Does the Mutation Rate change? If so how, if not then why not.

[mark kennedy]

Does the mutation rate change when the divergence goes from 1.33% to 4%. A simple question and by all means feel free to respond as you see fit:

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Table 3. Estimates of mutation rate assuming different divergence times and different ancestral population sizes

4.5 mya, pop.= 10,000 mutation rate is 2.7 x 10^-8
4.5 mya, pop.= 100,000 mutation rate is 1.6 x 10^-8
5.0 mya, pop.= 10,000 mutation rate is 2.5 x 10^-8
5.0 mya, pop.= 10,0000 mutation rate is 1.5 x 10^-8
5.5 mya, pop.= 10,000 mutation rate is 2.3 x 10^-8
5.5 mya, pop.= 10,000 mutation rate is 1.4 x 10^-8
6.0 mya, pop.= 10,000 mutation rate is 2.1 x 10^-8
6.0 mya, pop.= 100,000 mutation rate is 1.3 x 10^-8

Table 4. Estimates of mutation rate for different sites and different classes of mutation

Transition at CpG mutation rate 1.6 x 10^-7
Transversion at CpG mutation rate 4.4 x 10^-8
Transition at non-CpG mutation rate 4.4 x 10^-8
Transversion at non-CpG mutation rate 5.5 x 10^-9
All nucleotide subs mutation rate 2.3 x 10^-8
Length mutations mutation rate 2.3 x 10^-9
All mutations mutation rate 2.5 x 10^-8

Rates calculated on the basis of a divergence time of 5 mya, ancestral population size of 10,000, generation length of 20 yr, and rates of molecular evolution given in Table 1.


Calculations are based on a generation length of 20 years and average autosomal sequence divergence of 1.33%
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Estimate of the Mutation Rate per Nucleotide in Humans (Michael W. Nachmana and Susan L. Crowella Genetics, 297-304, September 2000)

When the actual divergence is found to be between 4% and 5% does the calculation of the mutation rate change? It's a simple question.

 

[I_Love_Cheese]

Does the mutation rate change when the divergence goes from 1.33% to 4%. A simple question and by all means feel free to respond as you see fit:

---------------------------------------------------
Table 3. Estimates of mutation rate assuming different divergence times and different ancestral population sizes

4.5 mya, pop.= 10,000 mutation rate is 2.7 x 10^-8
4.5 mya, pop.= 100,000 mutation rate is 1.6 x 10^-8
5.0 mya, pop.= 10,000 mutation rate is 2.5 x 10^-8
5.0 mya, pop.= 10,0000 mutation rate is 1.5 x 10^-8
5.5 mya, pop.= 10,000 mutation rate is 2.3 x 10^-8
5.5 mya, pop.= 10,000 mutation rate is 1.4 x 10^-8
6.0 mya, pop.= 10,000 mutation rate is 2.1 x 10^-8
6.0 mya, pop.= 100,000 mutation rate is 1.3 x 10^-8

Table 4. Estimates of mutation rate for different sites and different classes of mutation

Transition at CpG mutation rate 1.6 x 10^-7
Transversion at CpG mutation rate 4.4 x 10^-8
Transition at non-CpG mutation rate 4.4 x 10^-8
Transversion at non-CpG mutation rate 5.5 x 10^-9
All nucleotide subs mutation rate 2.3 x 10^-8
Length mutations mutation rate 2.3 x 10^-9
All mutations mutation rate 2.5 x 10^-8

Rates calculated on the basis of a divergence time of 5 mya, ancestral population size of 10,000, generation length of 20 yr, and rates of molecular evolution given in Table 1.


Calculations are based on a generation length of 20 years and average autosomal sequence divergence of 1.33%
-----------------------------------------------------

Estimate of the Mutation Rate per Nucleotide in Humans (Michael W. Nachmana and Susan L. Crowella Genetics, 297-304, September 2000)

When the actual divergence is found to be between 4% and 5% does the calculation of the mutation rate change? It's a simple question.

The above seems familiar, maybe the following will as well.

Under a neutral model, the amount of divergence, k, between sequences drawn from two species is given by

where t is the time since the species have diverged measured in generations, µ is the mutation rate, and Ne is the ancestral effective population size (K[SIZE=-1]IMURA[/SIZE] 1983[SIZE=-1]A[/SIZE]

from http://www.genetics.org/cgi/content/full/156/1/297#T1

Solving for u puts k in the numerator, and thus multiplying u by three when you arbitrarily change k from 1.33 to 4 as you seem wont to do for some unknown reason.

I assume you could have done the basic algebra if you read the paper, what I really want to know is why you arbitrarily changed k from the value used in the paper without apparent reason. Is your value of k appropriate for this calculation and where did it come from?

 

[sfs]

When the actual divergence is found to be between 4% and 5% does the calculation of the mutation rate change? It's a simple question.

The comparisons in question are for humans and chimpazees. The answer hasn't changed since the last dozen times Mark asked this question. You cannot calculate the mutation rate directly from the 4% or 5% divergence you quote, since the mutation rate measures the number of mutations while the divergence measures the number of base pairs difference between the two genomes. To calculate the mutation rate, you need to know the number of mutations, not the total amount of sequence changed by mutation.

For single-base substitutions, the distinction doesn't matter, since each mutation changes a single base. It's when you add in length mutations (insertions and deletions) that you have to remember what it is you're trying to calculate, since some of those mutations add or subtract large amounts of sequence. If you keep track of the mutations rather than the total amount of sequence, then you will find that the mutation rate hardly changes at all when the divergence estimates increased from 1.3% to 4-5%. According to Table 4, the mutation rate was predicted to be 2.3 x 10-8 (single-base substitutions) + 0.2 x 10-8 (insertions and deletions) = 2.5 x 10-8. When the genomes were compared, it was found that the insertion and deletion rate was actually one-seventh the single-base rate, rather than 1/10th, so the table would now read (making the same assumptions about generation and time since speciation), 2.3 x 10-8 + 0.3 x 10-8 = 2.6 x 10-8.

So yes, the mutation rate changed with the improved data, but by a very small amount. What did change was the estimate of the average size of insertions and deletions; it was not known when Nachman and Crowell published that mutations of this type that change very large amounts of DNA in a single mutation were not all that uncommon.

 

[shernren]

The actual citation is Nachman and Crowell, Genetics, 297-304, 2000. Interestingly, googling mark's typoed authors reveals two other hits, both from heated crevo discussions. Copy and paste citation?

Anyways, here're two questions. One will be easy for readers of the paper to answer, and the second should show why mark is wrong:

What constituents of the genome were surveyed to obtain those rates of mutation, and how many?

How representative are they of the whole genome?