wolfgang Misof, Bernhard |
| description | The aim of our study was to test the robustness and efficiency of maximum likelihood with respect to different long branch effects on multiple-taxon trees. We simulated data of different alignment lengths under two different 11-taxon trees and a broad range of different branch length conditions. The data were analyzed with the true model parameters as well as with estimated and incorrect assumptions about among-site rate variation. If length differences between connected branches strongly increase, tree inference with the correct likelihood model assumptions can fail. We found that incorporating invariant sites together with Γ distributed site rates in the tree reconstruction (Γ+I) increases the robustness of maximum likelihood in comparison with models using only Γ. The results show that for some topologies and branch lengths the reconstruction success of maximum likelihood under the correct model is still low for alignments with a length of 100,000 base positions. Altogether, the high confidence that is put in maximum likelihood trees is not always justified under certain tree shapes even if alignment lengths reach 100,000 base positions. |
| doi_str_mv | 10.1371/journal.pone.0036593 |
| format | Article |
| fullrecord | <record><control><sourceid>gale_plos_</sourceid><recordid>TN_cdi_plos_journals_1324602267</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><galeid>A477127297</galeid><doaj_id>oai_doaj_org_article_70770b4dc6d54641999127320502187a</doaj_id><sourcerecordid>A477127297</sourcerecordid><originalsourceid>FETCH-LOGICAL-c758t-745217fe68c10dc8d7fdfb6ecc1a02b96fdf429aa05248ea477e50db9f81658a3</originalsourceid><addsrcrecordid>eNqNk9tq3DAQhk1padK0b1BaQaG0F7vVwZbsm0IIPSwsBHq6FbI8XmsrWxtJLsnbV5t1wrrkovjC1uj7_9GMNVn2kuAlYYJ82LrRD8oud26AJcaMFxV7lJ2SitEFp5g9Pvo-yZ6FsMW4YCXnT7MTSjmnhOLTbLd2wwbVXg26Q9C2oGNAjQnR-Yh6dW36sUfW_AZrOucatOturNvAYCAgM6CQ9q2Kxg1JBWFnIqAANrmkEHItih0g7bxPEdS7Buzz7EmrbIAX0_ss-_n504-Lr4v15ZfVxfl6oUVRxoXIC0pEC7zUBDe6bETbtDUHrYnCtK54Wua0UgoXNC9B5UJAgZu6akvCi1Kxs-z1wXdnXZBTs4IkjOYcp_pFIlYHonFqK3fe9MrfSKeMvA04v5HKR6MtSIGFwHXeaN4UOc9JVVWECkZxgSkpxT7bxynbWPfQaBiiV3ZmOt8ZTCc37o9krKiwwMng3WTg3dUIIcreBA3WqgHcmM6NSckZEbhK6Jt_0Ierm6iNSgWYoXUpr96byvPUrHR8Wu2p5QNUehrojU43qzUpPhO8nwkSE-E6btQYglx9__b_7OWvOfv2iO1A2dgFZ8fbqzUH8wOovQvBQ3vfZILlfjDuuiH3gyGnwUiyV8c_6F50NwnsL6JgCSo</addsrcrecordid><sourcetype>Open Website</sourcetype><iscdi>true</iscdi><recordtype>article</recordtype><pqid>1324602267</pqid></control><display><type>article</type><title>Long branch effects distort maximum likelihood phylogenies in simulations despite selection of the correct model</title><source>MEDLINE</source><source>DOAJ Directory of Open Access Journals</source><source>Public Library of Science (PLoS) Journals Open Access</source><source>EZB-FREE-00999 freely available EZB journals</source><source>PubMed Central</source><source>Free Full-Text Journals in Chemistry</source><creator>Kück, Patrick ; Mayer, Christoph ; Wägele, Johann-Wolfgang ; Misof, Bernhard</creator><contributor>Stiller, John W.</contributor><creatorcontrib>Kück, Patrick ; Mayer, Christoph ; Wägele, Johann-Wolfgang ; Misof, Bernhard ; Stiller, John W.</creatorcontrib><description>The aim of our study was to test the robustness and efficiency of maximum likelihood with respect to different long branch effects on multiple-taxon trees. We simulated data of different alignment lengths under two different 11-taxon trees and a broad range of different branch length conditions. The data were analyzed with the true model parameters as well as with estimated and incorrect assumptions about among-site rate variation. If length differences between connected branches strongly increase, tree inference with the correct likelihood model assumptions can fail. We found that incorporating invariant sites together with Γ distributed site rates in the tree reconstruction (Γ+I) increases the robustness of maximum likelihood in comparison with models using only Γ. The results show that for some topologies and branch lengths the reconstruction success of maximum likelihood under the correct model is still low for alignments with a length of 100,000 base positions. Altogether, the high confidence that is put in maximum likelihood trees is not always justified under certain tree shapes even if alignment lengths reach 100,000 base positions.