1. What are the advantages of being asexual? Sexual?

Asexuals have a higher reproductive rate because they do not need two individuals to reproduce; thus each clone can produce twice as many offspring as a sexual (if all else is equal). Asexuals also do not lose combinations of genes that do well together (sexuals do through recombination). Sexuals can purge deletarious mutations through recombination (by having DNA from two different adults). Sexuals also gain novel gene combinations that are successful (through recombination).

2. Explain the Red Queen hypothesis, and how it relates to parasite-host cycling.

The Red Queen says "you can run and run and run, but you don’t go anywhere". Which we interpret as an evolutionary Arms Race. A parasite infects a host, the host in turn evolves defense mechanisms against the parasite to increase it’s own survival, and in turn the parasite evolves a mechanism to more efficiently infect the host (to increase transmission), etc….

3. Draw an imaginary phylogenetic tree to identify all of the key features discussed in class. (node, branches, outgroup, sister taxa, root, taxa)
4. Explain how "Muller’s ratchet" can be used to explain the evolution of sex.

Muller’s ratchet is the concept that asexuals can not purge mutations. All individuals (sexual and asexual) gain mutations, and because asexual offspring are clones they all inherit their mom’s mutations. They can only acquire more mutations, but never less. Thus the number of mutations increases in most generations, and eventually one of those mutations will be deleterious and an entire line of clones will die. Sexuals can purge mutations through recombination of gametes and therefore a smaller proportion of the entire population will die from deleterious mutations.

5) What is the neutral theory of evolution?

The neutral theory refers to mutations that are "neutral", meaning that selection does not act on them. These can be any mutation in 1) non-coding regions (introns….), 2) any change in one of the 3 base pairs of a codon that does not change the amino acid that is coded for by that codon, 3) or any switch of one amino acid for another that does not give a drastic change in polarity or size. Neutral mutations do not get hidden by selection, and are thus useful time markers (assuming a constant rate) in phylogenetic analysis.

6. What is a molecular clock, and how can it be used in the study of evolution?

A molecular clock is a reference to time information that can be inferred from the rates of mutation in particular sites of the genome. If we assume that rates of mutation are fairly constant within a region of DNA (over a long period of time), we can count the number of base pair changes in that region between two species and extrapolate back to a time when they both had the same DNA sequence: ie when they diverged from a common ancestor.

7. Why would parasites become less nasty? And how do hosts respond?

Parasites may become less nasty if they pass on more copies of themselves by not killing the host as rapidly than if they decimate the host immediately. The benefit of passing on more "progeny" will be selected for in the subsequent generations. A host may develop resistance to a parasite, because if fitness (# of offspring) is reduced by having the parasite, those who are no susceptible to the parasite (or who get a novel mutation for resistance) will leave more offspring in the next few generations (strong selection for that trait).

8. How does "Rice’s ratchet" differ from "Muller’s ratchet".

Rice’s concept adds the possibility of longitudinal parasites (parasites passed on to progeny). Thus not only are asexuals not able to purge mutations, but they also can receive a parasite that has infected their mom. Because the offspring are clones of their mom, they will not have a resistance gene unless and thus have lower fitness than asexuals that do. So very few asexuals survive a parasite (and will probably die off from a deleterious mutation!!). Sexuals who have the resistance gene pass it on to progeny, but since each offspring has two parents, they only need to get the gene from one of the adults.

9. Draw the most parsimonious phylogenetic tree using the below data. Be sure to indicate the appearance of traits on your tree.

	Spots	Poison	Strong legs	Sticky tongue
Tree frog	-	-	+	+
Rock frog	-	-	-	+
Arrow frog	+	+	+	+
Jumping frog	+	-	+	+
Giant Iguana	-	-	-	-



10. Why are phylogenetic trees useful in the study of traits?

Phylogenetic trees can sometimes allow you to make inferences about when traits arose in relation to other traits. For example, when studying sexual selection, you might wonder which came first: female preference for some "trait", or the development of the "trait" in males. The example of Swordtail fish, is an example of this type of analysis. By creating a phylogeny based on genetic data and comparing it to choice experiments using a few different species (but still closely related), Basolo was able to show that female preference predates the male "sword" trait. However, there are two important things to remember: 1) a phylogeny is only a hypothesis and could change depending on the data used to build it, and on how unresolved branches are placed 2) the characters used to construct the tree can not be the same characters which you are interested in. (so don’t use the presence of a sword to construct the tree for the above example!!!).

11. Ring species: All morphs (A-G) can interbreed with their neighbor but with nobody else. (ie B can interbreed with A and C but not with any of the others). The only exception is A cannot interbreed with G. Are these separate species? If so which ones?