We're going to try a different approach in discussion section. We'll see how it works. If you have suggestions or preferences, please let Jackie or me know (but bear in mind that there are about 400 other opinions in the class, and we need to consider all of the feedback we receive, as well as our own teaching experience).
There are 11 questions below. The first 3 are from the first three lectures I gave on March 2-4. The next 8 questions are based on the material I will present in class during this week (March 16-18). You should work through these problems and be prepared to discuss them during the discussion section on Friday.
thanks,
-CWO
1. You go to two different sites (one "wet" and one "dry") and observe a particular "species" of lizard. Although the local herpetologist claims that these lizards all belong to the same species, you notice that the two populations have very different color patterns and head morphology. How would you determine a) if the variation in color pattern and head morphology was the result of an evolutionary change? and b) if these populations represented different species?
Part a) You want to determine if the different color patterns and head morphologies are due to genetic differences or a plastic response to the environment. First, you would want to sample the dry and wet areas intensively to make sure you do not miss any overlap of the two color or head morphologies in the two areas. You could also do a more broad survey over the range of this "species" and look for possible overlaps of the two color and head morphologies. Next, you could do a "commongarden experiment" (grow animals from the two populations under similar conditions and see if differences remain after a couple of generations)-if the stocks from the two populations remain phenotypically distinct, then the original differences were due to genetic differentiation. If not, then the 2 populations of lizards are most likely one species that have a plastic response (color pattern and head morphology) to the environment.2. A veteran scuba diver has told you that she consistently observes three species of sea urchin under the same types of coral heads on reefs in the Florida Keys (i.e., the three species occur in the same habitats). Because you are a BSC 2011 student, you know that urchins have external fertilization and don't exhibit courtship. Your scuba diving friend wants to know what keeps these urchins from interbreeding. What would you tell her, and how would your answer change if you were discussing fishes with internal fertilization ?You could also do a reciprocal transplant study where you rear offspring from both populations under both environmental conditions (wet and dry conditions). This would allow you to understand the relationship between phenotype and environment for each genetic group. You would be able to assess the effect of genetic differentiation and the environment and assess how much those two effects modified each other (i.e.,whether each genetic group responded to the environment in similar ways or showed the same amount of phenotypic plasticity).
Part b) According to the biological species concept, if these were two different species of lizards, they would not be able to interbreed. However, remember that what breeds under laboratory conditions may not be indicative of what happens in nature. So, you could also find a closely related lizard species, and do genetic work (like RFLP's or DNA sequencing) on the closely related lizard species and on your two populations of lizards. If you determine that the popluations are as genetically different as the closely related species, then you would have evidence to suggest that the two populations are indeed separate species.
Part a) Prezygotic mechanisms that could isolate the three urchin species could be temporal isolation (prevents mating) (gametes of each urchin species are released at different times), and gametic isolation (prevents fertilization) (egg and sperm of different species can not fuse). All the postzygotic mechanisms could occur: reduced hybrid viability, reduced hybrid fertility and hybrid breakdown.3. Define homology and analogy. Can you provide some examples, in addition to those we discussed in class?Part b) Prezygotic mechanisms that could isolate fish species with internal fertilization could be temporal isolation as above and behavioral isolation (where different fish species aren't attracted to one another) (both mechanisms prevent mating) . Mechanisms which prevent fertilization could be mechanical isolation (reproductive morphology of different species is incompatible) and gametic isolation. And, all three postzygotic mechanisms mentioned above could isolate fish species with internal fertilization.
Homology-a character shared by 2 species that was present in a common ancestor.4. Using a bunch of friends and their children, make some morphological measurements. For an easy one, I'd suggest the length of their lower arm (or hand) and total height. Here's one data point already: I'm 6'0", and my lower arm is 12 1/8" (my hand is 7 5/8" long). Try to get a range of body sizes (e.g., from infants up to basketball players). Plot arm lengths against total height (or hand length against total height, or hand length against arm length). What does this relationship look like? Now try plotting these data on log-axes. What does the relationship look like? What's the approximate slope of the two relationships? What is you had used measured (and plotted) body weight instead of arm length. What would this relationship have looked like (on arithmetic axes vs. log-axes)?
Some examples are feathers in blue jays and hummingbirds and forearms of humans, cats, whales and bats.
Analogy-a similar character that arose independently on different lineages (i.e., a case of convergent evolution)
An example is wings in birds, bats, and butterflies.
After measuring ~ 11 graduate students, I plotted the relationship between arm length and hand length vs. total height. These relationships appeared linear (see linked files below), and the slopes were both less than one. In other words, arm and hand length appeared to scale proportionally with total height or be isometric on an arithmetic scale. However, it is difficult to evaluate isometric vs. allometric relationships on arithmetic scales, so I also plotted these measurements on a log scale. Remember, if arm and hand length do scale proportionally with total height, we would expect to see a slope around 1 for each of these relationships on a log scale. If the slopes are different from 1, this would suggest an allometric relationship. We see that the slope of arm length vs. total height is just about 1, suggesting isometry. However, the slope of hand length vs. total height is greater than 1, suggesting an allomtric relationship between these characters. Since the slope is greater than 1, this suggests that hand size changes at a faster rate than total height. Why did we not see a curved relationship on our arithmetic scale? Remember, I only sampled a narrow range of subjects; if I had measurements from infants all the way to basketball players, then we probably would have seen a curvilinear relationship between hand length and total height on an arithmetic scale. What we actually observe is a very small part of that curved relationship, so it appears linear.