</description><identifier>ISSN: 1932-6203</identifier><identifier>EISSN: 1932-6203</identifier><identifier>DOI: 10.1371/journal.pone.0036593</identifier><identifier>PMID: 22662120</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>Algorithms ; Alignment ; Analysis ; Arthropods ; Biology ; Branches ; Computer Simulation ; Data processing ; Estimates ; Genomes ; Hymenoptera ; Hypotheses ; Likelihood Functions ; MicroRNAs ; Models, Genetic ; Morphology ; Parameter estimation ; Phylogenetics ; Phylogeny ; Reconstruction ; Robustness ; Sample variance ; Trees</subject><ispartof>PloS one, 2012-05, Vol.7 (5), p.e36593-e36593</ispartof><rights>COPYRIGHT 2012 Public Library of Science</rights><rights>2012 Kück et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License: https://creativecommons.org/licenses/by/4.0/ (the “License”), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><rights>Kück et al. 2012</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c758t-745217fe68c10dc8d7fdfb6ecc1a02b96fdf429aa05248ea477e50db9f81658a3</citedby><cites>FETCH-LOGICAL-c758t-745217fe68c10dc8d7fdfb6ecc1a02b96fdf429aa05248ea477e50db9f81658a3</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC3359070/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC3359070/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,727,780,784,864,885,2102,2928,23866,27924,27925,53791,53793,79600,79601</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/22662120$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><contributor>Stiller, John W.</contributor><creatorcontrib>Kück, Patrick</creatorcontrib><creatorcontrib>Mayer, Christoph</creatorcontrib><creatorcontrib>Wägele, Johann-Wolfgang</creatorcontrib><creatorcontrib>Misof, Bernhard</creatorcontrib><title>Long branch effects distort maximum likelihood phylogenies in simulations despite selection of the correct model</title><title>PloS one</title><addtitle>PLoS One</addtitle><description>The aim of our study was to test the robustness and efficiency of maximum likelihood with respect to different long branch effects on multiple-taxon trees. We simulated data of different alignment lengths under two different 11-taxon trees and a broad range of different branch length conditions. The data were analyzed with the true model parameters as well as with estimated and incorrect assumptions about among-site rate variation. If length differences between connected branches strongly increase, tree inference with the correct likelihood model assumptions can fail. We found that incorporating invariant sites together with Γ distributed site rates in the tree reconstruction (Γ+I) increases the robustness of maximum likelihood in comparison with models using only Γ. The results show that for some topologies and branch lengths the reconstruction success of maximum likelihood under the correct model is still low for alignments with a length of 100,000 base positions. Altogether, the high confidence that is put in maximum likelihood trees is not always justified under certain tree shapes even if alignment lengths reach 100,000 base positions.