Download - 4 phylogeny-ch26
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Lecture 4: Phylogeny and the Tree of Life
Campbell & Reece:
Chapter 26
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HumansRattlesnakePine treeAmoebaBacterium
All life is interconnected by descent
How to determine the pattern of descent?
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Systematics - field of biology dealing with diversity and evolutionary history of life
Includes Taxonomy: DINCDescription Identification NomenclatureClassification
Goal:– Determine Evolutionary History (Phylogeny) of Life
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Description
= assign features
Character = a feature (e.g., “petal color”)
Character states = two or more forms of a character (e.g., “red,” “white”).
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Identification
= associate an unknown with a knownHow? One way: Taxonomic Key, e.g.,
Tree …………………………………….…………… Species A Leaves simple …….………………………… Species B Leaves pinnate …….………..…..…..…… Species C
Herb Flowers red …….…………………………… Species D Flowers white …….…………………..…… Species E
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Nomenclature
Naming, according to a formal system.
Binomial: Species are two names (Linnaeus):
E.g., Homo sapiensHomo = genus namesapiens = specific epithetHomo sapiens = species name
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Nomenclature
Hierarchical Ranks:Domain
KingdomPhylum
ClassOrder
FamilyGenus
Species
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Classification
• Placing objects, e.g., life, into some type of order.
• Taxon = a taxonomic group (plural = taxa).
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How to classify life
• Phenetic classification
– Based on overall similarity
– Those organisms most similar are classified more “closely” together.
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Problem with phenetic classification:• Can be arbitrary,
e.g., classify these:
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Phylogenetic classification
• Based on known (inferred) evolutionary history.
• Advantage:– Classification reflects pattern of evolution– Classification not ambiguous
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TIME
lineage or clade
Cladogram or Phylogenetic Tree
= representation of the history of life
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A B C D E F
TIME
lineage or clade
Cladogram or Phylogenetic Tree
TAXA
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A B C D E F
TIME
speciation
Cladogram or Phylogenetic Tree
TAXA
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Ingroup – group studied
Outgroup – group not part of ingroup, used to “root” tree
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Fig. 26-5
Sistertaxa
ANCESTRALLINEAGE
Taxon A
PolytomyCommon ancestor oftaxa A–F
Branch point(node)
Taxon B
Taxon C
Taxon D
Taxon E
Taxon F
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Apomorphy (derived trait)
= a new, derived feature= a new, derived featureE.g., for this evolutionary transformationE.g., for this evolutionary transformation
scales --------> feathers scales --------> feathers(ancestral feature)(ancestral feature) (derived feature) (derived feature)
Presence of feathers is an Presence of feathers is an apomorphyapomorphy for birds.for birds.
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Taxa are grouped by apomorphies
Apomorphies are the result of evolution.
Taxa sharing apomorphies underwent same evolutionary history should be grouped together.
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Principle of ParsimonyThat cladogram (tree) having the fewest number
of “steps” (evolutionary changes) is the one accepted.
Okham’s razor: the simplest explanation, with fewest number of “ad hoc” hypotheses, is accepted.
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Other methods of phylogeny reconstruction:
• Maximum Likelihood or Bayesian analysis– Uses probabilities– Advantage: can use evolutionary models.
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apomorphies (for Taxa B & C)
apomorphy (for Taxon D)
apomorphy (for Taxa B,C,D,E,F)
A B C D E F
TIME
Cladogram or Phylogenetic Tree
TAXA
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Fig. 26-11
TAXA
Lan
cele
t(o
utg
rou
p)
Lam
pre
y
Sal
aman
der
Leo
par
d
Tu
rtle
Tu
na
Vertebral column(backbone)
Hinged jaws
Four walking legs
Amniotic (shelled) egg
CH
AR
AC
TE
RS
Hair
(a) Character table
Hair
Hinged jaws
Vertebralcolumn
Four walking legs
Amniotic egg
(b) Phylogenetic tree
Salamander
Leopard
Turtle
Lamprey
Tuna
Lancelet(outgroup)
0
0 0
0
0
0
0 0
0
0
0 0
0 0 0 1
11
111
1
11
1
1
11
11
Sequentially group taxa by shared derived character states (apomorphies)
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Fig. 26-8a
Deletion
Insertion
1
2
DNA sequence data – most important type of data
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Fig. 26-8b
3
4
DNA sequence data - alignment
Each nucleotide position = CharacterCharacter states = specific nucleotide
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Homology
• Similarity resulting from common ancestry.
– E.g., the forelimb bones of a bird, bat, and cat.
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Homoplasy (analogy)
• Similarity not due to common ancestry
• Reversal – loss of new (apomorphic) feature, resembles ancestral (old) feature.
• Convergence (parallelism) – gain of new, similar features independently.
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Convergent evolution:spines of cacti & euphorbs
Cactus EuphorbEuphorb
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euphorb spines cactus spines
Convergent evolution:spines of cacti & euphorbs
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Both examples of reversal within Tetrapods: loss of a derived feature – forelimbs.
