Novel versus unsupported clades: assessing the qualitative support for clades in MRP supertrees. Export

@article{Bininda-Emonds2003, abstract = {Matrix representation with parsimony (MRP) supertree construction has been criticized because the supertree may specify clades that are contradicted by every source tree contributing to it. Such unsupported clades may also occur using other supertree methods; however, their incidence is largely unknown. In this study, I investigated the frequency of unsupported clades in both simulated and empirical MRP supertrees. Here, I propose a new index, QS, to quantify the qualitative support for a supertree and its clades among the set of source trees. Results show that unsupported clades are very rare in MRP supertrees, occurring most often when there are few source trees that all possess the same set of taxa. However, even under these conditions the frequency of unsupported clades was <0.2\%. Unsupported clades were absent from both the Carnivora and Lagomorpha supertrees, reflecting the use of large numbers of source trees for both. The proposed QS indices are correlated broadly with another measure of quantitative clade support (bootstrap frequencies, as derived from resampling of the MRP matrix) but appear to be more sensitive. More importantly, they sample at the level of the source trees and thus, unlike the bootstrap, are suitable for summarizing the support of MRP supertree clades.}, author = {Olaf}, citeulike-article-id = {757474}, journal = {Syst Biol}, keywords = {14668120, algorithms, alignment, alligators, analysis, and, angiosperms, animals, array, bibtex-import, biodiversity, calibration, carnivora, classification, cluster, comparative, computer, crocodiles, data, design, dna, evolution, factors, fossils, genetic, genetics, govt, graphics, interface, interpretation, meta-analysis, models, molecular, mutational, non-phs, non-us, oligonucleotide, pedigree, phylogeny, population, re, research, search, sequence, simulation, software, statistical, study, support, theoretical, time, us, user-computer, variation}, month = {Dec}, number = {6}, pages = {839--48}, pdf = {Bininda-Emonds2003.pdf}, posted-at = {2006-07-13 16:23:28}, priority = {2}, title = {Novel versus unsupported clades: assessing the qualitative support for clades in {MRP} supertrees.}, volume = {52}, year = {2003} }

TY - JOUR ID - Bininda-Emonds2003 L3 - citeulike-article-id:757474 N2 - Matrix representation with parsimony (MRP) supertree construction has been criticized because the supertree may specify clades that are contradicted by every source tree contributing to it. Such unsupported clades may also occur using other supertree methods; however, their incidence is largely unknown. In this study, I investigated the frequency of unsupported clades in both simulated and empirical MRP supertrees. Here, I propose a new index, QS, to quantify the qualitative support for a supertree and its clades among the set of source trees. Results show that unsupported clades are very rare in MRP supertrees, occurring most often when there are few source trees that all possess the same set of taxa. However, even under these conditions the frequency of unsupported clades was <0.2\%. Unsupported clades were absent from both the Carnivora and Lagomorpha supertrees, reflecting the use of large numbers of source trees for both. The proposed QS indices are correlated broadly with another measure of quantitative clade support (bootstrap frequencies, as derived from resampling of the MRP matrix) but appear to be more sensitive. More importantly, they sample at the level of the source trees and thus, unlike the bootstrap, are suitable for summarizing the support of MRP supertree clades. IS - 6 JF - Syst Biol EP - 48 TI - Novel versus unsupported clades: assessing the qualitative support for clades in {MRP} supertrees. VL - 52 SP - 839 KW - 14668120 KW - algorithms KW - alignment KW - alligators KW - analysis KW - and KW - angiosperms KW - animals KW - array KW - bibtex-import KW - biodiversity KW - calibration KW - carnivora KW - classification KW - cluster KW - comparative KW - computer KW - crocodiles KW - data KW - design KW - dna KW - evolution KW - factors KW - fossils KW - genetic KW - genetics KW - govt KW - graphics KW - interface KW - interpretation KW - meta-analysis KW - models KW - molecular KW - mutational KW - non-phs KW - non-us KW - oligonucleotide KW - pedigree KW - phylogeny KW - population KW - re KW - research KW - search KW - sequence KW - simulation KW - software KW - statistical KW - study KW - support KW - theoretical KW - time KW - us KW - user-computer KW - variation AU - Olaf PY - 2003/Dec// ER -