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MBE Advance Access published online on August 5, 2004
Molecular Biology and Evolution, doi:10.1093/molbev/msh219
Molecular Biology and Evolution © Society for Molecular Biology and Evolution 2004; all rights reserved
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Accepted July 19, 2004

Original Article

Molecular Claims of Gondwanan Age for Australian Agamid Lizards Are Untenable

Andrew F. Hugall 1* Michael S. Y. Lee 2

1 Centre for Evolutionary Biology and Biodiversity, School of Earth and Environmental Sciences, University of Adelaide, SA 5005, Australia
2 Centre for Evolutionary Biology and Biodiversity, School of Earth and Environmental Sciences, University of Adelaide, SA 5005, Australia; Natural Sciences Division, The South Australian Museum, North Terrace, Adelaide SA 5000, Australia

* To whom correspondence should be addressed. E-mail: Andrew.Hugall{at}adelaide.edu.au.


  Abstract

A recent mtDNA study proposes a surprisingly deep (~150 mya) divergence between SE Asian and Australasian agamid lizards (Schulte et al. 2003), consistent with ancient Gondwanan vicariance rather than dispersal across the Indonesian archipelago. However, the analysis contains a fundamental error: using rates of molecular evolution inferred from uncorrected sequence divergence to put a time frame on a tree with branch lengths greatly elongated by complex likelihood and rate-smoothing models. Furthermore, this date implies that basal splits within agamids occurred implausibly early, at least 300 mya (100mya before the first fossil lizards and coincident with the earliest fossil reptiles). Analyses of the mtDNA data using more appropriate methods, and new information from nuclear (c-mos) sequences, both suggest a much more recent divergence between SE Asian and Australian agamids (around 30 mya). Using two fossil boundary dates, bootstrapping the c-mos data gives a 95% confidence interval for this divergence time that is sufficiently recent (14-41 mya) to exclude an ancient Gondwanan vicariance, and is more consistent with Miocene overwater dispersal. As with the mtDNA, the c-mos data implies implausibly old basal divergences among agamids if a Gondwanan age is assumed for the Australasian clade. The analyses also highlight how methods for creating ultrametric trees (especially nonparametric rate smoothing) can greatly modify branch lengths and thus always require internal calibrations. The errors associated with inferred dates in the previous study (inferred through parametric bootstrapping) were also unjustifiably low, as this method only considers stochasticity in the substitution model and ignores much larger sources of uncertainty, such as variation in character sampling, tree topology, and calibration accuracy.

Keywords: molecular clock; rate-smoothing; ultrametric trees; Agamidae; Wallace line; Gondwanan biogeography.
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