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Is Congruence between Data Partitions a Reliable Predictor of Phylogenetic Accuracy? Empirically Testing an Iterative Procedure for Choosing among Phylogenetic Methods
The relationship between phylogenetic accuracy and congruence between data partitions collected from the same taxa was explored for mitochondrial DNA sequences from two well-supported vertebrate phylogenies. An iterative procedure was adopted whereby accuracy, phylogenetic signal, and congruence wer...
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| Published in: | Systematic biology 1997-09, Vol.46 (3), p.464-478 |
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| Format: | Article |
| Language: | English |
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| container_end_page | 478 |
| container_issue | 3 |
| container_start_page | 464 |
| container_title | Systematic biology |
| container_volume | 46 |
| creator | Cunningham, Clifford W. |
| description | The relationship between phylogenetic accuracy and congruence between data partitions collected from the same taxa was explored for mitochondrial DNA sequences from two well-supported vertebrate phylogenies. An iterative procedure was adopted whereby accuracy, phylogenetic signal, and congruence were measured before and after modifying a simple reconstruction model, equally weighted parsimony. These modifications included transversion parsimony, successive weighting, and six-parameter parsimony. For the data partitions examined, there is a generally positive relationship between congruence and phylogenetic accuracy. If congruence increased without decreasing resolution or phylogenetic signal, this increased congruence was a good predictor of accuracy. If congruence increased as a result of poor resolution, the degree of congruence was not a good predictor of accuracy. For all sets of data partitions, six-parameter parsimony methods show a consistently positive relationship between congruence and accuracy. Unlike successive weighting, six-parameter parsimony methods were not strongly influenced by the starting tree. |
| doi_str_mv | 10.1093/sysbio/46.3.464 |
| format | article |
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For the data partitions examined, there is a generally positive relationship between congruence and phylogenetic accuracy. If congruence increased without decreasing resolution or phylogenetic signal, this increased congruence was a good predictor of accuracy. If congruence increased as a result of poor resolution, the degree of congruence was not a good predictor of accuracy. For all sets of data partitions, six-parameter parsimony methods show a consistently positive relationship between congruence and accuracy. Unlike successive weighting, six-parameter parsimony methods were not strongly influenced by the starting tree.</description><identifier>ISSN: 1063-5157</identifier><identifier>EISSN: 1076-836X</identifier><identifier>DOI: 10.1093/sysbio/46.3.464</identifier><identifier>PMID: 11975330</identifier><language>eng</language><publisher>England: Society of Systematic Biologists</publisher><subject>Animals ; Biometry - methods ; Codon - genetics ; Codons ; Congruence ; Data Interpretation, Statistical ; DNA, Mitochondrial - genetics ; Evolution ; incongruence tests ; Likelihood Functions ; Mathematical congruence ; maximum likelihood ; Models, Genetic ; Muridae - classification ; Muridae - genetics ; Nucleotide sequences ; Parsimony ; Peromyscus - classification ; Peromyscus - genetics ; phylogenetic accuracy ; Phylogenetics ; Phylogeny ; six-parameter parsimony ; successive weighting ; Taxa ; Term weighting ; transversion parsimony ; Vertebrates ; weighted parsimony</subject><ispartof>Systematic biology, 1997-09, Vol.46 (3), p.464-478</ispartof><rights>1997 Society of Systematic Biologists 1997</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c3514-f2c763556a0046603f1375b09f757aff68cf1bfab493edeeca46b4345e90e073</citedby></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.jstor.org/stable/pdf/2413692$$EPDF$$P50$$Gjstor$$H</linktopdf><linktohtml>$$Uhttps://www.jstor.org/stable/2413692$$EHTML$$P50$$Gjstor$$H</linktohtml><link.rule.ids>314,780,784,27924,27925,58238,58471</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/11975330$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><contributor>Simon, Chris</contributor><contributor>Simon, Chris</contributor><creatorcontrib>Cunningham, Clifford W.