In a molecular phylogeny of fishes produced using a cytb marker of 704 bp, Sota et al. (2005) (http://www.ncbi.nlm.nih.gov/pubmed/15684588) calibrated an ML clock tree with a node corresponding to the MRCA of two lineages that are assumed to have diverged in allopatry for 3.5 million years.
The 'node height' of this calibrated node is 0.047 (in Fig. 3, illustrating the ML clock tree, 'node height' apparently = number of substitutions per site).
The authors state that the calibration resulted in a "substitution rate of 2.7% per million years". Later on, they state that "3.5 million years corresponds to 9.4% sequence difference, giving a molecular clock of 2.7% per My".
I suppose that: 9.4/3.5 = 2.7 ...
The node height (0.047) should in fact be the branch length, or the number of substitutions separating the MRCA to one of the two sister lineages, divided by the length of the sequence (704), that is, the (average) number of substitutions per site. In this case, the 'divergence' between the two sister sequences should be twice this amount (the number of substitutions per site between the two sequences, along both branches), or 0.094.
By dividing the divergence (0.094 or 9.4/100, or '9.4%') by 3.4 million years, the authors found a 'divergence rate' of 2.7% per million year.
This however is referred to as the "molecular clock", or the "substitution rate".
Indeed, many authors (including me) would in this case use the term 'substitution rate' to indicate the average number of substitutions per site between the MRCA and one of its descendants, that is 0.047/3.5 = 0.0134 per million year, or '1.3% per million year'.
(incidentally, it always puzzled me why this complication of the '%', which should correspond to a 'rate per 100 million years').
When Sota et al. (2005) compare their "fish cytb molecular clock" of 2.7% per million year with the estimates of different studies (Orti et al. 1994; Cantatore et al. 1994), they find a range 0.8-2.8% per million year that is perfectly compatible with both the 'divergence rate' (2.7%) and the 'substitution rate' (1.3%) calculated above ... a misunderstanding of these rates is obviously very easy, since it is entirely possible that these other authors reported 'substitution rates', and not 'divergence rates'.
I'd be happy to share your thoughts about this topic.
Gianluca
yes Artur ... but that small amount of info is invariably the only stuff we have :-)
The % expression is an expression of the molecular divergence. It should be read as "per 100 base pairs". Also, the rate of molecular divergence should be the same regardless of how it is calculated. It does not matter if you call it divergence rate or substitution rate. It is all the same thing. If one rate is about half of the other rate, then someone has miscalculated. Of course, the date estimates of fossils have a large amount of error. This should be taken into account in proposing dates. When possible, multiple fossil calibrations should be used.
If you calculate a rate from the MRCA, as represented by a fossil, then you need to divide the observed divergence between the OTUs in half. (This would be the same as using the node height on an ultrametric tree.) If you are using someone else's rate, you can get the divergence time by dividing the divergence by the rate (all units cancel except time); in that case, you don't divide in half.
You are right, this is easily confusing. It looks like the authors, editors, and reviewers of that 2005 paper were confused as well. The question is: Is the error in how they used the term "node height" , or is the calculated rate inflated by 100%? Their figure defines node height as substitutions per site. But, we don't know if this is an estimate from the MRCA or a divergence between the OTUs. You could check this by using their NS model to calculate divergence between the OTUs, using sequences from GenBank. Also, you could ask them.
yes, I see that the percent notation indicates the percentage of substitutions, both in the divergence rate and in the substitution rate. Hence "2.7% per million year" means "2.7% of the sites were substituted in one million year".
However, I still see terminological confusion. That 2.7% per million year is a divergence rate, or the divergence between the two sister sequences, per million year.
Instead, the 'substitution rate' is "the percentage of substituted sites per million year between the MRCA and one of the two sister sequences". This counts the substitutions along one branch only between the MRCA and the descendant (= branch length). This rate is half the divergence rate. Indeed, this is the "molecular clock" of the marker, or how fast the marker changes in time.
This should be what you mean when you say "if you calculate a rate from the MRCA..."
About the rest of your reply: the figure clearly defines the node height as the average number of substitutions per site (0.047), or the branch length between the MRCA and one of the two sequences. That is obviously half the divergence between the two sequences (0.094), and that is why I wrote that the substitution rate is 0.047/3.5 = 0.0134 substitutions per million year, or 1.34% per million year.
Perhaps I am misunderstanding you... I still stress that there is only one actual rate. If we assume the authors made the mistake you are saying they made, then the 2.7% is not a rate of molecular change for this part of the DNA in these taxa. It is simply an error. I get the feeling we agree, but are just saying this differently.
I think you are likely correct about the nature of the error in the 2005 paper. It does not seem likely they would accidentally replace node heights with divergences in their figure. Still, I think it is possible.
Cheers!
Allen
No I think there is a misunderstanding.
I say that there are:
A) one rate which is the average number of substitutions per site (or the percentage of substitutions) per unit time, between the two sister sequences (= divergence rate = 2.7% per million year in this case);
AND
B) one rate which is the average number of substitutions per site (or the percentage of substitutions) per unit time, between the MRCA and one of the two sister sequences (= substitution rate = 1.3% per million year in this case).
B=1/2A
Let's fix this first.
yes that is what I was implying: only the substitution rate should be used as the 'molecular clock': 1.3% per million year
Now the second terminological issue:
Is the reported 'node height' (0.047) the 'branch length', or the number of substitutions separating the MRCA to one of the two sister lineages, divided by the length of the sequence (704), or the '(average) number of substitutions per site'?
Would you consider these three terms synonymous?
- Badges
- Science topic
- Similar topics
- Biological Science
- Biota
- Eukaryota
- Fungi