BIOLOGY 1001
FALL 2004
WEEK 12 LABORATORY
Evolution and Systematics
Our planet houses a fantastic array of organisms that range from tiny bacteria that live only in hot
springs, to giant sequoia trees, to over 35,000 different species of spiders. Biologists who work
in the field of systematics try to understand how this amazing diversity arose. Taxonomy, a
subfield of systematics, focuses on naming organisms and classifying them into groups. Each
distinct organism is given a unique binomial name, the genus and species. Organisms are then
categorized in a hierarchical scheme (domain, kingdom, phylum, class, order, family) that helps
us to organize our knowledge of the natural world.
Ideally, most contemporary biologists would like these taxonomic groups to reflect evolutionary
relationships among organisms. In other words, they want the organisms within a category to be
more closely related to one another than they are to organisms outside the category [see Chapter
19 of Tobin and Dusheck (3rd edition) for more information]. Systematists and taxonomists,
then, spend much of their time trying to reconstruct evolutionary history.
Reconstructing evolutionary history presents quite a challenge! We can’t actually know with
certainty what occurred in the past. Instead, we can only propose hypotheses about what might
have happened, based on information we can obtain from fossils and contemporary organisms.
The primary tool for formulating hypotheses about the relationships among organisms is the
construction of phylogenetic trees. Phylogenetic trees can be constructed using several methods;
the methods vary in the type of information about the organism used and how much weight is
given to each piece of information.
For many years, systematists constructed trees based on differences in various morphological
features, such as number of limbs or shape of toes. These types of morphological data have been
accumulated through years of field trips and detailed laboratory observations. More recently,
scientists have begun to use the information contained in biological molecules. Differences in
DNA base pair sequences, amino acid sequences and whole proteins can be used to construct
phylogenetic trees (Tobin and Dusheck 2005). This approach became available with the
development of techniques for analyzing these molecules such as chromatography,
electrophoresis, and DNA sequencing. Please note that many of the “trees” in Asking About Life
are not really phylogenetic trees; many of them show groupings of organisms but are not
arranged in a way that illustrates hypotheses about evolutionary history.
Taxonomists also must ensure that everyone can easily identify the organisms that have been
named and classified. Some biologists therefore spend their time constructing identification
keys. A key is simply an organized list of characteristics, such as distinctive morphological and
chemical features, that differ among organisms. Field guides often contain rudimentary keys.
For example, a guide to seaweed might include pictures of algae that are grouped by the color of
Lab12-1
the tissue. A very handy type of key is a dichotomous key; once you know how to use one, it’s
much more efficient than flipping through a field guide.
In laboratory today, you will explore the world of systematics. First, you will take a classical
approach to phylogenetic tree construction by using morphological characters. Instead of using
organisms, you will construct a phylogenetic tree illustrating the proposed relationships among
objects purchased at a hardware store. Second, you will use a dichotomous key to identify
different kinds of photosynthetic organisms.
*
*
*
I. Construction of a phylogenetic tree
II. Using a dichotomous key to identify “algae”
===========================================
Tobin and Dusheck, 3rd edition: I. pp. 396-409; II. pp. 430-439.
I. PROBLEMS IN SYSTEMATICS: CONSTRUCTION OF A PHYLOGENETIC TREE
A. BACKGROUND
Systematists create phylogenetic trees by grouping together those organisms that share character
states, i.e., similar versions of a particular trait. When a systematist begins to study of a group of
organisms that is new to her, she must follow five basic steps.
1.
She must identify the characters with which she will work.
2.
She must identify the different states of these characters. For example, if the
character under study is "the number of toes on the foot," having three toes represents
one character state and having four toes represents another.
3.
She must actually describe these characters in all of the organisms under study.
4.
She must hypothesize a pattern or sequence of evolution for each of these characters,
i.e., which version of the character is the oldest (the ancestral state), and which
versions are more recently evolved (the derived states).
5.
Finally, she must use a statistical procedure to organize the findings into the desired
format, the phylogenetic tree. As you know from lecture, systematists who use
cladistic methods follow the convention of grouping together those organisms that
share derived character states.
Lab12-2
B. CONSTRUCTION OF A PHYLOGENENTIC TREE—please work individually
Today in lab you will study a set of inanimate objects purchased at a hardware store. Your goal
is the construction of a "tree of relatedness" for these objects. You will identify characters and
character states but will not attempt to identify which states are ancestral and which are derived.
Instead of using statistics to compile your data, you will arrange the pieces of hardware on a large
sheet of paper and draw the "evolutionary divergences" that might have led to the set of objects
with which you are working.
