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An examination of the monophyly of morning glory taxa using Bayesian phylogenetic inference.

Publication ,  Journal Article
Miller, RE; Buckley, TR; Manos, PS
Published in: Systematic biology
October 2002

The objective of this study was to obtain a quantitative assessment of the monophyly of morning glory taxa, specifically the genus Ipomoea and the tribe Argyreieae. Previous systematic studies of morning glories intimated the paraphyly of Ipomoea by suggesting that the genera within the tribe Argyreieae are derived from within Ipomoea; however, no quantitative estimates of statistical support were developed to address these questions. We applied a Bayesian analysis to provide quantitative estimates of monophyly in an investigation of morning glory relationships using DNA sequence data. We also explored various approaches for examining convergence of the Markov chain Monte Carlo (MCMC) simulation of the Bayesian analysis by running 18 separate analyses varying in length. We found convergence of the important components of the phylogenetic model (the tree with the maximum posterior probability, branch lengths, the parameter values from the DNA substitution model, and the posterior probabilities for clade support) for these data after one million generations of the MCMC simulations. In the process, we identified a run where the parameter values obtained were often outside the range of values obtained from the other runs, suggesting an aberrant result. In addition, we compared the Bayesian method of phylogenetic analysis to maximum likelihood and maximum parsimony. The results from the Bayesian analysis and the maximum likelihood analysis were similar for topology, branch lengths, and parameters of the DNA substitution model. Topologies also were similar in the comparison between the Bayesian analysis and maximum parsimony, although the posterior probabilities and the bootstrap proportions exhibited some striking differences. In a Bayesian analysis of three data sets (ITS sequences, waxy sequences, and ITS + waxy sequences) no supoort for the monophyly of the genus Ipomoea, or for the tribe Argyreieae, was observed, with the estimate of the probability of the monophyly of these taxa being less than 3.4 x 10(-7).

Duke Scholars

Published In

Systematic biology

DOI

EISSN

1076-836X

ISSN

1063-5157

Publication Date

October 2002

Volume

51

Issue

5

Start / End Page

740 / 753

Related Subject Headings

  • Phylogeny
  • Monte Carlo Method
  • Models, Genetic
  • Markov Chains
  • Likelihood Functions
  • Ipomoea
  • Genes, Plant
  • Evolutionary Biology
  • DNA
  • Bayes Theorem
 

Citation

APA
Chicago
ICMJE
MLA
NLM
Miller, R. E., Buckley, T. R., & Manos, P. S. (2002). An examination of the monophyly of morning glory taxa using Bayesian phylogenetic inference. Systematic Biology, 51(5), 740–753. https://doi.org/10.1080/10635150290102401
Miller, Richard E., Thomas R. Buckley, and Paul S. Manos. “An examination of the monophyly of morning glory taxa using Bayesian phylogenetic inference.Systematic Biology 51, no. 5 (October 2002): 740–53. https://doi.org/10.1080/10635150290102401.
Miller RE, Buckley TR, Manos PS. An examination of the monophyly of morning glory taxa using Bayesian phylogenetic inference. Systematic biology. 2002 Oct;51(5):740–53.
Miller, Richard E., et al. “An examination of the monophyly of morning glory taxa using Bayesian phylogenetic inference.Systematic Biology, vol. 51, no. 5, Oct. 2002, pp. 740–53. Epmc, doi:10.1080/10635150290102401.
Miller RE, Buckley TR, Manos PS. An examination of the monophyly of morning glory taxa using Bayesian phylogenetic inference. Systematic biology. 2002 Oct;51(5):740–753.
Journal cover image

Published In

Systematic biology

DOI

EISSN

1076-836X

ISSN

1063-5157

Publication Date

October 2002

Volume

51

Issue

5

Start / End Page

740 / 753

Related Subject Headings

  • Phylogeny
  • Monte Carlo Method
  • Models, Genetic
  • Markov Chains
  • Likelihood Functions
  • Ipomoea
  • Genes, Plant
  • Evolutionary Biology
  • DNA
  • Bayes Theorem