INTRODUCTION.
A major theme of this course, both in the classroom and in the lab, is
diversity. In labs 1-5, we encounter the spectacular biological
diversity (“biodiversity”) of Earth and consider the differences
and similarities among the major groups of organisms. Then in labs 6-10
we study the diversity of organ systems and learn how organisms
function. Since there are between 5 and 30 million species on Earth, we
are immediately confronted with two important issues: 1) how
do we classify and name all of these species?, and 2) how did
this remarkable biodiversity arise? In today’s laboratory
session we will learn about the related endeavors of taxonomy and
systematics, two fields that help biologists classify species and
determine their evolutionary relationships.
The term taxonomy is derived from the Greek taxis (meaning
'arrangement') and nomos (meaning ‘law’). Taxonomy can be defined as
the theory and practice of classifying organisms. Classification is
vital in order to make the bewildering array of organic diversity
available to workers in other disciplines where proper identification of
organisms is vital, e. g. ecology, fishery biology, medical parasitology,
molecular biology. Systematics, from the latinized Greek systema
(meaning 'an ordered arrangement') can be defined as the theory and
practice of the scientific study of the kinds and diversity of organisms
and of all of the relationships among them. These relationships
include, but are not limited to, evolutionary or phylogenetic
relationships. Defined in this way systematics is a large and synthetic
discipline that properly includes taxonomy as well as ecology, genetics,
developmental biology, and nearly every other subdiscipline of biology.
One of the major goals of biology is to establish working phylogenies of
all living things. The term phylogeny is derived from the Greek phylon
(meaning 'race' or 'kind') and geneia (meaning 'origin') and refers to
the evolutionary descent of a single organism or group of organisms. The
sciences of taxonomy and systematics are central to the study of the
phylogenetic (evolutionary) relationships that exist among organisms.
While sometimes confused or considered synonyms of each another, these
two disciplines can be seen as separable, yet related.
The fundamental unit of taxonomy is the species. Each
species has a unique Latin binomial, consisting of a genus
name and the specific epithet that follows, e.g., Homo sapiens,
the human species. Note that by convention the genus (plural: genera) is
always capitalized and that the entire Latin name is either
italicized or underlined. The Latin names of species may be derived
from classical Greek or Latin names (e.g., Homo = man), or they may be
descriptive terms (e.g., sapiens = wise). Sometimes, the binomial is
followed by an abbreviation for the “authority,” or taxonomist who first
applied that name to that particular species. For example, in
Liriodendron tulipifera L., “L.” stands for Linnaeus, the father of
modern taxonomy and the man who named the tulip tree, which we will
encounter in today’s lab.
In making the diversity of organisms available to workers in other
fields, taxonomists will often produce a dichotomous key to a
particular group of organisms. Many times these keys are designed to
work for a particular group from a particular area, e.g. a key to the
trees and shrubs of eastern North America or a key to the beetles of the
family Carabidae from Peru. The best keys are those that can be used by
specialists and non-specialists alike, although the latter group might
need to become familiar with a set of specialized terms that relate to
the morphology, ecology, etc. of the group under consideration.
Dichotomous keys are groups of pairs (couplets) of choices that
relate to specific characters displayed by the organisms that the key is
designed to treat. A character is any feature of an organism that can be
measured in some way. These are often morphological/anatomical features
(e. g. number of appendages, type of coelom, presence of a vascular
tissue) but can also include behavioral features such as songs in the
case of birds, color, or ecological features such as the time of day an
organism is active (nocturnal, crepuscular, etc.). The most helpful
characters in terms of identifying organisms are those that have more
than one state represented among the group of organisms under study. A
character state is defined as an alternate form of a
particular character. For example, if the character is the
arrangement of leaves on a plant stem, then opposite, alternate, and
whorled are all character states for this one character. Leaf
arrangement then is a multistate character, because it can appear in
more than one state. Another example would be the shape of the edge of a
leaf. This single character could have multiple states: smooth, wavy,
saw-tooth, etc. Dichotomous keys proceed by giving the user a choice
between two different characters, character states, or groupings of
characters and character states. Each choice of the two (hence the use
of the term dichotomy) leads the user through the key until finally the
last couplet leads to the name of the organism at hand.
