Evolution Lecture: Phylogenetic Inference I

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Evolution Lecture Phylogenetic Inference I
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Phylogenetics and Population Genetics

• We have focused on how alleles change within
  populations
• Now we focus on change between populations and
  species
• Instead of examining differences between
  generations we are examining the differences
  between species that changed over hundreds or
  millions of yearsmacroevolution

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Phylogenetics

• A phylogeny is a graphical summary of the
  evolutionary relationship of taxa or populations
• It is a hypothesis
• It shows the sequence of the appearance of
  species and documents the relationships of
  species
• Phylogenies are inferred from data, we do not
  have direct evidence for most species

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Phylogenetic Inference and Questions

• What data do we use to infer phylogenies?
• How do we read trees?
• How do we determine the number of taxa to use?
• How do we know when we have found an accurate
  phylogeny
• Where do we derive statistical support for a tree?

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The Logic of Phylogeny Inference

• Inference is not simple and much more involved
  than the animals that share the greatest number
  of similarities are closely related and those
  with greater distance are less related
• Characters used to estimate phylogeny should be
  independent
• Synapomorphies--shared derived traits link
  relativesfeathers unite birds b/c their common
  ancestors (Dromaeosaurs) had feathers.
  Therefore, feathers are a synapomorphy that
  define living dinosaursbirds
• Synapomorphies are used to join taxa at any
  level population, species, genera, families etc

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Feathered Dinos
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Synapomorphies

• Define branching points
• When genetic separation occurs, species form, and
  homologous traits undergo changes due to mutation
  selection or drift
• Synapomorphies are nestedas you move through
  time and trace a tree from the root, each
  branching event adds another derived trait
• This describes a hierarchy of branching events
• Cladistics is this field of study and may be most
  appropriate for morphological data

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Character vs. Character State

• A character is a particular attribute of a
  specimen (for limb)
• Character states are the different forms of that
  character (fin, arm, wing)
• Synapomorphies join taxa using the derived
  homologous states
• Symplesiomorphies shared primitive states
• Autapomorphies are advanced character states
  found in a singe taxon and do not help resolve
  phylogenies

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Character Matrices

• We can represent characters and states in matrix
  form, with taxa, characters and character states
  (0,1,2). The states are different between taxa,
  even though the same numbers are used.
• Taxa 1 2 3
• A 0 0 0
• B 0 0 0
• C 0 1 0
• D 0 1 1

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Autapomorphy
B
C
A
D
Character 3 Two States
Character 2 Two States
Synapomorphy Uniting Taxa A and B
Synapomorphy Uniting Taxa C and D
Character 1 One state
Synplesiomorphies
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How do we make trees from data?

• 1) Grouping by overall similarity or grouping by
  shared derived characters.
• 2) Cladistics believe that evolution proceeds
  from primitive to derived, therefore, groupings
  should be by shared derived characters
• The phylogenies can be very different

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Example of Different Phylogenetic Groupings
Primitive0 Derived1
Characters 1 2 3 4 5 Taxa A 0
0 0 0 0 B 1 1 0 0 0 C
0 1 1 1 1
Shared Derived
B
C
A
B
A
C
Char 2 State 1
Char 3,4,5 State 0
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Must Establish which Characters are Homologous

• Homologous traits are found in closely related
  groups
• We can document this using structure types,
  developmental features, and genetic similarities
• To establish derived or primitive, we must
  understand the polarity of the state
• Outgroups analysis, the character state in the
  ingroup is compared to the character state in the
  outgroup (close relative that branched off
  earlier than all of the ingroup taxa)
• To determine the appropriate outgroup may be
  difficult, but usually involves information from
  other phylogenetic hypotheses

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If Z is the appropriate outgroup, then what would
you expect the States are for the characters?
Primitive0 Derived1
Characters 1 2 3 4 5 Taxa A
1 0 0 0 0 B 1 1 1 0
0 C 1 1 1 1 1
Shared Derived
B
C
A
Z
Char 2,3 State 1
Char 1 State 1
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Homoplasy

• When shared traits are not due to inheritance
  from a common ancestor
• Flippers in penguins and seals are the result of
  homoplasyconvergent evolution
• Derived traits can also mutate back to a
  primitive formreversals. For example, in DNA, a
  A can mutate into an T during a mistake in
  replication and unite two taxa, but it can also
  mutate back to an A
• Convergence and reversals give rise to homoplasy.
  Noise in the system. They prevent accurate
  reconstruction of phylogeny

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