Branch-length estimation bias misleads molecular dating for a vertebrate mitochondrial phylogeny

Phillips, Matthew J. (2009) Branch-length estimation bias misleads molecular dating for a vertebrate mitochondrial phylogeny. Gene, 441(1-2), pp. 132-140.

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Despite recent methodological advances in inferring the time-scale of biological evolution from molecular data, the fundamental question of whether our substitution models are sufficiently well specified to accurately estimate branch-lengths has received little attention. I examine this implicit assumption of all molecular dating methods, on a vertebrate mitochondrial protein-coding dataset. Comparison with analyses in which the data are RY-coded (AG → R; CT → Y) suggests that even rates-across-sites maximum likelihood greatly under-compensates for multiple substitutions among the standard (ACGT) NT-coded data, which has been subject to greater phylogenetic signal erosion. Accordingly, the fossil record indicates that branch-lengths inferred from the NT-coded data translate into divergence time overestimates when calibrated from deeper in the tree. Intriguingly, RY-coding led to the opposite result. The underlying NT and RY substitution model misspecifications likely relate respectively to “hidden” rate heterogeneity and changes in substitution processes across the tree, for which I provide simulated examples. Given the magnitude of the inferred molecular dating errors, branch-length estimation biases may partly explain current conflicts with some palaeontological dating estimates.

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57 citations in Web of Science®
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ID Code: 50539
Item Type: Journal Article
Refereed: Yes
Keywords: Fossil calibration, Maximum likelihood, Mitochondrion, Model misspecification, RY-coding
DOI: 10.1016/j.gene.2008.08.017
ISSN: 0378-1119
Subjects: Australian and New Zealand Standard Research Classification > BIOLOGICAL SCIENCES (060000) > GENETICS (060400)
Divisions: Current > QUT Faculties and Divisions > Science & Engineering Faculty
Deposited On: 23 May 2012 21:52
Last Modified: 23 May 2012 21:52

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