You must make the following assumptions about the hardware that you are classifying:
1. Each piece of hardware represents one "living" taxon, and all members of the taxon
are identical.
2. None of the taxa are extinct.
3. No taxon is the ancestor of another taxon in the set. All the ancestors in the tree
are hypothetical because there is no evidence about "fossil hardware."
4. All taxa are at the same taxonomic level. They are either "species" or "genera."
5. Neither color nor size can be used as a character state.
In constructing your tree, you will hypothesize a sequence of evolutionary bifurcations, i.e.,
identify characters with two alternative character states. To get started, use the "presence or
absence of a head" as the first character. The two character states, then, are "with head" and
"without head." This then, is the most basic character, the one that represents the earliest
bifurcation, and therefore, the most distant evolutionary split in the whole lineage.
After dividing the hardware into the two groups, with a head and without a head, choose another
character that will identify two sublineages within one of these two groups. Name the character,
identify two character states, and subdivide these objects into two appropriate groups again.
Continue to do this with as many characters as necessary to construct a tree with only one object
at the end of each branch.
Work on a large sheet of paper and write down the character states on the paper as you separate
the objects into smaller and smaller groups. The groups need not include the same number of
objects. Larger groups will require more characters and splits in lineages to separate out all of
the component taxa.
Lab12-3
Try to minimize the number of times that any character state evolves. This leads to the most
"parsimonious" tree. For example, if one of your characters is the presence of threads on the
shaft, the two character states are "present" versus "absent." This character split should occur
only once in the phylogenetic tree. Avoid having threads or any other important character state
evolve in more than one lineage.
Also, try to minimize the number of "evolutionary reversals" represented in the phylogenetic tree.
For example, if one branch of the tree includes hardware that has evolved threads on the shaft,
try to avoid having a "twig" on the phylogenetic tree that includes hardware in which the threads
have been "lost over evolutionary time."
The summary for this part of today's lab should include a list of the characters used, with the
character states indicated diagrammatically in the form of a tree. Do not attempt to be artistic in
depicting a "tree." The diagram should be simple and clear. Sketch the piece of hardware that
belongs at the tip of each branch.
After you have constructed your tree, your instructor will give you a piece of hardware
representing a newly discovered form. This piece should be classified in the most appropriate
place in your tree.
Lab12-4
II. USING A DICHOTOMOUS KEY TO IDENTIFY “ALGAE”
A. INTRODUCTION TO DICHOTOMOUS KEYS
Let’s say that you’ve found a piece of seaweed on the beach, and you want to determine its name
so that you can learn more about its physiology or its ecological importance. A dichotomous key
is a terrific tool for identifying an such an organism. In a dichotomous key, distinguishing
characteristics are listed in pairs (for example, presence or absence of a pigment). When you
choose the characteristic that best describes the organism that you’re trying to identify, you are
directed to a second pair of alternative characteristics.
By working through the key, you will eventually arrive at a point where no more alternatives are
presented. When you reach this end point, you may have identified your organism! (It’s also
possible that your particular organism isn’t listed, which means that you’ve identified something
with similar characteristics). The key you will use today will lead you only to the organism’s
genus; you would need another, more detailed key to learn precisely which species you have.
A key may seem similar to a phylogenetic tree because organisms with shared characteristics
tend to be grouped together. However, a key’s purpose is simply to aid in identification rather
than to illustrate evolutionary relationships. As you use your key today, keep in mind the two
paired organisms on a key may, in fact, be only distantly related.
B. INTRODUCTION TO THE DIVERSITY OF PHOTOSYNTHETIC ORGANISMS
In lecture, you have learned primarily about photosynthesis in land plants. However,
photosynthesis occurs in a diverse set of organisms that are classified into a number of groups.
Distinctions among groups of photosynthetic organisms can be made on the basis of cell
structure, cellular chemistry, and reproductive strategies. Some important differences in cellular
chemistry include the kinds of photosynthetic pigments present, the carbohydrate storage
products made, and the polysaccharides incorporated into the cell wall.
These distinctions have been used to organize photosynthetic organisms into domains, kingdoms,
and phyla (sometimes called divisions). Some taxonomic information about the photosynthetic
organisms that you will be looking at today is summarized in Table 10-1. Many of the
photosynthetic organisms that live in water are collectively referred to as algae, regardless of
their evolutionary history.
