Best Practices for Justifying Fossil Calibrations
James F. Parham1,2,*, Philip C. J. Donoghue3, Christopher J. Bell4, Tyler D. Calway5, Jason J. Head6, Patricia A. Holroyd7, Jun G. Inoue8, Randall B. Irmis9, Walter G. Joyce10, Daniel T. Ksepka11,12, José S. L. Patané13, Nathan D. Smith14,15, James E. Tarver3,16, Marcel van Tuinen17, Ziheng Yang18, Kenneth D. Angielczyk15, Jenny M. Greenwood3, Christy A. Hipsley19,20, Louis Jacobs21, Peter J. Makovicky15, Johannes Müller19, Krister T. Smith22, Jessica M. Theodor23 and Rachel C. M. Warnock3
- Author Affiliations
1Alabama Museum of Natural History, University of Alabama, 427 6th Avenue, Smith Hall, Box 870340, Tuscaloosa, AL 35487, USA
2BioSynC, The Field Museum of Natural History, 1400 S Lake Shore Drive, Chicago, IL 60657, USA
3School of Earth Sciences, University of Bristol, Bristol BS8 1RJ, UK
4Department of Geological Sciences, The University of Texas at Austin, 1 University Station, C1100, Austin, TX 78712, USA
5Department of the Geophysical Sciences, University of Chicago, 5734 South Ellis Avenue, Chicago, IL 60637, USA
6Department of Earth and Atmospheric Sciences, University of Nebraska-Lincoln, 228 Bessey Hall, Lincoln, NE 68588-0340, USA
7Museum of Paleontology, University of California, 1101 Valley Life Sciences Building, Berkeley, CA 94720, USA
8Atmosphere and Ocean Research Institute, University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8564, Japan
9Utah Museum of Natural History and Department of Geology & Geophysics, University of Utah, Salt Lake City, UT 84112, USA
10Institut für Geowissenschaften, University of Tübingen, Sigwartstraße 10, 72076 Tübingen, Germany
11Department of Marine, Earth and Atmospheric Sciences, North Carolina State University, Raleigh, NC 27695, USA
12Department of Paleontology, North Carolina Museum of Natural Sciences, Raleigh, NC 27601, USA
13Laboratorio de Ecologia e Evolucao, Instituto Butantan, Av. Dr. Vital Brasil, 1500, 05503-900 Sao Paulo, SP, Brazil
14Committee on Evolutionary Biology, University of Chicago, 1027 E. 57th Street, Chicago, IL 60637, USA
15Department of Geology, Field Museum of Natural History, 1400 S. Lake Shore Drive, Chicago, IL 60605, USA
16Department of Biological Sciences, Dartmouth College, Hanover, NH 03755, USA
17Department of Biology and Marine Biology, University of North Carolina at Wilmington, NC 28403, USA
18Department of Biology, University College London, Gower Street, London WC1E 6BT, UK
19Museum für Naturkunde, Leibniz-Institut für Evolutions- und Biodiversitätsforschung an der Humboldt-Universität zu Berlin, Invalidenstr. 43, 10115 Berlin, Germany
20Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, A316 Earth and Marine Sciences Building, Santa Cruz, CA 95064, USA
21Department of Earth Sciences, Southern Methodist University, Dallas, TX 75275, USA
22Department of Paleoanthropology and Messel Research, Senckenberg Museum, Senckenberganlage 25, 60325 Frankfurt am Main, Germany
23Department of Biological Sciences, University of Calgary, 2500 University Dr. NW, Calgary, AB T2N 1N4, Canada
↵*Correspondence to be sent to: Department of Biology, California State University, 9001 Stockdale Highway, Bakersfield, CA 93311-1099, USA; E-mail: jparham@csub.edu.
Received September 13, 2011.
Revision received September 22, 2011.
Accepted November 14, 2011.
Abstract
Our ability to correlate biological evolution with climate change, geological evolution, and other historical patterns is essential to understanding the processes that shape biodiversity. Combining data from the fossil record with molecular phylogenetics represents an exciting synthetic approach to this challenge. The first molecular divergence dating analysis (Zuckerkandl and Pauling 1962) was based on a measure of the amino acid differences in the hemoglobin molecule, with replacement rates established (calibrated) using paleontological age estimates from textbooks (e.g., Dodson 1960). Since that time, the amount of molecular sequence data has increased dramatically, affording ever-greater opportunities to apply molecular divergence approaches to fundamental problems in evolutionary biology. To capitalize on these opportunities, increasingly sophisticated divergence dating methods have been, and continue to be, developed. In contrast, comparatively, little attention has been devoted to critically assessing the paleontological and associated geological data used in divergence dating analyses. The lack of rigorous protocols for assigning calibrations based on fossils raises serious questions about the credibility of divergence dating results (e.g., Shaul and Graur 2002; Brochu et al. 2004; Graur and Martin 2004; Hedges and Kumar 2004; Reisz and Müller 2004a, 2004b; Theodor 2004; van Tuinen and Hadly 2004a, 2004b; van Tuinen et al. 2004; Benton and Donoghue 2007; Donoghue and Benton 2007; Parham and Irmis 2008; Ksepka 2009; Benton et al. 2009; Heads 2011).
© The Author(s) 2012. Published by Oxford University Press on behalf of the Society of Systematic Biologists. All rights reserved.
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
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