Common ancestry of humans and chimpanzees: mutations
I am going to describe here a small part of the genetic evidence for common ancestry of humans and chimpanzees, which is one tiny piece of the overall evolutionary picture of life. I hope it will give some idea of what geneticists see when they compare species, and why they rely on evolution for interpreting their observations. The data come two sources: first, the comparison of the human and chimpanzee genomes (in whole or in part), which gives detailed information about huma-chimpanzee genetic divergence, and second, the study of genetic variation between humans, which gives information about human genetic diversity.
First, some background. Humans and chimpanzees are thought to have diverged from a common ancestral species about five to seven million years ago. This means that if you compare a human chromosome with the corresponding chimpanzee chromosome, the two pieces of DNA were originally identical, because they were once the same chromosome. (Note: the last common ancestor of the two chromosomes is actually somewhat further back in time than the species split, by a million years or so. This is because you also have to include the time to get back to the common ancestor of two chromosomes within the ancestral species. So I will use seven million years as the time to the last common ancestral chromosome.) Of course, this assumes that the evolutionary picture is true.
Humans and chimpanzees differ genetically because during those seven million years, mutations have been accumulating in both species' genomes. The great majority, perhaps 95%, of these can be treated as being selectively neutral, neither helping nor hurting the organism; mostly, in fact, they do nothing at all. These are the mutations I am interested in. Since they do not have any effect on survival, these mutations accumulate steadily, with a new crop being added every generation. Similarly, all genetic differences between individual humans are the result of mutations accumulated over the last several hundred thousand years. Presumably this is very different from most creationist scenarios, in which the human and chimpanzee genomes were indidually created with whatever characteristics and genes the creator desired, while human variants are either the result of a short period of mutation or were created in Adam and Eve. (I say presumably because there are not many detailed creationist models of genetics.)
What are these mutations? They are any change in genetic information that can be passed to offspring. The genome can be thought of as a string of letters (called nucleotides, or bases), some of which spell out words (genes). (In this alphabet, though, there are only four letters, A, C, G and T). In the human or chimpanzee genome there are three billion of these letters, grouped into a couple of dozen chromosomes. A mutation can be a change from one letter to another (an A to a T, for example), or it can be the deletion of a group of nucleotides, or the addition or inversion of a group, or the fusion or splitting of whole chromosomes. The first of these, the single-base substitution (the replacement of a single nucleotide by another) is the most common kind of mutation and the best studied, so that is what I will focus on.
The scientific question then is this: Do genetic differences between humans and chimpanzees
look like they are the result of lots of accumulated mutations? What predictions about the differences can one make, based on the hypothesis that they are all the result of mutation?
Total divergence
For starters, we should be able to predict how different the genomes should be. The seven million years of evolution in each lineage represents about 350,000 generations in each (assuming 20 years per generation). How many mutations happen per generation? Estimating mutation rates is not easy (at least without assuming common descent): it is hard to find a few changed nucleotides out of 3 billion that have not changed. By studying new cases of genetic diseases, individuals whose parents' do not have the disease, however, it is possible to identify and count new mutations, at least in a small number of genes. Using this technique, it has been estimated[1] that the single-base substitution rate for humans is approximately 1.7 x 10^-8 substitutions/nucleotide/generation, that is, 17 changes per billion nucleotides. That translates into ~100 new mutations for every human birth. (17 x 3, for the 3 billion nucleotides in the genome, x 2 for the two genome copies we each carry). At that rate, in 350,000 generations a copy of the human genome should have accumulated about 18 million mutations, while the chimpanzee genome should have accumulated a similar number.
The evolutionary prediction, then, is that there should be roughly 36 million single-base differences between humans and chimpanzees. The actual number could be determined when both the chimpanzee and human genomes had been completely sequenced. When the two genomes were compared[2], thirty-five million substitutions were found, in remarkably good agreement with the evolutionary expectation. Fortuitously good agreement, in fact: the uncertainty on most of the numbers used in the estimate is large enough that it took luck to come that close.
