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Parsimony, likelihood, and simplicity
(Wiley Blackwell Publishing, Inc, 2003-02)
The latest charge against parsimony in phylogenetic inference is that it involves estimating too many parameters. The charge is derived from the fact that, when each character is allowed a branch length vector of its own ...
Evaluating the clade size effect in alternative measures of branch support
(Wiley, 2013-11)
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 ...
Methods of phylogenetic inferenceMétodos de inferencia filogenética
(Universidad Nacional Mayor de San Marcos, Facultad de Ciencias Biológicas, 2011)
An artifact caused by undersampling optimal trees in supermatrix analyses of locally sampled characters
(Elsevier Inc, 2013-06)
Empirical and simulated examples are used to demonstrate an artifact caused by undersampling optimal trees in data matrices that consist mostly or entirely of locally sampled (as opposed to globally, for most or all ...
On defining a unique phylogenetic tree with homoplastic characters
(Academic Press Inc Elsevier Science, 2018-05)
This paper discusses the problem of whether creating a matrix with all the character state combinations that have a fixed number of steps (or extra steps) on a given tree T, produces the same tree T when analyzed with ...
Assessing topological congruence among concatenation-based phylogenomic approaches in empirical datasets
(Academic Press Inc Elsevier Science, 2021-08)
Assessing the effect of methodological decisions on the resulting hypotheses is critical in phylogenetics. Recent studies have focused on evaluating how model selection, orthology definition and confounding factors affect ...
Phylogenetic relationships in Bulbostylis (Abildgaardieae: Cyperaceae) inferred from nuclear and plastid DNA sequence data
(Taylor & Francis, 2018-07)
Previous molecular phylogenetic analyses of the family Cyperaceae based on rbcL sequences showed Bulbostylis as paraphyletic, with B. atrosanguinea and B. hispidula forming a clade with Nemum spadiceum. On the contrary, ...
Phylogenetic relationships in Bulbostylis (Abildgaardieae: Cyperaceae) inferred from nuclear and plastid DNA sequence data
(Taylor & Francis, 2018)
Previous molecular phylogenetic analyses of the family Cyperaceae based on rbcL sequences showed Bulbostylis as
paraphyletic, with B. atrosanguinea and B. hispidula forming a clade with Nemum spadiceum. On the contrary, ...
Phylogenetic analysis of the Brazilian microendemic Paepalanthus subgenus Xeractis (Eriocaulaceae) inferred from morphology
(WILEY-BLACKWELL, 2011)
Paepalanthus subgenus Xeractis (Eriocaulaceae) comprises 28 recognized species endemic to the Espinhaco Range, in Minas Gerais state, Brazil. Most species of the subgenus are restricted to small localities and critically ...
Phylogenetic relationships in Solanaceae and related species based on cpDNA sequence from plastid trnE-trnT region
(BRAZILIAN SOC PLANT BREEDING, 2008)
Intergenic spacers of chloroplast DNA (cpDNA) are very useful in phylogenetic and population genetic studies of plant species, to study their potential integration in phylogenetic analysis. The non-coding trnE-trnT intergenic ...