This document provides an introduction to reading phylogenetic trees and key phylogenetic concepts. It discusses polytomies, or nodes with more than two descendant branches, and the possible resolutions of polytomies. It also covers monophyletic, paraphyletic, and polyphyletic groups. Additionally, it defines important terms like synapomorphy, homoplasy, convergence, and evolutionary reversal. Examples are provided to illustrate these phylogenetic concepts and how to distinguish between homology and homoplasy.

1. Introduction to Phylogeny:
Reading Phylogenetic
Trees Part 2
“Nothing in biology makes sense except in
the light of evolution”
T.H. Dobzhansky (1973)
Dr. Rachel Mackelprang

2. Polytomies
So far we have been discussing bifurcating trees
These are trees in which each internal node gives
rise to two descendant branches

3. Polytomies
Some nodes have three or more descendent branches
Such nodes are called polytomies and usually reflect
uncertainty about phylogenetic relationships

4. Polytomies
Extreme case of ignorance: a completely unresolved
bush

5. Polytomies
There are three possible resolutions of this three-
branched polytomy.

6. Polytomies
Resolution 1: The beetle is more closely related to
(fly+moth) than the wasp is

7. Polytomies
Resolution 1: The beetle is more closely related to
(fly+moth) than the wasp is

8. Polytomies
Resolution 2: The wasp is more closely related to
(fly+moth) than the beetle

9. Polytomies
Resolution 2: The wasp is more closely related to
(fly+moth) than the beetle

10. Polytomies
What is the third possibility?

11. Polytomies
The wasp and beetle are each others closest
relatives

12. In-class polytomy exercise

13. Types of phylogenetic groups
•Monophyletic group: a group of organisms
consisting of their most recent common ancestor
(MCRA) and all of its descendants.
•Clade: a monophyletic group
•Paraphyletic group: a group of organisms
consisting of their MRCA but excluding some of its
descendants
•Polyphyletic group: a group of organisms that
excludes the MCRA

14. Monophyletic groups (clades)
Consider taxa f & g
Where is the most recent common ancestor?
a b c d e f g h

15. Monophyletic groups (clades)
Consider taxa f, g & h
a b c d e f g h
Is it a monophyletic group?

16. Monophyletic groups (clades)
a b c d e f g h

17. Monophyletic groups (clades)
a b c d e f g h

18. Monophyletic groups (clades)
a b c d e f g h

19. Monophyletic groups (clades)
a b c d e f g h
What is the relationship between the number of internal
nodes in the tree and the number of monophyletic groups?

20. Monophyletic groups (clades)
a b c d e f g h
If a tree has n internal nodes, how many monophyletic
groups are there in this tree (excluding terminal taxa)?

21. Non-monophyletic groups
a b c d e f g h
Non-monophyletic groups are groups that include some
but not all descendants of the most recent common
ancestor of that group

22. Paraphyletic groups
a b c d e f g h
This is a paraphyletic group: it contains the most
recent common ancestor but not all descendants
e, f, g, h are
excluded

23. Polyphyletic groups
a b c d e f g h
This is a polyphyletic group: it excludes the
most recent common ancestor
MCRA

24. Sister groups
a b c d e f g h
Sister groups: two clades or species that are each
other’s closest relatives (the two descendants of a
single node)

25. In and out
a b c d e f g h
Ingroup: the group of taxa under study
Outgroup: one or more taxa (usually closely related to
the ingroup) that are not members of the ingroup
Ingroup

26. In and out
a b c d e f g h
Ingroup
i j
Outgroup
Ingroup: the group of taxa under study
Outgroup: one or more taxa (usually closely related to
the ingroup) that are not members of the ingroup

27. Types of phylogenetic groups
•A heritable feature of an organism is known as a
character (also a character trait or trait)
•The form a character takes is known as its state
(also known as a character state)
•Note: presence/absence can also be a state
•Example:
•Character = heart
•Character state = presence/absent
•Character state = # of chambers

28. Character ancestry is critical to understand
•Characters that are inherited from a common
ancestor are homologous
•Species change over time
•Known (generally) as divergence, or divergent
evolution
•Species change over time due to the combined
processes of mutation, recombination, drift,
selection, etc

29. Example: trait present in ancestor and all
descendants
Most recent common ancestor (MCRA) has a “smiley face”

30. Example: trait present in ancestor and all
descendants
Descendants maintained “smiley face” over time

31. Example: trait present in ancestor and all
descendants
Descendants maintained “smiley face” over time, even through
other speciation events

32. Example: trait present in ancestor and all
descendants
All taxa (a-h) inherited the “smiley face” character

33. Example: trait present in ancestor and all
descendants
Simplify view: add branches

34. Example: trait present in ancestor and all
descendants
Simplify view: highlight nodes

35. Example: trait present in ancestor and all
descendants
Simplified view: show extant taxa

36. Example: trait present in ancestor and all
descendants
Most recent common ancestor (MCRA) has a “smiley face”

37. Example: trait present in ancestor and all
descendants
One lineage evolved into the frowning form

38. Example: trait present in ancestor and all
descendants
Descendants maintained “smiley face” or “frowny face” over time
through other splits

