A phylogenetic analysis is provided for 70% of the representatives of genus Gavilea, as well as f... more A phylogenetic analysis is provided for 70% of the representatives of genus Gavilea, as well as for several species of the remaining genera of subtribe Chloraeinae: Bipinnula, Chloraea and Geoblasta. Sequences from the plastid markers rpoC1, matK-trnK and atpB-rbcL and the nuclear marker ITS, were analyzed using Maximum Parsimony and Bayesian Inference. Monophyly of subtribe Chloraeinae was confirmed, as well as its position inside tribe Cranichideae. Neither Chloraea nor Bipinnula were recovered as monophyletic. Gavilea turned out polyphyletic, with Chloraeachica embedded in the genus while Gavilea supralabellata was related to Chloraea and might be a hybrid between both genera. None of the two sections of Gavilea were monophyletic, and the topologies obtained do not suggest a new division of the genus.
Journal of Zoological Systematics and Evolutionary Research, 2013
ABSTRACT The clade size effect refers to a bias that causes middle-sized clades to be less suppor... more ABSTRACT The clade size effect refers to a bias that causes middle-sized clades to be less supported than small or large-sized clades. This bias is present in resampling measures of support calculated under maximum likelihood and maximum parsimony and in Bayesian posterior probabilities. Previous analyses indicated that the clade size effect is worst in maximum parsimony, followed by maximum likelihood, while Bayesian inference is the least affected. Homoplasy was interpreted as the main cause of the effect. In this study, we explored the presence of the clade size effect in alternative measures of branch support under maximum parsimony: Bremer support and symmetric resampling, expressed as absolute frequencies and frequency differences. Analyses were performed using 50 molecular and morphological matrices. Symmetric resampling showed the same tendency that bootstrap and jackknife did for maximum parsimony and maximum likelihood. Few matrices showed a significant bias using Bremer support, presenting a better performance than resampling measures of support and comparable to Bayesian posterior probabilities. Our results indicate that the problem is not maximum parsimony, but resampling measures of support. We corroborated the role of homoplasy as a possible cause of the clade size effect, increasing the number of random trees during the resampling, which together with the higher chances that medium-sized clades have of being contradicted generates the bias during the perturbation of the original matrix, making it stronger in resampling measures of support.
... Geometric morphometrics. ... The application MakeFan6 of the IMP package (Sheets, 2003) was u... more ... Geometric morphometrics. ... The application MakeFan6 of the IMP package (Sheets, 2003) was used to guarantee consistent placement of the semi-landmarks; a comb of 25 lines was used for this purpose. Figure 1. Landmarks and semi-landmarks recorded on seeds. image. ...
A phylogenetic analysis is provided for 70% of the representatives of genus Gavilea, as well as f... more A phylogenetic analysis is provided for 70% of the representatives of genus Gavilea, as well as for several species of the remaining genera of subtribe Chloraeinae: Bipinnula, Chloraea and Geoblasta. Sequences from the plastid markers rpoC1, matK-trnK and atpB-rbcL and the nuclear marker ITS, were analyzed using Maximum Parsimony and Bayesian Inference. Monophyly of subtribe Chloraeinae was confirmed, as well as its position inside tribe Cranichideae. Neither Chloraea nor Bipinnula were recovered as monophyletic. Gavilea turned out polyphyletic, with Chloraeachica embedded in the genus while Gavilea supralabellata was related to Chloraea and might be a hybrid between both genera. None of the two sections of Gavilea were monophyletic, and the topologies obtained do not suggest a new division of the genus.
Journal of Zoological Systematics and Evolutionary Research, 2013
ABSTRACT The clade size effect refers to a bias that causes middle-sized clades to be less suppor... more ABSTRACT The clade size effect refers to a bias that causes middle-sized clades to be less supported than small or large-sized clades. This bias is present in resampling measures of support calculated under maximum likelihood and maximum parsimony and in Bayesian posterior probabilities. Previous analyses indicated that the clade size effect is worst in maximum parsimony, followed by maximum likelihood, while Bayesian inference is the least affected. Homoplasy was interpreted as the main cause of the effect. In this study, we explored the presence of the clade size effect in alternative measures of branch support under maximum parsimony: Bremer support and symmetric resampling, expressed as absolute frequencies and frequency differences. Analyses were performed using 50 molecular and morphological matrices. Symmetric resampling showed the same tendency that bootstrap and jackknife did for maximum parsimony and maximum likelihood. Few matrices showed a significant bias using Bremer support, presenting a better performance than resampling measures of support and comparable to Bayesian posterior probabilities. Our results indicate that the problem is not maximum parsimony, but resampling measures of support. We corroborated the role of homoplasy as a possible cause of the clade size effect, increasing the number of random trees during the resampling, which together with the higher chances that medium-sized clades have of being contradicted generates the bias during the perturbation of the original matrix, making it stronger in resampling measures of support.
... Geometric morphometrics. ... The application MakeFan6 of the IMP package (Sheets, 2003) was u... more ... Geometric morphometrics. ... The application MakeFan6 of the IMP package (Sheets, 2003) was used to guarantee consistent placement of the semi-landmarks; a comb of 25 lines was used for this purpose. Figure 1. Landmarks and semi-landmarks recorded on seeds. image. ...
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Papers by Amelia Chemisquy