Although sorting organisms into the prokaryotic or eukaryotic domains is pretty straightforward,
deciding how to assign the photosynthetic organisms to kingdoms and phyla within the domains
has proved problematic. Table 10-1 follows the taxonomic system used by Asking About Life,
which represents a common solution. All photosynthetic prokaryotes are grouped together. Land
plants are placed in their own kingdom. All eukaryotic photosynthetic organisms except land
plants have been placed together in the kingdom Protista.
Lab12-5
Table 10-1: Characteristics traditionally used to classify the oxygen-producing
photosynthetic organisms that will be observed in lab today* (adapted from Tobin and
Dusheck 2001 and 2005, Campbell and Reese 2002, and Price 2003).
Domain
Kingdom
Phylum
Common
name
Photosynthetic
pigments
Energy
storage
Eubacteria
?**
?**
Cyanobacteria
chlorophyll a,
phycobilins
No starch
Protista
Bacillariophyta
(Chrysophyta)
Diatoms
chlorophylls a & c,
carotenes (yellow)
xanthophylls (brown)
Lipids and nonstarch
polysaccharides
Non-starch
polysaccharides
Eukarya
Eukarya
Protista
Phaeophyta
Brown algae
chlorophylls a & c,
carotenes,
xanthophylls
Eukarya
Protista
Rhodophyta
Red algae
chlorophyll a,
phycoerythrin (red)
Starch
Eukarya
Protista
Chlorophyta
Green algae,
desmids
chlorophylls a & b,
carotenes,
xanthophylls
Starch
Eukarya
chlorophylls a & b,
carotenes,
Starch
xanthophylls
* Additional phyla of protists photosynthesize and produce oxygen, but you won’t be studying
them today. Also, some Eubacteria can photosynthesize without producing oxygen.
Plantae
Many phyla
Land plants
** Classification of bacteria is very tricky!
In many ways, though, this classification system conflicts with current hypotheses about the
evolutionary relationships among photosynthetic organisms. Phylogenetic trees constructed
using molecular information are rapidly leading to the generation of new hypotheses and new
taxonomic schemes. As a result, some systematists have proposed that groups of photosynthetic
organisms be re-categorized.
For example, some green alga might be more appropriately classified with the land plants than
with the protists (Campbell and Reese 2002). Similarly, some researchers have proposed that a
new Kingdom, the Chromista, be established to group together all of the organisms that use
chlorophyll c (UCMP Taxon Lift 2000). New information like this makes it an exciting time to
be a systematist. Unfortunately it’s a confusing time to be an onlooker – it sometimes seems as if
everyone is using her own taxonomic scheme, right now!
** For an overview of each algal phylum, read Asking About Life 3rd edition, p 430-439.
DO THIS BEFORE LAB – SOME INFO WILL BE INCLUDED ON THE PRE-LAB QUIZ
Lab12-6
C. USE OF A DICHOTOMOUS KEY FOR THE ALGAE—working in pairs
1. Become an algal identification expert! Use the dichotomous key in Table 10-2 to identify the
various algae on demonstration. For each specimen, be sure to provide a drawing and
describe the pathway taken through the dichotomous key. Make sure that you know how to
use the key, rather than relying on your partner! You’re likely to be asked to use a key on
your final lab practical.
Confirm with your instructor that you are expected to observe 4 different organisms.
Some of the vocabulary in the key may be unfamiliar to you. If you’re not sure what something
is, look it up!
2. For practical reasons, most keys include a relatively small number of organisms. Imagine
how long your key would be if it included every single one of the 7000 green alga! So, what
happens if your specific organism isn’t listed on the key? You can hypothesize that it is
related to, and therefore shares important characteristics with, an organism that is on the key.
You will be given an alga that is not listed in the dichotomous key but is a relative of one or
several. For your unknown, name its closest relative(s), provide a drawing, describe the
pathway taken through the key, and show how you would alter the key to allow the new
organism to be included.
REFERENCES CITED
Campbell NA and JB Reese. Biology. 6th edition. San Francisco: Benjamin Cummings. 2002.
Price N. 2003. Distinguishing Features of the Dominant Classes of Phytoplankton in the Sea.
Retrieved October 13, 2003 from
http://ww2.mcgill.ca/biology/undergrad/c441b/lect06/phytofeatures.htm
Tobin AJ and J Dusheck. Asking About Life. 2nd edition. Brooks/Cole. 2001.
UCMP Taxon Lift. 1996-2000. Retreived October 10, 2003 from
http://www.ucmp.berkeley.edu/help/taxaform.html
Lab12-7
TABLE 10-2. DICHOTOMOUS KEY FOR THE ALGAE
1a.
Macroscopic.....................................................................................……………….
