Lab 2

Evolution and Diversity

Background
From the time of the first fossil evidence of life 3.5 billion years ago, there has been a series of
spectacular explosions of organismal diversity alternating with extinctions that affected the majority
of living organisms. The amazing diversity of life we see today represents both long-surviving
lineages and recent diversification within groups of organisms whose history can be traced to a single
common single-celled ancestor that emerged from the ‘primordial soup’ of early Earth.
Exercise 1 Geologic Time (by Dr. Cruzan)
For the lab exercises today, neatly answer the questions on the answer sheet provided using complete
sentences. It is best to use pencil.
Materials:
- One 4.6 meter string
- Meter stick
- Masking tape
- Calculator
1) Obtain a 4.5 meter length of string. This string will represent the entire length of time (4.5 billion
years) since the Earth was formed. On this time line, you will attach masking tape labels to mark the
point when the events listed below occurred. Measure from the starting point with the meter stick.
(bya = billion years ago, mya = million years ago, ya = years ago).

Years ago Event

4.5 bya Formation of earth
3.5 bya First living prokaryotic cells
2.5 bya Oxygen-releasing photosynthetic pathway
1.7 bya Origin of eukaryotic cells
1.2 bya Origin of multicellularity
470 mya First vertebrate animals (marine fishes)
450 mya First vascular land plants and land animals
345 mya Great coal forests; amphibians and insects great adaptive radiation
250 mya Mass extinction of nearly all living organisms
225 mya Origin of mammals, dinosaurs; seed plants dominate
140 mya Origin of flowering plants
135 mya Dinosaurs reach peak
65 mya Mass extinction of dinosaurs and most marine organisms
63 mya Flowering plants, mammals, birds, and insects dominate
6 mya First hominin (upright walking) human ancestors
2.5 mya Human ancestors (Homo) using stone tools, forming social life
160,000 ya Evolution of Homo sapiens
6400 ya Egyptian pyramids constructed
2000 ya Peak of Roman Empire
225 ya Signing of the Declaration of Independence
In 1969 Humans step on the moon

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Question 1 – Over what proportion of the Earth’s history have modern humans (Homo sapiens)
existed?

Question 2 – Over what proportion of the Earth’s history have multicelled organisms existed?

Question 3 – Over what proportion of the Earth’s history have mammals been a dominant part
of the fauna?

Question 4 – Over what proportion (percentage) of the Earth’s history were there only
prokaryotes? Hint: Divide the length of time by the total and multiply by 100.

Exercise 2 Taxonomy
(adapted from Krempels and Lee)

We know that there is a lot of life on Earth, but we do not know exactly how many species exist.
Between 7,000 and 10,000 new species are identified every year. The total number of named species
is approximately 1.5 million. However, recent estimates of our planet's biological diversity suggest
that the species number between 5 and 50 million, or even more. Biodiversity is the total range of
species diversity. To effectively study the multitude of organisms that inhabit the Earth, we attempt
to classify organisms into groups that reflect evolutionary relationships. The science of describing,
classifying and naming organisms is known as taxonomy.

Strictly speaking, taxonomy is the sorting of living organisms into various taxonomic groups, or
taxa (singular = taxon). From most inclusive to least inclusive, the major taxonomic ranks are as
follows:

DOMAIN (e.g., Eukarya)

KINGDOM (e. g., Animalia)
PHYLUM (e. g., Chordata)
CLASS (e. g., Mammalia)
ORDER (e. g., Primates)
FAMILY (e. g., Hominidae)
GENUS (e. g., Homo)
SPECIES (e. g., Homo sapiens)

(Just remember, Dumb Kids Playing Chicken On Freeways Get Smashed)

Domain is the highest rank, and each domain is subdivided into kingdoms, which are subdivided into
phyla, which are subdivided into classes, which are subdivided into orders, which are subdivided
into families, which are subdivided into genera (singular: genus), which are subdivided into species.
Every described, named organism is classified into this nested hierarchy, from domain to species, as
shown above for our own species, Homo sapiens. You are probably most familiar with the genus and
species level of taxonomic classification because this constitutes the scientific name of an organism.
The scientific name of an organism is simply its genus (always capitalized and italicized) and species
(always italicized): e.g., Homo sapiens.

