Taxonomy &

Phylogeny
Introduction
Classification
Phylogeny
Cladograms
Quiz
 In this tutorial, you will learn:
 Thetraditional classification scheme of Linnaeus.
 Two theories of taxonomy:
 Traditional evolutionary taxonomy
 Cladistics
 How to read a cladogram

Credits:
Figures and images by N. Wheat unless otherwise noted.
Image of Linnaeus from Wikipedia
Funded by Title V-STEM grant P031S090007.
 Introduction
 The practice of categorizing organisms according
to similar features goes back to Aristotle.
 The goal of Taxonomy today is to produce a
formal system for naming and classifying species
to illustrate their evolutionary relationships.
 Classification
 In classification, the taxonomist asks whether the
species being classified contains the defining
feature of a certain taxonomic grouping.
 Focus is on features.
 Systematization
 In systematization, the taxonomist asks whether
the characteristics of a species support the
hypothesis that it descends from the most recent
common ancestor of the taxonomic group.
 Focus is on evolutionary origin of those features.
 Linnaeus and Classification
 In the 18th century, Carolus Linnaeus designed
the hierarchical classification system still in use
today.
 Kingdom
 Phylum
 Class
 Order
 Family
 Genus
 Species
 Taxa
 Taxa(singular = taxon) are the major groups of
organisms.
 Each rank can be subdivided into additional levels of
taxa.
 Superclass, suborder, etc.
 Binomial Nomenclature
 Binomialnomenclature is the system Linnaeus
developed for naming species.
 The two-part scientific name includes the genus and
species
 Names are latinized and italicized, only the genus is
capatilized.
 Sitta carolinensis
 Phylogeny
 Thegoal of systematics is to determine the
phylogeny – the evolutionary history – of a
species or group of related species.
 Phylogeny (2)

 Phylogenies are inferred by identifying organismal

features, characters, that vary among species.
 These characters can be:
 Morphological
 Chromosomal
 Molecular
 Behavioral or ecological
 Homology
 Homologous characters are shared characters that
result from common ancestry.
 Homoplasy
 Homoplasies are shared characters that are not a
result of common ancestry, but of independent
evolution of similar characters (they are not
homologous).
 Can result from convergent evolution.
 Convergent Evolution
 Convergent evolution occurs when natural
selection, working under similar environmental
pressures, produces similar (analogous)
adaptations in organisms from different
evolutionary lineages.
 Phylogeny
 When trying to determine evolutionary
relationships (inferring a phylogeny), we only
want to consider homologous characters.
 Homoplasies can create errors.
Shared Primitive and Shared Derived
Characteristics
 Focusing on homologous structures, we need to
determine when that character arose.
 Newer characters tell us more!
 Primitive (older) vs. derived (newer) characters
Shared Primitive Characteristics
A shared primitive character is a homologous
structure that is older than the branching of a
particular clade from other members of that clade.
 It is shared by more than just the taxon we are trying
to define.
 Example – mammals all have a backbone, but so do
other vertebrates.
 Shared Derived Characteristics
A shared derived character is a new evolutionary
feature, unique to a particular group.
 Example - all mammals have hair, and no other
animals have hair.

 Theseare the features that are most useful for

determining evolutionary relationships!
 Ancestral Character States
 The ancestral character state is the form of the
character that was present in the common ancestor
of the group.
 Variations of the character that arose later are
called derived character states.
 Polarity
 Polarity(which version of the trait is ancestral) is
determined by using outgroup comparison.
 An outgroup is closely related, but not part of the
group being examined (the ingroup).
 Polarity (2)

 An ancestral character is one that is found in both

the study group and the outgroup.
 Derived character groups are those found in the
study groups but not the outgroups.
 Clades
 Cladesare groups that share derived characters
and form a subset within a larger group.
 A clade is a unit of common evolutionary descent.
 Synapomorphy
A synapomorphy is a derived character that is
shared by all the members of the clade.
 Using synapomorphies to define clades will result in a
nested hierarchy of clades.
 Symplesiomorphy
 Ancestral character states for a taxon are called
plesiomorphic.
 Symplesiomorphies are shared ancestral
characters.
 Symplesiomorphies do not provide useful
information for forming a nested series of clades.
 Cladogram
 The nested hierarchy
of clades can be
shown as a
cladogram that is
based on
synapomorphies.
 Monophyletic
A valid clade is
monophyletic, it
consists of the ancestor
species and all its
descendants.
 Paraphyletic
A paraphyletic clade
consists of an ancestral
species and some, but
not all, of the
descendants.
 Polyphyletic
A polyphyletic
clade includes
many species that
lack a common
ancestor.
 Cladistics
 Cladistics,also called phylogenetic systematics,
is a taxonomic theory that is based on cladograms.
 All taxa must be monophyletic!
 Evolutionary Taxonomy
 Traditional Evolutionary
taxonomy is based on
common descent and the
amount of evolutionary
change to rank higher
taxa.
 Sometimes this type of
classification includes
paraphyletic groupings.
 Cladistics (2)