</description><subject>Algorithms</subject><subject>Alignment</subject><subject>Analysis</subject><subject>Arthropods</subject><subject>Biology</subject><subject>Branches</subject><subject>Computer Simulation</subject><subject>Data processing</subject><subject>Estimates</subject><subject>Genomes</subject><subject>Hymenoptera</subject><subject>Hypotheses</subject><subject>Likelihood Functions</subject><subject>MicroRNAs</subject><subject>Models, Genetic</subject><subject>Morphology</subject><subject>Parameter estimation</subject><subject>Phylogenetics</subject><subject>Phylogeny</subject><subject>Reconstruction</subject><subject>Robustness</subject><subject>Sample variance</subject><subject>Trees</subject><issn>1932-6203</issn><issn>1932-6203</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2012</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>ABUWG</sourceid><sourceid>AFKRA</sourceid><sourceid>AZQEC</sourceid><sourceid>BENPR</sourceid><sourceid>CCPQU</sourceid><sourceid>DWQXO</sourceid><sourceid>GNUQQ</sourceid><sourceid>DOA</sourceid><recordid>eNqNk9tq3DAQhk1padK0b1BaQaG0F7vVwZbsm0IIPSwsBHq6FbI8XmsrWxtJLsnbV5t1wrrkovjC1uj7_9GMNVn2kuAlYYJ82LrRD8oud26AJcaMFxV7lJ2SitEFp5g9Pvo-yZ6FsMW4YCXnT7MTSjmnhOLTbLd2wwbVXg26Q9C2oGNAjQnR-Yh6dW36sUfW_AZrOucatOturNvAYCAgM6CQ9q2Kxg1JBWFnIqAANrmkEHItih0g7bxPEdS7Buzz7EmrbIAX0_ss-_n504-Lr4v15ZfVxfl6oUVRxoXIC0pEC7zUBDe6bETbtDUHrYnCtK54Wua0UgoXNC9B5UJAgZu6akvCi1Kxs-z1wXdnXZBTs4IkjOYcp_pFIlYHonFqK3fe9MrfSKeMvA04v5HKR6MtSIGFwHXeaN4UOc9JVVWECkZxgSkpxT7bxynbWPfQaBiiV3ZmOt8ZTCc37o9krKiwwMng3WTg3dUIIcreBA3WqgHcmM6NSckZEbhK6Jt_0Ierm6iNSgWYoXUpr96byvPUrHR8Wu2p5QNUehrojU43qzUpPhO8nwkSE-E6btQYglx9__b_7OWvOfv2iO1A2dgFZ8fbqzUH8wOovQvBQ3vfZILlfjDuuiH3gyGnwUiyV8c_6F50NwnsL6JgCSo</recordid><startdate>20120509</startdate><enddate>20120509</enddate><creator>Kück, Patrick</creator><creator>Mayer, Christoph</creator><creator>Wägele, Johann-Wolfgang</creator><creator>Misof, Bernhard</creator><general>Public Library of Science</general><general>Public Library of Science (PLoS)</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>IOV</scope><scope>ISR</scope><scope>3V.</scope><scope>7QG</scope><scope>7QL</scope><scope>7QO</scope><scope>7RV</scope><scope>7SN</scope><scope>7SS</scope><scope>7T5</scope><scope>7TG</scope><scope>7TM</scope><scope>7U9</scope><scope>7X2</scope><scope>7X7</scope><scope>7XB</scope><scope>88E</scope><scope>8AO</scope><scope>8C1</scope><scope>8FD</scope><scope>8FE</scope><scope>8FG</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>ABJCF</scope><scope>ABUWG</scope><scope>AFKRA</scope><scope>ARAPS</scope><scope>ATCPS</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BGLVJ</scope><scope>BHPHI</scope><scope>C1K</scope><scope>CCPQU</scope><scope>D1I</scope><scope>DWQXO</scope><scope>FR3</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>H94</scope><scope>HCIFZ</scope><scope>K9.</scope><scope>KB.</scope><scope>KB0</scope><scope>KL.</scope><scope>L6V</scope><scope>LK8</scope><scope>M0K</scope><scope>M0S</scope><scope>M1P</scope><scope>M7N</scope><scope>M7P</scope><scope>M7S</scope><scope>NAPCQ</scope><scope>P5Z</scope><scope>P62</scope><scope>P64</scope><scope>PATMY</scope><scope>PDBOC</scope><scope>PIMPY</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PRINS</scope><scope>PTHSS</scope><scope>PYCSY</scope><scope>RC3</scope><scope>7X8</scope><scope>5PM</scope><scope>DOA</scope></search><sort><creationdate>20120509</creationdate><title>Long branch effects distort maximum likelihood phylogenies in simulations despite selection of the correct model</title><author>Kück, Patrick ; Mayer, Christoph ; Wägele, Johann-Wolfgang ; Misof, Bernhard</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c758t-745217fe68c10dc8d7fdfb6ecc1a02b96fdf429aa05248ea477e50db9f81658a3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2012</creationdate><topic>Algorithms</topic><topic>Alignment</topic><topic>Analysis</topic><topic>Arthropods</topic><topic>Biology</topic><topic>Branches</topic><topic>Computer Simulation</topic><topic>Data processing</topic><topic>Estimates</topic><topic>Genomes</topic><topic>Hymenoptera</topic><topic>Hypotheses</topic><topic>Likelihood Functions</topic><topic>MicroRNAs</topic><topic>Models, Genetic</topic><topic>Morphology</topic><topic>Parameter estimation</topic><topic>Phylogenetics</topic><topic>Phylogeny</topic><topic>Reconstruction</topic><topic>Robustness</topic><topic>Sample variance</topic><topic>Trees</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Kück, Patrick</creatorcontrib><creatorcontrib>Mayer, Christoph</creatorcontrib><creatorcontrib>Wägele, Johann-Wolfgang</creatorcontrib><creatorcontrib>Misof, Bernhard</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Gale