</creatorcontrib><title>Is Congruence between Data Partitions a Reliable Predictor of Phylogenetic Accuracy? Empirically Testing an Iterative Procedure for Choosing among Phylogenetic Methods</title><title>Systematic biology</title><addtitle>Syst Biol</addtitle><description>The relationship between phylogenetic accuracy and congruence between data partitions collected from the same taxa was explored for mitochondrial DNA sequences from two well-supported vertebrate phylogenies. An iterative procedure was adopted whereby accuracy, phylogenetic signal, and congruence were measured before and after modifying a simple reconstruction model, equally weighted parsimony. These modifications included transversion parsimony, successive weighting, and six-parameter parsimony. For the data partitions examined, there is a generally positive relationship between congruence and phylogenetic accuracy. If congruence increased without decreasing resolution or phylogenetic signal, this increased congruence was a good predictor of accuracy. If congruence increased as a result of poor resolution, the degree of congruence was not a good predictor of accuracy. For all sets of data partitions, six-parameter parsimony methods show a consistently positive relationship between congruence and accuracy. Unlike successive weighting, six-parameter parsimony methods were not strongly influenced by the starting tree.</description><subject>Animals</subject><subject>Biometry - methods</subject><subject>Codon - genetics</subject><subject>Codons</subject><subject>Congruence</subject><subject>Data Interpretation, Statistical</subject><subject>DNA, Mitochondrial - genetics</subject><subject>Evolution</subject><subject>incongruence tests</subject><subject>Likelihood Functions</subject><subject>Mathematical congruence</subject><subject>maximum likelihood</subject><subject>Models, Genetic</subject><subject>Muridae - classification</subject><subject>Muridae - genetics</subject><subject>Nucleotide sequences</subject><subject>Parsimony</subject><subject>Peromyscus - classification</subject><subject>Peromyscus - genetics</subject><subject>phylogenetic accuracy</subject><subject>Phylogenetics</subject><subject>Phylogeny</subject><subject>six-parameter parsimony</subject><subject>successive weighting</subject><subject>Taxa</subject><subject>Term weighting</subject><subject>transversion parsimony</subject><subject>Vertebrates</subject><subject>weighted parsimony</subject><issn>1063-5157</issn><issn>1076-836X</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>1997</creationdate><recordtype>article</recordtype><recordid>eNqN0cuO0zAUBuAIgZgLrNkhLxALpLR27djJCo3KdFppEB1UoYqN5TjHrYckLrYzkCfiNUlJxWXHxvbi86-j8yfJC4InBBd0GvpQWjdlfEInjLNHyTnBgqc55dvHxzenaUYycZZchHCPMSE8I0-TM0IKkVGKz5Mfq4Dmrt35DloNqIT4DaBF71RUaK18tNG6NiCFPkJtVVkDWnuorI7OI2fQet_XbgctRKvRldadV7p_i66bg_VWq7ru0QZCtO0OqRatIngV7cMxxGmoOg_IDEHzvXPhl2mGUf4NfQ9x76rwLHliVB3g-em-TDaL6818md5-uFnNr25TTTPCUjPTgtMs4wpjxjmmhlCRlbgwIhPKGJ5rQ0qjSlZQqAC0YrxklGVQYMCCXiavx9iDd1-7YXLZ2KChrlULrgtS5CKnOD_C6Qi1dyF4MPLgbaN8LwmWx2rkWI1kXNLhYMOPl6formyg-uNPXQzgzQhcd_iPtFcjvg9DFX_zGcVCzhihvJgNLB2ZDRG-_2bKf5FcDJuRy-1nebNY3H3a3i3lgv4EKt23_Q</recordid><startdate>199709</startdate><enddate>199709</enddate><creator>Cunningham, Clifford W.</creator><general>Society of Systematic Biologists</general><scope>BSCLL</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>7X8</scope></search><sort><creationdate>199709</creationdate><title>Is Congruence between Data Partitions a Reliable Predictor of Phylogenetic Accuracy? Empirically Testing an Iterative Procedure for Choosing among Phylogenetic Methods</title><author>Cunningham, Clifford W.