Comparing Bootstrap and Posterior Probability Values in the Four-Taxon Case

DMCA

Comparing Bootstrap and Posterior Probability Values in the Four-Taxon Case (2003)

Cached

Download Links

by Michael P. Cummings , Scott A. Handley , Daniel S. Myers , David L. Reed , Antonis Rokas , KATARINA WINKA

Citations:

61 - 4 self

BibTeX

@MISC{Cummings03comparingbootstrap,
    author = {Michael P. Cummings and Scott A. Handley and Daniel S. Myers and David L. Reed and Antonis Rokas and KATARINA WINKA},
    title = { Comparing Bootstrap and Posterior Probability Values in the Four-Taxon Case},
    year = {2003}
}

OpenURL

Abstract

Assessment of the reliability of a given phylogenetic hypothesis is an important step in phylogenetic analysis. Historically, the nonparametric bootstrap procedure has been the most frequently used method for assessing the support for specific phylogenetic relationships. The recent employment of Bayesian methods for phylogenetic inference problems has resulted in clade support being expressed in terms of posterior probabilities. We used simulated data and the four-taxon case to explore the relationship between nonparametric bootstrap values (as inferred by maximum likelihood) and posterior probabilities (as inferred by Bayesian analysis). The results suggest a complex association between the two measures. Three general regions of tree space can be identified: (1) the neutral zone, where differences between mean bootstrap and mean posterior probability values are not significant, (2) near the two-branch corner, and (3) deep in the two-branch corner. In the last two regions, significant differences occur between mean bootstrap and mean posterior probability values. Whether bootstrap or posterior probability values are higher depends on the data in support of alternative topologies. Examination of star topologies revealed that both bootstrap and posterior probability values differ significantly from theoretical expectations;

Keyphrases

posterior probability value four-taxon case comparing bootstrap mean posterior probability value mean bootstrap posterior probability two-branch corner significant difference bayesian analysis complex association phylogenetic inference problem tree space nonparametric bootstrap procedure neutral zone whether bootstrap star topology alternative topology maximum likelihood clade support phylogenetic hypothesis nonparametric bootstrap value important step general region phylogenetic analysis bayesian method theoretical expectation recent employment specific phylogenetic relationship

DMCA