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Classification
Taxonomy
method of classifying organisms
As the science of biology developed
in the 18th & 19th centuries, a
major goal was to name and
classify Earth's diverse species.
You might think this task would be
fairly complete by now—but in
fact that is not the case. New
discoveries, methods, technology,
and molecular evidence have
revitalized the field, making it one
of today's most exciting areas of
biological research.
What Is Taxonomy?
A branch of biology that involves the identification, naming, and
classification of species.
Assigning scientific names to species is an important part of studying
the history of life.
Although common names such as monkey, fruit fly, and pine generally
work well in everyday language, common names can also cause
confusion. Each of the names above actually refers to many different
species. And sometimes the same common name can even refer to
very different organisms.
For example, a tortoise might be called a gopher in Florida, but in
Kansas, "gopher" might refer to either a ground squirrel or a pocket
gopher.
Often, a common name doesn't accurately reflect the organism.
Consider the names catfish, crayfish, and silverfish—the first is a fish,
the second is a small freshwater lobster, and the third is an insect.
Then there's the fact that organisms have different common names in
different languages. Yet biologists must be able to communicate with
one another about the species they study, no matter what language
they speak.
Scientific Names
To reduce this confusion in
discussing organisms, one goal
of taxonomy is to assign a
universal scientific name to
each known species.
Taxonomists also attempt to
organize the diversity of life by
classifying species into larger
groups of related species. This
section describes some of their
methods.
Astrophytum myriostigma
This poison frog's
scientific name,
Dendrobates azureus,
means “blue tree-walker”. Binomial Nomenclature
Carolus Linnaeus (1700’s)
System for naming things using Genus and
species (two names)
Used by all countries in all languages to
avoid confusion among scientists.
• Ex. Homo sapiens, Canus lupus, Felis domesticus
• Genus comes 1st and is Upper case , Species
comes 2nd is lower case
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The Linnaeus binomial system also
groups species into broader categories.
Closely related species are grouped into
the same genus.
• For example the leopard (Panthera
pardus) , and the African lion
(Panthera leo) both belong to the
genus Panthera. Taxonomists
group similar genera in the same
family. Next, similar families are
placed into orders, orders into
classes, and classes into phyla
(singular, phylum). Phyla are
grouped into kingdoms.
• Classifying a species by kingdom,
phylum, and so on, is like placing
students in a large school system.
First a student might be identified by
school, then by specific grade, and
finally as a unique individual by
name.
Classification and Evolution
Darwin viewed Linnaeus's system of
classification in the context of
evolution. Ever since, biologists
have strived to have classification
represent the evolutionary
relationships among species.
A diagram that reflects such
hypotheses of evolutionary
relationships has a branching pattern
called a phylogenetic tree . (The
diagram's name comes from the
word phylogeny, meaning
"evolutionary history.")
In a phylogenetic tree, each
branch point represents a
common ancestor of the species
above that point. In this diagram,
the branches are labeled to
reinforce how taxonomy reflects
the branching pattern of evolution.
Phylogenetic Tree 1, 2
How do we classify?
Based on Morphology
- branch of biology dealing with the study of form &
structure of organisms
How do we classify?
Structural (anatomy and physiology)
Biochemical (enzymes, proteins,
DNA)
Cytological (cell structure)
Embryological (development)
Behavioral (patterns of actions)
Fossil (common ancestor)
Evolutionary relations

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Homologous structures are one of the best
clues to assess how closely organisms are
related.
Homologous structures—like a
whale's flipper and a bat's wing—
may look different and function
very differently in different species.
However, they will have basic
underlying similarities if they both
evolved from a single structure in
a common ancestor.
The greater the number of
homologous structures 2
species have, the more closely the
species are thought to be related.
Convergent EvolutionConvergent Evolution
process in which unrelated species from similar environments
have adaptations that seem very similar.
There are, however, pitfalls in the
search for homologous
characteristics. Not all similar
structures are inherited from a
common ancestor. Similar
adaptations that result from
convergent evolution are called
analogous structures.
For example, the wings of insects
and those of birds are analogous,
not homologous, flight
equipment—they evolved
independently. And, they are built
from entirely different structures.
There is no evidence that insects
and birds shared a common
winged ancestor.
Homology & Analogy
Molecular Data as a Taxonomic Tool
The relatedness of species can be measured by comparing
their genes and gene products (proteins). The more the
sequences match up, the more closely the species are probably
related. Researchers are now sequencing the genomes of
species at a rapid rate. The data—readily available on the
Internet—have sparked a boom in the study of evolutionary
history. Such molecular data are independent of the structural
data that have traditionally been used for classification.
Such molecular comparisons provide a new way to test
hypotheses about evolutionary history. The strongest support
for any such hypothesis is when molecular data agree with
evidence from other sources, such as anatomy (body
structure). For instance, fossil data have indicated that whales
are closely related to the group of mammals that includes
hippos, cows, deer, and pigs. Molecular data have backed up
this hypothesis.
Taxonomy began a new era in the 1960s. One advance that led the way occurred when the molecular
methods just described became available for comparing species' DNA. At the same time, computer
technology provided greater power to analyze information. These innovations coincided with a new
ways of building phylogenetic trees as hypotheses about evolutionary relationships.
A key feature of a phylogenetic tree is the pattern of branches. A particular branching in the cat
familycould be represented as the diagram on the right. The tree can be expanded to include
additional species, as in the diagram on the left. The "deeper" branch point represents the
evolutionary split from a common ancestor of the wolf and cat groups. This phylogenetic tree
represents the hypothesis that the wolf and cat groups diverged earlier in their evolution than did
leopards and house cats.
Leopards and house cats compose a branch of two species that share a common ancestor
(right). A larger branch that also includes wolves (left) has a common ancestor that would have
lived longer ago than the ancestor of leopards and house cats.
Cladistics
Cladistics - is a branch of biology that determines
the evolutionary relationships between organisms
based on derived similarities
Cladistics is a particular method of hypothesizing
relationships among organisms. Like other methods,
it has its own set of assumptions, procedures, and
limitations. Cladistics is now accepted as the best
method available for phylogenetic analysis, for it
provides an explicit and testable hypothesis of
organismal relationships.