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The table below illustrates how four species are classified using this taxonomic system.

DOMAIN Eukarya
KINGDOM Animalia Plantae
PHYLUM Chordata Arthropoda Angiospermophyta
CLASS Mammalia Insecta Monocotyledoneae
ORDER Primate Carnivora Hymenoptera Liliales
FAMILY Hominidae Canidae Apidae Liliaceae
GENUS Homo Canis Apis Alium
SPECIES sapiens lupus mellifera sativum
(human) (wolf) (honeybee) (garlic)
Biological nomenclature is the application of names to organisms recognized to be part of a
particular taxon. Organisms are grouped according to their similarities and evolutionary closeness.
For example, the name of the taxon containing all domestic dogs is Canis familiaris. The order to
which all dogs belong (along with a host of other flesh-eating mammals with specialized cutting teeth
called carnassials) is Carnivora. The scientific name of a group of similar organisms has no more
significance than any other convenient label used to describe a group of similar items. Don't let names
confuse or intimidate you. Often, once you know the Latin or Greek word roots, seemingly
complicated names make perfect sense and become easier to remember. For example, the name of
Eleutherodactylus planirostris, a frog naturalized in southern Florida gardens, can be broken down
into its Greek roots: eleuthero, meaning "free," dactyl, meaning "toe," plani, meaning "flat" and
rostris, meaning nose." This little guy is a flat-nosed frog with unwebbed toes.

In many cases, a biologist must identify an unknown specimen in the field. The most common (and
simple) method of identifying an unknown species is through the use of a dichotomous taxonomic
key. The taxonomic key is developed on the basis of similarities and differences between taxa. The
key is called dichotomous because at each stage of identification, the choices branch in two (Greek:
dicho = “in two” or “split, tom = “cut”). Each branch of identification involves paired statements
which describe two contrasting characteristics (usually based on morphology) found in the organisms
being classified. With the specimen at hand, you just select which of the paired statements best
matches the organism. The statement selected may immediately identify the specimen, but more often
it will direct the user to another set of paired statements. At the end, the organism should be identified
by name.

1. Work in pairs for this exercise. At your station you will find a container containing several
"species" of pasta. Let's key out (yes, this is the verb commonly used to describe the process of
identifying things with a taxonomic key) some pasta. Select one individual from your container, and
use the taxonomic key below to identify its genus and species. Once you have done this, identify each
different "species" of pasta in your container.

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A Taxonomic Key to Pasta of the Pacific Northwest
1a. Body tubular in shape ……...…...…………………..............….......……...…......… 2
1b. Body not tubular …………….……………………….......................…........…....… 4

2a. Skin lined with small, symmetrical ridges ……....................…...……...…......…… 3

2b. Skin smooth …………………………….......….....................................… Penna rigata

3a. Ridges erupt as a spiral pattern along the axis of the body ………............. Ziti edulis
3b. Ridges erupt as vertical lines along the axis of the body ………..…. Rigatonii deliciosus

4a. Skin lined with small, symmetrical ridges ………........……...........… Conchus crispus
4b. Skin not lined with ridges ………………………..….....…...............……………… 5

5a. Body cylindrical in overall shape ……………............................…… Rotinii spiralis

5b. Body dorsoventrally flattened in shape ……....................................... Farfalla aurea
(dorsoventral = extending from the back to the belly)

Question 5: Your pasta is labeled 1-6. Key out each and record the species name of each
number.

Exercise 3 Creating a Taxonomic Key

Now that you know how to use a taxonomic key, it’s your turn to create one. Work in groups for this
exercise. In another container at your station you will find several "species" of hardware. At this point,
it's not important that you can tell their evolutionary relationships to one another. You are merely
trying to create a tool that a person who found these species in the field could use to identify them.
Create a dichotomous key to your hardware species, using the pasta key on the previous page as a
guide for its construction. Use the guide to Greek and Latin root words to help with the naming for
each of your species, and try to be as descriptive as possible with the name. (Some of your individuals
might be in the same genus. It's up to you to decide.) Remember, genus is capitalized, species is lower
case, and the entire name is italicized (or underlined if you are writing and not typing the name).

