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Molecular clocks and avian diversification

 Mol Biol Evol. 2006 Sep;23(9):1731-40. Epub 2006 Jun
14.  Links 
A mitogenomic timescale for birds detects variable
phylogenetic rates of molecular evolution and refutes
the standard molecular clock.Pereira SL, Baker AJ. 
Department of Natural History, Royal Ontario Museum,
Toronto, Ontario, Canada. sergio.pereira@utoronto.ca

Current understanding of the diversification of birds
is hindered by their incomplete fossil record and
uncertainty in phylogenetic relationships and
phylogenetic rates of molecular evolution. Here we
performed the first comprehensive analysis of
mitogenomic data of 48 vertebrates, including 35
birds, to derive a Bayesian timescale for avian
evolution and to estimate rates of DNA evolution. Our
approach used multiple fossil time constraints
scattered throughout the phylogenetic tree and
accounts for uncertainties in time constraints, branch
lengths, and heterogeneity of rates of DNA evolution.
We estimated that the major vertebrate lineages
originated in the Permian; the 95% credible intervals
of our estimated ages of the origin of archosaurs (258
MYA), the amniote-amphibian split (356 MYA), and the
archosaur-lizard divergence (278 MYA) bracket
estimates from the fossil record. The origin of modern
orders of birds was estimated to have occurred
throughout the Cretaceous beginning about 139 MYA,
arguing against a cataclysmic extinction of lineages
at the Cretaceous/Tertiary boundary. We identified
fossils that are useful as time constraints within
vertebrates. Our timescale reveals that rates of
molecular evolution vary across genes and among taxa
through time, thereby refuting the widely used
mitogenomic or cytochrome b molecular clock in birds.
Moreover, the 5-Myr divergence time assumed between 2
genera of geese (Branta and Anser) to originally
calibrate the standard mitochondrial clock rate of
0.01 substitutions per site per lineage per Myr
(s/s/l/Myr) in birds was shown to be underestimated by
about 9.5 Myr. Phylogenetic rates in birds vary
between 0.0009 and 0.012 s/s/l/Myr, indicating that
many phylogenetic splits among avian taxa also have
been underestimated and need to be revised. We found
no support for the hypothesis that the molecular clock
in birds "ticks" according to a constant rate of
substitution per unit of mass-specific metabolic
energy rather than per unit of time, as recently
suggested. Our analysis advances knowledge of rates of
DNA evolution across birds and other vertebrates and
will, therefore, aid comparative biology studies that
seek to infer the origin and timing of major adaptive
shifts in vertebrates.