Biology 2900 Principles of Evolution and Systematics

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Biology 2900Principles of Evolutionand
Systematics

• Dr. David Innes
• Jennifer Gosse
• Valerie Power

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Announcements

• Lab 4 Group 1 starts Monday, March 3
• Download from Webpage
• Pass in a copy of article used for Lab 5
  presentation ( 2 marks)

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Encyclopedia of life
YouTube Video
E. O. Wilson
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Topics

• Diversity
• Classification and phylogeny (Lab 4)
• Species and speciation
• Patterns of evolution
• Evolution in the fossil record
• History of life on earth
• The geography of evolution
• The evolution of biodiversity

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Terms (Futuyma Ch. 2)

• Plesiomorphic Character states
• Apomorphic Ancestral
• Synapomorphic Derived
• Autapomorphic Convergent
• Homology Reversal
• Homoplasy Outgroup
• Parsimony Sister group
• Polytomy Nodes
• Taxa (Taxon) Common Ancestor
• Monophyletic Polyphyletic

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Darwin and Evolution

• All living organisms related
• Phylogenetic Tree
• - ancestor - descendant

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Phylogenetic Tree

• Tree-like Phylogeny
• Consequence of a branching process
• D
• B
• - single species A E
• F
• C
• G

Descendants evolve differences Process repeated
over millions of years
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Plants
Eucarya
Fig. 2.1 The Tree of Life http//www.tolweb.org/
Animals
Root
Archaea
Bacteria
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Phylogeny

• Genealogical relationship among organisms
• - share a recent common ancestor
• - share more distant common ancestors
• Phylogeny estimated, reconstructed,
  assembled

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Phylogeny

• Useful for understanding
• Which organisms share a common ancestor
• Pathway by which characteristics have evolved
• (adaptation)

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Phylogeny

• Evolutionary history
• - not observed directly
• - can not know the true evolutionary
  history
• - deduced from evidence
• some fossil, but mostly living
  organisms

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Phylogeny

• Inferring phylogenetic history
• Species become steadily more different from one
  another
• Therefore,
• Can infer history of branching by measuring
  degree of similarity or difference

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Characteristics of Organisms

• Phenotypic characters
• - external and internal morphology
• - behaviour, physiology, biochemistry
• DNA sequences acgtcggagcctt
• - nucleotide site in a sequence a character

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Character States

• Each character can occur as different forms
• 1. a c g t c g g a g a c g a c g g a g
• 2. Turtle shell shape
• 3. Neck length

1 2 3 4 5 6 7 8
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1 2 3 4 5 6 7
8 9
rounded saddle
long short
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Phylogenetic Analysis

• Example (Fig. 2.4) 4 taxa (species)
• Arrange into a phylogenetic tree
• Which species derived from
• - recent common ancestors
• - ancient common ancestors

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Phylogenetic Analysis

• Characters
• (A)
• Species 1 0 0 1 1 1 0 0 0 0 0
• Species 2 0 0 1 0 0 1 1 1 1 0
• Species 3 0 0 1 0 0 1 1 0 0 1
• Species 4 1 1 0 0 0 0 0 0 0 0
• Calculate similarity matrix of each pair
• as shared character states

0 ancestral 1 derived
a b c d e f g h i j
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(A)
Monophyletic groups Sp2 Sp3 Sp2
Sp3Sp1 Sp2Sp3Sp1Sp4
0 ? 1 Evolved
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Phylogenetic Analysis

• Ancestral and derived character states known
• Two types of similarity
• 1. Overall similarity
• shared ancestral shared derived
• 2. Shared derived (Synapomorphies)
• count only shared characters
• that evolved

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Phylogenetic Analysis

• Phylogeny in
• Fig. 2.4 (A) Approximately equal rates of
  evolution along branches
• Fig. 2.4 (B) Complications
• Accelerated evolution in one branch
• Consequence overall similarity indicates
  Sp1
• and Sp3 most similar
• Suggests they share a most recent common
  ancestor

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(B)
Other autapomorphies?
Autapomorphy Derived in single lineage No
indication of relationship
Accelerated rate of evolution Suggests Sp 1 and
Sp3 most similar
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Phylogenetic Analysis

• Phylogeny Fig. 2.4 (B) Complications
• Overall similarity indicates Sp1 and Sp3 most
  similar
• Suggests they share a most recent common
  ancestor
• Similarity not an adequate indicator of
  relationship
• (Degree of relationship relative recency
  of common ancestor
• ? similarity)
• However,
• Shared derived characters does accurately
  indicate relationship

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Phylogenetic Analysis

• Interpretation
• Taxa similar because they share
• ancestral derived character states
• But, only shared derived states (synapomorphies)
• indicate monophyletic groups
• Also,
• derived states restricted to a single lineage
  (autapomorphies)? no indication of relationship

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Phylogenetic Analysis

• Previous examples each character changed once
• (0 ?
  1)
• Taxa sharing a character state
• inherited without change from common ancestor
• Homologous characters (states) shared through
  inheritance from a common ancestor

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Phylogenetic Analysis

• Phylogeny Fig. 2.4 (C) Further complications
• Homoplasy (homoplasious)
• - convergence a character state independently
  evolved two or more times (ie. does not have a
  unique origin)
• - reversals derived state evolves back to
  ancestral
• Consequence taxa with shared homoplasious
  characters have not inherited it from their
  common ancestor

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(C)
Spot the error!!
Autapomorphy ?
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(C)
0 1 1 1 1 1 1 0 1 1
g and h evolved twice
3 homoplasious characters - g and h
convergence - j reversal
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Phylogenetic Analysis