Leg-less lizards Snake
Example of convergence relative to one another!Independently evolved.
snakesleg-lesslizards
leggedlizards
**
*= loss of legs
gain of legs (Tetrapods)
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Convergent evolution:wings of some animals evolved independently
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Fig. 26-7
Convergent evolution:Australian “mole” and N. Am. “mole”
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Fig. 26-18
(b) Paralogous genes
(a) Orthologous genes
Ancestral gene
Paralogous genes
Ancestral species
Speciation withdivergence of gene
Gene duplication and divergence
Species A after many generations
Species A Species B
Species A
Orthologous genes
Orthology – genes homologous
Paralogy – genes not homologous
Gene Duplicationcan occur!
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A B C D E F
TIME
Cladogram or Phylogenetic Tree
TAXA
common ancestor (of taxon A & taxa B-F)
common ancestor (of taxon D, E, & F)
Common ancestry
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Monophyletic Group
• a group consisting of: – a common ancestor +– all descendents of that common ancestor
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monophyletic group
A B C D E F
TIME
Cladogram or Phylogenetic Tree
TAXA
common ancestor (of taxon A & taxa B-F)
common ancestor (of taxon D, E, & F)
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monophyletic group
A B C D E F
TIME
Cladogram or Phylogenetic Tree
TAXA
common ancestor (of taxon A & taxa B-F)
common ancestor (of taxon D, E, & F)
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monophyletic group
A B C D E F
TIME
Cladogram or Phylogenetic Tree
TAXA
common ancestor (of taxon A & taxa B-F)
common ancestor (of taxon D, E, & F)
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monophyletic group
A B C D E F
TIME
Cladogram or Phylogenetic Tree
TAXA
common ancestor (of taxon A & taxa B-F)
common ancestor (of taxon D, E, & F)
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monophyletic group
A B C D E F
TIME
Cladogram or Phylogenetic Tree
TAXA
common ancestor (of taxon A & taxa B-F)
common ancestor (of taxon D, E, & F)
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A B C D E F
TIME
speciation
Cladogram or Phylogenetic Tree
TAXA
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A B C D E F
TIME
speciation
Cladogram or Phylogenetic Tree
TAXA
C B F E D A
Cladograms can be “flipped” at nodes, show same relationships
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Fig. 26-13
Drosophila
Lancelet
Zebrafish
Frog
Human
Chicken
Mouse
CENOZOIC
Present65.5
MESOZOIC
251
Millions of years ago
PALEOZOIC
542
One can date divergence times with molecular clock and fossils
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Relationship
• = recency of common ancestry
i.e., taxa sharing a common ancestor more recent in time are more closely related than those sharing common ancestors more distant in time.
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Example:
• Are fish more closely related to sharks or to humans?
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Shark Fish Humans
TIME
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Shark Fish Humans
TIME
common ancestor of Fish and Humans
common ancestor of Sharks, Fish, and Humans
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monophyletic group
Osteichthyes Vertebrata
Shark Fish Humans
TIME
common ancestor of Fish and Humans
common ancestor of Sharks, Fish, and Humans
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Example:
• Are crocodyles more closely related to lizards or to birds?
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Lizards & Snakes Crocodyles Birds Turtles
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Lizards & Snakes Crocodyles Birds Turtles
"Reptilia"
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Paraphyletic group
• Consist of common ancestor but not all descendents
• Paraphyletic groups are unnatural, distort evolutionary history, and should not be recognized.
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Lizards & Snakes Crocodyles Birds Turtles
"Reptilia"
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Lizards & Snakes Crocodyles Birds Turtles
"Reptilia"
“Reptilia” here paraphyletic
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Lizards & Snakes Crocodyles Birds Turtles
Reptilia
Re-defined Reptilia monophyletic
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Lizards & Snakes Crocodyles Birds Turtles
Dinosaurs
† † †
Reptilia
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Importance of a name:Did humans evolve from apes?
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Gorilla Chimpanzees Humans Orangatan
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Gorilla Chimpanzees Humans Orangatan
HominidaePongidae
“Great Apes”
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Hominidae
Gorilla Chimpanzees Humans Orangatan
Pongidae“Great Apes”Pongidae orHominidae
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Hominidae
Gorilla Chimpanzees Humans Orangatan
Pongidae orHominidae
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Hominidae
Gorilla Chimpanzees Humans Orangatan
Pongidae orHominidae
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We are human, butwe are also apes.
• We share unique human features.
• We also share features with other apes (and with other animals, plants, fungi, bacteria, etc.).
• Humans didn’t evolve from apes, humans are apes.
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Importance of systematics & evolution:
1) Foundation of biology - study of biodiversity2) Basis for classification of life3) Gives insight into biological processes:
speciation processesadaptation to environment
4) Can be aesthetically/intellectually pleasing!
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E.g., schistosomiasis
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Schistosomiasis:
knowledge of species diversity and evolutionary history of primary host can aid in controlling parasite
(Schistosoma, a fluke)
Phylogeny of Oncomelania snails
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All of life is interconnectedby descent.
A B C D E F
TIME
lineage or clade
Cladogram or Phylogenetic Tree
TAXA
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There are no “higher” or “lower” species.
A B C D E F
TIME
lineage or clade
Cladogram or Phylogenetic Tree
TAXA