Arrange all your species of hardware so that everyone in the group can list their obvious physical
characteristics. (Are they made of metal or plastic? Both? Are they elongate or flat? Disc shaped or
cylindrical?) Make a list of the general physical characteristics of each species.

Once you have included all your species in your key, and feel confident that anyone using your key
could identify any of these species of hardware, let your TA know you're finished so that he/she can
take a look.

Exercise 4 Phylogeny Reconstruction

(adapted from R. Gendron and L. Ruedas)

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Organisms are not randomly classified into the various taxa. Biologists compare similarities in
morphology (physical traits), DNA sequences, behavior, development, protein composition,
chromosome structure, metabolic pathways, and other traits to determine relationships between taxa.
Comparisons of these traits are useful because classifications are actually reflections of evolutionary
history. For example, humans and wolves are both in the class Mammalia within the phylum
Chordata because they share certain characteristics (e.g., backbone, hair, homeothermy, etc.). This
similarity is not a coincidence; both species inherited these traits from the same common ancestor.
In general, the greater the resemblance between two species, the more recently they diverged from a
common ancestor. Thus, when we say that the human and wolf are more closely related to each other
than either is to a honeybee, we mean that they share a common ancestor that is not shared with the
honeybee.

Another way of showing the evolutionary relationship between organisms is in the form of a
phylogenetic tree (Greek: phylon = “stock” or “tribe” + genus = “birth”, “origin”):

Figure 2.1. Phylogeny of Primates.

On the tree, a node exists everywhere a branch bifurcates (splits into two) and each node represents
an ancestral species. In the tree in Figure 2.1, the nodes from which branches bifurcate (A, B, C, D,
etc.) represent the hypothetical common ancestor of all of the taxa that extend from that node. The
endpoints of the branches represent the living descendants of that ancestor. For example, in Figure
2.1, we see that humans and chimps have diverged approximately six million years ago. The most
recent common ancestor shared by chimps and humans is indicated by the letter “G”. Taxa are
grouped together based on shared, derived characters known as synapomorphies – characters shared
by two or more species as a result of inheritance. For example, synapomorphies of orangutans,

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gorillas, chimpanzees and humans include relatively large brains, the absence of a tail, and increased
flexibility of wrists and thumbs. These are characteristics that set the orangutans, gorillas,
chimpanzees and humans apart from the rest of the primates because these traits were present in their
common ancestor (denoted by “E” in Figure 2.1). Because these traits are not present in other taxa,
we conclude that they arose at some point during the evolution of ancestor E (you can write these
traits on the tree, putting them on the line leading to ancestor E).

When you look at the tree, you should see the following:
The Ancestral Primate gave rise to all primates.
Ancestor A gave rise to Tarsiers and Anthropoids, but not Lemurs and their kin.
Ancestor E is the most recent common ancestor of orangutans, gorillas, chimpanzees and humans
Ancestor G gave only rise to humans, chimpanzees and bonobos.
…and so on.

The following is a simplified example of how trees are constructed. In practice, trees may take into
consideration hundreds (or more) of discreet characters, requiring the use of computer programs to
find the most parsimonious tree (parsimony is a concept stating that the most straightforward answer
most likely is the most correct answer). In this example, let’s consider the relationship of the four
animals below. Observe the physical characteristics of each animal as noted in the character chart.
The character chart documents the presence of novel adaptations. Not having these traits is
considered to be the ancestral form.

A B C D

EYES EYE STALKS FOUR LEGS TEETH

Animal A Yes Yes Yes No
Animal B Yes No Yes No
Animal C Yes No No No
Animal D Yes Yes Yes Yes

Notice that all the animals have developed eyes; three groups have developed four legs; two have
developed eye stalks; and only one group has developed teeth. After examining the characters
represented in each animal, the next step is to construct our tree so that groups that share traits are
nestled properly; we could produce 16 different trees if we place the traits and animals randomly, so
let’s use some reasoning to help us out. The characters shared by the largest number of animals
should theoretically be placed lowest (most ancient) on the tree. Eyes are a character shared by all
the animals, so eyes will be a synapomorphy that unites all the animals. Four legs is a trait that is
only shared by three of the animals. Animal C does not have four legs, so we will represent it as a
branch before the node defined by the presence of four legs. If we continue this line of reasoning we
will create the tree below.

