Terraces in Phylogenetic Tree Space
A key step in assembling the tree of life is the construction of species-rich phylogenies from multilocus—but often incomplete—sequence data sets. We describe previously unknown structure in the landscape of solutions to the tree reconstruction problem, comprising sometimes vast "terraces"...
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| Veröffentlicht in: | Science (American Association for the Advancement of Science) 2011-07, Vol.333 (6041), p.448-450 |
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| creator | Sanderson, Michael J. McMahon, Michelle M. Steel, Mike |
| description | A key step in assembling the tree of life is the construction of species-rich phylogenies from multilocus—but often incomplete—sequence data sets. We describe previously unknown structure in the landscape of solutions to the tree reconstruction problem, comprising sometimes vast "terraces" of trees with identical quality, arranged on islands of phylogenetically similar trees. Phylogenetic ambiguity within a terrace can be characterized efficiently and then ameliorated by new algorithms for obtaining a terrace's maximum-agreement subtree or by identifying the smallest set of new targets for additional sequencing. Algorithms to find optimal trees or estimate Bayesian posterior tree distributions may need to navigate strategically in the neighborhood of large terraces in tree space. |
| doi_str_mv | 10.1126/science.1206357 |
| format | Article |
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We describe previously unknown structure in the landscape of solutions to the tree reconstruction problem, comprising sometimes vast "terraces" of trees with identical quality, arranged on islands of phylogenetically similar trees. Phylogenetic ambiguity within a terrace can be characterized efficiently and then ameliorated by new algorithms for obtaining a terrace's maximum-agreement subtree or by identifying the smallest set of new targets for additional sequencing. 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We describe previously unknown structure in the landscape of solutions to the tree reconstruction problem, comprising sometimes vast "terraces" of trees with identical quality, arranged on islands of phylogenetically similar trees. Phylogenetic ambiguity within a terrace can be characterized efficiently and then ameliorated by new algorithms for obtaining a terrace's maximum-agreement subtree or by identifying the smallest set of new targets for additional sequencing. 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Biological and molecular evolution</subject><subject>Genomics - methods</subject><subject>Heuristics</subject><subject>Landscapes</subject><subject>Likelihood Functions</subject><subject>Magnoliopsida - classification</subject><subject>Magnoliopsida - genetics</subject><subject>Models, Statistical</subject><subject>Phylogenetics</subject><subject>Phylogeny</subject><subject>Poaceae - classification</subject><subject>Poaceae - genetics</subject><subject>Sequence Alignment</subject><subject>Taxa</subject><subject>Terraces</subject><issn>0036-8075</issn><issn>1095-9203</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2011</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNqF0E1Lw0AQBuBFFFurZ09KUcRT2tmddD-OUvyCgoL1HDabiaakSd1ND_33pjRa8OJpD-8zM-zL2DmHEedCjoMrqHI04gIkTtQB63Mwk8gIwEPWB0AZaVCTHjsJYQHQZgaPWU9wqUFz6LPrOXlvHYVhUQ1fPzdl_UEVNYUbzj3R8G3VZqfsKLdloLPuHbD3h_v59CmavTw-T-9mkYsVNpHTPCNUMraZ0qlxeiIyBTrPMEtzB1Yiyqw9LFACoclEruIcUDhjUkNxigN2u9u78vXXmkKTLIvgqCxtRfU6JAaUkVJq_q_USmtudNvCgF39kYt67av2G1skkUsRt2i8Q87XIXjKk5UvltZvEg7Jtuek6znpem4nLru163RJ2a__KbYFNx2wwdky97ZyRdi7GI1A3LqLnVuEpvb7XBmlhdb4DayIjZE</recordid><startdate>20110722</startdate><enddate>20110722</enddate><creator>Sanderson, Michael J.</creator><creator>McMahon, Michelle M.</creator><creator>Steel, Mike</creator><general>American Association for the Advancement of Science</general><general>The American Association for the Advancement of Science</general><scope>IQODW</scope><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>7QF</scope><scope>7QG</scope><scope>7QL</scope><scope>7QP</scope><scope>7QQ</scope><scope>7QR</scope><scope>7SC</scope><scope>7SE</scope><scope>7SN</scope><scope>7SP</scope><scope>7SR</scope><scope>7SS</scope><scope>7T7</scope><scope>7TA</scope><scope>7TB</scope><scope>7TK</scope><scope>7TM</scope><scope>7U5</scope><scope>7U9</scope><scope>8BQ</scope><scope>8FD</scope><scope>C1K</scope><scope>F28</scope><scope>FR3</scope><scope>H8D</scope><scope>H8G</scope><scope>H94</scope><scope>JG9</scope><scope>JQ2</scope><scope>K9.</scope><scope>KR7</scope><scope>L7M</scope><scope>L~C</scope><scope>L~D</scope><scope>M7N</scope><scope>P64</scope><scope>RC3</scope><scope>7X8</scope></search><sort><creationdate>20110722</creationdate><title>Terraces in Phylogenetic Tree Space</title><author>Sanderson, Michael J. ; McMahon, Michelle M. ; Steel, Mike</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c473t-c81de3764ad78b9c852d708fd3dbfc0a6336d1682360e39d2f74f032c99b9e4b3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2011</creationdate><topic>Algorithms</topic><topic>Animals</topic><topic>Arthropods - classification</topic><topic>Arthropods - genetics</topic><topic>Bayes Theorem</topic><topic>Biodiversity</topic><topic>Biological and medical sciences</topic><topic>Biological Evolution</topic><topic>Colubridae - classification</topic><topic>Colubridae - genetics</topic><topic>Data Interpretation, Statistical</topic><topic>Datasets</topic><topic>Ecological genetics</topic><topic>Ecology</topic><topic>Evolutionary biology</topic><topic>Fundamental and applied biological sciences. 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| ispartof | Science (American Association for the Advancement of Science), 2011-07, Vol.333 (6041), p.448-450 |
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| subjects | Algorithms Animals Arthropods - classification Arthropods - genetics Bayes Theorem Biodiversity Biological and medical sciences Biological Evolution Colubridae - classification Colubridae - genetics Data Interpretation, Statistical Datasets Ecological genetics Ecology Evolutionary biology Fundamental and applied biological sciences. Psychology Genetic loci Genetics Genetics of eukaryotes. Biological and molecular evolution Genomics - methods Heuristics Landscapes Likelihood Functions Magnoliopsida - classification Magnoliopsida - genetics Models, Statistical Phylogenetics Phylogeny Poaceae - classification Poaceae - genetics Sequence Alignment Taxa Terraces |
| title | Terraces in Phylogenetic Tree Space |
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