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Re: Molecular clocks and avian diversification

At 17:06 2006-10-24, David Marjanovic wrote:
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.

Major ouch time!

It's embarrassing that anyone used this as late as 2006. (It has recently been refuted, I think in the latest paper on the phylogeny of Neornithes.)

Especially since both Branta and Anser have fossil records going back at least to the mid-Miocene. And yet Branta and Anser can still interbreed! The offspring seems to be sterile though.

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

What a pity.


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.

A nice way of putting what a biomedical researcher seeking major founding would without doubt have called "...will revolutionize our understanding of..."

Where's the revolution?

Instead, let me doubt the dates. A Permian date for the basal divergence of the crown of Archosauria is suspect. An Early Cretaceous date for the basal divergence of Neornithes is highly suspect. And so on... I've recently done some molecular dating; some programs let you fiddle with several parameters that can greatly influence the results, others seem to have them inbuilt and inalterable...

This is an interesting paper in this context:

van Tuinen, M., Stidham, T. A. & Hadly, E. A. 2006. Tempo and mode of modern bird evolution observed with large-scale taxonomic sampling. Historical Biology 18(2):205-221.

Macroevolutionists continue to disagree about the evolutionary history of birds. Their debate centers on the apparent
discrepancy between molecular- and fossil-derived times of certain events. In this study we will show that there is much
more agreement than discrepancy. We do it by simultaneously using both molecules (DNA hybridization and DNA sequence) and
fossils to study a large set of avian taxa. Our analysis focuses on the time of origin and diversification of most of the orders
and families of extant birds. Both tools show that the Cretaceous-Tertiary transition witnessed a major ordinal
diversification within extant birds. Both also show a pulse of family diversification near the Eocene-Oligocene transition. Thus
both of these pulses occurred close to times of mass extinction. The presented evolutionary time scale for extant birds launches
testing of novel inter-disciplinary hypotheses.

This implies that most of the older avian orders are each descended from a single species at the KT boundary which seems plenty cataclysmic to me.

Tommy Tyrberg