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They ARE the actual amounts of change in the branch between the LCA and the taxon in question.
Not to belabor this, but they are the average rates, by definition.
Considering how I am one of the authors of the paper in question, I think I know what we were looking at, and rates - average or otherwise - had nothing to do with it. You are confusing the comparison of total changes in branch lengths to glean differences in rates of mutation accumulation to some sort of statement about the average rates of mutation.
So when you wrote: "...and then give us average rates of change for each segment in between while saying that these are the actual rates of change in those groups for those periods." you were totally off base. Nowhere did we say anything about average rates at all, in terms of absolute rates per lineage. If you read the paper, the discussion of rates entailed observations of comparisons between branch lengths of various taxa. We did not assign them any rates, we did not conclude that their rate of mutation was X, we merely compared the resulting branch lengths and described what we saw.
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You do not know when each individual fixed selected mutation occurred, you don't even know if half occurred in the first half of the time period and half occurred in the second half or whether 90% occurred in the first half and 10% in the second. All you have is (n) mutations occurred in (t) time and the average rate of mutation over time (t) was (n/t). Within that time period (t) the specific rate of change could have varied considerably: you don't know.
A most astute and insightful series of proclamations. Now, if only we had done what you appear to insist we did, there might be some relevance here, but as we were not assigning rates - average or otherwise - your criticisms are still baseless and bordering on the hysterical.
What is more, the distribution of the occurrence of mutations along some spectrum is utterly irrelevant as to the analyses we performed. The observations about differences in mutation accumulation in different lineages was a by-product of what we were really interested in.
For example, we wrote:
"We further utilized the percentages of nucleotide change on the branches of the phylogenetic trees in Figs. 3 and 4 along with the estimated ages of the branch points (Table 4) to obtain estimates of evolutionary rates for noncoding DNA. These results are presented in Table 5. They indicate that noncoding DNA accumulated change at a slower rate."
See? We were concerned with rates of accumulation, we were not postulating anything about the rate of occurrance:
"It has been observed that during primate evolution the rate of accumulation of nucleotide substitutions in noncoding DNA markedly slowed in anthropoids and..."
It simply does not matter when the rates of occurrance might have been faster or slower. We were looking at the total - the end results.
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I fail to see the relevance of this.
["this" refers to: "My main criticism of molecular clocks is that it cannot differentiate between survival selection and sexual selection. In the case of human evolution there is pretty good evidence for fisherian runaway sexual selection,..."]
They would de facto have different rates of fixing selected mutations.
And it would still be irrelevant for the our purposes.
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This is irrelevant to the general 'accuracy' of local clock calculations. The goal of such calculations is not to make such differentiations. Your criticisms seem similar to Paul Nelson's criticism of molecular phylogenetics as being a diversion because they do not explain what the mechancim behind the changes is.
Again the rate of fixing selected mutations would be de facto different under punctuated versus stasis conditions.
And it would still be irrelevant to the study in question.
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Well of course, but criticising a paper in which the goal was not to do that for not doing that seems superfluous.
You were the one that introduced the paper in answer to my criticism. If it doesn't do that it is not my fault.
Um, well, OK, but I recall
introducing the paper to address this:
Now when we compare "molecular clocks" for mtDNA Eve and yChrom Adam what do we see? More change in Eve than in Adam? Longer change in Eve than in Adam or slower change in Adam than in Eve? We don't know. There is no connection to fossils, hard data, to be able to say at this point.
In my reply, I wrote:
"Again, that is not always the case. Local molecular clocks use fossil divergence dates as calibration points. This paper, for example, employs such clocks and its results are quite congruent with dates inferred from fossil data when applicable. "
So, I think it pretty clear why I introduced it and in reference to what, and it was not inreference ot criticisms about knowing when mutations took place of whether or not the mutations were in coding DNA or not and whether they were beneficial or not, etc.
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Yes. Since local molecular clocks do not rely on any assumptions about mutation rates or rate differentials, a sufficiently large data set will not suffer from potential short term bursts of mutation and selection or the lack thereof.
Nor will it be able to identify short term bursts or conditions under which they may apply.
Totally insightful! And here is more shocking news - shovels don't work well when you want to chop down trees...
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Thus it will be unable to identify when a period could be high rate or low rate. By identifying average rates as uniform rates over long periods it also ignores the fact that different rates occur during different times.
No, it does not. If for the sake of discussion we adopt your forced position that we were assigning average rates, the very term 'average' means that such differences have been taken into account. That is how one gets averages. Again, for the purposes of the paper in question, such criticisms are superfluous and irrelevant.
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One thing I do note from your paper is that the different rates are significantly different even in spite of the averaging of the rates over the time periods involved. To me this is validation that different rates occur regularly during evolution. I would think that the question of rate changes and maximum rates of change would be of high interest.
They may well be for some, but it is a mistake to presume that all researchers are interested in and will devote time to all things that appear to be of interest.
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It is logical for me that the rates of selecting and fixing change away from other daughter species would be higher for one or both than the average rate of selecting and fixing change.
This would make understanding the magnitudes of different rates of fixing selected mutations fairly critical to the understanding of speciation and the causes of different rates. Especially if you are doing studies involving multiple speciation events or periods of intense selection pressure.
Different rates of selecting and fixing mutations is part of evolution, and understanding those different rates, and the conditions under which they occur, is also part of understanding evolution.
That may well be, but such understanding is not required when doing analyses in which such differentiations are irrelevant.
Perhaps an analogy is in order.
I am in the business of starting with endpoints and trying to figure out starting points, or stops along the way to the end point, say for cars in a road race. When the cars get to the finish line, I try to figure out where they started from (crazy road race). Upon discerning a starting point for the race, we can observe that car A took much longer than car B to reach the end, even though they started from the same place. I might then conclude that car A drove more slowly than car B. Now, car A might have gone full speed for several miles, then pulled off the side of the road for a rest, then coasted for a time, etc., while car B drove at a steady pace for the entire race.
Would that really matter if my only concern was how long it took each car to get to the end? Regardless of car A's driver's habits, it still took longer to get to the end, even if car A drove super fast for a long tiome and only then slowed down.
Your complaint seems to be that because I did not map out when and for how long car A went super fast then slow, that I cannot draw conclusions about who won the race.
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