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Reliability of Bayesian posterior probabilities and bootstrap frequencies in phylogenetics.
It is shown that Bayesian posterior probabilities are significantly higher than corresponding nonparametric bootstrap frequencies for true clades, but also that erroneous conclusions will be made more often. Expand
Improvements to resampling measures of group support
Several aspects of current resampling methods to assess group support are reviewed. When the characters have different prior weights or some state transformation costs are different, the frequenciesExpand
Piecing together the "new" Plantaginaceae.
In a phylogenetic study of 47 members of Plantaginaceae and seven outgroups based on 3561 aligned characters from four DNA regions, the relationships within this clade were analyzed and the results from parsimony and Bayesian analyses support the removal of the Lindernieae from Gratioleae to a position outsideplantaginaceae. Expand
DISSECT: an assignment-free Bayesian discovery method for species delimitation under the multispecies coalescent
MOTIVATION The multispecies coalescent model provides a formal framework for the assignment of individual organisms to species, where the species are modeled as the branches of the sp tree. None ofExpand
Further disintegration of Scrophulariaceae
A novel, strongly supported, clade of taxa earlier assigned to Scrophulariaceae was found and possibly represents the tribe Lindernieae, diagnosed by geniculate anterior filaments, usually with a basal swelling. Expand
Phylogenies without roots? A plea for the use of vouchers in molecular phylogenetic studies.
A plea for the use of vouchers in molecular phylogenetic studies is made and it is suggested that vouchers should be placed in the phylogenetic tree for the sake of clarity. Expand
Whole-Gene Positive Selection, Elevated Synonymous Substitution Rates, Duplication, and Indel Evolution of the Chloroplast clpP1 Gene
Light is shed on the controversial issue of whether negative or positive selection is to be expected after gene duplications by providing evidence for the latter alternative, and the observed increase in synonymous substitution rates indicates that the detection of positive selection may be obscured under such circumstances. Expand
Phylogenetic relationships within the Gentianales based on NDHF and RBCL sequences, with particular reference to the Loganiaceae.
Phylogenetic relationships in the Gentianales with focus on Loganiaceae sensu lato are evaluated using parsimony analyses of nucleotide sequence data from the plastid genes rbcL and ndhF, which indicate that the family Rubiaceae forms the sister group to the successively nested Gentianaceae, Apocynaceae, and Logania, all of which are well supported. Expand
More characters or more taxa for a robust phylogeny--case study from the coffee family (Rubiaceae).
It is concluded that the monophyly of the Rubiaceae is supported and within the family there are three well supported, but not easily characterized, large subfamilies, Rubioideae, Cinchonoideae s.s. and Ixoroideae l.l. Expand
Generic boundaries in the tribe Sileneae (Caryophyllaceae) as inferred from nuclear rDNA sequences
The relationships within the tribe Sileneae (Caryophyllaceae, Caryophylloideae) were deduced from nucleotide sequence variation in the nuclear ribosomal DNA, and Polyschemone, previously often misplaced in Lychnis, is apparently closely related to Silene acaulis. Expand