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Reexamining Traditional Classification
In most cases, cladistic analysis has supported traditional classification.
However, basing phylogenetic trees strictly on derived characters produces
some surprises.
For instance, biologists have traditionally placed birds and reptiles (lizards,
snakes, and crocodiles) in separate classes of vertebrates. Cladistic analysis
now suggests that crocodiles are more closely related to birds than they are to
lizards and snakes.
This cladogram shows birds and crocodiles in one clade, and lizards and
snakes in another. Now look at the larger clade that includes the ancestor that
crocodiles share with lizards and snakes. In this scheme, the reptile group
must also include birds. This classification seems to go against common
sense and tradition. For many people, the unique flight adaptations of birds
justify separating them from the crocodiles and other reptiles.
Keeping birds in a separate group from reptiles may be more comfortable, but
it probably does not accurately reflect evolutionary relationships.
Cladogram: Major Groups of
Plants
Section 2 How Biologists
Classify OrganismsChapter 14
Comparing Classification
Schemes
Phylogenetic trees and classifications
represent hypotheses about evolutionary
history. Like all hypotheses, they are revised to
correspond with the discovery of new
evidence. In some cases they are even
rejected. Cladistic analysis of molecular data is
changing scientists' understanding of certain
evolutionary relationships. The changes even
affect classification at the kingdom level.
Two- and Three-Kingdom Schemes
Biologists have traditionally considered the kingdom to be the broadest taxonomic
category. In high school, your grandparents learned that there are only two kingdoms of
life—plants and animals.
The two-kingdom system had a long tradition in taxonomy. Linnaeus divided all known
forms of life between the plant and animal kingdoms. The two-kingdom system prevailed
for over 200 years, but it had its problems. Where do prokaryotes fit in such a system?
Can they be considered members of the plant kingdom? And what about fungi?
Two- and Three-
Kingdom Schemes
Later on your grandparents
learned a three-kingdom
model. This model placed
protists such as
protozoans into their own
kingdom. But this model
also failed to fit new
evidence about the biology
and evolutionary history of
certain forms of life.
A Five-Kingdom Scheme
In 1969, American ecologist Robert H. Whittaker
proposed a five-kingdom system.
It places prokaryotes such as
bacteria in the kingdom Monera.
Organisms of the other 4 kingdoms
all consist of eukaryotic cells.
The kingdoms for plants, fungi, and
animals consist of multicellular
eukaryotes. Among eukaryotes, these
kingdoms differ in structure,
development, and modes of nutrition.
Plants make their own food by
photosynthesis.
Fungi live by decomposing the
remains of other organisms and
absorbing small organic molecules.
Most animals live by ingesting food
and digesting it within their bodies.
MONERA

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In the five-kingdom system, the kingdom
Protista contains all eukaryotes that do not fit
the definitions of plant, fungus, or animal.
Most protists are
unicellular. Amoebas and
other so-called protozoa
are examples.
But protists also include
certain large, multicellular
organisms (green Ulva)
that are thought to be close
relatives of unicellular
protists.
Three Domains
In the last decade, molecular data and
cladistics have led to a reevaluation of the
five-kingdom system. A three-domain system
is one alternative to the five-kingdom system.
A domain is a taxonomic category above the
kingdom level.
Three-domains of Life:
- Archaea – no nuclear membrane (Live in very
harsh conditions)
- Bacteria (Monera) – no nuclear membrane
- Eukarya – Nuclear membrane
What is most important to understand here is
that classifying Earth's diverse species of life
is a work in progress. As more is learned
about organisms and their evolution,
classification schemes will continue to be
revised. It is quite possible that if you continue
your study of biology in the coming years, you
may learn about new and different taxonomic
systems.
Kingdom and Domain
Characteristics
Section 1 Introduction to
Kingdoms and Domains
Chapter 19
Dichotomous Key
Tool used by biologists to identify an unknown
organism
Series of paired statements of anatomical
description that leads to an identification.
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What bird am I ?

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Bird W is Geospiza
Bird X is Platyspiza
Bird Y is Certhidea
Bird Z is Camarhynchus
Key for Vertebrate Identification
1. a) animal has a spine…………………..go to 2
b) animal has no spine………..…invertebrate
2. a) animal has no gills and fins……..…. go to 3
b) animal has gills and fins…………….. Fish
3. a) animal has no scales…………..........go to 4
b) animal has scales………………..….reptile
4. a) animal has feathers …………………..bird
b) animal has no feathers ……………..go to 5
5. a) animal has hair…………………….mammal
b) animal has no hair………………..amphibian
What am I ???
1. Give two reasons why common names of organisms can
lead to confusion.
2. Why are analogous structures not useful for classifying
species in an evolutionary context?
3. What does a branch point in a cladogram represent?
4. How does the three-domain model of classification differ
from the five-kingdom model?
Concept Check
Online Review
Taxonomy Quiz 1
Phylogenetic Tree Quiz 1, 2
Homology and Analogy
Convergent Evolution
Vertebrate Flight
Cladistics Quiz 1, 2, 3