Taxonomy and Classification
Taxonomy is the science dealing with description, identification, nomenclature,
and classification of living things.
A dichotomous key is a tool that allows users to identify items or organisms in a
systematic and reproducible fashion. Dichotomous keys may be used in a variety
of situations, such as for identifying rocks and minerals as well as for identifying
unknown organisms to some taxonomic level (e.g., species, genus, family, etc.).
What makes these keys distinctive is that they are ordered in such a way that a
series of choices is made that leads the user to the correct identity of the item
they are looking at. "Dichotomous" means, "divided into two parts." Therefore,
dichotomous keys always offer two choices for each step, each of which
describes key characteristics of a particular organism or group of organisms.
Imagine that you are trying to construct a dichotomous key for the students in
your biology laboratory class. To do this you would need to make a list of some
characteristics possessed by the members of the group, such as gender, hair
color, height, type of clothing (jeans, dress pants, shorts, dress), whether or not
they wear glasses, and so forth. You would then construct your key by setting
up a series of bifurcating characteristics, starting with the most general
characters and moving to the most specific such that, in the end, each member
of the group can be clearly identified. For example:
1. Sex female---2
Sex male---5
2. Hair color red---Sally
Hair color not red---3
3. Hair color blonde---Julie
Hair color black---4
4. Glasses worn---Deanna
&nbseanna
Glasses not worn---Leslie
5. Shoes high-top sneakers---Joseph
Shoes not high-tops---6
6. Hair color blonde--Michael
Hair color brown--David
Thus if we are looking at a male student with brown hair wearing cowboy boots
we would start at step 1. Because he is male, we would be instructed to go to
point 5. At point 5 we would establish that his shoes are not high-tops, and so be
directed to step 6, where the fact that our specimen has brown hair would allow
us to determine that we are looking at David.
Exercise 1
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Imagine that you meet a blonde male member of this class wearing teva
sandals. Who is it?
Imagine that his girl friend has black hair but doesn't wear glasses. Who is
he dating?
Exercise 2
Use the dichotomous key to the principle orders insects provided to determine
the identity of the following organisms:
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Click here for specimen 1.
Click here for specimen 2.
Click here for specimen 3.
Systematic Approaches to Phylogeny
What is Systematics?
Systematics is a discipline within biology whose goal is the determination of the
evolutionary history and relationships among organisms (termed phylogeny) and
then the use of that phylogeny in classifying organisms. To achieve that goal, a
systematist will utilize evidence from a wide variety of sources including
paleontology, embryology, morphology, behavior, and molecular biology.
Over the last few centuries systematists have developed a number of different
approaches for trying to show the relationships of organisms. As a result,
different schemes have emerged for ordering these relationships into a
classification scheme. The main approaches in the last 50 or so years may be
classified as follows:
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Phenetic (or numerical taxonomy)
Cladistic (or phylogenetic)
Evolutionary (or synthetic)
Phenetics
In the "old days" (before the twentieth century), classification was largely carried
out by "gentlemen" scientists who based their identifications of organisms upon a
few "important" characteristics and a "gut feeling" developed during many years
experience. Phenetic classification methods were invented by systematists who
thought that this type of classification scheme was too subjective. These
scientists argue that taxonomy should not be based on a few characteristics
arbitrarily judged to be "important," but rather upon the degree of overall similarity
between organisms. Thus they collect data on as many characteristics of the
organisms being classified as possible. Each organism is then compared with
every other for all characters measured, and the number of similarities (or
differences) is calculated. The organisms are then clustered in such a way that
the most similar are grouped close together and the more different ones are
linked more distantly. Because of the enormous amount of data involved in this
process, these calculations are usually made using specially programmed
computers1. The taxonomic clusters (phenograms) that result from such an
analysis do not necessarily reflect genetic similarity or evolutionary relatedness.
Pheneticists would argue that this is OK, because nobody really knows the true
evolutionary histories of these organisms and at least this system is objective.
However, the lack of evolutionary significance in phenetics has meant that this
system has had little impact on animal classification, and as a consequence
interest in and use of phenetics has been declining in recent years.
1
The dependence of Phenetics on the use of computers made it particularly unpopular with some
"old-school" biologists. Paul Ehrlich, one of the early converts to Phenetics, was reportedly once
asked by an irate taxonomist at a conference, "You mean to tell me that taxonomists can be
replaced by computers?" Ehrlich responded, "No, some of you can be replaced by an abacus!"