In Context: Opposing Viewpoints</collection><collection>Gale In Context: Science</collection><collection>ProQuest Central (Corporate)</collection><collection>Animal Behavior Abstracts</collection><collection>Bacteriology Abstracts (Microbiology B)</collection><collection>Biotechnology Research Abstracts</collection><collection>Proquest Nursing & Allied Health Source</collection><collection>Ecology Abstracts</collection><collection>Entomology Abstracts (Full archive)</collection><collection>Immunology Abstracts</collection><collection>Meteorological & Geoastrophysical Abstracts</collection><collection>Nucleic Acids Abstracts</collection><collection>Virology and AIDS Abstracts</collection><collection>Agricultural Science Collection</collection><collection>Health & Medical Collection</collection><collection>ProQuest Central (purchase pre-March 2016)</collection><collection>Medical Database (Alumni Edition)</collection><collection>ProQuest Pharma Collection</collection><collection>Public Health Database</collection><collection>Technology Research Database</collection><collection>ProQuest SciTech Collection</collection><collection>ProQuest Technology Collection</collection><collection>ProQuest Natural Science Collection</collection><collection>Hospital Premium Collection</collection><collection>Hospital Premium Collection (Alumni Edition)</collection><collection>ProQuest Central (Alumni) (purchase pre-March 2016)</collection><collection>Materials Science & Engineering Collection</collection><collection>ProQuest Central (Alumni Edition)</collection><collection>ProQuest Central UK/Ireland</collection><collection>Advanced Technologies & Aerospace Collection</collection><collection>Agricultural & Environmental Science Collection</collection><collection>ProQuest Central Essentials</collection><collection>Biological Science Collection</collection><collection>ProQuest Central</collection><collection>Technology Collection</collection><collection>Natural Science Collection</collection><collection>Environmental Sciences and Pollution Management</collection><collection>ProQuest One Community College</collection><collection>ProQuest Materials Science Collection</collection><collection>ProQuest Central Korea</collection><collection>Engineering Research Database</collection><collection>Health Research Premium Collection</collection><collection>Health Research Premium Collection (Alumni)</collection><collection>ProQuest Central Student</collection><collection>AIDS and Cancer Research Abstracts</collection><collection>SciTech Premium Collection</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>Materials Science Database</collection><collection>Nursing & Allied Health Database (Alumni Edition)</collection><collection>Meteorological & Geoastrophysical Abstracts - Academic</collection><collection>ProQuest Engineering Collection</collection><collection>ProQuest Biological Science Collection</collection><collection>Agricultural Science Database</collection><collection>Health & Medical Collection (Alumni Edition)</collection><collection>Medical Database</collection><collection>Algology Mycology and Protozoology Abstracts (Microbiology C)</collection><collection>Biological Science Database</collection><collection>Engineering Database</collection><collection>Nursing & Allied Health Premium</collection><collection>Advanced Technologies & Aerospace Database</collection><collection>ProQuest Advanced Technologies & Aerospace Collection</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Environmental Science Database</collection><collection>Materials Science Collection</collection><collection>Publicly Available Content Database</collection><collection>ProQuest One Academic Eastern Edition (DO NOT USE)</collection><collection>ProQuest One Academic</collection><collection>ProQuest One Academic UKI Edition</collection><collection>ProQuest Central China</collection><collection>Engineering Collection</collection><collection>Environmental Science Collection</collection><collection>Genetics Abstracts</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><collection>DOAJ Directory of Open Access Journals</collection><jtitle>PloS one</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Kück, Patrick</au><au>Mayer, Christoph</au><au>Wägele, Johann-Wolfgang</au><au>Misof, Bernhard</au><au>Stiller, John W.