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Instructor Notes

Make sure to read CH 22. Be familiar with the following terms/concepts/people:

Archaea

Bacteria

Binomial nomeclature

Biological species concept (BSC)

Carl Woese

Carolus Linnaeus

Character states

Charles Darwin

Cladistics

Clade

Cladogram

Class

Classification

Compartmentalization (in eukaryotes)

Convergent evolution

Derived characters

Domain

Endosymbiosis

Eukarya

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Extremophile

Family

Genera

Homologous characters

Homoplasy

Horizontal gene transfer

Kingdom

Methanogen

Molecular clock

Monophyletic

Multicellularity

Nonextreme archaea

Order

Outgroup

Paraphyletic

Phylum

Phylogeny

Phylogenetic species concept (PSC)

Plesiomorphy

Polyphyletic

Principle of parsimony

Prokaryotic

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Sexual reproduction

Shared derived characters

Sister group

Specific epithet

Stymplesiomorphy

Synapomorphy

Systematics

Taxa

Taxonomy

Viridiplantae

A peculiar characteristic of humans beginning with the early Greeks to present-day is to pigeonhole
organisms into groups based on traits, first by looking at physical traits, then only recently by including
physiological, genetic and behavior traits. Classification systems have existed for thousands of years;
however, Carolus Linneaus in the mid-1700s created the system in use today, illustrated in the figure
below.

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Taxonomy as a science is a necessary part of biology in that it provides reference points for further
discussion of various organisms, their habitats, interactions, genetic relationships, biochemistry,
behavior and more. Without it scientists would never be sure whether they were examining the same
type of individual or group of organisms. The most widely accepted classification scheme is hierarchal
with each subunit encompassing a smaller but more similar group of organisms. The arrangement from
the most inclusive to the least inclusive is: domain-kingdom–phylum–class–order–family–genus–
species. The binomial nomenclature system created by Linnaeus further enhanced taxonomy by
providing convenience and precision in standardizing names for all organisms.

On the surface, defining a species seems simple, but the criteria are not always absolute. The biological
species concept states that organisms capable of producing fertile offspring are the same species. This
concept, when expanded over evolutionary time, states that a species is a single linage and maintains
its distinctive identity from other lineages within a population. To understand evolutionary
relationships among populations of lineages through time, scientists use systematics and cladistics.
Systematics studies evolutionary relationships by looking at similarities and differences between
species by constructing an evolutionary tree or phylogeny. Cladistics through cladogram construction
focuses on certain key characteristics of a group that are shared being inherited from a common
ancestor as well as shared derived traits in which similarities arose within the group. Cladograms do

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not identify ancestors, but are useful hypotheses in understanding evolutionary relationships in
providing insights for how, when, and at what rate traits evolved through adaptation, selective
pressure or some other means. The proposed ancestors in traditional phylogenies are indicated at the
nodes between branches. The comparisons in cladistics are objective and based on so many characters
with assigned importance values that computers are required to make the assessments.

The diversity of all living things is astounding! All organisms with characteristics of organization,
response to stimuli, growth, development, reproduction, regulation and homeostasis are classified into
three domains (a taxonomic level higher than the kingdom) Archaea, Bacteria, and Eukarya; and, the
six-kingdom system proposed by Carl Woese that further separates the domains into kingdoms of:
archaebacteria, bacteria, protista, fungi, plantae, and animalia. The Domain Archaea includes the
kingdom archaebacteria that seem to have diverged from the bacteria and are more similar to eukarya
than bacteria. Archaebacteria include the prokaryotic methanogens, the extremophiles (halophiles,
thermophiles, pressure-tolerant archaebacteria) and the nonextreme archaebacteria that inhabit the
same environments as bacteria. Domain Bacteria includes the prokaryotic kingdom bacteria whose
members are the most abundant organisms on earth and are so tiny they cannot be seen with the
naked eye. They play a critical role in the earth’s ecology as decomposers and recyclers of carbon,
nitrogen, and sulfur. Still others are pathogenic and cause many diseases. Domain Eukarya include the
four eukaryotic kingdoms of protista, fungi, plantae, and animalia. Analysis of the two major metabolic
organelles, mitochondria and chloroplasts, indicates an origin associated with bacteria. The
endosymbiosis hypothesis states that early in the history of eukaryotes, some bacteria became
endosymbionts and eventually became the mitochondria and chloroplast organelles found in
eukaryotic cells. All Domain Eukarya members, even though extraordinary diverse, share three
characteristics not found in prokaryotes: compartmentalization, multicellularity in some, and sexual
reproduction. All Eukarya kingdoms have discrete compartments providing for specialization within
the cell. Kingdom protista is primarily unicellular, while the other three Eukarya kingdoms exhibit
multicellularity (with the exception of yeast in kingdom fungi). Another key characteristic of
eukaryotes is sexual reproduction. The genetic exchange that occurs in bacteria is not a predictable
event. In kingdom protista the process of sexual reproduction occurs only occasionally, but in the
Eukarya kingdoms of fungi, plantae and animalia sexual reproduction is regular with predictable
results and often includes an alternation between syngamy and meiosis.

