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Sunday, May 30, 2010

Calibrating the Molecular Clock

John Hawks is discussing the evolution of hominids on his blog and, in particular, whether Ardipithecus (Ardi) is a hominid [Ardipithecus challenge explication: the molecular clock].

This is a complex issue. One of the problems is that Ardi is supposed to have lived 5.5 million years ago, according to John Hawks, but all estimates of the human-chimp divergence say it occurred between 3 and 5 million years ago. If that's true then Ardi is not in either the chimp or human lineages.

The human-chimp divergence is based on calibrating the molecule clock and that's what John addresses in his post. He seems to think that this calibration is accurate [Reviewing the clock, and phylogenomics] but I'm not so sure. Many of these studies (but not all) require calibrating the rate of change by using fixed time points inferred from the fossil record. For example, if you assume that primates and rodents last shared a common ancestor 100 million years ago then you can get a rate of change by adding up the number of changes in each lineage and dividing by 100 (substitutions per million years). Then you look at the number of substitutions in the human and chimp lineages and calculate the years since they diverged.

This is an over-simplification, as John explains on his blog, because the calibrations are also based on known mutation rates and population genetics. The theoretical models agree on a human-chimp divergence time of 3-5 million years.

I've been skeptical of the fossil record calibrations for many years because they give some very unreasonable divergence times and because the so-called "fixed" standards also seem unreasonable. The molecular clock ticks at an approximately constant rate but we just don't know what that rate is. I would have no problem accepting that humans and chimps diverged 6-7 million years ago.

[Reconstructions: Copyright 2009, J.H. Matternes.]


John Hawks said...

Many thanks!

It's such a tough problem to work through. We can make any fossil consistent with any tree by assuming the right substitution rate. But that assumption will have effects that propagate through the whole tree. You're absolutely correct -- that means we focus too much on "charismatic" fossils.

The "Cretaceous anthropoid" series I've been writing is focused on this problem at a deeper time scale. One of the consequences of a substitution rate that makes Ardi a hominin, is that it predicts monkeys to be much older than we've ever found them. Which some paleontologists think is very possible based on the number of lineages missed in the later primate fossil record.

The Archaeologist said...

G’day Larry,
The problem with molecular clocks is that they are bound by assumptions. They are guides, they are not actual clocks. I suspect with refined ancient DNA techniques and applications to actual fossil populations, rather than individuals we will find that the molecular clock is not as clock like as we first thought.

This link is on some recent work on the ancient dna of penguins which I think is probably the most robust study of its kind and yet is rarely brought up in these molecular clock debates. It argues that the molecular clock underestimates divergence times, which fits in with your thinking.

Larry Moran said...

The Archaeologist says,

I suspect with refined ancient DNA techniques and applications to actual fossil populations, rather than individuals we will find that the molecular clock is not as clock like as we first thought.

We don't need to know the exact rate of change in order to test whether the clock ticks at an approximately constant rate. We already have thousands of trees that tell us how clocklike the change really is. It's pretty good at the scale of millions of years.

With respect to ancient DNA, you're thinking like an archaelogist! :-)

In my opinion, the molecular clock is only good for large scale changes over millions of years. It's very unreliable for short term measurements like we see in hominid evolution. It's a stochastic clock, not a digital clock!

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