Next, I plotted the body mass of the same individuals vs. their total height. We might have expected to see a curvilinear relationship between body mass and height, since, for instance, adding 1 inch on someone four feet tall does not add as much weight as adding 1 inch on someone six feet tall. However, if you look at the plot of body mass vs. total height on an arithmetic scale, you seen that it is linear. But, when we plot this on a log scale, we see that the slope is greater than 1, indeed suggesting that body mass and total height have an allometric relationship where body mass changes at a faster rate than total height. Again, since I only sampled a very narrow range of individuals, we only captured a small part of the curved relationship between body mass and total height on an arithmetic scale, so our relationship appears linear (if I had sampled across a broader range of total heights, we would have observed this curvilinear relationship).
Figure of arm length and hand length vs. total height5. Why is phylogenetics considered a more useful way to classify organisms than phenetics?
Figure of body mass vs. total height
Phylogenetics seeks to reconstruct evolutionary relationships and is based on explicit consideration of common ancestry. Phenetics may result in grouping unrelated taxa based on superficial similarities.
For the Questions 6-10, consider the following phylogeny (for Group ABCD), which was derived from the following character matrix (presumed ancestors are indicated as E, F, and G):
| Taxon | a | b | c | d |
| X (outgroup) | 0 | 0 | 0 | 0 |
| A | 1 | 1 | 0 | 0 |
| B | 1 | 1 | 0 | 0 |
| C | 1 | 0 | 1 | 0 |
| D | 1 | 0 | 1 | 1 |
E has derived states for characters a and b; it has ancestral states for characters c and d (a1, b1, c0, d0).7. Which ancestral taxon is the closest shared relative of Species a) A + B; b) A + C; c) B + D; d) B, C + D?
F has derived states for characters a and c; it has ancestral states for characters b and d (a1, b0, c1, d0) .
G has a derived state for character a; it has ancestral states for characters b, c, and d (a1, b0, c0, d0).
a) E8. Which character(s) was (were) not useful in constructing the tree? Why?
b) G
c) G
d) G
Character d was not helpful because its derived state was present in only one species (D) and was therefore not shared by any taxa. Thus, it provided no information about common ancestry. Try building the tree without d to convince yourself. You can also try re-building the tree without the other characters to demonstrate that they do provide useful information.9. Give an example of a monophyletic group (i.e., name the species that comprise it).
Examples of monophyletic groups are A + B, C + D, and A, B, C + D. X, A, B, C + D do NOT represent a monophyletic group. Dr. Osenberg mentioned in class that you can break the bottom of the tree into a monophyletic group if you know information about that entire tree (as in the example of an entire Kingdom being designated as a monophyletic group). However, in this example, X is simply an outgroup and without more information about this tree, you can not assume X, A, B, C + D would comprise a monophyletic group like an entire Kingdom.10. The outgroup (X) also possesses a variety of character states that are shared with Species A, B, C, and D. Why weren't these states used in constructing the tree?
Character states that are present in all of the taxa do not provide any information to distinguish patterns of common ancestry. These traits represent ancestral homologies. Remember, phylogenetics is based on shared derived characters.
11. Using the following Character Matrix, construct the most parsimonious
tree(s). In doing this, you'll probably generate a number of other trees
- keep them - they'll be useful for discussing your final answer (i.e.,
hypothesis):
| Taxon | Characters and States | ||||
| a | b | c | d | e | |
| X (outgroup) | 0 | 0 | 0 | 0 | 0 |
| W | 1 | 1 | 1 | 1 | 1 |
| Y | 1 | 0 | 1 | 1 | 0 |
| Z | 1 | 1 | 1 | 0 | 1 |
In discussion we came up with a variety of trees that were equally parsimonious (i.e., they all required 6 evolutionary steps). I know you can come with even more than what we did in discussion. However, we would need more information to determine the sequence of species W, Y and Z (or sequence of branches containing W, Y and Z) in our trees. To do this you could increase your database and come up with more characters to measure. You could also come up with "better" characters (ones that aren't as labile) to use in your character matrix, and you could also clarify the likely sequence of evolutionary events.12. What is the Principle of Parsimony and why is it useful?
The Principle of Parsimony is the simplest explanation (i.e., the one with the fewest transitions between character states) that is assumed to be the most likely to have occurred. Without some criteria, we would be left with on means to evaluate the plausibility of different trees (there are many possible trees for even a simple character matrix as we proved in #11). Of course, this does not guarantee that the most parsimonious tree is correct--it is only a hypothesis--a more complicated tree may actually be correct. We use the Principle of Parsimony as a tool. It does not necessarily represent the “true” phylogeny, but it generates estimates of the least amount of change in evolutionary history of taxa.