Cladistics (Phylogenetic Systematics)
Phenetics has been criticized because phenograms resulting from such analyses
do not necessarily correspond to evolutionary histories (degree of relatedness)
between organisms. Thus an alternative approach to diagramming relationships
between taxa was developed, called cladistics. The basic assumption behind
cladistics is that members of a group share a common evolutionary history, and
are thus more "closely related" to one another than they are to other groups of
organisms. Related groups of organisms are recognized because they share a
set of unique features (apomorphies) which were not present in distant
ancestors, but which are shared by most or all of the organisms within the group.
These shared derived characteristics are called synapomorphies.
In contrast to phenetics, in cladistics groupings do not depend on whether
organisms share physical traits, but on their evolutionary relationships. Indeed, in
cladistic analyses two organisms may share numerous characteristics but still be
considered members of different groups. For example, a jellyfish, a sea star, and
a human: jellyfish and sea stars both live in the ocean, have radial symmetry and
are invertebrates, so phenetic analysis might place them together in a group.
However, this would not reflect evolutionary relationships, as sea stars are
actually more closely related to humans than they are to jellyfish (both are
deuterostomes). Thus in cladistics, the emphasis is not upon the presence of all
shared traits, but upon the presence of shared derived (apomorphic) traits. In the
example above radial symmetry, aquatic habitat and invertebrate structure are all
traits that are believed to have been present in the common ancestor of all
animals, and so such traits are not considered to be very useful in determining
relationships using cladistic analysis.
Cladistic analyses have some pretty strict rules. For example, cladists always
assume that new species arise by bifurcations of the original lineage (the lineage
always splits in two). Most cladists assume that the original ancestral species no
longer exists after this bifurcation, so each branching event results in two new
species. In addition, cladistic groupings must possess the following
characteristics:
1. All species in a grouping must share a common ancestor.
2. All species derived from a common ancestor must be included in the
taxon.
The application of these requirements results in the following terms being used to
describe the different ways in which groupings can be made:
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A monophyletic grouping is one in which all species share a common
ancestor and all species derived from that common ancestor are included.
This is the only form of grouping accepted as valid by cladists. (For
example, turtles, lizards, crocodilians and birds are all derived from a
shared common ancestor. Thus a monophyletic grouping would place all
of these together, rather than placing birds into a separate group.)
A paraphyletic grouping is one in which all species share a common
ancestor, but not all species derived from that common ancestor are
included (for example, grouping turtles, lizards and crocodiles as "reptiles"
and separating that grouping from the birds).
A polyphyletic grouping is one in which species that do not share an
immediate common ancestor are lumped together, while excluding other
members that would link them (for example, a hypothetical group the
"lizmams" made by grouping together the lizards and the mammals).
Thus, in cladistics, no matter how divergent in appearance B might be from C,
relative to A, if B and C share a common ancestor that is not shared by A, then B
and C must be grouped together and separated from lineage A. In the cladogram
of the reptiles and birds above, you can see an example of such a situation.
Steps for Constructing a Cladogram
1. Select a taxonomic group to be analyzed; for example, a group of
vertebrates.
2. For each member of the group, determine some observable traits
(characters), and note their "states" (a "character state" is one of two [or
more] possible forms of that character). For example, for a character
"fins," the possible states may be "present" and "absent." For the
character "number of forelimb digits," possible states may be 1, 2, 3, 4, or
5
3. For each character, determine which state is ancestral (primitive or
plesiomorphic) and which is derived (apomorphic). This is usually done
by comparison with a more distantly related organism termed the
"outgroup." It is hypothesized that traits shared with the more distantly
related organism(s) are likely to be "ancient" or plesiomorphic traits.
Similarly, traits that differ from the outgroup are postulated to have arisen
since the group being considered branched from its shared common
ancestor with the outgroup, and thus are likely to be "derived" or
apomorphic.
4. Group taxa by shared derived character states (synapomorphines).
5. When in doubt, choose the most parsimonious tree. While similar
structures may evolve independently in separate lineages facing similar
selective pressures (convergent evolution), this is assumed to be a rare
event. Most major structures (eyes, horns, tails, fur, etc.) are assumed to
have evolved or to be lost only rarely. Thus, when in doubt, choose a
pathway that minimizes the number of times a feature must be postulated
to have arisen (or lost) separately.
