Reading the Entrails of Chickens

Dan Graur has a recent post on the phylogeny of placental mammals [The Root of the Placental Phylogenetic Tree: Are we Overlooking Something?]. He refers to a recent review in Molecular Biology and Evolution (MBE) that discusses various options. Graur believes that the question has been settled by examining transposon insertions.

But that's not the part that caught my attention. At the end of his post he says,

Finally, there is a small sentence in the Teeling and Hedges commentary that drove me up the wall: “The timing of the splitting event—approximately 100 Ma based on molecular clocks—is not in debate, at least among molecular evolutionists (Hedges et al. 1996…” Actually, dear Blair, it is. And whether you like it or not, both William Martin and I are fine molecular evolutionists.

The reference is to a paper by Dan Graur and Bill Martin—a formidable team that you want on your side because the alternative can be very embarrassing. You really, really don't want to mess with these guys.

We need more papers like this one.

Graur, D. & Martin, W. (2004) Reading the entrails of chickens: molecular timescales of evolution and the illusion of precision. TRENDS in Genetics 20:80-86 [doi: 10.1016/j.tig.2003.12.003] [PDF]

The Graur & Martin paper attacks molecular clock calibrations, pointing out that there are very few solid time points in the fossil record that can be used to calibrate the rate of molecular changes (in years). Here's the abstract ....

For almost a decade now, a team of molecular evolutionists has produced a plethora of seemingly precise molecular clock estimates for divergence events ranging from the speciation of cats and dogs to lineage separations that might have occurred, 4 billion years ago. Because the appearance of accuracy has an irresistible allure, non-specialists frequently treat these estimates as factual. In this article, we show that all of these divergence-time estimates were generated through improper methodology on the basis of a single calibration point that has been unjustly denuded of error. The illusion of precision was achieved mainly through the conversion of statistical estimates (which by definition possess standard errors, ranges and confidence intervals) into errorless numbers. By employing such techniques successively, the time estimates of even the most ancient divergence events were made to look deceptively precise. For example, on the basis of just 15 genes, the arthropod – nematode divergence event was ‘calculated’ to have occurred 1167 +/- 83 million years ago (i.e. within a 95% confidence interval of, 350 million years). Were calibration and derivation uncertainties taken into proper consideration, the 95% confidence interval would have turned out to be at least 40 times larger (~ 14.2 billion years).

They point out that the mammalian radiation is commonly assumed to be about 110 My but there's no justification for that assumption.

The fossil record indicates that mammals (placental and marsupial) were already a diverse group 175 My ago. Two recent papers in Nature document early mammal-like species. One of the papers suggests that mammals may have originated about 215 My ago see Palaeontology: Jurassic fossils and mammalian antiquity]. Like it or not, there's still disagreement between the fossil data and molecular clock estimates.

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