Taxonomy

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Taxonomy Phylogeny

• Introduction
• Classification
• Phylogeny
• Cladograms
• Quiz

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In this tutorial, you will learn

• The traditional 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.
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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.

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Classification vs. Systematization

• In classification, the taxonomist asks whether
  the species being classified contains the
  defining feature of a certain taxonomic grouping.
• Focus is on features.

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Classification vs. 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.

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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

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Taxa

• Taxa (singular taxon) are the major groups of
  organisms.
• Each rank can be subdivided into additional
  levels of taxa.
• Superclass, suborder, etc.

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Binomial Nomenclature

• Binomial nomenclature 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

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Phylogeny

• The goal of systematics is to determine the
  phylogeny the evolutionary history of a
  species or group of related species.

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Phylogeny

• Phylogenies are inferred by identifying
  organismal features, characters, that vary among
  species.
• These characters can be
• Morphological
• Chromosomal
• Molecular
• Behavioral or ecological

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Homology

• Homologous characters are shared characters that
  result from common ancestry.

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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.

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Convergent Evolution

• Convergent evolution occurs when natural
  selection, working under similar environmental
  pressures, produces similar (analogous)
  adaptations in organisms from different
  evolutionary lineages.

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Phylogeny

• When trying to determine evolutionary
  relationships (inferring a phylogeny), we only
  want to consider homologous characters.
• Homoplasies can create errors.

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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

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Shared Primitive and Shared Derived
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.

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Shared Primitive and 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.
• These are the features that are most useful for
  determining evolutionary relationships!

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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.

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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).

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Polarity

• 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.

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Clades

• Clades are groups that share derived characters
  and form a subset within a larger group.
• A clade is a unit of common evolutionary descent.

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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.

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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.

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Cladogram

• The nested hierarchy of clades can be shown as a
  cladogram that is based on synapomorphies.

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Monophyletic

• A valid clade is monophyletic, it consists of the
  ancestor species and all its descendants.

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Paraphyletic

• A paraphyletic clade consists of an ancestral
  species and some, but not all, of the
  descendants.

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Polyphyletic

• A polyphyletic clade includes many species that
  lack a common ancestor.

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Cladistics

• Cladistics, also called phylogenetic systematics,
  is a taxonomic theory that is based on
  cladograms.
• All taxa must be monophyletic!

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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.

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Cladistics

• Since all groupings must be monophyletic in
  cladistics, the paraphyletic arrangement of ape
  families doesnt work.
• Humans, chimpanzees, gorillas, and orangutans are
  now all included together in one monophyletic
  family - Hominidae.

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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.

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Cladistics vs. Evolutionary Taxonomy

• The important 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.

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Who developed the classification system including
the binomial scientific name in use today?
Question 1

• Darwin
• Mendel
• Linnaeus
• Aristotle

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Sorry!
Question 1

• That is incorrect.
• Try again!

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Congratulations!
Question 1

• You are correct!

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Which of the following are considered to be taxa?
Question 2

• Phylum
• Class
• Family
• Species
• All of the above

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Question 2

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• Try again!

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Congratulations!
Question 2

• You are correct!

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Which example of binomial nomenclature is
formatted correctly?
Question 3

• Homo sapiens
• homo sapiens
• Homo Sapiens
• Homo Sapiens
• It doesnt matter, they are all correct

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Question 3

• That is incorrect.
• Try again!

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Congratulations!
Question 3

• You are correct!

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Which of these terms is associated with
characters that share common ancestry.
Question 4

• Homology
• Convergent evolution
• Homoplasy
• Analogy
• All of the above

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Question 4

• That is incorrect.
• Try again!

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Congratulations!
Question 4

• You are correct!

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When defining a clade, what type of characters
should we use?
Question 5

• Homoplasies
• Shared primitive characters symplesiomorphies
• Shared derived characters synapomorphies
• All of the above

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Question 5

• That is incorrect.
• Try again!

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Congratulations!
Question 5

• You are correct!

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The branching diagram that illustrates the
nesting hierarchy of clades is called a
Question 6

• Family tree
• Cladogram
• Phylogenetic diagram
• Taxonomic web

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Question 6

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Question 6

• You are correct!

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A monophyletic clade is one that contains
Question 7

• An ancestor and all of its descendants.
• An ancestor and some of its descendants.
• Several species that lack a common ancestor.
• One species.

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Question 7

• That is incorrect.
• Try again!

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Congratulations!
Question 7

• You are correct!

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A polyphyletic clade is one that contains
Question 8

• An ancestor and all of its descendants.
• An ancestor and some of its descendants.
• Several species that lack a common ancestor.
• One species.

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Question 8

• That is incorrect.
• Try again!

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Congratulations!
Question 8

• You are correct!

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A paraphyletic clade is one that contains
Question 9

• An ancestor and all of its descendants.
• An ancestor and some of its descendants.
• Several species that lack a common ancestor.
• One species.

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Question 9

• That is incorrect.
• Try again!

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Congratulations!
Question 9

• You are correct!

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This cladogram illustrates a ________________
clade.
Question 10

• Monophyletic
• Paraphyletic
• Polyphyletic
• None of the above

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Question 10

• That is incorrect.
• Try again!

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Congratulations!
Question 10

• You are correct!

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Which of the following statements about the
difference between cladistics and traditional
evolutionary taxonomy is false?
Question 11

• Both accept monophyletic clades
• Both accept paraphyletic clades
• Cladistics rejects paraphyletic clades, while
  evolutionary taxonomy sometimes accepts them.
• Both reject polyphyletic clades.

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Question 11

• That is incorrect.
• Try again!

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Congratulations!
Question 11

• You are correct!

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Which of the following cladograms incorrectly
illustrates sister groups?
Question 12
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Question 12

• That is incorrect.
• Try again!

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Congratulations!
Question 12

• You are correct!