Mitochondrial sequence data and Dipsacales phylogeny: Mixed models, partitioned Bayesian analyses, and model selection
Contribuinte(s) |
UNIVERSIDADE DE SÃO PAULO |
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Data(s) |
20/10/2012
20/10/2012
2008
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Resumo |
Phylogenetic analyses of chloroplast DNA sequences, morphology, and combined data have provided consistent support for many of the major branches within the angiosperm, clade Dipsacales. Here we use sequences from three mitochondrial loci to test the existing broad scale phylogeny and in an attempt to resolve several relationships that have remained uncertain. Parsimony, maximum likelihood, and Bayesian analyses of a combined mitochondrial data set recover trees broadly consistent with previous studies, although resolution and support are lower than in the largest chloroplast analyses. Combining chloroplast and mitochondrial data results in a generally well-resolved and very strongly supported topology but the previously recognized problem areas remain. To investigate why these relationships have been difficult to resolve we conducted a series of experiments using different data partitions and heterogeneous substitution models. Usually more complex modeling schemes are favored regardless of the partitions recognized but model choice had little effect on topology or support values. In contrast there are consistent but weakly supported differences in the topologies recovered from coding and non-coding matrices. These conflicts directly correspond to relationships that were poorly resolved in analyses of the full combined chloroplast-mitochondrial data set. We suggest incongruent signal has contributed to our inability to confidently resolve these problem areas. (c) 2007 Elsevier Inc. All rights reserved. |
Identificador |
MOLECULAR PHYLOGENETICS AND EVOLUTION, v.46, n.3, p.830-843, 2008 1055-7903 http://producao.usp.br/handle/BDPI/27716 10.1016/j.ympev.2007.11.021 |
Idioma(s) |
eng |
Publicador |
ACADEMIC PRESS INC ELSEVIER SCIENCE |
Relação |
Molecular Phylogenetics and Evolution |
Direitos |
restrictedAccess Copyright ACADEMIC PRESS INC ELSEVIER SCIENCE |
Palavras-Chave | #Bayesian inference #caprifolieae #dipsacales #heptacodium #linnaeeae #mitochondrial DNA #mixed models #data partitions #PLANT MITOCHONDRIAL #VALERIANACEAE DIPSACALES #NUCLEOTIDE SUBSTITUTION #CHLOROPLAST #EVOLUTION #DNA #BIOGEOGRAPHY #LIKELIHOOD #INFERENCE #NUCLEAR #Biochemistry & Molecular Biology #Evolutionary Biology #Genetics & Heredity |
Tipo |
article original article publishedVersion |