Two diploid species of closely related frogs, which we will call species A and species B, were analyzed with regard to genes that encode an enzyme called hexokinase. Species A has two distinct copies of this gene: $A 1$ and $A 2$. In other words, this diploid species is A1A1 A2A2. The other species has three copies of the hexokinase gene, which we will call $B 1, B 2$, and $B 3$. A diploid individual of species $\mathrm{B}$ would be $B 1 B 1 B 2 B 2 B 3 B 3$. These hexokinase genes from the two species were subjected to DNA sequencing, and the percentage of sequence identity was compared among these genes. The results are shown here:

$$\begin{aligned} &\text { Percentage of DNA Sequence Identity }\\ &\begin{array}{rrrrrr} & A 1 & A 2 & B 1 & B 2 & B 3 \\ \hline A 1 & 100 & 62 & 54 & 94 & 53 \\ \text { A2 } & 62 & 100 & 91 & 49 & 92 \\ \text { B1 } & 54 & 91 & 100 & 67 & 90 \\ \text { B2 } & 94 & 49 & 67 & 100 & 64 \\ \text { B3 } & 53 & 92 & 90 & 64 & 100 \end{array} \end{aligned}$$

If we assume that hexokinase genes were never lost in the evolution of these frog species, how many distinct hexokinase genes do you think there were in the most recent ancestor that preceded the divergence of these two species? Explain your answer. Also explain why species $B$ has three distinct copies of this gene, whereas species A has only two.

Genetic variation is prevalent in natural populations. This variation is revealed in the DNA sequencing of genes. According to the neutral theory of evolution, discuss the relative importance of natural selection against detrimental mutations, natural selection in favor of beneficial mutations, and neutral mutations in accounting for the genetic variation we see in natural populations.

For each of the following examples, discuss whether it would be the result of neutral mutation or mutation that has been acted on by natural selection, or both:
A. When comparing sequences of homologous genes, differences in the coding sequence are most common at the wobble base (i.e., the third base in each codon).
B. For a structural gene, the regions that encode portions of the polypeptide that are vital for structure and function are less likely to incur mutations compared to other regions of the gene.
C. When comparing the sequences of homologous genes, introns usually have more sequence differences compared to exons.

Compare and contrast the neutral theory of evolution versus the Darwinian (i.e., selectionist) theory of evolution. Explain why the neutral theory of evolution is sometimes called non-Darwinian evolution.

Take a look at the $\alpha$-globin and $\beta$-globin sequences. Which sequences are more similar, the $\alpha$ globin in humans and the $\alpha$ globin in horses, or the $\alpha$ globin in humans and the $\beta$ globin in humans? Based on your answer, would you conclude that the gene duplication that gave rise to the $\alpha$-globin and $\beta$-globin genes occurred before or after the divergence of humans and horses? Explain your reasoning.

Evolution, which involves genetic change in a population of organisms over time, is often described as the unifying theme in biology. Discuss how evolution is unifying at the molecular and cellular levels.

Sympatric speciation by allotetraploid has been proposed as a common mechanism for speciation. Let's suppose you were interested in the origin of certain grass species in southern California. Experimentally, how would you go about determining if some of the grass species are the result of allotetraploid?

Compare the forms of speciation that are slow with those that occur more rapidly. Make a list of the slow and fast forms. With regard to mechanisms of genetic change, what features do slow and rapid speciation have in common? What features are different?

Aphylogenetic tree of all life on Earth based on $16 \mathrm{~S}$ rRNA data. Based on your understanding of molecular genetics (in this and other chapters), describe three or more observations that suggest that all life-forms on Earth evolved from a common ancestor or group of ancestors.

Plant seeds contain storage proteins that are encoded by plant genes. When the seed germinates, these proteins are rapidly hydrolyzed (i.e., the covalent bonds between amino acids within the polypeptides are broken), which releases amino acids for the developing seedling. Would you expect the genes that encode plant storage proteins to evolve slowly or rapidly compared with genes that encode enzymes? Explain your answer.

When comparing the coding region of structural genes among closely related species, it is commonly found that certain regions of the gene have evolved more rapidly (i.e., have tolerated more changes in sequence) than other regions of the gene. Explain why different regions of a structural gene evolve at different rates.

Which would you expect to exhibit a faster rate of evolutionary change, the nucleotide sequence of a gene or the amino acid sequence of the encoded polypeptide of the same gene? Explain your answer.

Would the rate of deleterious or beneficial mutations be a good molecular clock? Why or why not?

If a researcher used genetic engineering techniques to express the Drosophila eyeless gene in the embryo at the region that will become the tip of the mouse's tail, what results would you expect in the resulting offspring?