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 Teeth
Eye stalks
Four
Eyes

Notice that in this example, once each character has developed (in the “ancestral area” indicated by
the circle), it remains present in each species that shares that ancestor. Trees are not always this
straightforward: sometimes, traits that evolve in a common ancestor are lost (and sometimes gained
again!) by subsequent descendants. Sometimes, traits have similar functions but evolved from very
different sources (wings of butterflies and wings of bats). We would say that these characters are
analogous (share a function) rather than homologous (share an evolutionary origin due to common
ancestry and genetic constitution of the character regardless of its current function). For example, the
wings of a bat are homologous with the arms and hands of a human (they share the same basic
underlying skeletal morphology), but they are analogous with the wings of an insect because the
primary function of both sets of wings is flight
In this exercise, you will develop a taxonomic classification and phylogenetic tree for a group of
imaginary organisms called Caminalcules after the taxonomist Joseph Camin who devised them.
1. Carefully examine the eight Caminalcules illustrated below. You can think of them as distinct
biological species and refer to them by their number.

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2. Group your species together on the basis of shared, derived characters (synapomorphies). To
accomplish this, select a series of characters that can be expressed as binary (i.e., two state). Use the
following characters:

Character a: "eyes present" (+) versus "eyes absent" (-); (note one eye, as seen in #1, counts as a +,
and eyes on stalks also count as a +)
Character b: "body mantle present" (+) versus "body mantle absent" (-); (note, a body mantle gives
the animal a tube, or rounded body shape)
Character c: "paired, anterior non-jointed appendages present" (+) versus "paired, anterior non-
jointed appendages not present" (-)
Character d: "anterior appendages flipperlike" (+) versus "anterior appendages not flipperlike" (-)
Character e: "eyes stalked" (+) versus "eyes not stalked" (-)
Character f: "body mantle posterior bulbous" (+) versus "body mantle posterior not bulbous" (-)
Character g: "eyes fused into one" (+) versus "eyes separate" (-)
Character h. "forelimbs with digits" (+) versus "forelimbs without digits" (-)

3. Examine all your organisms and determine which character state they each exhibit.

Enter the data in Table 2.1.

Question 6: Character a (presence or absence of eyes) and character b (presence or absence of

body mantle) is the same in all eight species. Is this character useful for building a phylogeny?
Why or why not?

Build the tree provided below by placing each caminalcule on the proper branch of the tree,
and by labeling your characters (synapomorphies) on the branches. Characters a, b, and c have
been added to the tree for you already.

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A Key to the Hardware of The Pacific Northwest

1a. ____________________________________________________________________________

________________________________________________……………………...______________

1b. ____________________________________________________________________________

________________________________________________……………………...______________

2a. ____________________________________________________________________________

________________________________________________……………………...______________

2b. ____________________________________________________________________________

________________________________________________……………………...______________

3a. ____________________________________________________________________________

________________________________________________……………………...______________

3b. ____________________________________________________________________________

________________________________________________……………………...______________

4a. ____________________________________________________________________________

________________________________________________……………………...______________

4b. ____________________________________________________________________________

________________________________________________……………………...______________

5a. ____________________________________________________________________________

_______________________________________________……………………...______________

5b. ____________________________________________________________________________

________________________________________________……………………...______________

6a. ____________________________________________________________________________

________________________________________________……………………...______________

6b. ____________________________________________________________________________

________________________________________________……………………...______________

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Answer Sheet
Please print this before class and be sure to show it to your TA for credit before you leave the
laboratory
Question 1

Question 2

Question 3

Question 4
Question 5
Taxa 1
Taxa 2
Taxa 3
Taxa 4
Taxa 5
Taxa 6

Question 6

Table 2.1 Character states of characters a-h in Caminalcules (enter + or -)

Character 1 2 3 4 5 6 7 8
A + + + + + + + +
B + + + + + + + +
C + - - + - + - +
D
E
F
G
H

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Be sure to show your answers, keys, tables and tree to your TA before you leave today.

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