2
1b.
Microscopic.....................................................................................……………......
6
2a.
No obvious differentiation of tissues......................................................…………....
3
2b.
Differentiated tissues clearly apparent (e.g., holdfasts, floats, blades, stipes) ...........
4
3a.
Reddish; filamentous........................................………….....
3b.
Deep green; appearance like cellophane.................................
4a.
Several blades per plant; floats present........................................…….......…….......
4b.
Single flattened blade, much longer than the stipe; no floats……. Laminaria (Phaeophyta)
5a.
Floats are small and spherical................................……….....
5b.
Floats are prominent and oblong with a variable shape and with white spots in their
surface.................................................................…………....
Fucus (Phaeophyta)
6a.
Cells single; not grouped in a colony or filament........................…….....................
7
6b.
Cells grouped in a colony or end to end in a filament..............................……........
9
7a.
Cells longer than broad.........................................................................……………
8
7b.
Round cells with a branching pattern..........................…………………...Micrasterias (Chlorophyta)
8a.
Cells golden-brown; from the top view the tips taper to rounded points
while from the side view the cells are blunted and squared.........................Synedra (Bacillariophyta)
8b.
Cells bright green, long and slightly crescent shaped; round vacuoles at
each tip may be filled with granules; a row of doughnut-shaped bodies
(pyrenoids) runs the length of the cell..........................................................Closterium (Chlorophyta)
Lab12-8
Polysiphonia (Rhodophyta)
Ulva (Chlorophyta)
5
Sargassum (Phaeophyta)
9a.
Cells joined end to end in a long filament...............................................…….…....
10
9b.
Cells as clusters, aggregates, or spheres but not as filament........................……....
13
10a.
Cells with obvious chloroplasts and distinct internal structures; cells about 2-3 times as
long as broad...............................................................................………………......
11
10b.
Cells without obvious chloroplasts or distinct internal structures; interior of cell dense
and granular; filament interrupted by large thick-walled structures (heterocysts); cells
dark green or blue-green in color............................…........... Anabaena (Cyanobacteria)
11a.
Chloroplasts evenly distributed throughout the cell...........................…….............
11b.
Chloroplasts concentrated in a band in the center of the cell, leaving large empty spaces
on either side ....................................................…………........
Ulothrix (Chlorophyta)
12a.
Filamentous with many cells nearly filled with chloroplasts; large clear areas are not
present in young cells; large, dark, round spheres (female structures) larger than the cell
may be interspersed along the filament, as may be small plate-like cells (male
structures)...................................................……………......
Oedogonium (Chlorophyta)
12b.
Chloroplasts arranged in a spiral within the cells; two filaments may be connected by
bridges...............................................................…………..
Spirogyra (Chlorophyta)
13a.
Colony small and composed of 3 to 24 cells; not motile; one cell thick.........….......
13b.
Colony large; round, hollow ball composed of 500 or more very small cells; some
colonies contain dark, smaller hollow balls of cells within; motile, swimming with a
rolling motion.....................................................…………......
Volvox (Chlorophyta)
14a.
Colony a flat plate of 6 to 24 polygonal cells; colony somewhat
circular........................................................………........
Pediastrum (Chlorophyta)
14b.
Colony usually of 4 oblong cells connected side by side; tips of cells on ends often have
long spines....................................................……….....
Scenedesmus (Chlorophyta)
Lab12-9
12
14
BIOLOGY 1001
NAME_________________________________
DATA SHEETS: LABORATORY 10--Evolution and Systematics
I.
Systematics: Construction of a Phylogenetic Tree
Attach your hardware phytogenetic tree.
1. Would you expect any two hypothetical phylogenetic trees to be exactly alike within
your lab section? Explain your answer.
2. What are the implications of your answer to the previous question for classifying the
variety of living organisms on earth?
Lab12-10
II.
Using a dichotomous key to identify photosynthetic protists and bacteria
1. For each of the algae you observed, provide a drawing and describe the pathway you
took through the dichotomous key.
Lab12-11
2. For your unknown, name the organism on the key that had the most similar features, provide
a drawing, describe the pathway taken through the key, and show how you would alter the
key to allow the new organism to be included.
3. Most of the organisms that you had the chance to observe today have some economic or
ecological significance. Please help us build a database of fun facts about photosynthetic
organisms. Choose one of the genera on the key and perform a quick internet search to
learn something about your chosen organism.
 Summarize (using only the space below) the most interesting tidbit that you
learned.
 Include the website’s address so that we have it for future reference!
Lab12-12