Types of mutation
Next, we can analyze different types of substitution. This is worth doing because not all sites in the genome mutate at the same rate, which means that we should expect to find different levels of divergence at different kinds of site. One important consideration is simply which nucleotide is doing the mutating. The bases A and G are chemically similar to one another, as are C and T. A nucleotide is more likely to be replaced by a similar one; as a result, rates for mutations between similar nucleotides (called transitions) are higher than for mutations between dissimilar ones (called transversions). Another important effect is that one particular combination of nucleotides is unusually prone to mutation: a C followed by a G (called a "CpG") is chemically unstable under some circumstances, and is known to mutate at very high rates. Thus, in the disease study mentioned above, the mutation rate at CpG sites was 11 times higher than the non-CpG rate. The rate for transitions was also found to be higher than the transversion rate, by more than a factor of three.
The prediction from common descent is that human-chimpanzee differences should show the same pattern. They do. In a human-chimpanzee comparison[3], transition differences were 2.4 times
as common as transversions, and substitutions at CpG sites were 17 times as common as at non-CpG sites; the agreement with the mutation rate estimates is quite good, considering the large uncertainties on the latter. In other words, we see the same pattern in new mutations occurring in humans today as in the genetic differences between humans and chimpanzees. This is to be expected if the same process, random mutation, is driving both phenomena; it doesn't seem to make a lot of sense in other models.
It is also possible to make a better test than the crude mutation rate estimates permit. We can do this by looking at the genetic differences between individual humans, since these differences are also (according to standard evolutionary thinking) the result of accumulated mutations. The test is to see whether patterns in genetic diversity within humans match those already described for human-chimpanzee divergence. This comparison has been done[3]. Here are the results:
The first plot shows the pattern for the human-chimpanzee comparison, while the second shows the pattern for human diversity. Differences are broken down into CpG and non-CpG, and into transitions ("Ti") and the three kinds of transversion (G<->C, A<->T, and A<->C/G<->T). The similarity of the two patterns is striking. It is difficult to escape the conclusion that genetic diversity among humans and genetic divergence between humans and chimpanzees have both been produced by accumulated mutations.
Local mutation rate
We can use the same technique, comparing human diversity with human-chimpanzee divergence, to look at various regions of the genome, rather than at different kinds of sites. It is well known that the mutation rate varies somewhat from place to place on the chromosomes. If the hypothesis of common descent is correct, parts of the genome with higher mutation rates should show both a larger divergence between species and more variation within a single species. It is a simple matter to compare the two and see if there really is this kind of correlation. Here is the comparison:
For the figure, I divided the genome into 1 million nucleotide windows and calculated divergence and diversity within each window. Each point on the plot represents one window, with the human diversity along the x axis and the human-chimpanzee divergence along the y axis. As expected, there is a strong correlation between the two: spots with large divergence are very likely to have large diversity as well. Again, this is a simple prediction from common descent, and I cannot think of any reason why it should be true in a creationist model.
Mutation on the sex chromosomes
Yet another way that mutation rates vary is by the sex of the parent. For many mutations, it is known that males have a higher rate of mutation than females, at least in part because it takes many more cycles of cell division to generate sperm than eggs. One implication of this is that the X and Y chromosomes should accumulate mutations at different rates from the rest of the chromosomes (the autosomes), since the Y chromosome is only found in males, while the X chromosome spends two/thirds of its evolutionary life in females. The prediction from common descent, therefore, is that human-chimpanzee divergence should be higher on the Y and lower on the X than on the autosomes. In this case a quantitative prediction is hard to make, since the size of the effect can only be measured by assuming common ancestry. The qualitative prediction, however, has been confirmed very nicely by observation[2]: divergence on the X chromosome, the Y chromosome and the autosomes is, respectively, 0.94%, 1.90% and 1.23%.
Conclusion
Consistently, the hypothesis of common ancestry makes accurate predictions about the comparative genetics of humans and chimpanzees. No other hypothesis has been offered that provides any kind of useful prediction. Not surprisingly, geneticists overwhelming use evolution, because that is what works.
References
[1] Kondrashov AS. Direct estimates of human per nucleotide mutation rates at 20 loci causing Mendelian diseases. Human Mutation 21:12-27 (2003).
[2] The Chimpanzee Sequencing and Analysis Consortium. Initial sequencing of the chimpanzee genome and comparison with the human genome. Nature 437:69-87 (2005).
[3] Ingo Ebersberger, Dirk Metzler, Carsten Schwarz, and Svante Paabo. Genomewide Comparison of DNA Sequences between Humans and Chimpanzees. Am. J. Hum. Genet. 70:1490-1497 (2002).
