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

• Biology Department
• Open House
• Wednesday February 27, 2008
• 500 700 PM
• SN-2109 Pizza!!

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Evolution in the News

• Bat flight, echo location
• Flight evolved first,
• echolocation later
• Onychonycteris
• Its large claws, primitive wings, broad tail and
  especially its underdeveloped cochlea - the part
  of the inner ear that makes echolocation possible
  - all set it apart from existing species.
• Nature Feb. 14, 2008 CBC Quirks Quarks

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• The study of Evolution
• - how populations change in response to their
  environment
• - formation of new species
• The Study of Adaptation and Diversity

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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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Darwin The great tree of life
Extant
Extinct
Time
Angle rate of evolution
Evolutionary divergence
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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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Tree of Life

• Overview
• Life on Earth shares a common, genetic history
  with complex origins
• Don't draw conclusions about the relative
  diversity of different groups of organisms
• Don't interpret relative branch lengths as
  indicators of levels of evolutionary
  advancement
• No organism alive today represents the ancestor
  of any other living creature

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Cataloguing Life
The Tree of Life
Encyclopedia of life
Consortium for the barcode of life
Barcode of Life (BOLD)
Bolnet.ca
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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, Systematics Classification

• Phylogenetic analysis study of relationships
  among organisms
• Classification cataloguing and organizing living
  organisms
• Taxonomy naming of organisms
• Systematics Classification Taxonomy

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Classification

• Binomial Nomenclature
• Hierarchical (nested) classification
• Taxonomic categories
• K, P, C, O, F, G, S
• No objective basis for classification
• Without an evolutionary framework

Linnaeus
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Classification

• Classification after Origin of Species
• - provided the basis for the hierarchical
• organisation of life (descent from common
  ancestor)
• Gave meaning to closely related species
• recently descended from a common ancestor
• Common features that group species inherited from
  common ancestor species

Darwin
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Classification

• Hierarchical Classification reflects
• - a real historical process
• - true genealogical relationships
• Natural Classification
• - high information content
• - predictive

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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 ? 10 a j
• States 0 ancestral
• 1 derived (has evolved 0 ? 1)
• Plesiomorphic ancestral
• Apomorphic derived
• Data on character states used to infer
  phylogenetic relationships

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Phylogenetic Analysis

• Fig. 2.4 (A) Hypothetical phylogeny
• 4 species 3 species 1 outgroup
• Outgroup taxon known to be more distantly
  related than any
• of the ingroup
  species
• Branch point (Node) common ancestor
• Evolutionary change (a0 ? a1) tick on branch
• Monophyletic group set of species derived from a
  common ancestor

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(A)
Monophyletic groups Sp2 Sp3 Sp2
Sp3Sp1 Sp2Sp3Sp1Sp4
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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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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

• Complications
• Example 2.4A ? rate of evolution equal among
• lineages
• Example 2.4B ? greater rate of evolution between
• ancestor 3 ------gt Sp
  2
• Overall similarity indicates Sp1 and Sp3 most
  similar
• Suggests they share a most recent common
  ancestor

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(B)
Accelerated rate of evolution
Autapomorphy
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Phylogenetic Analysis

• 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
• 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

• Further complications
• Homoplasy (homoplasious)
• - 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!!
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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

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(C)
0 1 1 1 1 1 1 0 1 1
autapomorphy
3 homoplasious characters - g and h
convergence - j reversal
g and h evolve twice
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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 for the 4 species where homoplasy
  incorrectly groups Sp 1 and Sp 2 based on shared
  character states

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Homework Assignment

• 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
• 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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Phylogenetic Analysis

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

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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)
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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 (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
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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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Number of Phylogenetic Trees

• Number of Trees

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Phylogeny Software

• http//evolution.genetics.washington.edu/phylip/so
  ftware.html

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