</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Long branch effects distort maximum likelihood phylogenies in simulations despite selection of the correct model</atitle><jtitle>PloS one</jtitle><addtitle>PLoS One</addtitle><date>2012-05-09</date><risdate>2012</risdate><volume>7</volume><issue>5</issue><spage>e36593</spage><epage>e36593</epage><pages>e36593-e36593</pages><issn>1932-6203</issn><eissn>1932-6203</eissn><abstract>The aim of our study was to test the robustness and efficiency of maximum likelihood with respect to different long branch effects on multiple-taxon trees. We simulated data of different alignment lengths under two different 11-taxon trees and a broad range of different branch length conditions. The data were analyzed with the true model parameters as well as with estimated and incorrect assumptions about among-site rate variation. If length differences between connected branches strongly increase, tree inference with the correct likelihood model assumptions can fail. We found that incorporating invariant sites together with Γ distributed site rates in the tree reconstruction (Γ+I) increases the robustness of maximum likelihood in comparison with models using only Γ. The results show that for some topologies and branch lengths the reconstruction success of maximum likelihood under the correct model is still low for alignments with a length of 100,000 base positions. Altogether, the high confidence that is put in maximum likelihood trees is not always justified under certain tree shapes even if alignment lengths reach 100,000 base positions.</abstract><cop>United States</cop><pub>Public Library of Science</pub><pmid>22662120</pmid><doi>10.1371/journal.pone.0036593</doi><tpages>e36593</tpages><oa>free_for_read</oa></addata></record> |
| fulltext | fulltext |
| identifier | ISSN: 1932-6203 |
| ispartof | PloS one, 2012-05, Vol.7 (5), p.e36593-e36593 |
| issn | 1932-6203 1932-6203 |
| language | eng |
| recordid | cdi_plos_journals_1324602267 |
| source | MEDLINE; DOAJ Directory of Open Access Journals; Public Library of Science (PLoS) Journals Open Access; EZB-FREE-00999 freely available EZB journals; PubMed Central; Free Full-Text Journals in Chemistry |
| subjects | Algorithms Alignment Analysis Arthropods Biology Branches Computer Simulation Data processing Estimates Genomes Hymenoptera Hypotheses Likelihood Functions MicroRNAs Models, Genetic Morphology Parameter estimation Phylogenetics Phylogeny Reconstruction Robustness Sample variance Trees |
| title | Long branch effects distort maximum likelihood phylogenies in simulations despite selection of the correct model |
| url | https://sfx.bib-bvb.de/sfx_tum?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2024-12-27T00%3A39%3A04IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-gale_plos_&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=Long%20branch%20effects%20distort%20maximum%20likelihood%20phylogenies%20in%20simulations%20despite%20selection%20of%20the%20correct%20model&rft.jtitle=PloS%20one&rft.au=K%C3%BCck,%20Patrick&rft.date=2012-05-09&rft.volume=7&rft.issue=5&rft.spage=e36593&rft.epage=e36593&rft.pages=e36593-e36593&rft.issn=1932-6203&rft.eissn=1932-6203&rft_id=info:doi/10.1371/journal.pone.0036593&rft_dat=%3Cgale_plos_%3EA477127297%3C/gale_plos_%3E%3Curl%3E%3C/url%3E&disable_directlink=true&sfx.directlink=off&sfx.report_link=0&rft_id=info:oai/&rft_pqid=1324602267&rft_id=info:pmid/22662120&rft_galeid=A477127297&rft_doaj_id=oai_doaj_org_article_70770b4dc6d54641999127320502187a&rfr_iscdi=true |