[Taxacom] Molecular dates are NOT necessarily minimums

[Rob Smissen]

Once again Michael Heads promotes his self-serving slogan, claiming "As discussed, fossil-calibrated, molecular clock dates for clades can only ever be minimums."
Current Bayesian molecular dating software gives a probability distribution of dates. How can a distribution of dates (a range) be a minimum? Well, Heads takes the oldest date from a published range and transmogrifies that into minimum.

But that is only the beginning. The "only ever minimum" argument ignores the fact that other sources of error can contribute to misleadingly old date estimates. These include

  1.  Ancestral polymorphism (splits in gene lineages are older than splits among populations). This has the opposite effect to the missing fossil problem. Gene lineage divergences necessarily predate population divergences, and therefore one might (wrongly) infer using Heads' logic that molecular date estimate are necessarily maximum.
  2.  Rate variation among lineages.
  3.  Miss-specified models.
  4.  Incorrect attribution of fossils to extant lineage.
  5.  Imprecise ages of fossils (often themselves given as ranges).
  6.  Stochastic effects when sequences are short.

Sometimes the data underpinning molecular dating papers is consistent with a 0 age (by which I mean that the samples could as well have been taken from a single panmictic population), yet Heads transmogrifies an age of millions of years into a so called minimum. I don't believe intelligent people would support that, at least not if they were honest.

We should all take molecular clock dates with a big grain of salt, but slogans don't make for good science. I don't mind an argument that molecular date estimates may be underestimates, but I do mind the slogan that they are necessarily minimum. That is sophistry.

Using the current generation of software, it is possible to explore the effect of using different priors. In fact it is quite easy. In particular, it is easy to explore the effect of increasing a calibration age to make dates older. It is also easy to constrain or relax the allowed rate variation among lineages.  If Heads was serious he could undertake these analyses. He could make the calibrations as old as he likes. Or stipulate that conspecific allopatric populations diverged in the Mesozoic as he oft claims. Then he could quantify how much rate variation, and how old the earth has to be, to accommodate his "biogeographic" assumptions. Despite claiming an understanding of molecular data and the workings of Bayesian analyses, and the fact that the software is free, Heads seems remarkably slow to provide analyses of how much older than their oldest fossils clades needs to be to fit his paradigm.




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