Within the coding region of a gene, where would you most likely find silent polymorphisms?

A segment of DNA in an individual may differ at several nucleotide positions from a corresponding DNA segment in another individual. For instance, one individual may have the sequence $\dotsb$A $\dotsb$ G $\dotsb$ C $\dotsb$ and another individual may have the sequence $\dotsb$ T $\dotsb$ A $\dotsb$ A $\dotsb$ . These two DNA segments differ in three nucleotide positions.Because the nucleotides within each segment are tightly linked, they will tend to be inherited together as a unit, that is, without being scrambled by recombination. We call such heritable units DNA haplotypes. Through sampling and DNA sequencing, researchers can determine which DNA haplotypes are present in a particular population. When this kind of analysis is performed on human populations by sequencing, for example, a segment of mitochondrial DNA, it is found that samples from Africa exhibit more haplotype diversity than samples from other continents. What does this observation tell us about human evolution?

The prune gene (symbol pn) is X-linked in Drosophilavmelanogaster. Mutant alleles of this gene cause the eyes to be brown instead of red. A dominant mutant allele of another gene located on a large autosome causes hemizygous or homozygous pn flies to die; this dominant mutant allele is therefore called Killer of prune (symbol Kpn). How could mutants such as these play a role in the evolution of reproductive isolation between populations?

Distinguish between allopatric and sympatric modes of speciation.

Drosophila mauritiana inhabits the island of Mauritius in the Indian Ocean. Drosophila simulans, a close relative, is widely distributed throughout the world. What experimental tests would you perform to determine if D. mauritiana and D. simulans are genetically different species?

Exon shuffling is a mechanism that combines exons from different sources into a coherent sequence that can encode a composite protein—one that contains peptides from each of the contributing exons. Alternate splicing is a mechanism that allows exons to be deleted during the expression of a gene; the mRNAs produced by alternate splicing may encode different, but related, polypeptides. What bearing do these two mechanisms have on the number of genes in a eukaryotic genome? Do these mechanisms help to explain why the gene number in the nematode Caenorabditis elegans is not too different from the gene number in Homo sapiens?

Darwin stressed that species evolve by natural selection. What was the main gap in his theory?

Dispersed, repetitive sequences such as transposable elements may have played a role in duplicating short regions in a genome. Can you suggest a mechanism?

A geneticist has studied the sequence of a gene in each of three species, A, B, and C. Species A and species B are sister species; species C is more distantly related. The geneticist has calculated the ratio of nonsynonymous (NS) to synonymous (S) nucleotide substitutions in the coding region of the gene in two ways—first, by comparing the gene sequences of species A and C, and second, by comparing the gene sequences of species B and C. The NS:S ratio for the comparison of species B and C is five times greater than it is for the comparison of species A and C. What might this difference in the NS:S ratios suggest?

How might you explain the thousandfold difference in the evolutionary rates of fibrinopeptide and histone $3$?

The coding sequence of the alcohol dehydrogenase (Adh) gene of Drosophila melanogaster consists of $765$ nucleotides ($255$ codons); $192$ of these nucleotides are functionally silent—that is, they can be changed without changing an amino acid in the Adh polypeptide. In a study of genetic variation in the Adh gene, Martin Kreitman observed that $13$ of the $192$ silent nucleotides were polymorphic. If the same level of polymorphisms existed among the nonsilent nucleotides of the Adh gene, how many amino acid polymorphisms would Kreitman have observed in the populations he studied?

If the evolutionary rate of amino acid substitution in a protein is K, what is the average length of time between successive amino acid substitutions in this protein?

If a randomly mating population is segregating n selectively neutral alleles of a gene and each allele has the same frequency, what is the frequency of all the homozygotes in the population?

Ribonuclease, a protein that degrades RNA, is $124$ amino acids long. A comparison between the amino acid sequences of cow and rat ribonucleases reveals $40$ differences. What is the average number of amino acid substitutions that have occurred per site in these two evolutionary lineages? If the cow and the rat lineages diverged from a common ancestor $80$ million years ago, what is the rate of ribonuclease evolution?