An Example of Cladogram Construction for Vertebrates
Trait
Outgroup
Frog
(Lobefinned fish)
Turtle
Kangaroo Mouse
Human
Dorsal Nerve Yes
Cord
Yes
Yes
Yes
Yes
Yes
Legs
No
Yes
Yes
Yes
Yes
Yes
Nature of
egg
Requires
water
Requires Hard shell
water
prevents
drying
Develops
inside the
mother
Develops
inside the
mother
Develops inside
the mother
Nature of
In egg
development
In egg
In egg
Marsupial
Placental
Placental
Hair
No
No
No
Yes
Yes
Reduced
Presence of
pouch
No
No
No
Yes
No
No
Bidpedal
posture
No
No
No
Yes
No
Yes
In this example, frogs share all major traits with the outgroup (i.e., they show
mostly ancestral or plesiomorphic traits), except that they have legs and slightly
enlarged brains. These last two features are apomorphies that are widespread in
the vertebrate lineage. Frogs are thus postulated to have branched from the main
vertebrate lineage relatively early in the evolutionary process.
Turtles show further modifications from the outgroup, most markedly the
presence of a hard shelled egg, as well as an increased tendency toward larger
brain size; therefore we would suggest that their lineage branched next from the
ancestral lineage.
All three of the remaining groups are characterized by an egg that develops
inside the mother, suggesting that these three share a common ancestor not
shared by frogs and turtles. Mice and kangaroos share similar hair amounts,
while humans and kangaroos share a generally bipedal posture. So how do we
know how to group these three organisms? Firstly, we would suspect that the
possession of hair, even in reduced amounts, might link humans to kangaroos
and mice. Secondly, we would look to the other traits possessed by these
groups. Both mice and humans show placental development and thus lack a
pouch. Thus we would tend to link these two groups together more closely and
the kangaroo more distantly. We would thus conclude that the cladogram for this
group of organisms (minus the outgroup, which is not usually shown in these
figures) should look something like the one below.
You will note that, in this solution, the tendency toward a bipedal posture was
postulated to have evolved twice; once in the marsupial lineage (kangaroos) and
once in the placental lineage (humans). Such features are said to be analogous
and to have resulted from convergent evolution. However, it is possible to draw
the cladogram such that humans and kangaroos are postulated to have a
common bipedal ancestor not shared by mice. However, in this solution, the
tendency towards placental development, along with all the required anatomical
changes (absence of a pouch etc.) must be postulated to have occurred twice
(once in the mouse lineage and once in the human lineage). Such a solution
would require more evolutionary steps than the sequence that we have proposed
here and, consequently, would not be as efficient or "parsimonious" as our
initial solution.
Exercises
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Click here for Exercise 1.
Click here for Exercise 2.
Click here for Exercise 3.
Click here for Exercise 4.
Evolutionary (Synthetic) Systematics
Like cladistics, evolutionary systematics is based strongly on evolutionary
relationships. However, its supporters suggest that the degree of genetic
differences between lineages should be used in addition to their genealogical
(evolutionary) similarities when developing taxonomic classifications. Among
other ways in which evolutionary systematics and a cladistic analyses differ:
evolutionary taxonomists are more tolerant of multiple branches developing
synchronously from an ancestral line (rather then just two as in cladistics), and
they tend to treat organisms that are unchanged when a new branch arises from
their lineage as the same species that existed before the branching event (i.e.,
the original species is not always believed to become extinct every time a
branching event occurs). However, the biggest difference between the two
approaches is that, when creating groupings, evolutionary taxonomists seek to
maximize the way in which the groupings they create communicate information
about the group of organisms in that taxon (in the way the word "mammal" or
"reptile" does for even an untrained person). This type of division is also intended
to increase the ease with which a field biologist, or even someone coming in from
outside, can retrieve information about a group of organisms of interest to
him/her using the taxonomic divisions formed. Taxa generated by an evolutionary
biologist will never be polyphyletic, but may be either monophyletic or
paraphyletic in nature. For example, as we saw earlier, birds and crocodilians
diverged from the same ancestral reptilian line. A cladist would insist that these
"sister groups" be placed in the same taxon, even though the amount of change
from the common ancestor is much greater for the birds than it is for the
crocodiles. An evolutionary taxonomist would suggest that the large number of
similarities between crocodilians and reptiles would justify grouping them within
the same general taxon, while placing birds in a separate taxon due to the large
number of unique characters possessed by members of this group.