What is the neutral theory of molecular evolution as proposed by Kimura (1968)? What determines the frequency of neutral alleles in a population?

What types of nucleotide substitutions will not be detected by amino acid sequencing of a gene’s protein product?

What are the two groups of reproductive isolating mechanisms? Which of these is regarded as more efficient, and why?

List the barriers that prevent interbreeding and give an example of each.

A recent study examining the mutation rates of 5669 mammalian genes (17,208 sequences) indicates that, contrary to popular belief, mutation rates among lineages with vastly different generation lengths and physiological attributes are remarkably constant (Kumar, S., and Subramanian, S. 2002. Proc. Natl. Acad. Sci. [USA] 99: 803-808). The average rate is estimated at $12.2 \times 10^{-9}$ per bp per year. What is the significance of this finding in terms of mammalian evolution?

Achondroplasia is a dominant trait that causes a characteristic form of dwarfism. In a survey of 50,000 births, five infants with achondroplasia were identified. Three of the affected infants had affected parents, while two had normal parents. Calculate the mutation rate for achondroplasia and express the rate as the number of mutant genes per given number of gametes.

One of the first Mendelian traits identified in humans was a dominant condition known as brachydactyly. This gene causes an abnormal shortening of the fingers or toes (or both). At the time, some researchers thought that the dominant trait would spread until 75 percent of the population would be affected (because the phenotypic ratio of dominant to recessive is $3: 1$ ). Show that the reasoning was incorrect.

Under what circumstances might a lethal dominant allele persist in a population?

Consider a population in which the frequency of allele $A$ is $p=0.7$ and the frequency of allele $a$ is $q=0.3$, and where the alleles are codominant. What will be the allele frequencies after one generation if the following occurs?
(a) $w_{A A}=1, w_{A a}=0.9, w_{a a}=0.8$
(b) $w_{A A}=1, w_{A a}=0.95, w_{a a}=0.9$
(c) $w_{A A}=1, w_{A a}=0.99, w_{a a}=0.98$
(d) $w_{A A}=0.8, w_{A a}=1, w_{a a}=0.8$

The ability to taste the compound PTC is controlled by a dominant allele T, while individuals homozygous for the recessive allele t are unable to taste PTC. In a genetics class of 125 students, 88 can taste PTC, and 37 cannot. Calculate the frequency of the T and t alleles in this population and the frequency of the genotypes.

In this chapter, we focused on how changes in gene frequency are related to the process of species formation. At the same time, we found many opportunities to consider the methods and reasoning by which much of this information was acquired. From the explanations given in the chapter, what answers would you propose to the following fundamental questions?
(a) How do we determine how much genetic variation exists in a population?
(b) What evidence has been obtained from laboratory studies to indicate that natural selection is the cause of genetic differences among natural populations of a species?
(c) How can the minimum genetic divergence between two species be determined?
(d) How can we determine the last common ancestor shared by two divergent species?

Genetic variation is a characteristic of most populations. In some cases, this can be observed at the phenotypic level, but analysis at the amino acid and nucleotide levels provides a more direct way to estimate genetic variation.

The sequencing of Neanderthal DNA shows that it is so different from ours that Neanderthals may have been a separate species and that Neanderthals and H. sapiens diverged about 600,000 years ago. However, the debate continues about whether H. sapiens and Neanderthals interbred, and if so, to what extent. Discuss the evidence that supports, and refutes, the idea that Neanderthals and H. sapiens interbred.

Use VSEPR theory to predict the probable geometric structures of the molecules
(b) $\mathrm{O}_3 \mathrm{XeF}_2$;