Humans and Chimps

[Sherlock Holmes]

The subject of human and chimp genome similarities and differences came up in another thread recently along with the suspicion that the genetic differences between humans and chimps is too large to have occurred within time available.

This is a crude no doubt poor analysis but I wanted to get the basic numbers up and some basic data:

One way to state the difference is that human DNA and chimp DNA are largely the same but approx. 35,000,000 base pairs are different between us.

If we descended from a common ancestor then this is believed to have taken place about 7,000,000 years ago. If we assume that the 35,000,000 base pair differences represent the cumulative effects of evolution, then we can guess that chimps and humans each differ from the common ancestor by about half the difference between humans and chimps. That is humans differ by around 17,500,000 base pairs from the common ancestor and likewise chimps.

If we assume new generations arise approx. every 15 years then in 7,000,000 years we'd see 467,000 generations. Again if we assume a constant rate of genome change (in terms of base pair changes) over this period we can estimate that each generation between the ancestor and us today, will have incurred about 37 base pair changes per generation.

Having said that we also see that the rate of mutation based on recent data seems to be about 1 in 30,000,000 base pairs per generation. Since the genome itself about 35,000,000 we can expect at most - 1.7 - base pair mutations per generation yet for us to share a common ancestor with chimps we'd need to see a mutation rate of 37 per generation, some 21 times higher.

Is this analysis representative? and if so how can we reconcile the true rate (1.7 BP/gen) with the necessary rate (37 BP/gen)?

[Jose Fly]

The subject of human and chimp genome similarities and differences came up in another thread recently along with the suspicion that the genetic differences between humans and chimps is too large to have occurred within time available.

That's an interesting characterization of your reaction to the paper Alex linked you. Your reaction to that paper was to deny that evolution even happens.

One way to state the difference is that human DNA and chimp DNA are largely the same but approx. 35,000,000 base pairs are different between us.

Let's start here. Are you assuming that each BP difference requires it's own individual mutation?

[Difflugia]

One way to state the difference is that human DNA and chimp DNA are largely the same but approx. 35,000,000 base pairs are different between us.

[...]

Having said that we also see that the rate of mutation based on recent data seems to be about 1 in 30,000,000 base pairs per generation. Since the genome itself about 35,000,000 we can expect at most - 1.7 - base pair mutations per generation yet for us to share a common ancestor with chimps we'd need to see a mutation rate of 37 per generation, some 21 times higher.

Is this analysis representative? and if so how can we reconcile the true rate (1.7 BP/gen) with the necessary rate (37 BP/gen)?

Where'd you get your first set of numbers? Does that refer to coding regions only or does that include non-coding DNA?

The blog doesn't link to it, but I'm assuming that the primary research is "Human Y Chromosome Base-Substitution Mutation Rate Measured by Direct Sequencing in a Deep-Rooting Pedigree". The abstract includes this:

Twelve mutations were confirmed in ∼10.15 Mb; eight of these had occurred in vitro and four in vivo. The latter could be placed in different positions on the pedigree and led to a mutation-rate measurement of 3.0 × 10−8 mutations/nucleotide/generation (95% CI: 8.9 × 10−9–7.0 × 10−8), consistent with estimates of 2.3 × 10−8–6.3 × 10−8 mutations/nucleotide/generation for the same Y-chromosomal region from published human-chimpanzee comparisons depending on the generation and split times assumed.

Since the mutation rate is "consistent with estimates" based on chimpanzee sequences and there appears to be no conflict between published sequences and observed rate of mutation, perhaps you'd like to either rephrase your original question or perhaps narrow it a bit.

[Sherlock Holmes]

One way to state the difference is that human DNA and chimp DNA are largely the same but approx. 35,000,000 base pairs are different between us.

[...]

Having said that we also see that the rate of mutation based on recent data seems to be about 1 in 30,000,000 base pairs per generation. Since the genome itself about 35,000,000 we can expect at most - 1.7 - base pair mutations per generation yet for us to share a common ancestor with chimps we'd need to see a mutation rate of 37 per generation, some 21 times higher.

Is this analysis representative? and if so how can we reconcile the true rate (1.7 BP/gen) with the necessary rate (37 BP/gen)?

Where'd you get your first set of numbers? Does that refer to coding regions only or does that include non-coding DNA?

The blog doesn't link to it, but I'm assuming that the primary research is "Human Y Chromosome Base-Substitution Mutation Rate Measured by Direct Sequencing in a Deep-Rooting Pedigree". The abstract includes this:

Twelve mutations were confirmed in ∼10.15 Mb; eight of these had occurred in vitro and four in vivo. The latter could be placed in different positions on the pedigree and led to a mutation-rate measurement of 3.0 × 10−8 mutations/nucleotide/generation (95% CI: 8.9 × 10−9–7.0 × 10−8), consistent with estimates of 2.3 × 10−8–6.3 × 10−8 mutations/nucleotide/generation for the same Y-chromosomal region from published human-chimpanzee comparisons depending on the generation and split times assumed.