Most identification keys are said to be “artificial,” meaning that
they do not necessarily reflect the true evolutionary relationships,
or phylogenies, of organisms. The phylogeny of any group of organisms is
most commonly thought of as an evolutionary tree wherein the branching
pattern of the tree indicates the evolutionary relatedness among the
member taxa. A key, although it also has a branching structure, is
merely a convenient device for distinguishing one species from another;
therefore, the branching patterns of a key and a phylogeny will often
not coincide with one another. An illustrative example is taken from the
Key to Wesleyan College Trees that follows. Southern magnolia and tulip
tree are closely related, evolutionarily, and are therefore placed in
the same family, Magnoliaceae, the magnolias. However, in the artificial
key, these species do not key out close to each other because the
southern magnolia is evergreen and the tulip tree is deciduous.
After completing this laboratory you should be able to:
1) Define, compare, and contrast the practices of
taxonomy and systematics;
2) Use a dichotomous key to identify an unknown
organism;
3) Explain how characters and character state
analyses can be used to infer phylogenetic (evolutionary)
relationships among taxa.
4) Produce an evolutionary tree for a hypothetical
group of organisms.
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Lab 1 Worksheet
Insect Key
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PART I. USE OF DICHOTOMOUS KEYS.
As described below, practice using the dichotomous key in the
blue area below to identify common local woody plants.
Materials:
Dichotomous key to selected woody plants of Wesleyan College.
Herbarium specimens of the plant species.
Procedure:
1. Starting at any specimen, attempt to identify it by following
each option presented in the Dichotomous Key until all choices
end.
2. Be able to recognize all specimens, as well as their
distinguishing characteristics.
Study suggestions:
1. Make detailed sketches and notes on specimens. This will help
you to look at the specimens more closely, as well as to help
you study later.
2. Plan to come view the specimens once or twice more before the
lab test. Test yourself by attempting to identify the specimens
using the key.
KEY TO SELECTED WOODY PLANTS OF WESLEYAN COLLEGE
Note: this key includes only 10
species, about 10 percent of the woody plant
diversity in the Wesleyan College Arboretum. The key
will therefore not work, or may give an erroneous
result, if used to identify a species not included
in the key. More complete keys are available from
the Biology Department and in books about Georgia
trees.
1. Trees; bearing woody cones with seeds naked (not enclosed in
ovary); leaves evergreen or deciduous; leaves needle-like or
scale-like:
2. Deciduous; leaves short, scale-like; cones 2-3 cm,
disintegrating when mature; woody “knees” at or near base of
tree; wetlands Baldcypress (Taxodium
distichum)
2. Evergreen; leaves long (15 cm), needle-like, in bundles of 3;
cones 10-15 cm, persistent; “knees” absent; uplands
Loblolly Pine (Pinus taeda)
1. Trees or shrubs; bearing true fruits (fleshy or dry) with
seeds enclosed in ovary; leaves evergreen or deciduous;
broad-leaved
2. Leaves evergreen
3. Leaves opposite on twigs; shrub, parasitic on trees; berries
white
American Mistletoe (Phoradendron
serotinum)
3. Leaves alternate on twigs; trees; fruit or seeds red
4. Leaves 15-20 cm; margins smooth, untoothed; leaves
brown-hairy below; fruit a cone-like aggregate, ca. 10 cm; seeds
with red fleshy coat Southern Magnolia
(Magnolia grandiflora)
4. Leaves 5-8 cm; margins with sharp prickles; leaves hairless
below; fruit red berries American Holly
(Ilex opaca)
2. Leaves deciduous (or tardily deciduous)
3. Leaves or buds opposite on twigs
4. Twigs and buds reddish; buds with many overlapping scales;
buds similar in size; fruit dry, winged
Red Maple (Acer rubrum)
4. Twigs and buds green; buds with two scales; larger, globular
flower buds may be present; fruit fleshy, red
Flowering Dogwood (Cornus florida)
3. Leaves or buds alternate on twigs
4. Buds clustered at tips of twigs; some leaves may persist in
winter; fruit an acorn Water Oak (Quercus
nigra)
4. Buds not clustered at tips of twigs; fruit a spiky ball or a
cone-like aggregate; seeds winged
5. Buds with many overlapping scales; twigs lacking scars
encircling twigs at leaf scars; twigs may have corky “wings”;
fruit a spiky ball with 1 cm winged seeds
Sweetgum (Liquidambar styraciflua)
5. Buds with two scales; twigs with scars encircling twigs at
leaf scars; twigs lacking corky “wings”; fruit a cone-like
aggregate of 3 cm winged seeds Tulip Tree
(Liriodendron tulipifera)
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PART II. RECONSTRUCTING PHYLOGENY
Determining the branching evolutionary history of any group of
organisms is a daunting task that requires evidence of many
different types. Systematists rely on the following sources of
evidence: molecular data (amino acid sequences of proteins, DNA
sequences), fossils, biogeography, embryology, and morphology.
