Molecular Clocks, Part 3: Rocks vs. Clocks

It’s probably obvious by now that I’m not a big fan of the molecular clock. You may think that I’m misrepresenting the method or making it look too simple. The point of this post is to take four representative examples to compare what palaeontology tells us and what the molecular clock tells us.


Our first example is a classic: the origin of the modern birds. The earliest fossil we have is Vegavis iaai [Free PDF here!], from the latest Creataceous (66 Ma) of Antarctica.

Vegavis iaai. Clarke et al., 2005.

It’s a duck – and not a basal one either, it’s relatively derived. It’s presence means that the stem group ducks and chickens and, by extension, of the modern birds lies before the K-T boundary. That’s a pretty vague statement though. To put a soft maximum time on it, we look at when the most primitive birds lived (i.e. birds with teeth) and we come to a soft maximum time of 86.5 Ma. This is as old as we can go, palaeontologically.

Now let’s see what the molecular clock tells us. I have chosen this paper [warning, .pdf] by Brown et al. from 2008, because it was a rather honest paper that dealt with the problem and acknowledged the limitations of the molecular clock. In fact, on page 8, you can see the same dataset run through four different algorithms and compare the differences. The dot we’re interested in is the purple one: palaeontology gives us a maximum age for it at 86.5 Ma. As you can see, the one that comes closest to it is the PATHd8 algorithm, but it’s still off by ~ 10 Ma.

Looking at their final tree [I will not upload it here, too big] on the next page, you’ll see that they did not go for that one. Instead, they went for an early Cretaceous origin (~ 120 Ma) and diversification right after. The fossil evidence for this does not exist. As far as we know, there were no modern birds that early on.

Molecular systematists have different arguments they use to justify their results. They might say that half the bird fossil record is missing. They might say basal birds were cryptic and just weren’t preserved. This is basically the argument that the fossil record is shit. And I’ll admit, birds aren’t the most easily fossilised animals. Their bones are small, hollow and delicate. But molecular systematists tend to be ignorant of fossils and they don’t seem to know that there are several Cretaceous fossil sites where small, terrestrial animals are preserved (e.g. lizards, mammals, amphibians). There is no reason to have such skeletons but no birds – except that the birds did not exist. The point is: stick to what we have, not calculations pulled out of thin air.


Let’s look at this concept of a poor fossil record with an example where we have an excellent, albeit hard to interpret, fossil record, namely the origin of arthropods in the Cambrian. We’ve already looked at the palaeontological aspects </shameless self-promotion>, now let’s see what the mollies tell us. This is an example from The Time Tree of Life, a book with a large number of molecular clock studies. The book is available for free download at their website (Chapter 4, ‘Calibrating and constraining the molecular clock’, is an extremely useful palaeontological counterpart to the book), and you can also enjoy yourself by putting 2 random taxa into their search field and seeing what the molecular time of divergence is.

Arthropod Molecular Clock. Pisani, 2009.

First of all, Myriochelata? This is a grouping of chelicerates and myriapods with absolutely no morphological evidence. It only comes out of molecular studies and should be looked down upon and shamed. But let’s humour them and assume Myriochelata is a valid taxon. Point 1 is the last common ancestor of the arthropods, at ~700 Ma. Palaeontology tells us they originated in the early Cambrian and probably in the Neoproterozoic. The maximum palaeontological time is 590 Ma.

The implication of this is that the Cambrian Radiation is just an example of how the fossil record is inadequate. They’ll talk about a phylogenetic fuse: the ancestors were small, impossible to fossilise, larvae-like animals, gradually evolving until the environmental conditions allowed for biomineralisation to occur. In other words, the fossil record is shitty.


But let’s look at this concept of a phylogenetic fuse some more, this time with the origin of land plants, the embryophytes. The first fossil land plants we have are from the mid-Silurian (Cooksonia, 425 Ma).

Embryophyte Molecular Clock. Magallon, 2009.

This is the studfy from the Time Tree of Life (TToL). The land plants originate in the Neoproterozoic, 175 Ma earlier than the fossil record. Let’s ignore the date and look at the pattern though. Soon after the embryophytes diverged, there was a radiation – this is just as predicted by the geological record. The reason is simple: the first organisms to live on land must have been subjected to abnormally high mutation rates due to the lack of an ozone layer. These extraordinary mutation rates are too high to fit into the regular algorithms; this split cannot possibly be dated.


If you’re like me, you’ve probably formed your own conclusion about molecular clocks by now. But let’s give them an advantage for once: so far, we’ve had real physical evidence to back our assertions up. Let’s look at the very first eukaryotes – single-celled organisms for which there is virtually no fossil record.

Eukaryote Molecular Clock. Bhattacharya et al., 2009.

The molecular clock from TToL gives us an origin at ~ 1600 Ma. Reading their method for getting that date though, it’s pretty questionable: they took a weighted average from previous studies on the root. Looking at the tree’s topology, we see some dubious taxa, like Chromalveolata and Excavata, which suffer from the same problem as Myriochelata.

However one thing to notice is the origin of the Plantae (Point 3). It fits surprisingly well with the geological record of oceanic oxygen! But then again, one good result means nothing if it’s within the wrong framework.

Those are our four examples. I hope you now have an idea of where the differences between palaeontology and molecular clocks are. The next post will have my own conclusions and explanations for why these dates are so different, and I will also suggest if the fossil record and molecular clocks are actually compatible (the answer may surprise you!).

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