Since the mutation rate is "consistent with estimates" based on chimpanzee sequences and there appears to be no conflict between published sequences and observed rate of mutation, perhaps you'd like to either rephrase your original question or perhaps narrow it a bit.

About 35 million DNA base pairs differ between the shared portions of the two genomes, each of which, like most mammalian genomes, contains about 3 billion base pairs.

https://www.genome.gov/15515096/2005-re ... -dna-level

[Difflugia]

If we descended from a common ancestor then this is believed to have taken place about 7,000,000 years ago. If we assume that the 35,000,000 base pair differences represent the cumulative effects of evolution, then we can guess that chimps and humans each differ from the common ancestor by about half the difference between humans and chimps. That is humans differ by around 17,500,000 base pairs from the common ancestor and likewise chimps.

If we assume new generations arise approx. every 15 years then in 7,000,000 years we'd see 467,000 generations. Again if we assume a constant rate of genome change (in terms of base pair changes) over this period we can estimate that each generation between the ancestor and us today, will have incurred about 37 base pair changes per generation.

Having said that we also see that the rate of mutation based on recent data seems to be about 1 in 30,000,000 base pairs per generation. Since the genome itself about 35,000,000 we can expect at most - 1.7 - base pair mutations per generation yet for us to share a common ancestor with chimps we'd need to see a mutation rate of 37 per generation, some 21 times higher.

Is this analysis representative? and if so how can we reconcile the true rate (1.7 BP/gen) with the necessary rate (37 BP/gen)?

First, if you actually want to read the primary research instead of relying on yet another blog post, the chimp genome paper is here. Surprisingly (for Nature), the PDF is free to download.

I'm trying to figure out your math. If we start with the 3 billion base pair number, one in 30 million per generation comes out to 100 mutations per generation. 100 × 467,000 is 46,700,000 mutations. That's about three times your 17,500,000 number, and according to the paper in Nature, mutations in the Y chromosome are collected at a higher rate than in other chromosomes. A 3x difference doesn't seem anomalous and it's in the wrong direction than what you're claiming.

If we work back the other way, the 17,500,000 mutations over 467,000 generations is the 37 total mutations per generation that you quoted. Dividing 3 billion by 37 gives us one mutation per 80,000,000 base pairs per generation, which is just showing us that same factor of three.

Where did your 1.7 come from?

[Jose Fly]

Hello? SH.....Are you assuming that each BP difference requires it's own individual mutation?

[Sherlock Holmes]

If we descended from a common ancestor then this is believed to have taken place about 7,000,000 years ago. If we assume that the 35,000,000 base pair differences represent the cumulative effects of evolution, then we can guess that chimps and humans each differ from the common ancestor by about half the difference between humans and chimps. That is humans differ by around 17,500,000 base pairs from the common ancestor and likewise chimps.

If we assume new generations arise approx. every 15 years then in 7,000,000 years we'd see 467,000 generations. Again if we assume a constant rate of genome change (in terms of base pair changes) over this period we can estimate that each generation between the ancestor and us today, will have incurred about 37 base pair changes per generation.

Having said that we also see that the rate of mutation based on recent data seems to be about 1 in 30,000,000 base pairs per generation. Since the genome itself about 35,000,000 we can expect at most - 1.7 - base pair mutations per generation yet for us to share a common ancestor with chimps we'd need to see a mutation rate of 37 per generation, some 21 times higher.

Is this analysis representative? and if so how can we reconcile the true rate (1.7 BP/gen) with the necessary rate (37 BP/gen)?

First, if you actually want to read the primary research instead of relying on yet another blog post, the chimp genome paper is here. Surprisingly (for Nature), the PDF is free to download.

I'm trying to figure out your math. If we start with the 3 billion base pair number, one in 30 million per generation comes out to 100 mutations per generation. 100 × 467,000 is 46,700,000 mutations. That's about three times your 17,500,000 number, and according to the paper in Nature, mutations in the Y chromosome are collected at a higher rate than in other chromosomes. A 3x difference doesn't seem anomalous and it's in the wrong direction than what you're claiming.

If we work back the other way, the 17,500,000 mutations over 467,000 generations is the 37 total mutations per generation that you quoted. Dividing 3 billion by 37 gives us one mutation per 80,000,000 base pairs per generation, which is just showing us that same factor of three.

Where did your 1.7 come from?

You are correct, the latter steps in my logic are messed up.