BOT300 Home Page

Term Test 3 - 10 April 2003
answers (1, 2, 3, 4, 5, 6, 7, 8)


Please read and answer all eight questions.

Please use your time effectively by reading the questions carefully, and answering only what is asked in each one. Note the marks for each one (total = 80) and budget your time accordingly. You should give yourself at least two hours for this test; you may have up to four hours if you need it.

1. (5 marks) Arrange the following terms to reflect their hierarchical relationships (in terms of which encloses what; assume that all relate to an Angiosperm):

{Bract{Tepal{Stamen{Anther{Pollen grain{Microgametophyte{Sperm nucleus}}}}}}}

Back to Top


2. (7 marks) You are studying a section of a genus that comprises 4 species (A-D) with various pollen types. Other characters give you reason to believe that this section (section ABCD) is evolutionarily advanced in comparison with all other sections of the genus in which pollen grains are uniformly triporate.

Species

Pollen

A

tricolpate

B

polypantoporate

C

triporate

D

polypantoporate



a. What is the shortest tree for A-D that you can infer from these data?

This tree has two state changes on it.

b. If the tree for A-D has the shape shown below, what is the minimum number of state changes required to explain the pollen data tabulated above? Show where these occur on the tree, labeling the tips of the branches A-D as appropriate. Remember that sister groups must be supported by a synapomorphy.

Either of these two trees was accepted:

This tree also has only two state changes on it, but lacks a synapomorphy for the clade {A, C}. This tree shows support for clade {A, C}, but requires a reversal because C has triporate pollen.

c. How would you choose between the tree in (a) and the tree in (b) in arriving at your best estimate of the phylogeny of species A-D?

All things being equal, you would choose the shorter (i.e. with fewer state changes), more parsimonious tree.

Back to Top


3. (9 marks) Further study of the genus to which section ABCD belongs has led to amassing a comprehensive sample of specimens from not only species A, B, C, and D but also other species of the genus. Some of these have been associated with section ABCD by earlier workers, and then excluded from the section by other workers. Other species are new to science, having been discovered in the lower montane rain forest of eastern Peru. These species are at least superficially similar to species A, B, C, and D. These specimens have been scored for just over 40 characters, including linear measurements, ordered and unordered multistate, and binary characters.

On the following page are the results obtained after calculating between-specimen distances using a coefficient similar to Gower's for mixed data. The upper panel represents the first two axes from a principal coordinates analysis (PcoA). This analysis demonstrated that these data are effectively 8-dimensional, with the first eight eigenvalues (out of 75 that are greater than zero) accounting for 58% of the total variance in the sample (the first two axes account for 15.8% and 12.6%, respectively).

In the lower panel is the result of a cluster analysis based on the same resemblance matrix. In each of these two analyses the numbers 1-76 indicate the positions of specimens 1-76. The gray outline in the upper panel, and the gray shading in the lower one block out 49 specimens that include all of the specimens from species A, B, C, and D. Please answer the following questions about these two panels.

a. What can you conclude about species X (specimens 1, 2, and 68-72), based on each of these two panels? In each panel, be sure to outline the location of these specimens as part of your answer.

The specimens representing species X are markedly different from all the other 69 specimens in the analysis.

b. Identify at least one more group of specimens that could likely represent a distinct taxon, and explain why you think so.

I've used color in the two panels above to break out groups of specimens that might be considered distinct on the basis of their isolation from other specimens in the PCoA plot (upper panel) and in the dendrogram (lower panel). The three specimens outlined in turquoise are the best example since in the dendrogram it is made clear that these specimens are also quite different. Note the great difference in distance (vertical axis) between the level at which the three specimens form a group (approx. 1.6) and that at which they join with the rest of the sample other than the species X specimens (approx. 3.9). Note that the separation of this group likely involves variation along the third (or higher) PCoA axis (not shown) since in the plane of PCo1 and PCo2 these specimens appear to be quite close to the group outlined in purple.

c. Supposing that you based a classification of this part of the genus on these two panels. What kind of classification would this be? Why?

A phenetic classification.

Back to Top

 

4. (25 marks) After studying these results, one of your colleagues concludes that section ABCD also includes species Y and Z whose specimens are included among the 39 indicated by shading, and that species X (see above) is the sister group of section ABCD. S/he produces the data table on the following page in support of this contention (0 codes the ancestral state).

A

B

C

D

X

Y

Z

pollen not tricolpate (0)

1

0 0 0

0

0

1

pollen not polypantoporate (0)

0

1 0 1

0

0

0

3

1

0

1

0

0

1

1

4

0

0

0

0

0

1

1

5

1

1

0

1

0

0

0

6

1

1

0

1

0

1

1

7

0

0

1

0

0

0

0


Use the table below to evaluate character compatibility in these data.

Character-state combinations (1-1, 1-0, 0-1, 0-0) present in a given character comparison have been shaded pink. Where all four possible combinations are present the two characters are incompatible and their comparison is shaded red.

1

1

1

1

0

1

1

1

0

1

1

1

0

1

1

1

0

1

1

1

0

1

1

1

0

0

1

0

0

0

1

0

0

0

1

0

0

0

1

0

0

0

1

0

0

0

1

0

0

2

1

1

1

0

1

1

1

0

1

1

1

0

1

1

1

0

1

1

1

0

0

1

0

0

0

1

0

0

0

1

0

0

0

1

0

0

0

1

0

0

3

1

1

1

0

1

1

1

0

1

1

1

0

1

1

1

0

0

1

0

0

0

1

0

0

0

1

0

0

0

1

0

0

4

1

1

1

0

1

1

1

0

1

1

1

0

0

1

0

0

0

1

0

0

0

1

0

0

5

1

1

1

0

1

1

1

0

0

1

0

0

0

1

0

0

6

1

1

1

0

0

1

0

0

2

3

4

5

6

7

a. What characters are incompatible? Which ones make up the largest clique?

