[Taxacom] Hedges /Kumar (eds) The Timetree of Life

[Jason Mate]

I was going to reply to John but I guess their is no avoiding the collateral damage.

John, you are right, you were commenting on the title. But since the time part of it is supplied by fossils then maybe a better title would be A Tree of life based on DNA and fossil evidence?
As for the maximal ages and plenty of examples, please see below.

Michael, I read your article before and took the useful bits. Your article brought a salutary reminder of the uncertainties in using historical data. But even then the main thrust of the article bothered me. In particular the fact that the examples you brought up were more about semantics. Also the sweeping remarks such as p66:

In most phylogeographic studies the fossil record is taken at face value and the age of a clade is equated with
the age of its oldest known fossil. Node calibrations and the chronology of the whole phylogenetic tree are based
on these ages. As indicated above, this is simplistic and misleading.

Most? Further you later state regarding Koch et al:

1 Myr difference between oldest fossil and age of the group? Why not 2, 10 or 20 Myr?

Why indeed. Well, for one thing because even though 20myr is possible, it may not be probable. Now, the probability or possibility of an event may not be directly quantifiable
but, I am guessing here, they are making an educated guesstimate. You of course have the power to prove them wrong if you find evidence to the contrary, i.e. a fossil that is older. The lack
of evidence approach works both ways. They are weaving a story based on data at hand (it is a hypothesis) and as long as it fits the data it is valid. Mind you I am not saying it is 
right, just that it fits the evidence, as do many others I´m sure.

Further in the article a similar point is brought up regarding geological evidence:

A common error that biologists make in reading geology involves taking geologists’ suggestion that
‘‘there is no evidence for land’’ in a region for a particular period to mean ‘‘there is evidence for no
land’’.... Most of the standard correlations between distribution and paleogeographic events used to calibrate clocks
are highly simplistic. A classic example is the final rise of the Isthmus of Panama at about 3.5 Ma....

Now, maybe some researchers are as naive as you claim, assuming that flora and fauna were sitting at the edges of the continents, like traffic at a red-light, waiting
to cross over as soon as the bridge is up. Most though will take a more circumspect view. Geological events are datable ´´facts´´(who exactly knows when the 
first sandbar connecting both sides emerged from the sea) so they are evidence which can be brought into the interepretation of biogeographical patterns, even 
if semantically they are quite liberal in expressing their opinions.

And here lies the crux, on biogeographical patterns, and more specifically panbiogeography vs phylogeography:

With millions of species and now DNA sequencing, biology has an immense amount of information on
differentiation in space; virtually infinitely more than geology, with its few hundred major minerals. But
biology still lags a hundred years behind geology in all aspects of mapping (Heads, in press b) and the use of
‘‘chance dispersal’’ means biology has nothing to offer its sister science. Ideally, as in the work of Wegener
(1924), biology should be able to make fundamental contributions to tectonics. Molecular phylogenetic
work is invaluable, but the emphasis should be on intensive sampling phylogenetically and geographically.
Detailed mapping of clades is essential to permit correlation of distributions with different events in
earth history. This is not necessarily a straightforward process, as geological features such as major faults
and fracture zones are reactivated repeatedly over long periods of time. However, in the long term this should
be a more profitable line of inquiry than the current emphasis on calibrating molecular divergences with
fossils.

So the main article is to say that calibration is impossible, fossils and geology (completely it appears) unreliable, therefore, panbiogeography unrefutable. I have no problems with dispersion or vicariance
here, I know biogeography is messy, but this article hardly proves the point. 

Regarding the Timetree book:

> I looked up hystricognath rodents in the Timetree book. The group is a classic biogeographic 'problem', with the New World caviomorphs sister to the African phiomorphs. The oldest fossils of both caviomorphs and phiomorphs are c.37 Ma. The text states: 'Consequently, these dates are congruent with the hypothesis that the invasion of South America by African hystricognath ancestors involved overwater waif dispersal across a 1700-km expanse of the Atlantic subsequent to the separation of these two continents at a much earlier date'.
>  
>    But if the dates are treated as minima, they are just as congruent with vicariance as they are with dispersal. The reason the author does not mention vicariance is that the dates are being treated as maxima. The authors says the group evolved 'subsequent to' the opening of the Atlantic. This means that the date proposed is being treated as a maximum. If it were being treated as a minimum, the author wouldn't have said it evolved 'subsequent' to anything, he would only have been able to say it evolved 'before' such and such a date or event. Further on, the author says that the opening of the Atlantic was 'at a much earlier date' than the origin of the group. Again, the date, which is an estimate of minimum age, is being treated as an estimate of maximum (absolute) age. 

You again interchange possibility and probability. My understainding of the article is as follows: since the oldest fossil is c.37myr and the separation of of Africa predates this by a lot, and since the rodent fossil record is  c. 65myr, it is reasonable to assume that they dispersed over water.  If a fossil appears that negates this hypothesis then a new one that fits the data will have to be developed.

Goodnight

Jason