Introduction to phylogenetics

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Introduction to phylogenetics
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Phylogenetic Systematics

• The study of the evolutionary history of species,
  genes, and other biological entities
• The use of phylogenies to obtain information
  about evolutionary phenomena

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History of tree-thinking

• Evolutionary (transmutationist) views were
  original tied to ideas of progress up a ladder
  of life
• Charles Darwin was the first to see clearly that
  evolutionary biology implies a tree like form

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Jean-Baptiste Lamarck

• French Naturalist (1744-1829)
• Professor of Worms and Insects in Paris
• The first scientific theory of evolution

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Lamarcks beliefs

• Continuum between physical and biological world
  (followed Aristotle)
• Scala Naturae (Ladder of Life or Great Chain
  of Being)

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Charles Bonnet (Switzerland 1720-1792)
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Lamarcks evolution

• Life progresses upward due to an internal drive
  towards perfection
• Why are primitive organisms still around?
• Spontaneous generation of new life constantly
• Mechanisms of change? Inheritance of acquired
  characters

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Lamarcks ideas were dismissed

• Species seemed to have real boundaries
• There is no one linear ladder (Cuviers
  embranchements)
• Vertebrata, Insecta, Vermes (worms) and Radiata
  (radially symmetrical animals)

Georges Cuvier
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Charles Lyell (17971875)

• English Geologist, mentor to Charles Darwin
• Summarized (and attacked) Lamarcks views
• Anti-evolutionist
• Noted that evolution implies a tree-like form..

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Lyell, C. Principles of Geology, Vol. II, Chap. 1
Species 3
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Charles Darwin (1809 -1882)

• English Naturalist
• Best known for On the Origin of Species (1859)
• Abundant evidence for evolution
• Proposed a mechanism natural selection
• Accepted Lyells view that evolution implies a
  tree of life

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The affinities of all the beings of the same
class have sometimes be represented by a great
tree. I believe this simile largely speaks the
truth The green and budding twigs may
represent existing species and those produced
during former years may represent the long
succession of extinct species.. .the great Tree
of Life.covers the earth with ever-branching and
beautiful ramifications
Charles Darwin, On the Origin of Species pages
131-132
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The only figure in On the Origin of Species
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The next 100 years

• Trees were used frequently as a metaphor for
  evolution
• Most famously by Ernst Haeckel
• Formal phylogenetic theory was not developed

Haeckel (1866) Generelle Morphologie der
Organismen
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Systematic practice

• Until phylogenetic methods became generally
  accepted (less than 20 years ago), systematics
  continued to follow a ladder-of-life model
• Systematists looked for (and saw) continuity and
  directional trends among living species and used
  these to develop classifications

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The Germans

• Willi Hennig (entomologist) and Walter Zimmerman
  (botanist) developed formal methods for
  reconstructing phylogenies
• Hennigs book Phylogenetic Systematics was
  translated into English and ultimately stimulated
  great changes in systematic practice

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Argues for the centrality of phylogenetic trees
in evolution and systematics and provided a
framework for reconstructing phylogenies
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Ever since Hennig..

• Development of computational and molecular
  methods
• Phylogenetics has been reformulated as a series
  of statistical estimation problems
• It has become important for many biological
  problems..

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Classification is supposed to represent
evolutionary history

• Phylogenies are needed to build classifications

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Character evolution
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Biogeography
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Forensics
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Epidemiology
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Other uses of phylogenies

• Molecular evolution (constraints and patterns of
  sequence evolution)
• Comparative methods (finding general patterns of
  trait evolution)
• Diversification rates
• Molecular dating

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What a phylogenetic tree is

• A depiction of the descent relationships of a
  sample of tips (species, genes, etc.)

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Terms used to describe a phylogenetic tree
Terminal
branch Edge
Termina nodel
Taxon
Tip
Leaf
Internode
Internal branch Edge
Node Internal node
Root
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A phylogenetic tree
A
B
C
D
F
G
E
TIME
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The most important feature of a phylogenetic
trees is its topology (the order of branching)
A
B
C
D
F
G
F
G
C
D
A
B
E
E
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Which of the following has a different topology?
A
B
C
D
E
A
B
C
D
E
A
B
A
B
C
D
E
E
D
C
A
B
C
D