Presentation Detail

Phylogenetics, Methods and Theory

Bapst, David [1].

The Impact of Time-Scaling Methods on Phylogenetic Comparative Methods in the Fossil Record.

Tree-based studies of evolution hold considerable promise for furthering the unification of evolutionary biology and paleobiology. Applying these analyses in the fossil record often requires time-scaling a cladogram of morphotaxon relationships. Paleontological cladograms must be temporally scaled to apply phylogenetic analyses of macroevolution. However, temporal relationships are distorted in fossil data due to incomplete sampling. Several routines have been developed to secondarily time-scale cladograms of fossil taxa and I recently introduced the cal3 stochastic time-scaling method which utilizes a probabilistic model of sampling and diversification. However, no synthetic work has compared these methods and it is unclear how well different time-scaling methods reconstruct the true temporal relationships or how any such inaccuracy could impact tree-based evolutionary analyses. I developed a simulation framework for the comparison of empirical time-scaled trees to true time-scaled trees in the fossil record. I used these simulations to test the effect of time-scaling methods on the fidelity of several commonly applied tree-based analyses, across a range of simulation conditions. When the fidelity of time-scaling methods differed, the cal3 time-scaling method with ancestral inference produces preferable results. Estimating rates and models of continuous trait evolution was particularly sensitive to bias from scenarios which force the insertion of many short branch lengths, a bias which none of the time-scaling methods considered fully solves in all scenarios. The cal3 method of time-scaling can be recommended as the preferred time-scaling method of those tested, but caution must be exercised as tree-based analyses are prone to easily overlook biases.

1 - University of Chicago, Geophysical Sciences, 5734 South Ellis, Chicago, IL, 60637, USA

Keywords:
Paleobiology
phylogenetic comparative methods
macroevolution
trait evolution
Simulations
Sampling in the Fossil Record
diversification.

Presentation Type: Regular Oral Presentation
Session: 52
Location: Cotton A/Snowbird Center
Date: Sunday, June 23rd, 2013
Time: 9:45 AM
Number: 52006
Abstract ID:149
Candidate for Awards:W.D. Hamilton Award for Outstanding Student Presentation