It is important to note that viruses are not placed in any of the six kingdoms. They are not living
organisms as they do not exhibit all of the characteristics of organization, response to stimuli, growth,
development, reproduction, regulation, and homeostasis and are not, therefore, properly classified as
organisms. Viruses are fragments of eukaryotic or prokaryotic genomes or intracellular parasitic
chemicals capable of replication only in connection with a prokaryote or eukaryote host cell.

There are problems with the six-kingdom subjective approach in attempting to classify all living
organisms. Proposals have been suggested to increase the number of kingdoms to reflect the diversity
found within the established kingdoms. For example, kingdom protista with over 200,000 members is
the weakest of the six-kingdom classification system, as it is not grouped based on evolutionary

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relationships. This kingdom is often used as a catchall kingdom for any eukaryotic organism that is not
a plant, fungus, or animal. Many systematists are proposing a new kingdom called Virdiplantae, green
plant kingdom. Phylogenies are hypothesis and subjected to change as a result of new discoveries of
phylogenetic relationships. Additional phylogenetic problems include the relationships between
water/land plants, segmentation among animals, flight among animals, and differences in mammals to
name a few.

Some additional topics that may be worth spending additional time on in order to make sure that you
understand them include:

Evolution. Evolution is the accumulated inherited changes in a population over time A population is a

group of individuals of the same species (i.e. they can interbreed to produce viable offspring) living in
the same location

Evolution is one of the most powerful unifying concepts in science and is a critical underpinning to
modern biology. It has been stated that without evolution biology makes no sense (Dobzhansky, 1973).
Evolutionary processes can be thought of as having two distinct modes. 1.) microevolution: the short
term adaptations that result from changes in the environment (i.e. changes in allele frequency); and 2.)
macroevolution: the process of the development of new species from common ancestors

Phylogeny. Darwin recognized that the species he observed must be the modified descendants of
earlier ones. Distinct populations of an ancestral species separate and diverge through time, again and
again, giving rise to multiple descendant species. The result is the pattern of nested similarities
observed in nature. This history of descent with branching is called phylogeny, and is much like the
genealogy that records our own family histories. The process of speciation can be depicted in a
phylogenetic tree, where branches represent diverging populations. As species proliferate, their
evolutionary relationships to one another unfold in a treelike pattern, with present-day species as the
tips of branches and their last common ancestors at nodes from which they branched off. The
branching order found in a phylogenetic tree hypothesizes the evolutionary relationship within a
group.

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The tree above proposes that the closest living relatives of birds are crocodiles and alligators. It also
proposes that the closest relatives of all tetrapod (four-legged) vertebrates are lungfish. Two groups,
or taxons, are considered to be each other’s closest relatives if they share a common ancestor not
shared by any other group. Two groups that are each other’s closest relatives are called sister groups.
The closeness of the relationship is determined by looking to see how recently two groups share a
common ancestor.

Monophyletic, Paraphyletic, and Polyphyletic Groups. A monophyletic group (shown in blue below)
includes a common ancestor and all of it descendants. A paraphyletic group (shown in green) includes a
common ancestor and some, but not all, of its descendants. A polyphyletic group (shown in red) does
not include the common ancestor. Only monophyletic groups reflect evolutionary relationships
because only they include all the descendants of a common ancestor.

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Constructing a phylogenetic tree. When constructing a phylogenetic tree, the anatomical,

physiological, or molecular features that make up an organism are compared. These features, called
characters, can be similar for one of two reasons: 1.) Common descent from an ancestor that had the
same character state; or 2.) Convergent evolution, in which the character state evolved independently
in two separate groups. Common descent results in homologous characters, while adaptations by
different species to a similar environment result in homoplasy, similarities due to adaptations. In
general, characters have several observed conditions, called character states. Only shared derived
characters, or synapomorphies, are useful in constructing a phylogenetic tree because they are shared
by some, but not all, of the members of the group under consideration. Phylogenetic reconstruction on
the basis of synapomorphies is called cladistics. 

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To show how synapomorphies help us chart out evolutionary relationships, we look at four species of
animals in a group we wish to study—A, B, C, and D.

We believe them to be closely related, and compare them to a fifth group called the outgroup, which is
a group that we know falls on an earlier branch in the tree. We look at characters such as leg number,
presence of wings, and whether development of young to adult is direct or undergoes a pupal stage.
We focus on potential synapomorphies. When constructing a tree, the best-fit tree is the one that has
the fewest number of changes because it minimizes the total number of independent origins of
character states (the principle of parsimony).

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In this instance, the phylogeny requiring four changes is the best fit tree, according to the principle of
parsimony.

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