CALL FOR PROPOSALS:

ORGANIZERS

  • Harvey Thorleifson, Chair
    Minnesota Geological Survey
  • Carrie Jennings, Vice Chair
    Minnesota Geological Survey
  • David Bush, Technical Program Chair
    University of West Georgia
  • Jim Miller, Field Trip Chair
    University of Minnesota Duluth
  • Curtis M. Hudak, Sponsorship Chair
    Foth Infrastructure & Environment, LLC

 

Paper No. 15
Presentation Time: 5:15 PM

COMPARING METHODS FOR TIME-SCALING TREES OF EXTINCT TAXA


BAPST, David W., Dept of Geophysical Sciences, University of Chicago, 5734 S Ellis, Chicago, IL 60637, dwbapst@uchicago.edu

As phylogenetic approaches to paleobiology become increasingly common, it becomes necessary to assess the effect of methodology on our results. The temporal scaling of phylogenies is important in tree-based analyses that measure rates of trait evolution, reconstruct patterns of lineage diversity or estimate phylogenetic signal of a trait (a quantitative measure of fit to a Brownian model of trait evolution). In the recent paleobiological literature, various routines have been applied for scaling the phylogenetic branches to time. The most basic method for time-scaling a tree of extinct taxa produces many zero-length branches as an artifact and several alternatives have been suggested to deal with this. One alternative involves the use of a morphological clock, but this applied to phylogenies for which there is no information about character changes along branches, such as supertrees. Comparing time-scaling methods for such trees is thus especially important.

I present a new method for time-scaling phylogenies based on a stochastic weighted sampling procedure. This method uses estimates of sampling rates in the fossil record to produce large samples of time-scaled trees which bracket the uncertainty in branch lengths. Analyses are done across samples of trees to account for this uncertainty, rather than analyzing a single time-scaled tree. This new method also resolves soft polytomies and allows for the possibility of ancestor-descendant relationships among taxa.

In this study, I investigate the effect of this and other time-scaling methods on analyses of rates, phylogenetic signal and diversity. Using simulated fossil records and corresponding phylogenetic datasets, I produce time-scaled trees under various time-scaling methods, apply the analysis of interest and measure the fidelity of the result with the ‘true’ answer from the original simulation. In addition, I will also apply the new time-scaling method to real phylogenetic data in order to demonstrate the utility of this method in general.

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