In this exercise you will attempt to reconstruct the phylogeny
of a group of hypothetical trees based strictly on their
morphology. A similar exercise could be designed using molecular
data but the concepts of homology and parsimony
are easiest to convey with more tangible morphological features.
We will begin with a review of some basic terminology and
concepts used in systematics.
A major school of thought regarding phylogenetic analysis is
Cladistics. The word clade means branch, and thus the goal
of cladistics is to determine the evolutionary branching
patterns for groups of organisms. A cladistic approach to
phylogenetic reconstruction is based entirely on homologous
characters; characters believed to be analogous are never
considered as part of the analysis. Furthermore, cladistic
methods are designed to arrange organisms based on the principle
of shared derived characters.
Derived characters are those that represent a change or
departure from that of the ancestral character or character
state, the character or character state typically found in the
ancestral taxon. Derived characters, therefore, are typically
considered to be advanced with respect to the primitive
condition or state found in the ancestor. The primitive
condition is determined by comparison with an outgroup, a taxon
somewhat related to the group under study, but not as closely
related to them as they all are to each other. Shared derived
characters then are derived characters that are shared among
two or more descendent taxa from a common ancestor.
Again, the concept of common ancestor is central to the
cladistic approach because common ancestors will show homology
with their descendent taxa. Cladistic analysis typically
requires software to conduct the numerical computations. In any
case the output is a cladogram, a branching phylogenetic tree
where each branch point, or node, represents the common ancestor
to the taxa represented by the two branches leading away from
that node. Each descendent taxon can then be the ancestor to
another pair of descendent taxa, and so on until all of the
branches end at unbranched tips.
An important outcome of cladistic analysis is that only
monophyletic taxa are produced, i.e., groups consist of a
single ancestor and all of its descendent species. This is in
contrast to paraphyletic groups (not all of the
descendent species are included in a taxon) and polyphyletic
groups (taxa are derived from two different lineages that do not
share a recent common ancestor). Polyphyletic groupings result
if a systematist groups two species that have analogous traits,
i.e., traits that arose due to convergent evolution.
Convergent evolution occurs when two unrelated taxa evolve
similar traits because they are subject to the same selection
pressures; the adaptations therefore arise independently, and do
not represent true homologies.
Procedure:
You are presented with nine species of trees and must
reconstruct a reasonable phylogeny for these taxa based on their
morphological traits. One species is designated as the outgroup;
assume that this designation is based on fossil evidence,
biogeography, and morphology. You will use eight characters of
the taxa to determine the best phylogeny:
Evergreenness: evergreen vs. deciduous
Leaf shape: simple vs. lobed
Leaf margins: untoothed vs. toothed
Glands on the leaf stalk (“petiolar glands”): present vs. absent
(these glands produce nectar that attracts ants, which may
protect the
plant from destructive herbivores)
Fruit number per cluster: one vs. two
Fruit color: purple vs. red
Fruit texture: fuzzy vs. smooth
Leaf stalk: straight vs. curved
Build your phylogenetic tree (cladogram) by determining which
character states are primitive vs. which are derived, and try to
group species that have the same shared derived traits. Beware,
though, that just as in real species, some species may have
evolved the same traits due to convergent evolution. If you
suspect that one of your characters represents an analogy, but
you are not sure how to proceed, you should apply a fundamental
concept in phylogenetic reconstruction, namely the principle of
parsimony. The most parsimonious tree, and therefore the implied
“best” tree, is the one that is shortest, that is to say, the
one with the fewest number of changes in character states (and
therefore, the one with the smallest number of branching
points). It is important to recognize that the most parsimonious
tree is not necessarily the “correct” tree in terms of
faithfully representing the historical evolutionary pattern of
speciation. However, the less parsimonious the tree, the lower
the likelihood that it accurately depicts the real evolutionary
trends of the group under investigation.
TREE SPECIES FOR PHYLOGENETIC RECONSTRUCTION
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QUESTIONS:
1) For the cladogram produced in Part II, which trait(s),
if any, represent analogies? How can you tell, and what evidence
did you use instead to determine the best branching pattern?
2) Produce a simple matrix of taxa vs. their character
states, as shown on p. 497 in the Campbell textbook. For each
character in the matrix, use a “0” to represent ancestral
character states, and a “1” to represent the derived condition.
(Note: this matrix can be helpful in determining the branching
patterns of your cladogram.)
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