39. Example: trait present in ancestor and all
descendants
No additional changes in character state

40. Example: trait present in ancestor and all
descendants
Simplified view: add branches

41. Example: trait present in ancestor and all
descendants
Simplified view: highlight nodes

42. Example: trait present in ancestor and all
descendants
Simplified view: state change marker

43. Example: trait present in ancestor and all
descendants
Simplified view: terminal taxa

44. Example: trait present in ancestor and all
descendants
A character with the same form as in the ancestor of a group has
ancestor state: smiley face
A character with a different form as in the ancestor of a group has
derived state: frowny face

45. Synapomorphy
•Synapomorphy— shared derived traits
•Derivation: Greek
•Syn ~ with (aka shared)
•Apo ~ away from (aka derived)
•Morphy ~ shape (aka character)

46. Synapomorphy
Which represents the synapomorphy?

47. Synapomorphy
Which represents the synapomorphy?

48. Homoplasies or homoplastic traits
Traits that are similar for reasons OTHER than inheritance
from a common ancestor

49. Homoplasies or homoplastic traits
•Convergent evolution— independently evolved
traits subjected to similar selection pressures may
become similar
•Evolutionary reversal— a character reverts from a
derived state back to the ancestral state
Traits that are similar for reasons OTHER than inheritance
from a common ancestor

50. Convergence
MCRA had head but no face

51. Convergence
MCRA split into two branches. Each inherited a head but no
face

52. Convergence
One lineage evolves a face with a frown

53. Convergence
Descendants maintained “no face” or “frowny face” over time
through other splits

54. Convergence
A second lineage evolves frowny face due to selection for sad
features

55. Convergence
Descendants maintained “no face” or “frowny faces” over time
through other splits

56. Convergence
Mark on the tree where changes occurred

57. Evolutionary reversal
One of the lineages reverts due to selection for “no face” trait

58. Evolutionary reversal
One of the lineages reverts due to selection for “no face” trait

59. Examples of convergent evolution
Flying Squirrel Sugar Glider
Camera Eyes
Patagonian Cavy Kangaroo
Loss of body hair

60. Evolutionary reversal
•Example: Ancestors of whales and dolphins
returned to the ocean, and their limbs evolved
once again to resemble their ancestral state—
fins.
•The character reverted from a derived state
back to an ancestral state

61. Challenge
•Observation
•Two organisms have similar character traits and
states
•Possible explanations: homology, convergence,
or evolutionary reversal

62. Challenge
•Observation
•Two organisms have similar character traits and
states
•Possible explanations: homology, convergence,
or evolutionary reversal
How do we distinguish which occurred?

63. Answer
•Answer
•Reconstruct character state: overlay characters
onto a phylogenetic tree and infer likely history of
character state changes.
•Example: bird and bat flight
•

64. Example: bird and bat flight
Test two models: wings = ancestral or wings = derived
Mammals Reptiles
Bats Birds

65. Example: bird and bat flight
Test the model that wings=ancestral
Mammals Reptiles
Bats Birds

66. Example: bird and bat flight
Test the model that wings=ancestral
Mammals Reptiles
Bats Birds

67. Example: bird and bat flight
Test the model that wings=ancestral
Mammals Reptiles
Bats Birds

68. Example: bird and bat flight
Ancestral nodes of bats and birds must have wings
Mammals Reptiles
Bats Birds

69. Example: bird and bat flight
Multiple loss events required. Six for this tree. Many more if we
showed the full tree
Mammals Reptiles
Bats Birds

70. Example: bird and bat flight
Test the model that wings=derived
Mammals Reptiles
Bats Birds

71. Example: bird and bat flight
Reconstruct simplest history for nodes
Mammals Reptiles
Bats Birds

72. Example: bird and bat flight
Separate derivation in birds vs bats. Thus, convergence
Mammals Reptiles
Bats Birds

73. Kahoot
Take out your smart phone, tablet, or laptop
Go to kahoot.it

74. Kahoot question 1
Is tree 2 one of the possible resolutions of the polytomy
shown in tree 1?
1
a b c d e f g h a b c d e f g h
2

75. Kahoot question 1 answer
Is tree 2 one of the possible resolutions of the polytomy
shown in tree 1?
1
a b c d e f g h a b c d e f g h
2
NO

76. Kahoot question 2
Phylogentic groups
a b c d e f g h
What type of group is shown in this tree?

77. Kahoot question 2 answer
Phylogentic groups
a b c d e f g h
What type of group is shown in this tree?
Polyphyletic group

78. Kahoot question 3
Phylogentic groups
a b c d e f g h i
Which likely represents the outgroup?

79. Kahoot question 3 answer
Phylogentic groups
Taxon A
a b c d e f g h i
Which likely represents the outgroup?

80. Kahoot question 4
Which represents the synapomorphy? A or B?
A B

81. Kahoot question 4 answer
Which represents the synapomorphy? A or B?
A B
Group B