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Comparing cal3 and other a posteriori time-scaling approaches in a case study with the pterocephaliid trilobites

Published online by Cambridge University Press:  05 December 2016

David W. Bapst Open the ORCID record for David W. Bapst [Opens in a new window]  and
Melanie J. Hopkins
David W. Bapst
Affiliation:
Department of Earth & Planetary Sciences, University of California, Davis, One Shields Avenue, Davis, California 95616-8605, U.S.A. South Dakota School of Mines and Technology, 501 E. St. Joseph, Rapid City, South Dakota 57701, U.S.A. E-mail: [email protected]
Melanie J. Hopkins
Affiliation:
Division of Paleontology, American Museum of Natural History, Central Park West at 79th Street, New York, NY 10024, U.S.A. E-mail: [email protected]
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Abstract

Reconstructing the tree of life involves more than identifying relationships among lineages; it also entails accurately estimating when lineages diverged. Paleontologists typically scale cladograms to time a posteriori by direct reference to first appearances of taxa in the stratigraphic record. Some approaches use probabilistic models of branching, extinction, and sampling processes to date samples of trees, such as the recently developed cal3 method, which stochastically draws divergence dates given a set of rates for those processes. However, these models require estimates of the rates of those processes, which may be hard to obtain, particularly for sampling. Here, we contrast the use of cal3 and other a posteriori time-scaling approaches by examining a previous study that documented a decelerating rate of morphological evolution in pterocephaliid trilobites. Although aspects of the data set make estimation of branching, extinction, and sampling rates difficult, we use a multifaceted approach to calculate and evaluate the rate estimates needed for applying cal3. In agreement with previous simulation studies, we find that the choice of phylogenetic dating method impacts downstream macroevolutionary conclusions. We also find contradictory evolutionary inferences between analyses on ancestor–descendant contrasts (based on ancestor trait reconstruction methods) and maximum-likelihood parameter estimates. Ancestral taxon inference in cal3 corroborates previously hypothesized ancestor–descendant sequences, but cal3 suggests greater support for budding cladogenesis than anagenesis. This case study demonstrates the potential and wide applicability of the cal3 method and the benefits afforded by choosing cal3 over simpler a posteriori time-scaling approaches.

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Articles
Information
Paleobiology , Volume 43 , Issue 1 , February 2017 , pp. 49 - 67
Copyright
Copyright © 2016 The Paleontological Society. All rights reserved 

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