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Biology 2900 Principles of Evolution and Systematics

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'presence of a dorsal fin' Whales and Tuna form a monophyletic groups ... of changes = 10 (only dorsal fin homoplasious) Accepted Phylogeny ... – PowerPoint PPT presentation

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Title: Biology 2900 Principles of Evolution and Systematics


1
Biology 2900Principles of Evolutionand
Systematics
  • Dr. David Innes
  • Jennifer Gosse
  • Valerie Power

2
Announcements
  • Biology Department
  • Open House
  • Wednesday February 27, 2008
  • 500 700 PM
  • SN-2109 Pizza!!

3
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

4
  • The study of Evolution
  • - how populations change in response to their
    environment
  • - formation of new species
  • The Study of Adaptation and Diversity

5
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

6
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

7
Darwin and Evolution
  • All living organisms related
  • Phylogenetic Tree
  • - ancestor - descendant

8
Darwin The great tree of life
Extant
Extinct
Time
Angle rate of evolution
Evolutionary divergence
9
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
10
Plants
Eucarya
Fig. 2.1 The Tree of Life http//www.tolweb.org/
Animals
Root
Archaea
Bacteria
11
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

12
Cataloguing Life
The Tree of Life
Encyclopedia of life
Consortium for the barcode of life
Barcode of Life (BOLD)
Bolnet.ca
13
Phylogeny
  • Genealogical relationship among organisms
  • - share a recent common ancestor
  • - share more distant common ancestors
  • Phylogeny estimated, reconstructed,
    assembled

14
Phylogeny
  • Useful for understanding
  • Which organisms share a common ancestor
  • Pathway by which characteristics have evolved
  • (adaptation)

15
Phylogeny
  • Evolutionary history
  • - not observed directly
  • - can not know the true evolutionary
    history
  • - deduced from evidence
  • some fossil, but mostly living
    organisms

16
Phylogeny, Systematics Classification
  • Phylogenetic analysis study of relationships
    among organisms
  • Classification cataloguing and organizing living
    organisms
  • Taxonomy naming of organisms
  • Systematics Classification Taxonomy

17
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
18
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
19
Classification
  • Hierarchical Classification reflects
  • - a real historical process
  • - true genealogical relationships
  • Natural Classification
  • - high information content
  • - predictive

20
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

21
Characteristics of Organisms
  • Phenotypic characters
  • - external and internal morphology
  • - behaviour, physiology, biochemistry
  • DNA sequences acgtcggagcctt
  • - nucleotide site in a sequence a character

22
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
9
1 2 3 4 5 6 7
8 9
rounded saddle
long short
23
Phylogenetic Analysis
  • Example (Fig. 2.4) 4 taxa (species)
  • Arrange into a phylogenetic tree
  • Which species derived from
  • - recent common ancestors
  • - ancient common ancestors

24
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

25
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

26
(A)
Monophyletic groups Sp2 Sp3 Sp2
Sp3Sp1 Sp2Sp3Sp1Sp4
27
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
28
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

29
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

30
(B)
Accelerated rate of evolution
Autapomorphy
31
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

32
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

33
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

34
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

35
(C)
Spot the error!!
36
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

37
(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
38
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

39
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
40
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

41
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)
42
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

43
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

44
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)
45
Phylogenetic Reconstruction Using Parsimony
Accepted Phylogeny
of changes 10 (only dorsal fin homoplasious)
46
Phylogenetic Reconstruction Using Parsimony
  • the best phylogenetic hypothesis is the one
  • that requires the fewest homoplasious
  • changes

47
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

48
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
49
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
50
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
51
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
52
c and d convegence
53
c and d convegence e reversal
54
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)

55
Phylogenetic Methods
  • Other methods
  • Neighbor-joining
  • Maximum likelihood
  • Baysian
  • Software

56
Number of Phylogenetic Trees
  • Number of Trees

57
Phylogeny Software
  • http//evolution.genetics.washington.edu/phylip/so
    ftware.html

58
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