• Further complications
• Homoplasy misleading evidence about phylogeny
• Fig. 2.4C
• 1. characters g and j erroneously
  suggest
• Sp 1 and Sp 3 closest
  relatives
• 2. character h erroneously
  suggests
• Sp 1 and Sp 2 a monophyletic
  group
• only uniquely derived shared characters
  evidence for monophyletic groups

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Phylogenetic Analysis

• Fig. 2.4C
• Contains homoplasious character states
• but shared character states matrix
• and shared derived character states matrix
• both correctly group Sp 2 and Sp 3
• Homework assignment construct character state
  data
• in which
• - homoplasy incorrectly groups Sp 1 and Sp 3
  based on
• shared character states
• - correctly groups Sp 2 and Sp 3 based on
  shared derived character states

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Homework Assignment
0 ancestral 1 derived

• Characters
• Species 1 0 1 1 0 0 0 1 1 0 1
• Species 2 0 1 1 1 1 1 0 1 0 0
• Species 3 0 1 1 1 1 1 1 0 0 1
• Species 4 1 0 0 0 0 0 0 0 0 0

a b c d e f g h i j
1 2 3 4
Shared
Shared derived
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History of Classification and Phylogeny

• Numerical Taxonomy (1963)
• Classification (Phenetic)
• - objective
• - repeatable
• - large number of different types of characters
• - quantitative (based on distance or similarity
  matrix)
• - computer data analysis
• - produces a phenogram of overall similarity

Sokal and Sneath
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Numerical Taxonomy

• 22 species of the moss Didymodon
• Can a phenogram (dendrogram) of overall
  similarity represent a phylogenetic tree?

Not the primary purpose and Only if equal rates
of evolution among branches assumed
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History of Classification and Phylogeny

• Cladistics (Lab 4)
• Classification (Phylogenetic)
• - Classification based on evolutionary
  relationships
• - Character based (shared derived)
• - Branching pattern from common ancestor
• - Produces a cladogram of ancestors and
  descendants

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Phylogenetic Analysis

• Phylogenetic relationships
• German entomologist Willi Hennig
• Inferring phylogenetic relationships
• Taxa similar because they share
• - uniquely derived character states
  (Apomorphic)
• - ancestral character states (Plesiomorphic)
  1913 - 1976
• - homoplasious character states (Convergence,
  reversal)
• But only similarity due to uniquely derived
  character states evidence for monophyletic groups

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Systematics Journals
Systematic Botany
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Monophyletic Groups
Uniquely derived character states -
Tetrapod limb - Amnion -
Feathers Define monophyletic groups -
Tetrapods - Amniotes -
Birds Lack of the character is the ancestral
state and does not provide phylogenetic
information (ie. Lack of feathers does not form
a phylogenetic group)
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Phylogenetic Reconstruction

• Monophyletic groups defined by uniquely derived
  character states
• Difficulties
• 1. How to determine which state
  is derived?
• 2. How to determine if it is
  uniquely derived or
• homoplasious?
• Use the fossil record?
• - interpreting the relationship between fossil
  and living species
• - most species have very incomplete fossil
  records

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Phylogenetic Reconstruction

• Principle of Parsimony
• - the simplest explanation
• - requiring the fewest undocumented
  assumptions
• preferred over
• - more complicated explanations
• - requiring more assumption
• - for which evidence is lacking
• Phylogenetic relationship (Tree)
• best estimate requires fewest evolutionary
  changes

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Phylogenetic Reconstruction Using Parsimony
Hypothesis For the character presence of a
dorsal fin Whales and Tuna form a monophyletic
groups
of changes 17 (lots of homoplasy)
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Phylogenetic Reconstruction Using Parsimony
Accepted Phylogeny
of changes 10 (only dorsal fin homoplasious
due to ?)
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Phylogenetic Reconstruction Using Parsimony

• the best phylogenetic hypothesis is the one
• that requires the fewest homoplasious
• changes

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Maximum Parsimony

• Example Fig. 2.7
• Three species (1, 2, 3) form a monophyletic group
  relative to more distantly related outgroup
  species (4, 5).
• What is the phylogenetic relationship among the
  3 species?
• 3 possible trees

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Three-Species Trees
outgroups
1 2 3 4 5
2 3 1 4 5
1 3 2 4 5
Tree 3
Tree 1
Tree 2
Sister 1 2 1 3
2 3 taxa
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Character a C ?A (Why not A?C?)
b G?T c and d Define sp1 and sp2 as sister
groups e convergence f, g autapomorphies
Sister groups groups derived from a common
ancestor not shared with any other groups
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Character a C ?A (not A?C) b
G?T c and d Define sp1 and sp2 as sister
groups e convergence f, g autapomorphies
Sister groups groups derived from a common
ancestor not shared with any other groups
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Character a C ?A (not A?C) b
G?T c and d Define sp1 and sp2 as sister
groups e convergence f, g autapomorphies
Length (L) 8 character changes
Sister groups groups derived from a common
ancestor not shared with any other groups
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c and d convegence
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c and d convegence e reversal (T ? A? T)
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Parsimony

• Tree 1 best estimate
• - shortest tree
• - more characters support monophyly
• of sp1 and sp2 (c and d)
• than sp1 and sp3 (Tree 2) (e)
• or sp2 and sp3 (Tree 3) (none)

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Phylogenetic Methods

• Other methods
• Neighbor-joining
• Maximum likelihood
• Baysian
• Software

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Phylogenetic Methods

• Online analysis
• Biological Software
• Data Fig. 2.4 A
• 5 10
• Ancestor 0000000000
• species1 0011100000
• species2 0010011110
• species3 0010011001
• species4 1100000000

1 2 3 4
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Number of Phylogenetic Trees

• One true phylogenetic tree
• But many possible trees
• 10 species how many trees?
• Number of Trees