Cliques of compatible characters include {2,7}, {1,2,3,7}, and (the largest) {2,4,5,6,7}.

b. Draw the seven character trees.

Everyone did this well, so I don't see the need to do this here.

c. Draw a phylogeny for species A-D and X-Z. What is its length in steps (character-state changes)?

I think it's important to build up the phylogeny using what you know about character compatibility. Here are the trees for the three cliques above.

{2,7}

{1,2,3,7}

{2,4,5,6,7}. This suggests the shape of the tree onto which the other characters will have to be added.

Here is the tree with all the characters. See below re use of color to show homoplasy.

 

d. Homoplasy is defined as comprising the occurrence of reversals and parallelisms. Is there homoplasy in your tree? Where?

Yes; character 1 evolves twice (parallelism) as autapomorphies for A and Z, as shown in green. Character 3 shows a reversal (synapomorphy for {B,D}).

Back to Top

 

5. (5 marks) What concerns would you have about homology in using one of the following kinds of data: (a) presence/absence of different kinds of flavonoids; (b) fruit type, described as berry, capsule, or follicle; (c) habitat, described as prairie, forest, or marsh?

(a) Convergence; different biosynthetic pathways (i.e. controlled by different genes) could yield the same flavonoid.

(b) Fruit ontogeny could be different, even though at maturity it would be classified as the same type. Using the crude categories suggested above, for example, one could produce a "berry" from either an inferior ar a superior ovary. This wouldn't matter too much if the necessary floral characters were also included in the analysis, but this example should at least give you an idea of the kind of issues that could be involved.

(c) There's no necessary reason to think that the ability to grow in a particular habitat should be homologous. In fact, if you think of the diversity of clades represented in a given habitat it is apparent that habitat data are likely to be very homoplasious.

Back to Top

 

6. (5 marks) Compare and contrast botanical gardens and herbaria with respect to their contribution to plant systematics (ignore, for the purposes of this question the fact that most botanical gardens have herbaria associated with them, and concentrate on the difference between having living versus dead specimens).

Growing living specimens places a constraint on the number of individuals that can be grown, hence the sample size that can be studied and the range of variation that can be observed. On the other hand, however, living specimens can be observed over the course of their entire life history. The availability of living material greatly enhances the quality of the anatomical, morphological, and physiological observations that can be made, as compared with herbarium material. Moreover, it may be possible to observe critical life processes that it would be almost impossible to study using only herbarium material. One example could be the discovery of apomixis when an exclusively female tree at Kew set seed without there having been any chance of pollination occurring.

Because herbarium specimens take up such a small amount of space compared with living plants, it is possible to have many more of them for any given species. As a result, herbarium specimens lend themselves to the study of variation as it occurs in a taxon. In the same way, they also lend themselves to studies of geographic distribution, and to documenting the composition of plant communities. In any case, herbarium specimens are the ultimate record of any systematic study as they are more likely to outlast any given greenhouse or garden specimen.

Back to Top

 

7. (9 marks) From the perspective of phylogenetic classification, how would you characterize the following groups, going back to our section ABCD example: (a) {B, D, Y, Z}; (b) {A, B, C, D}; (c) {A, B, D, Y, Z}? If you were unable to construct a tree in question 4 then you should define the terms monophyletic, polyphyletic, and paraphyletic.

(a) polyphyletic

(b) paraphyletic

(c) monophyletic

Back to Top

 

8. (15 marks) Your colleague has provided you with the information tabulated below about the flowers and fruits found in section ABCD. Provide them with a key that will, as far as possible, serve the needs of the general public, and that will coincidentally demonstrate your understanding of flower and fruit terminology. You may find it helpful to sketch the fruits in order to figure out what the user of your key should look for (and you will get partial credit for your sketches if they are clear and labeled, even if you are unable to complete the key). Use the back of a page if you need the space.

Gynoecium

Fruit (or fruitlet) type

A

solitary pistil (superior ovary)

berry

B

solitary pistil (superior ovary)

capsule

C

solitary pistil (superior ovary)

achene

D

inferior ovary

berry

X

apocarpous gynoecium (i.e. many pistils per flower)

achene

Y

solitary pistil (superior ovary)

follicle

Z

apocarpous gynoecium (i.e. many pistils per flower)

follicle

 

1. Ovary inferior, fruit a berry................................................... D
1. Ovary superior.................................................................... 2
  2 (1). Pistil solitary............................................................. 3. (simple fruits)
  2 (1). Pistils >1 (apocarpous gynoecium).............................. 7. (aggregate fruits)
    3 (2). Fruit indehiscent................................................... 5
    3 (2). Fruit dehiscent...................................................... 6
      5 (3). Fruit dry, an achene.......................................... C
      5 (3). Fruit fleshy, a berry.......................................... A
      6 (3). Fruit dehiscing on one side only (a follicle)............ Y
      6 (3). Fruit dehiscing on more than one side (a capsule). B
    7 (2). Fruitlets indehiscent (achenes)................................ X
    7 (2). Fruitlets dehiscent (follicles).................................... Z

Of course, this is just one of the possible answers to this question, but it gives you an idea of what I was looking for.

Back to Top


|BOT300S Home Page | U of T Botany | University of Toronto |

© 2003 Botany Department, University of Toronto.

Please send your comments to tim.dickinson@utoronto.ca; last updated 30-May-2003