INFERRING SPECIATION RATES FROM PHYLOGENIES

INFERRING SPECIATION RATES FROM PHYLOGENIES Abstract It is possible to estimate the rate of diversification of clades from phylogenies with a temporal dimension. First, I present several methods for constructing confidence intervals for the speciation rate under the simple assumption of a pure birth process. I discuss the relationships among these methods in the hope of clarifying some fundamental theory in this area. Their performances are compared in a simulation study and one is recommended for use as a result. A variety of other questions that may, in fact, be the questions of primary interest (e.g., Has the rate of cladogenesis been declining?) are then recast as biological variants of the purely statistical question—Is the birth process model appropriate for my data? Seen in this way, a preexisting arsenal of statistical techniques is opened up for use in this area: in particular, techniques developed for the analysis of Poisson processes and the analysis of survival data. These two approaches start from different representations of the data—the branch lengths in the tree—and I explicitly relate the two. Aiming for a synoptic account of useful theory in this area, I briefly discuss some important results from the analysis of two distinct birth‐death processes: the one introduced into this area by Hey (1992) is refitted with some powerful statistical tools. http://www.deepdyve.com/assets/images/DeepDyve-Logo-lg.png Evolution Wiley

INFERRING SPECIATION RATES FROM PHYLOGENIES

Evolution, Volume 55 (4) – Apr 1, 2001

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Publisher
Wiley
Copyright
Copyright © 2001 Wiley Subscription Services, Inc., A Wiley Company
ISSN
0014-3820
eISSN
1558-5646
DOI
10.1111/j.0014-3820.2001.tb00801.x
Publisher site
See Article on Publisher Site

Abstract

Abstract It is possible to estimate the rate of diversification of clades from phylogenies with a temporal dimension. First, I present several methods for constructing confidence intervals for the speciation rate under the simple assumption of a pure birth process. I discuss the relationships among these methods in the hope of clarifying some fundamental theory in this area. Their performances are compared in a simulation study and one is recommended for use as a result. A variety of other questions that may, in fact, be the questions of primary interest (e.g., Has the rate of cladogenesis been declining?) are then recast as biological variants of the purely statistical question—Is the birth process model appropriate for my data? Seen in this way, a preexisting arsenal of statistical techniques is opened up for use in this area: in particular, techniques developed for the analysis of Poisson processes and the analysis of survival data. These two approaches start from different representations of the data—the branch lengths in the tree—and I explicitly relate the two. Aiming for a synoptic account of useful theory in this area, I briefly discuss some important results from the analysis of two distinct birth‐death processes: the one introduced into this area by Hey (1992) is refitted with some powerful statistical tools.

Journal

EvolutionWiley

Published: Apr 1, 2001

Keywords: ; ; ;

References

  • Inferring population history from molecular phylogenies.
    Nee, S.; Holmes, E. C.; Rambaut, A.; Harvey, P. H.

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