1. Lecture 4: Phylogeny and the Tree of Life Campbell: Chapter 26

2. All life is interconnected by descent
Humans
Rattlesnake
Pine tree
Amoeba
Bacterium
How to determine the pattern of descent?

3. Systematics - field of biology dealing with diversity and evolutionary history of life
Includes Taxonomy: DINC
Description
Identification
Nomenclature
Classification
Goal:
Determine Evolutionary History (Phylogeny) of Life

4. Description
= assign features Character = a feature (e.g., “petal color”) Character states = two or more forms of a character (e.g., “red,” “white”).

5. Identification = associate an unknown with a known How? One way:
Taxonomic Key, e.g.,
Tree
Leaves simple …….………………………… Species A
Leaves pinnate …….………..…..…..…… Species B
Herb
Flowers red …….…………………………… Species C
Flowers white …….…………………..…… Species D

6. Nomenclature
Naming, according to a formal system. Binomial: Species are two names (Linnaeus): E.g., Homo sapiens Homo = genus name sapiens = specific epithet Homo sapiens = species name

7. Nomenclature
Hierarchical Ranks: Domain Kingdom Phylum Class Order Family Genus Species

8. Classification Placing objects, e.g., life, into some type of order.
Taxon = a taxonomic group (plural = taxa).

9. How to classify life Phenetic classification
Based on overall similarity
Those organisms most similar are classified more “closely” together.

10. Problem with phenetic classification:
Can be arbitrary, e.g., classify these:

11. Phylogenetic classification
Based on known (inferred) evolutionary history.
Advantage:
Classification reflects pattern of evolution
Classification not ambiguous

12. = representation of the history of life

15. Ingroup – group studied Outgroup – group not part of ingroup, used to “root” tree

16. Branch point (node) Taxon A Taxon B Sister taxa Taxon C ANCESTRAL
Fig. 26-5
Branch point
(node)
Taxon A
Taxon B
Sister
taxa
Taxon C
ANCESTRAL
LINEAGE
Taxon D
Taxon E
Taxon F
Common ancestor of
taxa A–F
Polytomy

17. Apomorphy (derived trait)
= a new, derived feature E.g., for this evolutionary transformation scales > feathers (ancestral feature) (derived feature)
Presence of feathers is an apomorphy for birds.

18. Taxa are grouped by apomorphies
Apomorphies are the result of evolution. Taxa sharing apomorphies underwent same evolutionary history should be grouped together.

19. Principle of Parsimony
That 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.

20. Other methods of phylogeny reconstruction:
Maximum Likelihood or Bayesian analysis
Uses probabilities
Advantage: can use evolutionary models.

22. Sequentially group taxa by shared derived character states (apomorphies)
Lancelet
(outgroup)
(outgroup)
Lancelet
Salamander
Lamprey
Leopard
Lamprey
Tuna
Turtle
Vertebral column
(backbone)
Tuna 1 1 1 1 1
Vertebral
column
Hinged jaws 1 1 1 1
Salamander
Hinged jaws
CHARACTERS
Four walking legs 1 1 1
Turtle
Four walking legs
Amniotic (shelled) egg 1 1
Amniotic egg
Leopard
Hair 1
Hair
(a) Character table
(b) Phylogenetic tree
Fig

23. DNA sequence data – most important type of data1
Deletion 2
Insertion
Fig. 26-8a

24. DNA sequence data - alignment3
Fig. 26-8b 4
Each nucleotide position = Character
Character states = specific nucleotide

25. Homology Similarity resulting from common ancestry.
E.g., the forelimb bones of a bird, bat, and cat.

27. 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.

28. Convergent evolution: spines of cacti & euphorbs
Cactus
Euphorb

29. Convergent evolution: spines of cacti & euphorbs
euphorb spines
cactus spines

30. * * Leg-less lizards Snake
Both examples of reversal within Tetrapods: loss of a derived feature – forelimbs.
legged
lizards
leg-less
lizards
snakes * *
Example of convergence relative to one another! Independently evolved.
*= loss of legs
gain of legs (Tetrapods)

31. Convergent evolution: wings of some animals evolved independently

32. Convergent evolution: Australian “mole” and N. Am. “mole”
Fig. 26-7
Convergent evolution: Australian “mole” and N. Am. “mole”

33. Orthology – genes homologous
Gene Duplication
can occur!
Ancestral gene
Ancestral species
Speciation with
divergence of gene
Orthology – genes homologous
Orthologous genes
Species A
Species B
(a) Orthologous genes
Species A
Gene duplication and divergence
Paralogy – genes not homologous
Paralogous genes
Species A after many generations
(b) Paralogous genes
Fig

34. Monophyletic Group a group consisting of: a common ancestor +
all descendents of that common ancestor

41. C B F E D A
Cladograms can be “flipped” at nodes, show same relationships

42. One can date divergence times with molecular clock and fossils
Fig
One can date divergence times with molecular clock and fossils
Drosophila
Lancelet
Zebrafish
Frog
Chicken
Human
Mouse
PALEOZOIC
MESOZOIC
CENOZOIC
542
251
65.5
Present
Millions of years ago

43. 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.

44. Example:
Are fish more closely related to sharks or to humans?

48. Example:
Are crocodyles more closely related to lizards or to birds?

49. Lizards &
Turtles Snakes Crocodiles Birds

50. Lizards &
Turtles Snakes Crocodiles Birds

51. Is “E” more closely related to “D” or to “F”?
Is “E” more closely related to “B” or to “A”?
Is “E” more closely related to “B” or to “C”?
C B F E D A

52. Is “E” more closely related to “D” or to “F”?
Is “E” more closely related to “B” or to “A”?
Is “E” more closely related to “B” or to “C”?
C B F E D A
Answers: F, B, neither (equally to “B” & “C”)

53. Paraphyletic group Consist of common ancestor but not all descendents
Paraphyletic groups are unnatural, distort evolutionary history, and should not be recognized.

54. Lizards &
Turtles Snakes Crocodiles Birds

55. “Reptilia” here paraphyletic
Lizards &
Turtles Snakes Crocodiles Birds

56. Re-defined Reptilia monophyletic
Lizards &
Turtles Snakes Crocodiles Birds

57. Dinosaurs
Lizards &
Turtles Snakes Crocodiles
Birds

58. Did humans evolve from apes?
Importance of a name:
Did humans evolve from apes?

59. Orangutan Gorilla Chimpanzees Humans

60. Pongidae
“Great Apes”
Hominidae
Orangutan Gorilla Chimpanzees Humans

61. Pongidae
“Great Apes”
Pongidae or
Hominidae
Orangutan Gorilla Chimpanzees Humans

62. Pongidae or
Hominidae
Orangutan Gorilla Chimpanzees Humans

63. Pongidae or
Hominidae
Orangutan Gorilla Chimpanzees Humans

65. We are human, but we 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.

66. All of life is interconnected by descent.

67. There are no “higher” or “lower” species.

68. Importance of systematics & evolution:
1) Foundation of biology - study of biodiversity 2) Basis for classification of life 3) Gives insight into biological processes: speciation processes adaptation to environment 4) Can be aesthetically/intellectually pleasing!