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Mitochondrial sequence data and Dipsacales phylogeny: mixed models, partitioned Bayesian analyses, and model

Richard C Winkworth1, Charles D Bell, Michael J Donoghue

  • 1Department of Ecology and Evolutionary Biology, Yale University, PO Box 208106, New Haven, CT 06520, USA. rwinkworth@gmail.com

Molecular Phylogenetics and Evolution
|February 8, 2008
PubMed
Summary
This summary is machine-generated.

Mitochondrial DNA data in Dipsacales phylogeny confirm broad patterns but fail to resolve uncertain relationships. Incongruent evolutionary signals between coding and non-coding DNA regions may explain these persistent phylogenetic challenges.

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Area of Science:

  • Plant evolutionary biology
  • Molecular phylogenetics
  • Angiosperm systematics

Background:

  • Previous phylogenetic analyses of Dipsacales using chloroplast DNA and morphology provided robust support for major evolutionary lineages.
  • Certain relationships within Dipsacales have remained difficult to resolve using existing molecular and morphological data.

Purpose of the Study:

  • To investigate the utility of mitochondrial DNA sequences for resolving phylogenetic uncertainties in Dipsacales.
  • To explore the impact of data partitions and substitution models on phylogenetic resolution.
  • To identify potential sources of conflict in Dipsacales phylogeny.

Main Methods:

  • Phylogenetic analyses were conducted using sequences from three mitochondrial loci.
  • Parsimony, maximum likelihood, and Bayesian inference methods were applied to mitochondrial and combined chloroplast-mitochondrial data.
  • Experiments involved analyzing different data partitions (coding vs. non-coding) and employing heterogeneous substitution models.

Main Results:

  • Mitochondrial DNA analyses recovered a topology largely consistent with previous studies but with lower resolution and support.
  • Combining chloroplast and mitochondrial data yielded a well-resolved and strongly supported phylogeny, yet unresolved areas persisted.
  • Incongruent phylogenetic signals were detected between coding and non-coding mitochondrial DNA partitions, correlating with previously problematic relationships.

Conclusions:

  • Mitochondrial DNA alone offers limited improvement in resolving deep-level Dipsacales relationships compared to chloroplast data.
  • Incongruent evolutionary signals between different DNA sequence types are a significant factor hindering confident phylogenetic resolution in Dipsacales.
  • Further investigation into the nature of these conflicting signals is necessary to fully resolve the Dipsacales phylogeny.