Question

The molecular clock In eukaryotes, the majority of individual point mutations are thought to be "neutral" and have little or no effect on phenotype. Only a small fraction of the genome codes for proteins and critical DNA regulatory sequences. Even within coding regions, the redundancy of the genetic code is suffcient to render many mutations "synonymous" (that is, they do not change the amino acid, and hence the protein, encoded by the DNA). The slow accumulation of neutral mutations between two populations can be used as a "molecular clock" to estimate the length of time that has passed since the existence of their last common ancestor. In these estimates, it is common to make the simplifying approximations that (1) most mutations are neutral and (2) the rate of accumulation of neutral mutations is just the average point mutation rate per generation (that is, ignoring other kinds of mutations such as deletions, inversions, etc., as well as variations in and correlations among mutations). (a) With a crude estimate of the point mutation rate of humans of \(10^{-8}\) per base pair per generation, what fraction of the possible nucleotide differences would you expect there to be between chimpanzees and humans given that the fossil record and radiochemical dating indicate their lineages diverged about six million years ago? Compare your estimate with the observed result from sequencing of about \(1.5 \%\) (b) Some parasitic organisms (lice are an example) have specialized and co- evolved with humans and chimps separately. A natural hypothesis is that the most recent common ancestor of the human and chimp parasites existed at the same time as that of the human and chimp themselves. How might you test this from DNA sequence data and other information? What are likely to be the largest causes of uncertainty in the estimates? (Problem courtesy of Daniel Fisher.)

Short answer

The calculated fraction of nucleotide differences between humans and chimpanzees is approximately 0.6%, which is less than the observed difference of 1.5%. Possible sources of discrepancy could be other forms of mutations or an inaccurate estimate of the last common ancestor's divergence time. To test the hypothesis about human and chimp parasites, DNA sequencing of these parasites could be used. Various sources of uncertainty in these estimates would likely originate from the estimates of mutation rate, divergence time and generation time.

Step-by-step solution

Calculate the fraction of nucleotide differences

For each generation since humans and chimpanzees diverged, each lineage will have had separate opportunities for point mutations, or changes in the DNA sequence, to occur. If we sum up all these separate opportunities, we will get the total number of mutations. Since the human lineage and the chimpanzee lineage diverged \(6 \times 10^6\) years ago, and assuming about 20 years per generation, this will give us \(6 \times 10^6 / 20 = 3 \times 10^5\) generations. Each generation, each base pair has a \(10^{-8}\) probability of mutating. Hence, the expected fraction of nucleotide differences would be \(3 \times 10^5 \times 2 \times 10^{-8} = 0.006\) or 0.6\%.

Compare with observed sequencing result

The observed difference from sequencing is about 1.5%. The expected difference we calculated, from the point mutations alone, is 0.6%, which is smaller than the observed 1.5%. Other form of mutations and/or an inaccurate estimate of the divergence time could be responsible for this difference.

Creating a test hypothesis for human and chimp parasites

To test the hypothesis, one could sequence the DNA of both human and chimp parasites and calculate the differences in the same way as described above for the hosts. If these difference match the expected differences based on generation time and mutation rate, it would further support the hypothesis.

Identifying causes of uncertainty in these estimates

The biggest sources of uncertainty are likely to come from the estimates of the mutation rate, the generation time and the divergence time for the species. Any errors in these parameters could significantly impact the estimated fraction of nucleotide differences.

Key concepts

Understanding Point Mutations in Eukaryotes

Point mutations are a fundamental concept when it comes to genetic variations in eukaryotes. These are alterations where a single nucleotide in the DNA sequence is changed, which can have varying effects on an organism's phenotype. In the context of eukaryotes—the group that includes all plants, animals, fungi, and protists—many point mutations occur that do not necessarily affect the organism.

Neutral mutations are the ones that do not offer any advantage or disadvantage to the organism. In fact, a high proportion of mutations belong to this category, as only a small fraction of the eukaryotic genome actually codes for proteins or crucial regulatory sequences. Within these coding regions, because of the genetic code's redundancy, several mutations do not even change the amino acid sequence of the encoded protein. Such mutations are termed 'synonymous'.

Appreciating the frequency of these mutations and recognizing their neutral nature helps us understand how species diverge over time without the pressure of natural selection on every mutation. These mutations act as a form of genetic clock, providing insights into the evolutionary history and timings of lineage splits.

Genetic Code Redundancy and Its Role in Mutation Impact

The redundancy of the genetic code is a crucial buffer against the potential harmful effects of point mutations. This redundancy means that multiple triplets or 'codons' of DNA bases can code for the same amino acid. As a result, even if a point mutation occurs, the resultant amino acid sequence—and thus the protein itself—may remain unchanged. This feature is known as 'synonymous' or 'silent' mutation.

For example, the codons AAA and AAG both encode the amino acid lysine; thus, a mutation from AAA to AAG would not change the protein's structure or function. This inherent feature of the genetic code contributes to robustness against genetic damage and plays a pivotal role in the molecular clock concept. By allowing for a buffer where changes do not always lead to phenotypic effects, it provides a stable mechanism for tracking evolutionary changes over generations.

DNA Sequencing Comparison: A Tool for Understanding Evolution

DNA sequencing comparison is a powerful technique used to estimate the genetic relationship and evolutionary time between species. By comparing the DNA sequence of different organisms, scientists can quantify the genetic differences and make inferences about how long ago their last common ancestor lived.

However, this process isn't without its complexities. While comparing sequences, researchers have to account for several approximations. There's an assumption that most mutations are neutral and that these accumulate at a constant rate—which isn't always the case due to genetic drift, selection pressures, and other genetic mutation forms. As highlighted in the problem requiring the comparison between humans and chimpanzees, the observed genetic difference from DNA sequencing showed a 1.5% divergence, while the calculated point mutation rate estimated a lower divergence. This discrepancy suggests other factors might be at play, including other types of mutations or potential inaccuracies in generation time or divergence time estimates.

The use of DNA sequencing comparison also extends to understanding the co-evolution of species, such as humans, chimpanzees, and their respective parasites. By analyzing the genetic sequences of these parasites, one could test hypotheses about their common ancestry and co-evolution, while uncertainties such as mutation rates and generation times need to be carefully considered to ensure accurate estimates.