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

Genes are sometimes transferred between different species via horizontal gene transfer. Discuss how horizontal gene transfer might give misleading results when constructing a phylogenetic tree. How could you overcome this problem?

Discuss the major differences among allopatric, parapatric, and sympatric speciation.

Discuss how the principle of parsimony can be used in a cladistics approach to constructing a phylogenetic tree.

A team of researchers has obtained a dinosaur bone (Tyrannosaurus rex) and has attempted to extract ancient DNA from it. Using primers to the $12 \mathrm{~S}$ rRNA mitochondrial gene, they have used PCR and obtained a DNA segment that yields a sequence homologous to crocodile DNA. Other scientists are skeptical that this sequence is really from the dinosaur. Instead, they believe that it may be due to contamination from more recent DNA, such as the remains of a reptile that lived much more recently. What criteria might you use to establish the credibility of the dinosaur sequence?

Discuss whether the phenomenon of reproductive isolation applies to bacteria, which reproduce asexually. How would a geneticist divide bacteria into separate species?

Discuss the evidence in favor of the punctuated equilibrium model of evolution. What mechanisms could account for this pattern of evolution? In contrast, what type of genetic changes are consistent with gradualism?

We learned about a technique called fluorescence in situ hybridization (FISH), during which a labeled piece of DNA is hybridized into a set of chromosomes. Let's suppose that we cloned a piece of DNA from G. pubescent and used it as a labeled probe for in situ hybridization. What would you expect to happen if we hybridized it to the G. speciosa, the natural G. tetrahit, or the artificial G. tetrahit strains? Describe your expected results.

Two populations of snakes are separated by a river. The snakes cross the river only on rare occasions. The snakes in the two populations look very similar to each other except that the members of the population on the eastern bank of the river have a yellow spot on the top of their head, whereas the members of the western population have an orange spot on the top of their head. Discuss two experimental methods that you might follow to determine whether the two populations are members of the same species or members of different ones.

Discuss the two principles on which evolution is based.

The raw material for evolution is random mutation. Discuss whether or not you view evolution as a random process.

Write the balanced molecular equation for the neutralization reaction between $\ce{H2SO4}$ and $\ce{KOH}$.

What is the molecular geometry of methane (CH$_4$) and sulfite ion (SO$_3^{2-}$)?

How do the properties of metals differ from those of both ionic and molecular compounds?