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Open Access Research article

Integration of Bayesian molecular clock methods and fossil-based soft bounds reveals early Cenozoic origin of African lacertid lizards

Christy A Hipsley12, Lin Himmelmann3, Dirk Metzler4 and Johannes Müller1*

Author Affiliations

1 Museum für Naturkunde – Leibniz-Institut für Evolutions- und Biodiversitätsforschung an der Humboldt-Universität zu Berlin, Invalidenstr. 43, 10115 Berlin, Germany

2 Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, A316 Earth and Marine Sciences Building, CA 95064, USA

3 Institut für Informatik, Goethe-Universität, Robert Mayer Str. 11-15, D-60325 Frankfurt am Main, Germany

4 Department of Biology, University of Munich (LMU), Grosshaderner Str. 2, D-82152 Planegg-Martinsried, Germany

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BMC Evolutionary Biology 2009, 9:151  doi:10.1186/1471-2148-9-151

Published: 1 July 2009

Abstract

Background

Although current molecular clock methods offer greater flexibility in modelling evolutionary events, calibration of the clock with dates from the fossil record is still problematic for many groups. Here we implement several new approaches in molecular dating to estimate the evolutionary ages of Lacertidae, an Old World family of lizards with a poor fossil record and uncertain phylogeny. Four different models of rate variation are tested in a new program for Bayesian phylogenetic analysis called TreeTime, based on a combination of mitochondrial and nuclear gene sequences. We incorporate paleontological uncertainty into divergence estimates by expressing multiple calibration dates as a range of probabilistic distributions. We also test the reliability of our proposed calibrations by exploring effects of individual priors on posterior estimates.

Results

According to the most reliable model, as indicated by Bayes factor comparison, modern lacertids arose shortly after the K/T transition and entered Africa about 45 million years ago, with the majority of their African radiation occurring in the Eocene and Oligocene. Our findings indicate much earlier origins for these clades than previously reported, and we discuss our results in light of paleogeographic trends during the Cenozoic.

Conclusion

This study represents the first attempt to estimate evolutionary ages of a specific group of reptiles exhibiting uncertain phylogenetic relationships, molecular rate variation and a poor fossil record. Our results emphasize the sensitivity of molecular divergence dates to fossil calibrations, and support the use of combined molecular data sets and multiple, well-spaced dates from the fossil record as minimum node constraints. The bioinformatics program used here, TreeTime, is publicly available, and we recommend its use for molecular dating of taxa faced with similar challenges.