 Since all groupings must be

monophyletic in cladistics,
the paraphyletic
arrangement of ape families
doesn’t work.
 Humans, chimpanzees,
gorillas, and orangutans are
now all included together in
one monophyletic family -
Hominidae.
 Sister Groups
A sister group is a pair of taxa that are most
closely related to each other.
 Humans are most closely related to chimpanzees,
so humans & chimpanzees form a sister group.
 Gorillas form a sister group to the clade containing
humans and chimpanzees.
 Cladistics vs. Evolutionary
Taxonomy
 Theimportant difference between these two
theories of taxonomy is that traditional
evolutionary taxonomy sometimes accepts
paraphyletic clades, while cladistics does not.
 Both accept monophyletic clades.
 Both reject polyphyletic clades.
 Question 1

Who developed the classification system

including the binomial scientific name in
use today?
 Darwin
 Mendel
 Linnaeus
 Aristotle
 Question 1

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 That is incorrect.
 Try again!
 Question 1

Congratulations!
 You are correct!
 Question 2

Which of the following are

considered to be taxa?
 Phylum
 Class
 Family
 Species
 All of the above
 Question 2

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 That is incorrect.
 Try again!
 Question 2

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 You are correct!
 Question 3

Which example of binomial nomenclature

is formatted correctly?
 Homo sapiens
 homo sapiens
 Homo Sapiens
 Homo Sapiens
 It doesn’t matter, they are all correct
 Question 3

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 That is incorrect.
 Try again!
 Question 3

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 You are correct!
 Question 4

Which of these terms is associated with

characters that share common ancestry.
 Homology
 Convergent evolution
 Homoplasy
 Analogy
 All of the above
 Question 4

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 That is incorrect.
 Try again!
 Question 4

Congratulations!
 You are correct!
 Question 5

When defining a clade, what type of

characters should we use?
 Homoplasies
 Shared primitive characters = sympl
esiomorphies
 Shared derived characters = synapo
morphies
 All of the above
 Question 5

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 That is incorrect.
 Try again!
 Question 5

Congratulations!
 You are correct!
 Question 6

The branching diagram that illustrates the

nesting hierarchy of clades is called a
 Family tree
 Cladogram
 Phylogenetic diagram
 Taxonomic web
 Question 6

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 That is incorrect.
 Try again!
 Question 6

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 You are correct!
 Question 7

A monophyletic clade is one that

contains
 An ancestor and all of its
descendants.
 An ancestor and some of its
descendants.
 Several species that lack a common
ancestor.
 One species.
 Question 7

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 That is incorrect.
 Try again!
 Question 7

Congratulations!
 You are correct!
 Question 8

A polyphyletic clade is one that

contains
 An ancestor and all of its
descendants.
 An ancestor and some of its
descendants.
 Several species that lack a common
ancestor.
 One species.
 Question 8

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 That is incorrect.
 Try again!
 Question 8

Congratulations!
 You are correct!
 Question 9

A paraphyletic clade is one that

contains
 An ancestor and all of its
descendants.
 An ancestor and some of its
descendants.
 Several species that lack a common
ancestor.
 One species.
 Question 9

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 That is incorrect.
 Try again!
 Question 9

Congratulations!
 You are correct!
 Question 10

This cladogram illustrates a

________________ clade.
 Monophyletic
 Paraphyletic
 Polyphyletic
 None of the above
 Question 10

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 That is incorrect.
 Try again!
 Question 10

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 You are correct!
 Question 11

Which of the following statements about the difference

between cladistics and traditional evolutionary
taxonomy is false?
 Both accept monophyletic clades
 Both accept paraphyletic clades
 Cladistics rejects paraphyletic clades, while
evolutionary taxonomy sometimes accepts them.
 Both reject polyphyletic clades.
 Question 11

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 That is incorrect.
 Try again!
 Question 11

Congratulations!
 You are correct!
 Question 12

Which of the following cladograms

incorrectly illustrates sister groups?
 Question 12

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 That is incorrect.
 Try again!
 Question 12

Congratulations!
 You are correct!