</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c3514-f2c763556a0046603f1375b09f757aff68cf1bfab493edeeca46b4345e90e073</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>1997</creationdate><topic>Animals</topic><topic>Biometry - methods</topic><topic>Codon - genetics</topic><topic>Codons</topic><topic>Congruence</topic><topic>Data Interpretation, Statistical</topic><topic>DNA, Mitochondrial - genetics</topic><topic>Evolution</topic><topic>incongruence tests</topic><topic>Likelihood Functions</topic><topic>Mathematical congruence</topic><topic>maximum likelihood</topic><topic>Models, Genetic</topic><topic>Muridae - classification</topic><topic>Muridae - genetics</topic><topic>Nucleotide sequences</topic><topic>Parsimony</topic><topic>Peromyscus - classification</topic><topic>Peromyscus - genetics</topic><topic>phylogenetic accuracy</topic><topic>Phylogenetics</topic><topic>Phylogeny</topic><topic>six-parameter parsimony</topic><topic>successive weighting</topic><topic>Taxa</topic><topic>Term weighting</topic><topic>transversion parsimony</topic><topic>Vertebrates</topic><topic>weighted parsimony</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Cunningham, Clifford W.</creatorcontrib><collection>Istex</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>MEDLINE - Academic</collection><jtitle>Systematic biology</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Cunningham, Clifford W.</au><au>Simon, Chris</au><au>Simon, Chris</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Is Congruence between Data Partitions a Reliable Predictor of Phylogenetic Accuracy? Empirically Testing an Iterative Procedure for Choosing among Phylogenetic Methods</atitle><jtitle>Systematic biology</jtitle><addtitle>Syst Biol</addtitle><date>1997-09</date><risdate>1997</risdate><volume>46</volume><issue>3</issue><spage>464</spage><epage>478</epage><pages>464-478</pages><issn>1063-5157</issn><eissn>1076-836X</eissn><abstract>The relationship between phylogenetic accuracy and congruence between data partitions collected from the same taxa was explored for mitochondrial DNA sequences from two well-supported vertebrate phylogenies. An iterative procedure was adopted whereby accuracy, phylogenetic signal, and congruence were measured before and after modifying a simple reconstruction model, equally weighted parsimony. These modifications included transversion parsimony, successive weighting, and six-parameter parsimony. For the data partitions examined, there is a generally positive relationship between congruence and phylogenetic accuracy. If congruence increased without decreasing resolution or phylogenetic signal, this increased congruence was a good predictor of accuracy. If congruence increased as a result of poor resolution, the degree of congruence was not a good predictor of accuracy. For all sets of data partitions, six-parameter parsimony methods show a consistently positive relationship between congruence and accuracy. Unlike successive weighting, six-parameter parsimony methods were not strongly influenced by the starting tree.</abstract><cop>England</cop><pub>Society of Systematic Biologists</pub><pmid>11975330</pmid><doi>10.1093/sysbio/46.3.464</doi><tpages>15</tpages><oa>free_for_read</oa></addata></record> |
| fulltext | fulltext |
| identifier | ISSN: 1063-5157 |
| ispartof | Systematic biology, 1997-09, Vol.46 (3), p.464-478 |
| issn | 1063-5157 1076-836X |
| language | eng |
| recordid | cdi_proquest_miscellaneous_78783087 |
| source | JSTOR Archival Journals and Primary Sources Collection; Oxford Journals Online |
| subjects | Animals Biometry - methods Codon - genetics Codons Congruence Data Interpretation, Statistical DNA, Mitochondrial - genetics Evolution incongruence tests Likelihood Functions Mathematical congruence maximum likelihood Models, Genetic Muridae - classification Muridae - genetics Nucleotide sequences Parsimony Peromyscus - classification Peromyscus - genetics phylogenetic accuracy Phylogenetics Phylogeny six-parameter parsimony successive weighting Taxa Term weighting transversion parsimony Vertebrates weighted parsimony |
| title | Is Congruence between Data Partitions a Reliable Predictor of Phylogenetic Accuracy? Empirically Testing an Iterative Procedure for Choosing among Phylogenetic Methods |
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